@article{Vulovic2010,
  year = {2010},
  title = {A toolkit for the characterization of {CCD} cameras for transmission electron microscopy},
  pages = {97-109},
  journal = {Acta Crystallographica Section D},
  volume = {66},
  author = {Vulovic, M. and Rieger, B. and Vliet, L.J. van and Koster, A.J. and Ravelli, R.B.G.}
}
@article{Weber1981,
  year = {1981},
  title = {Resolution of the Fluorescence Lifetimes in a Heterogeneous System by Phase and Modulation Measurements},
  pages = {949-953},
  journal = {Journal of Physical Chemistry},
  volume = {85},
  author = {Weber, G.}
}
@article{Geman1984,
  number = {6},
  month = {November},
  year = {1984},
  title = {Stochastic Relaxation, {Gibbs} Distributions, and the {Bayesian} Restoration of Images},
  pages = {721--741},
  journal = {IEEE Transactions on Pattern Analysis and Machine Intelligence},
  volume = {6},
  author = {Geman, S. and Geman, D.}
}
@article{Fernandez2006,
  year = {2006},
  title = {{CTF} determination and correction in electron cryotomography},
  pages = {587-596},
  journal = {Ultramicroscopy},
  volume = {106},
  author = {Fernandez, J.J. and Li, S. and Crowther, R.A.}
}
@article{Clemons2001,
  year = {2001},
  title = {Crystal Structure of the {30S} Ribosomal Subunit from Thermus thermophilus: Purification, Crystallization and Structure Determination},
  pages = {827-843},
  journal = {Journal of Molecualar Biology},
  volume = {310},
  author = {Clemons, W.M. Jr. and Brodersen, D.E. and McCutcheon, J.P. and May, J.L.C. and Carter, A.P. and Morgan-Warren, R.J. and Wimberly, B.T. and Ramakrishnan, V.}
}
@article{Keller2006,
  number = {8},
  year = {2006},
  title = {A Signal Processing Approach to Symmetry Detection},
  pages = {2198-2207},
  journal = {IEEE Transactions on Image Processing},
  volume = {15},
  author = {Keller, Y. and Shkolnisky, Y.}
}
@book{Hilbert2001,
  year = {1971},
  title = {Foundations of Geometry},
  address = { La Salle, Illinois},
  publisher = {Open Court},
  author = {Hilbert, D.}
}
@article{Gabor1946a,
  number = {26},
  month = {November},
  year = {1946},
  title = {Theory of Communication: Part I: Analysis of Information},
  pages = {429-441},
  journal = {Journal of the Institution of Electrical Engineers},
  volume = {93},
  author = {Gabor, D.}
}
@inproceedings{Vliet1998,
  year = {1998},
  title = {Recursive Gaussian Derivative Filters},
  booktitle = {{ICPR'98}, Proc. 14th Int. Conference on Pattern Recognition},
  pages = {509--514},
  editor = {Jain, A.K. and Venkatesh, S. and Lovell, B.C.},
  volume = {I},
  publisher = {IEEE Computer Society Press, Los Alamitos},
  author = {Vliet, L.J. van and Young, I.T. and Verbeek, P.W.}
}
@article{Ziegler2004,
  year = {2004},
  title = {Interface structure and atomic bonding characteristic in silicon nitride ceramics},
  pages = {1768-1770},
  journal = {Science},
  volume = {306},
  author = {Ziegler, A. and Idrobo, J.C. and Cinibulk, M.K. and Kisielowski, C. and Browning, N.D. and Ritchie, R.O.}
}
@inproceedings{Verbeek1992a,
  year = {1992},
  title = {An estimator of edge length and surface area in digitized {2D} and {3D} images},
  booktitle = {Proc. 11th IAPR Int. Conf. on Pattern Recognition},
  pages = {1--5},
  volume = {3},
  publisher = {IEEE Computer Society Press},
  author = {Verbeek, P.W. and Vliet, L.J. van}
}
@article{Gove1995,
  number = {6},
  year = {1995},
  title = {Brightness Perception, Illusory Contours, and Corticogeniculate Feedback},
  pages = {1027--1052},
  journal = {Visual Neuroscience},
  volume = {12},
  author = {Gove, A. and Grossberg, S. and Mingolla, E.}
}
@article{Whitehouse1974,
  year = {1974},
  title = {The Quantitative Morphology of Anisotropy Trabecular Bone},
  pages = {153--168},
  journal = {Journal of Microscopy},
  volume = {101},
  author = {Whitehouse, W.J.}
}
@phdthesis{Vliet1993,
  month = {October},
  year = {1993},
  title = {Grey-Scale Measurements in Multi-Dimensional Digitized Images},
  address = {Delft, The Netherlands},
  school = {Delft University of Technology},
  author = {Vliet, L.J. van}
}
@article{Scalettar1996,
  year = {1996},
  title = {Dispersion, aberration and deconvolution in multi-wavelength fluorescence images},
  pages = {50--60},
  journal = {Journal of Microscopy},
  volume = {182},
  author = {Scalettar, B.A. and Swedlow, J.R. and Sedat, J.W. and Agard, D.A.}
}
@article{Vliet1990,
  number = {1},
  year = {1990},
  title = {The {Athena} Semi-Automated Katyotyping System},
  pages = {51--58},
  journal = {Cytometry},
  volume = {11},
  author = {Vliet, L.J. van and Young, I.T. and Mayall, B.H.}
}
@misc{Vliet1995,
  month = {October},
  year = {1995},
  title = {Segmentation of Overlapping Objects},
  howpublished = {in L.J. van Vliet and I.T. Young (eds), Abstracts of the ASCI Imaging Workshop, Venray, The Netherlands, 5-6},
  author = {Vliet, L.J. van. and Verbeek, P.W.}
}
@techreport{Vliet1996,
  number = {WC/40930},
  year = {1996},
  title = {Texture Analysis and Segmentation of Subsurface Images},
  institution = {Shell},
  author = {Vliet, L.J. van and Verbeek, P.W.}
}
@inproceedings{Vliet1994,
  year = {1994},
  title = {Better geometric measurements based on photometric information},
  booktitle = {Proc. IEEE Instrumentation and Measurement Technology Conf. IMTC94},
  pages = {1357--1360},
  author = {Vliet, L.J. van and Verbeek, P.W.}
}
@inproceedings{Vliet1999,
  month = {June 7-11},
  year = {1999},
  title = {Improving spatial resolution in exchange of temporal resolution in aliased image sequence},
  booktitle = {Proc. 11th Scandinavian Conference on Image Analysis},
  pages = {493--499},
  editor = {Ersboll, B.K. and Johansen,P. },
  address = {Lyngby},
  publisher = {Pattern Recognition Society of Denmark},
  author = {Vliet, L.J. van and Luengo Hendriks, C.L.}
}
@article{Haque1985,
  number = {6},
  month = {December},
  year = {1985},
  title = {A Two-Dimensional Fast Cosine Transform},
  pages = {1532--1538},
  journal = {IEEE Transactions on Acoustics, Speech and Signal Processing},
  volume = {33},
  annote = {key_fft},
  author = {Haque, M.A.}
}
@inproceedings{Ridder2000,
  month = {Bristol, UK},
  year = {2000},
  title = {Probabilistic {PCA} and {ICA} subspace mixture models for image segmentation},
  booktitle = {Proceedings British Machine Vision Conference 2000},
  pages = {112-121},
  editor = {Mirmehdi, M. and Thomas, B.},
  author = {Ridder, D. de and Kittler, J. and Duin, R.P.W.},
  organization = {BMVA}
}
@techreport{Nordberg1992,
  year = {1992},
  title = {Signal Representation using Operators},
  note = {LiTH-ISY-I-1342},
  institution = {{Link\"oping University}},
  author = {Nordberg, K. and Knutsson, H. and Granlund, G.H.}
}
@techreport{Nordberg1993,
  year = {1993},
  title = {On the Invariance of the Orientation and the Tensor Field Representation},
  note = {LiTH-ISY-R-1530 },
  address = {{Link\"oping}, Sweden},
  institution = {{Link\"oping} University},
  author = {Nordberg, K. and Knutsson, H. and Granlund, G.H.}
}
@inproceedings{Aguado1995,
  month = {4--6 July},
  year = {1995},
  title = {Ellipse Detection via Gradient Direction in the {Hough} Transform},
  booktitle = {Fifth International Conference on Image Processing and its Applications},
  pages = {375--378},
  author = {Aguado, A.S. and Montiel, M.E. and Nixon, M.S.}
}
@techreport{Nordberg1995,
  year = {1995},
  title = {Local Curvature from Gradients of the Orientation Tensor Field},
  note = {LiTH-ISY-R-1783},
  address = {{Link\"oping}, Sweden},
  institution = {{Link\"oping University}},
  author = {Nordberg, K. and Knutsson, H. and Granlund, G.H.}
}
@article{HautaKasari1999,
  year = {1999},
  title = {Multi-Spectral Texture Segmentation Based on the Spectral Co-occurrence Matrix},
  pages = {275--284},
  journal = {Pattern Analysis {\&} Applications},
  volume = {2},
  author = {Hauta-Kasari, M. and Parkkinen J. and Jaaskelainen, T. and Lenz, R.}
}
@book{Sethian1996,
  year = {1996},
  title = {Level Set Methods and Fast Marching Methods: Evolving Interfaces in Computational Geometry, Fluid Mechanics, Computer Vision, and Materials Science},
  address = {Cambridge},
  publisher = {Cambridge University Press},
  author = {Sethian, J. A.}
}
@techreport{Nordberg1994,
  number = {{LiTH-ISY-I-1552}},
  year = {1994},
  title = {Representation and Learning of Invariance},
  institution = {{Link\"oping University}},
  author = {Nordberg, K. and Granlund, G.H. and Knutsson, H.}
}
@article{Eberly1991,
  number = {6},
  month = {November},
  year = {1991},
  title = {On Gray Scale Image Measurements. {I}. Arc Length and Area},
  pages = {538--549},
  journal = {CVGIP: Graphical Models and Image Processing},
  volume = {53},
  author = {Eberly, D. and Lancaster, J.}
}
@book{Hearn1997,
  edition = {2},
  year = {1997},
  title = {Computer Graphics},
  address = {Englewood Cliffs, New Jersey},
  publisher = {Prentice Hall},
  author = {Hearn,D. and Baker, M.P. }
}
@inproceedings{Knutsson1985,
  month = {November 18-20},
  year = {1985},
  title = {Producing a Continuous and Distance Preserving 5-D Vector Representation of 3-D Orientation},
  booktitle = {IEEE Computer Society Workshop on Computer Architecture for Pattern Analysis and Image Database Management},
  pages = {175--182},
  publisher = {Miami Beach, Florida},
  author = {Knutsson, H.}
}
@article{Daulton2006,
  year = {2006},
  title = {Determination of chromium valence over the range {Cr(0)-Cr(VI)} by electron energy loss spectroscopy},
  pages = {561-573},
  journal = {Ultramicroscopy},
  volume = {106},
  author = {Daulton, T.L. and Little, B.J.}
}
@inproceedings{Knutsson1980,
  month = {December},
  year = {1980},
  title = {Fourier Domain Design of Line and Edge Detectors},
  booktitle = {Proceedings of the 5th International Conference on Pattern Recognition},
  address = {Miami, Florida},
  author = {Knutsson, H. and Granlund, G. H.}
}
@inproceedings{Knutsson1989,
  month = {June 19-22},
  year = {1989},
  title = {Representing Local Structure Using Tensors},
  booktitle = {The 6th Scandinavian Conference on Image Analysis},
  pages = {244--251},
  address = {Oulu, Finland},
  author = {Knutsson, H.}
}
@article{Knutsson1983,
  number = {3},
  month = {March},
  year = {1983},
  title = {Anisotropic Non-Stationary Image Estimation and its Applications --- {P}art {I}: {R}estoration of Noisy Images},
  pages = {388--397},
  note = {Report LiTH--ISY--I--0462, {Link\"oping} University, Sweden, 1981},
  journal = {IEEE Transactions on Communications},
  volume = {31},
  author = {Knutsson, H. and Wilson, R. and Granlund, G.H.}
}
@phdthesis{Knutsson1982,
  year = {1982},
  title = {Filtering and Reconstruction in Image Processing},
  address = {{Link\"oping, Sweden}},
  school = {{Link\"oping University}},
  author = {Knutsson, H.}
}
@article{Kothleitner2003,
  year = {2003},
  title = {{EELS} performance measurements on a new high energy resolution imaging filter},
  pages = {211-218},
  journal = {Micron},
  volume = {34},
  author = {Kothleitner, G. and Hofer, F.}
}
@article{Bowie1977,
  number = {5},
  year = {1977},
  title = {An Analysis Technique for Biological Shape -- {II}},
  pages = {455--464},
  journal = {Acta Cytologica},
  volume = {21},
  author = {Bowie, J.E. and Young, I.T.}
}
@article{Tiemeijer1999,
  year = {1999},
  title = {Measurement of Coulomb interactions in an electron beam monochromator},
  pages = {53-62},
  journal = {Ultramicroscopy},
  volume = {78},
  author = {Tiemeijer, P.C.}
}
@article{Osher1990,
  number = {4},
  month = {August},
  year = {1990},
  title = {Feature-Oriented Image Enhancement Using Shock Filters},
  pages = {919--940},
  journal = {SIAM J. Numer. Anal.},
  volume = {27},
  author = {Osher, S. and Rudin, L.I.}
}
@article{Hsu1990,
  year = {1990},
  title = {Partitioned {H}ough Transform for Ellipsoid Detection},
  pages = {275--282},
  journal = {Pattern Recognition},
  volume = {23},
  annote = {key_radon},
  author = {Hsu, C.-C. and Huang, J.S.}
}
@article{Fan2000,
  number = {1},
  year = {2000},
  title = {Digital imaging in transmission electron microscopy},
  pages = {1-13},
  journal = {Journal of Microscopy},
  volume = {200},
  author = {Fan, G.Y. and Ellisman, M.H.}
}
@inproceedings{Ramasse2004,
  year = {2004},
  title = {Diagnosis of aberrations from crystalline samples in aberration corrected {STEM}},
  booktitle = {13th European Microscopy Congress EMC 2004 (August 22-27, Antwerpen, Belgium)},
  pages = {1-2},
  author = {Ramasse, Q.M. and Bleloch, A.L.},
  organization = {European Microscopy Society}
}
@inproceedings{Weijer2001b,
  month = {Dec. },
  year = {2001},
  title = {Local Mode Filtering},
  booktitle = {CVPR'01},
  address = {Kauai, Hawaii, USA},
  author = {J. van de Weijer and R. van den Boomgaard}
}
@article{Krivanek1999,
  year = {1999},
  title = {Towards sub- electron beams},
  pages = {1-11},
  journal = {Ultramicroscopy},
  volume = {78},
  author = {Krivanek, O.L. and Dellby, N. and Lupini, A.R.}
}
@article{Stockwell1996,
  number = {4},
  month = {April},
  year = {1996},
  title = {Localization of the Complex Spectrum: the {S} Transform},
  pages = {998--1001},
  journal = {IEEE Transactions on Signal Processing},
  volume = {44},
  author = {Stockwell, R.G. and Mansinha, L. and Lowe, R.P.}
}
@article{Ramasse2005,
  year = {2005},
  title = {Diagnosis of aberrations from crystalline samples in scanning transmission electron microscopy},
  journal = {Ultramicroscopy},
  author = {Ramasse, Q.M. and Bleloch, A.L.}
}
@inproceedings{Ramasse2003,
  year = {2003},
  title = {Wavelet image analysis in aberration-corrected scanning transmission electrion microscopy},
  booktitle = {Elextron Microscopy and Analysis Group Conference EMAG2003 (Oxford, UK)},
  pages = {343-345},
  author = {Ramasse, Q.M. and Bleloch, A.L.},
  organization = {IOP Publishing Ltd}
}
@article{Dekker2001,
  year = {2001},
  title = {Does a monochromator improve the precision in quantitative {HRTEM}?},
  pages = {275-290},
  journal = {Ultramicroscopy},
  volume = {89},
  author = {Dekker, A.J. den and Aert, S. van and Dyck, D. van and Bos, A. van den and Geuens, P.}
}
@article{Ballard1981,
  number = {2},
  year = {1981},
  title = {Generalizing the {Hough} Transform to Detect Arbitrary Shapes},
  pages = {111--122},
  journal = {Pattern Recognition},
  volume = {13},
  annote = {key_radon},
  author = {Ballard, D.H.}
}
@book{Bass1995,
  year = {1995},
  title = {Handbook of Optics II},
  editor = {Bass, M},
  address = {New York},
  publisher = {McGraw-Hill}
}
@inproceedings{Worring1992,
  year = {1992},
  title = {The accuracy and precision of curvature estimation methods},
  booktitle = {Proceedings of the 11th IAPR International Conference on Pattern Recognition},
  pages = {139--142},
  address = {The Hague, The Netherlands},
  publisher = {IEEE Computer Society Press},
  author = {Worring, M. and Smeulders, A.W.M.}
}
@article{Uhlemann1998,
  year = {1998},
  title = {Residual wave aberrations in the first spherical aberration corrected transmission electron microscope},
  pages = {109-119},
  journal = {Ultramicroscopy},
  volume = {72},
  author = {Uhlemann, S. and Haider, M.}
}
@book{Sigel1988,
  year = {1988},
  title = {Nonparametric statistics for the behavioral sciences},
  address = {New York},
  publisher = {Mc Graw-Hill},
  author = {Siegel, S. and Castellan, N.J. Jr.}
}
@phdthesis{Eisele2002,
  month = {December},
  year = {2002},
  title = {Automatic Defect Detection and Evaluation in {X}-ray {CT} Images},
  address = {Heidelberg, Germany},
  school = {Ruprechts-Karls-{Universit\"at} University},
  author = {Eisele, H.}
}
@article{Lanzavecchia1999,
  year = {1999},
  title = {A Two-Exposure Technique for Ice-Embedded Samples Successfully Reconstructs the Chlorocruorin Pigment of Sabella spallanzanii at 2.1 nm Resolution},
  pages = {53-63},
  journal = {Journal of Structural Biology},
  volume = {127},
  author = {Lanzavecchia, S. and Wade, R.H. and Ghiretti Magaldi, A. and Tognon, G. and Bellon, P.L.}
}
@article{Demirel2005,
  year = {2005},
  title = {Clustering and diversity of fluctuations for proteins},
  pages = {41-46},
  journal = {Journal of Nanomedicine},
  volume = {1},
  author = {Demirel, M. and Cherny, D.I.}
}
@article{Cohen1997,
  number = {1},
  year = {1997},
  title = {Global minimum for active contour models: A minimal path approach},
  pages = {57-58},
  journal = {International Journal of Computer Vision},
  volume = {24},
  author = {Cohen, L.D. and Kimmel, R.}
}
@inproceedings{Geusebroek2002,
  series = {Lecture Notes in Computer Science},
  year = {2002},
  title = {Fast Anisotropic {G}auss Filtering},
  booktitle = {Proceedings of the ECCV 2002},
  pages = {99--112},
  editor = {Heyden, A.},
  volume = {2350},
  publisher = {Springer-Verlag},
  author = {Geusebroek, J.M. and Smeulders, A.W.M. and Weijer, J. van de}
}
@article{Geusebroek2003,
  number = {8},
  year = {2003},
  title = {Fast anisotropic gauss filtering},
  pages = {938-943},
  journal = {IEEE Transactions on Image Processing},
  volume = {12},
  author = {Geusebroek, J.M. and Smeulders, A.W.M. and Weijer, J. van de}
}
@article{Cohen1992,
  number = {3},
  month = {May},
  year = {1992},
  title = {Maximum Likelihood Unsupervised Textured Image Segmentation},
  pages = {239--251},
  journal = {CVGIP: Graphical Models and Image Processing},
  volume = {54},
  author = {Cohen, F.S. and Fan, Z.}
}
@article{Geusebroek2000,
  number = {1},
  year = {2000},
  title = {Robust autofocusing in microscopy},
  pages = {1-9},
  journal = {Cytometry},
  volume = {39},
  author = {Geusebroek, J.M. and Cornelissen, F. and Smeulders, A.W.M. and Geerts, H.}
}
@article{Delon2004,
  number = {3},
  title = {Photobleaching, Mobility, and Compartmentalisation: Inferences in Fluorescence Correlation Spectroscopy},
  pages = {255-267},
  journal = {Journal of Fluorescence},
  volume = {14},
  author = {Delon, A. and Usson, Y. and Derouard, J. and Biben, T. and Souchier, C.}
}
@article{Aldroubi2001,
  number = {4},
  year = {2001},
  title = {Nonuniform Sampling and Reconstruction in Shift-Invariant Spaces},
  pages = {585--620},
  journal = {SIAM Review},
  volume = {43},
  author = {Aldroubi, A. and {Gr\"ochenig}, K.}
}
@article{Barash2002,
  number = {6},
  year = {2002},
  title = {A Fundamental Relationship between Bilateral Filtering, Adaptive Smoothing, and the Nonlinear Diffusion Equation},
  pages = {844--847},
  journal = {IEEE Transactions on Pattern Analysis and Machine Intelligence},
  volume = {24},
  author = {Barash, D.}
}
@inproceedings{Lorenz1997,
  series = {Lecture Notes in Computer Science},
  year = {1997},
  title = {A Multi-scale Line Filter with Automatic Scale Selection based on the {Hessian} Matrix for Medical Image Segmentation},
  booktitle = {Scale-Space Theory in Computer Vision, First International Conference},
  pages = {152--163},
  editor = {Haar Romeny, B.M. ter and Florack, L. and Koenderink, J.J. and Viergever, M.A.},
  volume = {1252},
  address = {Utrecht, The Netherlands},
  publisher = {Springer},
  author = {Lorenz, C. and Carlsen, I.-C. and Buzug, T.M. and Fassnacht, C. and Weese, J.}
}
@article{Leavers2000a,
  number = {12},
  month = {December},
  year = {2000},
  title = {Use of the Two-Dimensional {Radon} Transform to Generate a Taxonomy of Shape for the Characterization of Abrasive Powder Particles},
  pages = {1411--1423},
  journal = {IEEE Transactions on Pattern Analysis and Machine Intelligence},
  volume = {22},
  annote = {key_radon},
  author = {Leavers, V.F.}
}
@book{Singh1992,
  year = {1992},
  title = {Optic Flow Computation: A Unified Perspective},
  publisher = {IEEE Computer Society Press},
  author = {Singh, A.}
}
@article{Foerster1948,
  number = {6},
  year = {1948},
  title = {{Zwischenmolekulare} {Energiewanderung} und {Fluoreszenz}},
  pages = {55--75},
  journal = {Annalen der Physik},
  volume = {2},
  author = {{F\"orster}, T.}
}
@article{Bigun1997,
  number = {3},
  year = {1997},
  title = {Pattern Recognition in Images by Symmetries and Coordinate Transformations},
  pages = {290--307},
  journal = {Computer Vision and Image Understanding},
  volume = {68},
  author = {{Big\"un}, J.}
}
@inproceedings{Bigun1996,
  month = {16--19 September},
  year = {1996},
  title = {Coordinate Transformations, Symmetries, and {GHT}},
  booktitle = {Proceedings of the International Conference on Image Processing},
  pages = {197--201},
  volume = {3},
  author = {{Big\"un}, J.}
}
@inproceedings{Bigun1994,
  title = {Speed, frequency, and orientation tuned 3-D Gabor filterbanks and their design},
  booktitle = {Proceedings of International Conference on Pattern Recognition, ICPR, Jerusalem},
  pages = {C-184--187},
  publisher = {IEEE Computer Society},
  author = {{Big\"un}, J.}
}
@book{Golub1996,
  edition = {3},
  year = {1996},
  title = {Matrix Computations},
  address = {Baltimore},
  publisher = {John Hopkins University Press},
  author = {G.H. Golub and C.F. van Loan}
}
@article{Jeulin1989,
  year = {1989},
  title = {Morphological Modeling of Images by Sequential Random Functions},
  pages = {403--431},
  journal = {Signal Processing},
  volume = {16},
  author = {Jeulin, D.}
}
@article{Kass1988,
  year = {1988},
  title = {Snakes: Active Contour Models},
  pages = {321--331},
  journal = {International Journal of Computer Vision},
  author = {Kass, M. and Witkin, A. and Terzopoulos, D.}
}
@article{Bigun1991,
  number = {8},
  year = {1991},
  title = {Multidimensional Orientation Estimation with Applications to Texture Analysis and Optical Flow},
  pages = {775--790},
  journal = {IEEE Transactions on Pattern Analysis and Machine Intelligence},
  volume = {13},
  author = {{Big\"un}, J. and Granlund, G.H. and Wiklund, J.}
}
@inproceedings{Luengo2000a,
  month = {June 14-16},
  year = {2000},
  title = {Morphological Scale-Space to Differentiate Microstructures of Food Products},
  booktitle = {Proceedings of the third annual conference of the Advanced School for Computing and Imaging (Heijen, the Netherlands)},
  pages = {289--293},
  editor = {{L.J. van Vliet et al.}},
  author = {Luengo Hendriks, C.L. and Vliet, L.J. van}
}
@article{Bahlmann2000,
  number = {5},
  year = {2000},
  title = {Depolarization by high aperture focusing},
  pages = {612-614},
  journal = {Applied Physics Letters},
  volume = {77},
  author = {Bahlmann, K. and Hell, S.W.}
}
@article{Dubuc2001,
  number = {1--2},
  year = {2001},
  title = {Complexity, Confusion, and Perceptual Grouping. Part {I}: The Curve-like Representation},
  pages = {55--82},
  journal = {Journal of Mathematical Imaging and Vision},
  volume = {15},
  author = {Dubuc, B. and Zucker, S.W.}
}
@book{Boor2001,
  year = {2001},
  title = {A Practical Guide to Splines},
  address = {New York},
  publisher = {Springer-Verlag},
  author = {de Boor, Carl}
}
@article{Vermolen2004,
  year = {2004},
  title = {{3D} Restoration With Multiple Images Acquired by a Modified Conventional Microscope},
  pages = {113-125},
  journal = {Microscopy Research and Technique},
  volume = {64},
  author = {Vermolen, B.J and Garini, Y. and Young, I.T.}
}
@article{Kass1987,
  year = {1987},
  title = {Analyzing Oriented Patterns},
  pages = {362--385},
  journal = {Computer Vision, Graphics and Image Processing},
  volume = {37},
  author = {Kass, M. and Witkin, A.}
}
@article{Ocuna1992,
  number = {3},
  month = {May},
  year = {1992},
  title = {Texture Modeling using {G}ibbs Distribution},
  pages = {210--222},
  journal = {CVGIP: Graphical Models and Image Processing},
  volume = {54},
  author = {Ocuna, C.O.}
}
@book{Jaehne1993,
  series = {Lecture Notes in Computer Science},
  number = {751},
  year = {1993},
  title = {Spatio-Temporal Image Processing},
  editor = {Goos, G. and Hartmanis, J.},
  address = {Berlin},
  publisher = {Springer-Verlag},
  author = {{J\"ahne}, B.}
}
@misc{Moller2000,
  year = {2000},
  title = {Aspects of Spatial Statistics, Stochastic Geometry and {Markov} Chain Monte Carlo Methods},
  note = {D. Sc. thesis},
  howpublished = {www},
  author = {{M\oe ller}, J.}
}
@article{Nagy2003,
  number = {1},
  year = {2003},
  title = {Small interfering {RNA}s suppress the expression of endogenous and {GFP}-fused epidermal growth factor receptor (erbB1) and induce apoptosis in erbB1-overexpressing cells},
  pages = {39-49},
  journal = {Experimental Cell Research},
  volume = {285},
  author = {Nagy, P. and Ardent-Jovin, D.J. and Jovin, T.M.}
}
@book{Greiner1993,
  edition = {2},
  year = {1993},
  title = {Theoretische Physik, Thermodynamik und statische Mechanik},
  address = {Frankfurt},
  publisher = {Verlag Harri Deutsch},
  author = {Greiner, W. and Neise, L. and {St\"ocker}, H.}
}
@inproceedings{Soille2000,
  series = {Lecture Notes on Computer Science},
  year = {2000},
  title = {Morphological Operators with Discrete Line Segments},
  booktitle = {DGCI 2000, 9th Discrete Geometry for Computer Imagery},
  pages = {78--98},
  editor = {Borgefors, G. and {Nystr\"om}, I. and Sanniti di Baja, G.},
  volume = {1953},
  publisher = {Springer},
  author = {Soille, P.}
}
@article{Ringach1996,
  number = {19},
  year = {1996},
  title = {Spatial and Temporal Properties of Illusory Contours and Amodal Boundary Completion},
  pages = {3037--3050},
  journal = {Vision Research},
  volume = {36},
  author = {Ringach, D.L. and Shapley, R.}
}
@article{Horn1981,
  year = {1981},
  title = {Determining Optical Flow},
  pages = {185--203},
  journal = {Artificial Intelligence},
  volume = {17},
  author = {Horn, B.K.P. and Schunck, B.G.}
}
@techreport{Horn1980,
  month = {April},
  year = {1980},
  title = {Determining Optical Flow},
  note = {A.I. Memo No. 572},
  institution = {Massachusetts Institute of Technology},
  author = {Horn, B.K.P. and Schunck, B.G.}
}
@misc{Verbeek1993a,
  year = {1993},
  title = {The {GST} as local mean squared friction},
  howpublished = {private communications},
  author = {Verbeek, P.W.}
}
@article{Boutin2000,
  number = {3},
  year = {2000},
  title = {Numerically Invariant Signature Curves},
  pages = {235--248},
  journal = {International Journal of Computer Vision},
  volume = {40},
  author = {Boutin, M.}
}
@article{Bettini1980,
  number = {9},
  year = {1980},
  title = {Microscopic persistence length of {DNA: Its} relation to average molecular dimensions},
  pages = {1689-1694},
  journal = {Biopolymers},
  volume = {19},
  author = {Bettini, A. and Pozzan, M.R. and Valdevit, E. and Frontali, C.}
}
@inproceedings{Ginkel2000,
  month = {June 14-16},
  year = {2000},
  title = {Robust Curvature Estimation by Finding Optimal Circular Segments in Orientation Space},
  booktitle = {ASCI2000, Proc. 6th Annual Conference of the Advanced School for Computing and Imaging (Lommel, Belgium)},
  pages = {299--306},
  editor = {Vliet, L.J. van and Heijnsdijk, J.W.K. and Kielmann, T. and Knijnenburg, P.M.W.},
  author = {Ginkel, M. van and Vliet, L.J. van and Verbeek, P.W.},
  organization = {ASCI, Delft}
}
@inproceedings{Ginkel2001,
  month = {May 30--June 1},
  year = {2001},
  title = {Robust Curve Detection using a Radon Transform in Orientation Space Applied to Fracture Detection in Borehole Images},
  booktitle = {ASCI2001, Proc. 7th Annual Conference of the Advanced School for Computing and Imaging (Heijen, the Netherlands)},
  pages = {84--91},
  editor = {Lagendijk, R.L. and Heijnsdijk, J.W.J. and Pimentel, A.D. and Wilkinson, M.H.F.},
  author = {Ginkel, M. van and Vliet, L.J. van and Verbeek, P.W. and Kraaijveld, M.A. and Reding, E.P.},
  organization = {ASCI, Delft}
}
@inproceedings{Ginkel2003,
  series = {Lecture Notes in Computer Science 2749},
  month = {June 29--July 2},
  year = {2003},
  title = {Robust Curve Detection Using a {Radon} Transform in Orientation Space},
  booktitle = {Proceedings of the 13th Scandinavian Conference on Image Analysis},
  pages = {125--132},
  editor = {{Big\"un}, J. and Gustavsson, T.},
  publisher = {Springer},
  author = {Ginkel, M. van and Kraaijveld, M.A. and Vliet, L.J. van and Reding, E.P. and Verbeek, P.W. and Lammers, H.J.}
}
@article{Jonker2002,
  number = {6},
  year = {2002},
  title = {Skeletons in {N} Dimensions using Shape Primitives},
  pages = {677--686},
  journal = {Pattern Recognition Letters},
  volume = {23},
  author = {Jonker, P.P.}
}
@phdthesis{Ginkel2002,
  year = {2002},
  title = {Image Analysis using Orientation Space based on Steerable Filters},
  note = {digital version available:\\\ {\small\tt http://www.ph.tn.tudelft.nl/PHDTheses/MvGinkel/thesis\_vanginkel.html}},
  address = {Delft, The Netherlands},
  school = {Delft University of Technology},
  author = {Ginkel, M. van}
}
@article{Chen1989a,
  number = {7},
  year = {1989},
  title = {A Multiscaling Approach Based on Morphological Filtering},
  pages = {694--700},
  journal = {IEEE Transactions on Pattern Analysis and Machine Intelligence},
  volume = {11},
  author = {Chen, M.-H. and Yan, P.-F.}
}
@article{Zhou2001a,
  number = {24},
  year = {2001},
  title = {Direct Evidence for the Size and Conformational Variability of the Pyruvate Dehydrogenase Complex Revealed by Three-dimensional Electron Microscopy},
  pages = {21704-21713},
  journal = {Journal of Biological Chemistry},
  volume = {276},
  author = {Zhou, Z.H. and Liao, W. and Cheng, R.H. and Lawson, J.E. and McCarthy, D.B. and Reed, L.J. and Stoops, J.K.}
}
@article{Verwer1989,
  number = {4},
  month = {April},
  year = {1989},
  title = {An Efficient Uniform Cost Algorithm Applied to Distance Transforms},
  pages = {425--429},
  journal = {IEEE Transactions on Pattern Analysis and Machine Intelligence},
  volume = {11},
  author = {Verwer, B.J.H. and Verbeek, P.W. and Dekker, S.T.}
}
@techreport{Ginkel2004,
  month = {December},
  year = {2003},
  title = {An short introduction to the Radon and Hough transforms and how they relate to each other},
  note = {Technical Report PH-2003-03},
  institution = {Pattern Recognition Group, Delft University of Technology},
  author = {Ginkel, M. van and Luengo Hendriks, C.L. and Vliet, L.J. van}
}
@inproceedings{Verwer1988,
  month = {November},
  year = {1988},
  title = {Improved metrics in image processing applied to the Hilditch skeleton},
  booktitle = {Proceedings of the 9th IAPR international conference on pattern recognition (ICPR), (Rome, Italy)},
  pages = {137--142},
  author = {Verwer, B.J.H.}
}
@article{Beaucage1997,
  year = {1997},
  title = {Persistence Length of Isotactic Poly(hydroxy butyrate)},
  pages = {4158-4162},
  journal = {Macromolecules},
  volume = {30},
  author = {Beaucage, G. and Rane, S. and Sukumaran, S. and Satkowski, M.M. and Schechtman, L.A. and Doi, Y.}
}
@article{Dyck2004,
  year = {2004},
  title = {Physical Limits on Atomic Resolution},
  pages = {153-157},
  journal = {Microscopy and Microanalysis},
  volume = {10},
  author = {Dyck, D. van and Aert, S. van and Dekker, A.J. den}
}
@article{Dyck2003,
  year = {2003},
  title = {Is atomic resolution transmission electron microscopy able to resolve and re ne amorphous structures?},
  pages = {27-42},
  journal = {Ultramicroscopy},
  volume = {98},
  author = {Dyck, D. van and Aert, S. van and Dekker, A.J. den and Bos, A. van den}
}
@article{Bastiaens1996,
  number = {16},
  year = {1996},
  title = {Imaging the intracellular trafficking and state of the {AB$_5$} quaternary structure of cholera toxin},
  pages = {4246-4253},
  journal = {The EMBO Journal},
  volume = {15},
  author = {Bastiaens, P.I.H. and Majoul, I.V. and Verveer, P.J. and {S\"oling}, H.-D. and Jovin, T.M.}
}
@article{Lanzavecchia2005,
  year = {2005},
  title = {Conical tomography of freeze-fracture replicas: a method for the study of integral membrane proteins inserted in phospholipid bilayers},
  pages = {87-98},
  journal = {Journal of Structural Biology},
  volume = {149},
  author = {Lanzavecchia, S. and Cantele, F. and Bellon, P.L. and Zampighi, L. and Kreman, M. and Wrigth, E. and Zampighi, G.A.}
}
@article{Chang1997,
  number = {2},
  year = {1997},
  title = {Fast algorithm for point pattern matching: {I}nvariant to translations, rotations and scale changes},
  pages = {311-320},
  journal = {Pattern Recognition},
  volume = {30},
  author = {Chang, S.-H. and Cheng, F.-H. and Hsu, W.-H.and Wu, G.-Z.}
}
@inproceedings{Froment1999,
  series = {Lecture Notes in Computer Science},
  year = {1999},
  title = {A Compact and Multiscale Image Model Based on Level Sets},
  booktitle = {Scale-Space Theories in Computer Vision},
  pages = {152--163},
  publisher = {Springer Verlag},
  author = {Froment, J.}
}
@article{Quintanilla1997,
  year = {1997},
  title = {Clustering in a Continuum Percolation Model},
  pages = {327--336},
  journal = {Adv. Appl. Probab.},
  volume = {29},
  author = {Quintanilla, J. and Torquato, S.}
}
@article{Quintanilla1999,
  number = {13},
  month = {October},
  year = {1999},
  title = {Percolation for a model of statistically inhomogeneous random media},
  journal = {Journal of Chemical Physics},
  volume = {111},
  author = {Quintanilla, J. and Torquato, S.}
}
@article{Lindeberg1994a,
  number = {2},
  year = {1994},
  title = {Scale-space Theory: A Basic Tool for Analyzing Structures at Different Scales},
  pages = {224--270},
  journal = {Journal of Applied Statistics},
  volume = {21},
  author = {Lindeberg, T.}
}
@inproceedings{Maragos1999,
  series = {Lecture Notes on Computer Science},
  month = {September},
  year = {1999},
  title = {Nonlinear PDEs and Numerical Algorithms for Modeling Levelings and Reconstruction Filters},
  booktitle = {Scale-Space Theories in Computer Vision (Second International Conference, Scale-Space'99, Corfu, Greece)},
  pages = {363--374},
  editor = {Nielsen, Mads and Johansen, Peter and Olsen, Ole F. and Weickert, Joachim},
  volume = {1682},
  address = {Berlin Heidelberg},
  publisher = {Springer-Verlag},
  author = {Maragos, Petros and Meyer, Fernand}
}
@article{Cooley1965,
  month = {April},
  year = {1965},
  title = {An algorithm for the machine calculation of complex {Fourier} series},
  pages = {297--301},
  journal = {Math. Comp.},
  volume = {19},
  annote = {key_fft},
  author = {Cooley, J.W. and Tukey, J.W.}
}
@article{Bruin2004,
  year = {2004},
  title = {Interactive {3D} segmentation using connected orthogonal contours},
  pages = {1-18},
  journal = {Computers in Biology and Medicine},
  volume = {34},
  author = {Bruin, P.W. de and Dercksen, V.J. and Post, F.H. and Vosselpoel, A.M. and Streekstra, G.J. and Vos, F.M.}
}
@incollection{Bastiaens1998,
  edition = {second},
  year = {1998},
  title = {Fluorescence Resonance Energy Transfer Microscopy},
  booktitle = {Cell Biology: A Laboratory Handbook},
  pages = {99-117},
  address = {New York},
  publisher = {Academic Press},
  author = {Bastiaens, I.H. and Jovin, T.M.}
}
@article{Maragos1995,
  number = {4},
  year = {1995},
  title = {Slope Transforms: Theory and Application to Nonlinear Signal Processing},
  pages = {864-877},
  journal = {IEEE Transactions on Signal Processing},
  volume = {43},
  author = {Maragos, Petros}
}
@inproceedings{Bakker1999,
  year = {1999},
  title = {Edge preserving orientation adaptive filtering},
  booktitle = {Conference on Computer Vision and Pattern Recognition},
  pages = {535--540},
  volume = {2},
  address = {Los Alamitos, CA, USA},
  publisher = {IEEE Computer Society Press},
  author = {Bakker, P. and Vliet, L.J. van and Verbeek, P.W.}
}
@article{Mokhtarian2001,
  year = {2001},
  title = {Curvature Computation on Free-Form 3-D Meshes at Multiple Scales},
  pages = {118--139},
  journal = {Computer Vision and Image Under Standing},
  volume = {83},
  author = {Mokhtarian, F. and Khalili, N. and Yuen, P.}
}
@phdthesis{Scharr2000,
  month = {May},
  year = {2000},
  title = {Optimale Operatoren in der Digitalen Bildverarbeitung},
  address = {Heidelberg, Germany},
  school = {Ruprechts-Karls-{Universit\"at} University},
  author = {Scharr, H.}
}
@article{Hell2003,
  number = {11},
  year = {2003},
  title = {Towards fluorescence nanoscopy},
  pages = {1347-1355},
  journal = {Nature Biotechnology},
  volume = {21},
  author = {Hell, S.W.}
}
@techreport{Goutsias1996,
  year = {1996},
  title = {{M}arkov Random Fields: Interacting Particle Systems for Statistical Image Modeling and Analysis},
  institution = {Department of Electrical and Computer Engineering, The Johns Hopkins University, USA},
  author = {Goutsias, J.}
}
@article{Hell2004,
  number = {5},
  year = {2004},
  title = {Concepts for nanoscale resolution in fluorescence microscopy},
  pages = {599-609},
  journal = {Current Opinion in Neurobiology},
  volume = {14},
  author = {Hell, S.W. and Dyba, M. and Jackobs, S.}
}
@article{Mouche1999,
  year = {1999},
  title = {Structural Comparison of Cephalopod Hemocyanins: Phylogenetic Significance},
  pages = {199-212},
  journal = {Journal of Structural Biology},
  volume = {127},
  author = {Mouche, F. and Boisset, N. and Lamy, J. and Zal, F. and Lamy, J.N.}
}
@book{Lipson2001,
  edition = {3rd edition},
  year = {2001},
  title = {Optical Physics},
  address = {Cambridge},
  publisher = {Cambridge University Press},
  author = {Lipson, S.G. and Lipson, H. and Tannhauser, D.S.}
}
@article{Winograd1978,
  number = {141},
  month = {January},
  year = {1978},
  title = {On Computing the Discrete {Fourier} Transform},
  pages = {175--199},
  journal = {Mathematics of Computation},
  volume = {32},
  annote = {key_fft},
  author = {Winograd, S.}
}
@article{Narasimha1978,
  month = {June},
  year = {1978},
  title = {On the computation of the discrete cosine transform},
  pages = {934--936},
  journal = {IEEE Transactions on Communications},
  volume = {26},
  annote = {key_fft},
  author = {Narasimha, M.J. and Peterson, A.M.}
}
@article{Rajagopal1959,
  number = {2},
  month = {February},
  year = {1959},
  title = {Statistical Theory of Particle Size Distributions in Emulsions and Suspensions},
  pages = {85--92},
  journal = {Kolloid-Zeitschrift},
  volume = {162},
  author = {Rajagopal, E.S.}
}
@article{Lindek1996,
  number = {3},
  year = {1996},
  title = {Optical transfer functions for confocal theta fluorescence microscopy},
  pages = {479--482},
  journal = {Journal of the Optical Society of America A},
  volume = {13},
  author = {Lindek, S. and Stelzer, E.H.K.}
}
@article{Winograd1976,
  number = {4},
  month = {April},
  year = {1976},
  title = {On Computing the Discrete {Fourier} Transform},
  pages = {1005--1006},
  journal = {Proc. Nat. Acad. Sci. USA},
  volume = {73},
  annote = {key_fft},
  author = {Winograd, S.}
}
@article{Genovesio2006,
  number = {5},
  year = {2006},
  title = {Tracking in {3-D+t} Microscopy: Method and Application to the Tracking of Endocytosed Quantum Dots},
  pages = {1062-1070},
  journal = {IEEE Transactions on Image Processing},
  volume = {15},
  author = {Genovesio, A. and Liedl, T. and Emiliani, V. and Parak, W.J. and Coppey-Moisan, M. and Olivo-Marin, J.-C.}
}
@article{Vliet1988,
  number = {1},
  year = {1988},
  title = { A contour processing method for fast binary neighbourhood operations},
  pages = {27--36},
  journal = {Pattern Recognition Letters},
  volume = {7},
  author = {Vliet, L.J. van and Verwer, B.J.H.}
}
@article{Vliet1989,
  number = {2},
  year = {1989},
  title = {A nonlinear Laplace operator as edge detector in noisy images},
  pages = {167--195},
  journal = {Computer Vision, Graphics and Image Processing},
  volume = {45},
  author = {Vliet, L.J. van and Young, I.T. and Beckers, A.L.D.}
}
@inproceedings{Rieger2002b,
  month = {August 11-15},
  year = {2002},
  title = {Curvature estimation of surfaces in 3D grey-value images},
  booktitle = {ICPR'02, Proc. 16th Int. Conf. on Pattern Recognition},
  editor = {R. Kasturi, D. Laurendeau, C. Suen},
  volume = {1},
  author = {Rieger, B. and Timmermans, F.J. and Vliet, L.J. van and Verbeek, P.W. },
  organization = {IEEE Computer Society}
}
@inproceedings{Hall1996,
  month = {June 16-19},
  year = {1996},
  title = {Automatic Extraction and Characterization of Geological Features and Textures from Borehole Images and Core Photographs},
  booktitle = {SPWLA 37th Annual Logging Symposium},
  author = {Hall, J. and Ponzi, M. and Gonfalini, M. and Maletti, G.}
}
@article{Herk1992,
  month = {July},
  year = {1992},
  title = {A Fast Algorithm for Local Minimum and Maximum Filters on Rectangular and Octagonal Kernels},
  pages = {517--521},
  journal = {Pattern Recognition Letters},
  volume = {13},
  author = {Herk, M. van}
}
@inproceedings{Rieger2002a,
  month = {June},
  year = {2002},
  title = {Estimation of curvature on surfaces in 3D grey-value images},
  booktitle = {Proc. ASCI 2002, 8th Annual Conf. of the Advanced School for Computing and Imaging},
  pages = {170--177},
  author = {Rieger, B. and Timmermans, F.J. and Vliet, L.J. van}
}
@article{Sethian1985,
  year = {1985},
  title = {Curvature and the Evolution of Fronts},
  pages = {487--499},
  journal = {Communications in Mathematical Physics},
  volume = {101},
  author = {Sethian, J.A.}
}
@book{Oneill1997,
  year = {1997},
  title = {Elementary Differential Geometry},
  address = {New York},
  annote = {ph2540},
  publisher = {Academic Press},
  author = {B. O'Neill}
}
@book{Gray1994,
  year = {1994},
  title = {Modern Differential Geometry of Curves and Surfaces},
  address = {Florida},
  publisher = {CRC Press},
  author = {Gray, A.}
}
@techreport{Knutsson1995,
  year = {1995},
  title = {Robust N-Dimensional Orientation Estimation using Quadrature Filters and Tensor Whitening},
  note = {LiTH-ISY-R-1798},
  institution = {{Link\"oping} University, Sweden},
  author = {Knutsson, H. and Andersson, M.T.}
}
@book{Fisher1993,
  year = {1993},
  title = {Statistical Analysis of Circular Data},
  publisher = {Cambridge University Press},
  author = {Fisher, N.I.}
}
@inproceedings{Knutsson1993,
  year = {1993},
  title = {Normalized Convolution - A Technique for Filtering Incomplete and Uncertain Data},
  booktitle = {SCIA'93, Proceedings of the 8th Scandinavian Conference on Image Analysis},
  pages = {997--1006},
  editor = {{H\o gda}, K. A. and Braathen, B. and Heia, K.},
  volume = {2},
  address = {{Troms\o} Norway},
  publisher = {Norwegian Society for Image Processing and Pattern Recognition},
  author = {Knutsson, H. and Westin, C.-F.}
}
@article{Eggers1998,
  number = {1},
  year = {1998},
  title = {Two fast Euclidean distance transformations in Z2 based on sufficient propagation},
  pages = {106-116},
  journal = {Comput. Vision Image Understanding},
  volume = {69},
  author = {Eggers, H.}
}
@inproceedings{Knutsson1991,
  month = {September},
  year = {1991},
  title = {A Tensor Based Approach to Structure Analysis and Enhancement in 2{D}, 3{D} and 4{D}},
  booktitle = {Workshop Program, Seventh Workshop on Multidimensional Signal Processing},
  address = {Lake Placid, New York, USA},
  publisher = {IEEE Signal Processing Society},
  author = {Knutsson, H. and Haglund, L. and {B\aa rman}, H.}
}
@article{Coster2001,
  year = {2001},
  title = {Image Analysis and Mathematical Morphology for Civil Engineering Materials},
  pages = {133--151},
  journal = {Cement {\&} Concrete Composites},
  volume = {23},
  author = {Coster, M. and Chermant, J.-L.}
}
@misc{Krivanek2002,
  year = {2002},
  title = {Autoadjusting charged-particle probe-forming apparatus},
  howpublished = {EP1197986},
  author = {Krivanek, O.L. and Dellby, N. and Lupini, A.R.}
}
@inproceedings{Granlund2000,
  month = {September 10--11},
  year = {2000},
  title = {An Associative Perception-Action Structure Using a Localized Space Variant Information Representation},
  booktitle = {Proceedings of Algebraic Frames for the Perception-Action Cycle (AFPAC)},
  address = {Kiel, Germany},
  author = {Granlund, G.H.}
}
@book{Papoulis2002,
  edition = {fourth},
  year = {2002, 1965},
  title = {Probability, Random Variables and Stochastic Processes},
  publisher = {McGraw-Hill},
  author = {Papoulis, A. and Pillai, S.U.}
}
@article{Brown1829,
  number = {34},
  year = {1829},
  title = {Additional Remarks on Active Molecules},
  pages = {161-166},
  journal = {The Philosophical Magazine and Annals of Philosophy},
  volume = {6},
  author = {Brown, R.}
}
@article{Unser1992,
  number = {1},
  month = {January},
  year = {1992},
  title = {Polynomial Spline Signal Approximations: Filter Design and Asymptotic Equivalence with Shannon's Sampling Theorem},
  pages = {95--103},
  journal = {IEEE Transactions on Information Theory},
  volume = {38},
  author = {Unser, Michael and Aldroubi, Akram and Eden, Murray}
}
@article{Worring1993,
  number = {3},
  year = {1993},
  title = {Digital curvature estimation},
  pages = {336--382},
  journal = {CVGIP: Image Understanding},
  volume = {58},
  author = {Worring, M. and Smeulders, A.W.M.}
}
@article{Medalia2002,
  year = {2002},
  title = {Macromolecular Architecture in Eukaryotic Cells Visualized by Cryoelectron Tomography},
  pages = {1209-1213},
  journal = {Ultramicroscopy},
  volume = {298},
  author = {Medalia, O. and Weber, I. and Frangakis, A.S. and Nicastro, D. and Gerisch, G. and Baumeister, W.}
}
@article{Wang1990,
  number = {1},
  year = {1990},
  title = {Electron-energy-loss and optical-transmittance investiationf of $Bi_2SR_2CaCu_2O_8$},
  pages = {420-425},
  journal = {Physical Review B},
  volume = {42},
  author = {Wang, Y.Y. and Feng, G. and Ritter, A.L.}
}
@misc{LeachXXXX,
  title = {Singular Value Decomposition -- A Primer},
  howpublished = {Web download-able. Department of Computer Science, Brown University, Providence, U.S.A.},
  author = {Leach, S.}
}
@article{Majumdar2000,
  number = {6},
  year = {2000},
  title = {Classification of Cereal Grains Using Machine Vision: {III}. Texture Models},
  pages = {1681--1687},
  journal = {Transactions of the American Society of Agricultural Engineers},
  volume = {43},
  author = {Majumdar, S. and Jayas, D.S.}
}
@techreport{Shewchuk1996,
  year = {1996},
  title = {Adaptive Precision Floating-Point Arithmetic and Fast Robust Geometric Predicates},
  institution = {School of Computer Science, Carnegie Mellon University, USA},
  author = {Shewchuk, J.R.}
}
@mastersthesis{Bezuijen2003,
  month = {September},
  year = {2003},
  title = {Improved sub-pixel shift estimation in 2D gray-value images},
  address = {Delft, The Netherlands},
  school = {Delft University of Technology},
  author = {Bezuijen, M.}
}
@article{Marr1980,
  year = {1980},
  title = {Theory of edge detection},
  pages = {187--217},
  journal = {Proceedings of the Royal Society of London B},
  volume = {207},
  author = {Marr, D. and Hildreth, E.}
}
@book{Marr1982,
  year = {1982},
  title = {Vision},
  address = {San Francisco, USA},
  publisher = {Freeman},
  author = {Marr, D.}
}
@article{Gerig1992,
  number = {2},
  month = {June},
  year = {1992},
  title = {Nonlinear anisotropic filtering of {MRI} data},
  pages = {221--232},
  journal = {IEEE Transactions on Medical Imaging},
  volume = {11},
  author = {Gerig, G. and {K\"ubler}, O. and Kikinis, R. and Jolesz, F.A.}
}
@article{Runnels1995,
  number = {4},
  year = {1995},
  title = {Theory and application of fluorescence homotransfer to melittin oligomerization},
  pages = {1569-1583},
  journal = {Biophysical Journal},
  volume = {69},
  author = {Runnels, L.W. and Scarlata, S.F.}
}
@article{Scharcanski1999,
  number = {11},
  month = {November},
  year = {1999},
  title = {Local Spatial Anisotropy and Its Variability},
  pages = {393--397},
  journal = {Journal of Pulp and Paper Science},
  volume = {25},
  author = {Scharcanski, J. and Dodson, C.T.J.}
}
@article{Pedersen2000,
  year = {2000},
  title = {The {Hausdorff} Dimension and Scale-Space Normalization of Natural Images},
  pages = {266--277},
  journal = {Journal of Visual Communication and Image Representation},
  volume = {11},
  author = {Pedersen, K.S. and Nielsen, M.}
}
@phdthesis{Fens2000,
  year = {2000},
  title = {Petrophysical Properties from Small Rock Samples using Image Analysis Techniques},
  school = {Delft University of Technology, Delft, The Netherlands},
  author = {Fens, T.W.}
}
@article{Keefe1992,
  year = {1992},
  title = {'Resolution' in high-resolution electron microscopy},
  pages = {282-297},
  journal = {Ultramicroscopy},
  volume = {47},
  author = {O'Keefe, M.A.}
}
@book{Hadwiger1957,
  year = {1957},
  title = {{V}orlesungen {\"uber} {I}nhalt, {Oberfl\"ache} und {I}soperimetrie},
  address = {Berlin},
  publisher = {Springer-Verlag},
  author = {Hadwiger, H.}
}
@book{Aguilera1999,
  edition = {second},
  year = {1999},
  title = {Microstructural Principles of Food Processing and Engineering},
  publisher = {Aspen Publishers, Inc.},
  author = {Aguilera, J.M. and Stanley, D.W.}
}
@article{Gramkov2001,
  year = {2001},
  title = {On Averaging Rotations},
  pages = {7--16},
  journal = {Journal of Mathematical Imaging and Vision},
  volume = {15},
  author = {Gramkov, C.}
}
@book{Bracewell2000,
  edition = {third},
  year = {2000,1965},
  title = {The {F}ourier Transform and its Applications},
  annote = {key_fft},
  publisher = {McGraw-Hill},
  author = {Bracewell, R.N.}
}
@article{Kimme1975,
  number = {2},
  month = {February},
  year = {1975},
  title = {Finding Circles by an Array of Accumulators},
  pages = {120--122},
  journal = {Communications of the ACM},
  volume = {18},
  author = {Kimme, C. and Ballard, D. and Sklansky, J.}
}
@article{Klar2001,
  number = {4},
  year = {2001},
  title = {Stimulated emission depletion microscopy with an offset depleting beam},
  pages = {393-395},
  journal = {Applied Physics Letters},
  volume = {78},
  author = {Klar, T. A. and Dyba, M. and Hell, S.W.}
}
@book{Madisetti1997,
  year = {1997},
  title = {The Digital Signal Processing Handbook},
  editor = {Madisetti, V.K. and Williams, D.B.},
  publisher = {IEEE Press/CRC Press}
}
@article{Granlund1978,
  year = {1978},
  title = {In Search of a General Picture Processing Operator},
  pages = {155--173},
  journal = {Computer Graphics and Image Processing},
  volume = {8},
  author = {Granlund, G.H.}
}
@book{Serra1982,
  year = {1982},
  title = {Image Analysis and Mathematical Morphology},
  address = {London},
  publisher = {Academic Press},
  author = {Serra, J.}
}
@book{Runge1924,
  year = {1924},
  title = {Vorlesungen {\"uber} Numerisches Rechnen},
  publisher = {Springer Verlag},
  author = {Runge, C. and Konitz, H.}
}
@article{Jeulin1992,
  number = {suppl. I},
  year = {1992},
  title = {Directional Mathematical Morphology for Oriented Image Restoration and Segmentation},
  pages = {545--550},
  journal = {Acta Stereology},
  volume = {11},
  author = {Jeulin, D. and Kurdy, M.B.}
}
@article{Jeulin1993,
  month = {October},
  year = {1993},
  title = {Random Models for Morphological Analysis of Powders},
  pages = {13--21},
  journal = {Journal of Microscopy},
  volume = {172, Pt 1},
  author = {Jeulin, D.}
}
@article{Westerweel1997,
  year = {1997},
  title = {Fundamentals of digital particle image velocimetry},
  pages = {1379-1392},
  journal = {Measurement Science and Technology},
  volume = {8},
  author = {Westerweel, J.}
}
@article{Vossepoel1979,
  year = {1979},
  title = {Dioda: Delineation and feature extraction of microscopical objects},
  pages = {231-244},
  journal = {Computer Programs in Biomedicine},
  volume = {10},
  author = {Vossepoel, A.M. and Smeulders, A.W.M and Broek, K. van den}
}
@inproceedings{Meyer1999a,
  series = {Lecture Notes on Computer Science},
  month = {September},
  year = {1999},
  title = {Morphological Scale-Space Representation with Levelings},
  booktitle = {Scale-Space Theories in Computer Vision (Second International Conference, Scale-Space'99, Corfu, Greece)},
  pages = {187--198},
  editor = {Nielsen, Mads and Johansen, Peter and Olsen, Ole F. and Weickert, Joachim},
  volume = {1682},
  address = {Berlin Heidelberg},
  publisher = {Springer-Verlag},
  author = {Meyer, Fernand and Maragos, Petros}
}
@article{Gerlich2001,
  year = {2001},
  title = {Four-dimensional imaging and quantitative reconstruction to analyse complex spatiotemporal processes in living cells},
  pages = {852-855},
  journal = {Nature Cell Biology},
  volume = {9},
  author = {Gerlich, D. and Beaudouin, J. and Gebhard, M. and Ellenberg, J. and Eils, R.}
}
@article{Sklansky1978,
  number = {10},
  month = {October},
  year = {1978},
  title = {On the {H}ough Technique for Curve Detection},
  pages = {923--926},
  journal = {IEEE Transactions on Computers},
  volume = {27},
  annote = {key_radon},
  author = {Sklansky, J.}
}
@article{Vliet1994a,
  number = {5},
  year = {1994},
  title = {Edge localization by MoG filters: Multiple-of-Gaussians},
  pages = {485--496},
  journal = {Pattern Recognition Letters},
  volume = {15},
  author = {Vliet, L.J. van and Verbeek, P.W.}
}
@book{doCarmo,
  year = {1976},
  title = {Differential Geometry of Curves and Surfaces},
  address = {New Jersey},
  publisher = {Prentice Hall},
  author = {do Carmo, M.P.}
}
@book{Dullien1979,
  edition = {second},
  year = {1979, 1992},
  title = {Porous Media - Fluid Transport and Pore Structure},
  publisher = {Academic Press},
  author = {Dullien, F.A.L.}
}
@article{Gerlich2003,
  year = {2003},
  title = {Quantitative motion analysis and visualization of cellular structures},
  pages = {3-13},
  journal = {Methods},
  volume = {29},
  author = {Gerlich, D. and Mattes, J. and Eils, R.}
}
@phdthesis{Eckley2001,
  month = {September},
  year = {2001},
  title = {Wavelet Methods for Time Series and Spatial Data},
  address = {Bristol, United Kingdom},
  school = {University of Bristol},
  author = {Eckley, I.A.}
}
@article{Verveer1999,
  number = {1},
  year = {1999},
  title = {A comparison of image restoration approaches applied to three-dimensional confocal and wide-field fluorescence microscopy},
  pages = {50-61},
  journal = {Journal of Microscopy},
  volume = {193},
  author = {Verveer, P.J. and Gemkow, M.J. and Jovin, T.M.}
}
@article{Verveer1998,
  number = {3},
  year = {1998},
  title = {Theory of confocal fluorescence imaging in the programmable array microscope (PAM)},
  pages = {192-198},
  journal = {Journal of Microscopy},
  volume = {198},
  author = {Verveer, P.J. and Hanley, Q.S. and Verbeek, P.W. and Vliet, L.J. van and Jovin, T.M.}
}
@misc{FastICA,
  year = {2004},
  title = {{FastICA}: An implementation of the fast fixed-point algorithm for independent component analysis in {MATLAB}, version 2.3},
  note = {Helsinki University of Technology, {\tt http://www.cis.hut.fi/projects/ica/fastica/}},
  author = {Hurri, J. and {G\"avert}, H. and {S\"arel\"a}, J. and {Hyv\"arinen}, A.}
}
@article{Lambacher1996,
  number = {3},
  year = {1996},
  title = {Fluorescence interference-contrast microscopy on oxidized silicon using a monomolecular dye layer},
  pages = {207--216},
  journal = {Applied Physics A},
  volume = {63},
  author = {Lambacher, A. and Fromherz, P.}
}
@phdthesis{Eijlers1993,
  year = {1993},
  title = {Scaling and Texture, Pyramids and Fractals},
  address = {Delft},
  school = {Information Theory Group, Department of Electrical Engineering, Delft University of Technology},
  author = {Eijlers, E.J.}
}
@article{Verveer1997,
  year = {1997},
  title = {Acceleration of the {ICTM} image restoration algorithm},
  pages = {191--195},
  journal = {Journal of Microscopy},
  volume = {188},
  author = {Verveer, P.J. and Jovin, T.M.}
}
@article{Weickert1999,
  year = {1999},
  title = {Coherence-enhancing diffusion of color images},
  pages = {201--212},
  journal = {Image and Vision Computing},
  volume = {17},
  author = {Weickert, J.}
}
@article{Young2003,
  number = {3},
  year = {2003},
  title = {Monitoring enzymatic reactions in nanolitre wells},
  pages = {254-263},
  journal = {Journal of Microscopy},
  volume = {212},
  author = {Young, I.T. and Moerman, R. and Doel, L.R. van den and Iordanov, V. and Kroon, A. and Dietrich, H.R.C. and Dedem, G.W.K. van and Bossche, A. and Gray, B.L. and Sarro, L. and Verbeek, P.W. and Vliet, L.J. van}
}
@article{Michielsen2001,
  year = {2001},
  title = {Integral-Geometry Morphological Image Analysis},
  pages = {461--538},
  journal = {Physics Report},
  volume = {347},
  author = {Michielsen, K. and Raedt, H. de}
}
@article{Young2002,
  number = {11},
  year = {2002},
  title = {Recursive Gabor filtering},
  pages = {2798--2805},
  journal = {IEEE Transactions on Signal Processing},
  volume = {50},
  author = {Young, I.T. and van Vliet, L.J. and van Ginkel, M. }
}
@inproceedings{Young2000,
  month = {September 3-7},
  year = {2000},
  title = {Recursive Gabor Filtering},
  booktitle = {ICPR15, Proc. 15th Int. Conference on Pattern Recognition (Barcelona, Spain)},
  pages = {342--345},
  editor = {Sanfeliu, A. and Villanueva, J.J. and Vanrell, M. and Alquezar, R. and Huang, T. and Serra, J.},
  volume = {3},
  publisher = {IEEE Computer Society Press, Los Alamitos},
  author = {Young, I.T. and Vliet, L.J. van and Ginkel, M. van}
}
@article{Kues2002,
  number = {4},
  year = {2002},
  title = {Single Molecule Motion Perpendicular to the Focal Plane of a Microscope: Application to Splicing Factor Dynamics within the Cell Nucleus},
  pages = {218-224},
  journal = {Single Molecule},
  volume = {3},
  author = {Kues, T. and Kubitscheck, U.}
}
@article{Buelow2001,
  number = {11},
  year = {2001},
  title = {Hypercomplex Signals - A Novel Extension of the Analytic Signal to the Multidimensional Case},
  pages = {2844--2852},
  journal = {IEEE Transactions on Signal Processing},
  volume = {49},
  author = {{B\"ulow}, T. and Sommer, G.}
}
@article{Grunewald2003,
  year = {2003},
  title = {Prospects of electron cryotomography to visualize macromolecular complexes inside cellular compartments: implications of crowding},
  pages = {577-591},
  journal = {Biophysical Chemistry},
  volume = {100},
  author = {{Gr\"unewald}, K. and Medalia, O. and Gross, A. and Steven, A.C. and Baumeister, W.}
}
@inproceedings{Haglund1993,
  month = {May},
  year = {1993},
  title = {Scale and Orientation Adaptive Filtering},
  booktitle = {Proceedings of the 8th Scandinavian Conference on Image Analysis},
  pages = {847--855},
  address = {{Troms\o}, Norway},
  author = {Haglund, L. and Knutsson, H. and Granlund, G.H.}
}
@phdthesis{Haglund1992,
  year = {1992},
  title = {Adaptive Multidimensional Filtering},
  address = {{Link\"oping, Sweden}},
  school = {{Link\"oping University}},
  author = {Haglund, L.}
}
@article{SaintMarc1991,
  number = {6},
  year = {1991},
  title = {Adaptive Smoothing: A General Tool for Early Vision},
  pages = {514},
  journal = {IEEE Transactions on Pattern Analysis and Machine Intelligence},
  volume = {13},
  author = {Saint-Marc, P. and Chen, J.S. and Medioni, G.}
}
@article{Verwer1993,
  number = {5},
  year = {1993},
  title = {Binary and Grey-Value Skeletons: Metrics and Algorithms},
  pages = {1287--1308},
  journal = {Int. Journal of Pattern Recognition and Artificial Intelligence},
  volume = {7},
  author = {Verwer, B.J.H. and van Vliet, L.J. and Verbeek, P.W.}
}
@article{Verwer1991,
  month = {November},
  year = {1991},
  title = {Local distances for distance transformations in two and three dimensions},
  pages = {671--682},
  journal = {Pattern Recognition Letters},
  volume = {12},
  author = {Verwer, B.J.H.}
}
@inproceedings{Johansen1986,
  year = {1986},
  title = {Representing Signals by their Toppoints in Scale Space},
  booktitle = {Proceeding of the 8th International Conference on Pattern Recognition},
  pages = {215--217},
  volume = {1},
  author = {Johansen, P. and Skelboe, S. and Grue, K. and Andersen, J.D.}
}
@book{Jahne1997,
  edition = {4th},
  year = {1997},
  title = {Digital Image Processing},
  address = {Berlin},
  publisher = {Springer},
  author = {{J\"ahne}, B.}
}
@inproceedings{Vulovic2010a,
  month = {April 14-17},
  year = {2010},
  title = {Estimation Of Defocus And Astigmatism In Transmission Electron Microscopy},
  booktitle = {IEEE International Symposium on Biomedical Imaging},
  pages = {1121-1124},
  address = {Rotterdam, The Netherlands},
  author = {Vulovic, M. and Brandt, P.L. and Ravelli, R.B.G. and Koster, A.J. and Vliet, L.J. van and Rieger, B.}
}
@article{Verwer1994,
  number = {5},
  year = {1994},
  title = {Binary and grey-value skeletons: Metrics and algorithms},
  pages = {1287--1308},
  journal = {Int. Journal of Pattern Recognition and Artificial Intelligence},
  volume = {7},
  author = {Verwer, B.J.H. and Vliet, L.J. van and Verbeek, P.W.}
}
@article{Shao1998,
  number = {11},
  year = {1998},
  title = {On the fifth order aberration in a sextupole corrected probe forming system},
  pages = {2428-2437},
  journal = {Review of Scientific Instruments},
  volume = {59},
  author = {Shao, Z.}
}
@article{Nitzberg1992,
  number = {8},
  month = {August},
  year = {1992},
  title = {Nonlinear Image Filtering with Edge and Corner Enhancement},
  pages = {826--833},
  journal = {IEEE Transactions on Pattern Analysis and Machine Intelligence},
  volume = {14},
  author = {Nitzberg, M. and Shiota, T.}
}
@article{Bernardini1994,
  number = {8},
  month = {August},
  year = {1994},
  title = {A New Technique for Twiddle-Factor Elimination in Multidimensional {FFT}'s},
  pages = {2176--2178},
  journal = {IEEE Transactions on Signal Processing},
  volume = {42},
  annote = {key_fft},
  author = {Bernardini, R. and Cortelazzo, G.M. and Mian, G.A.}
}
@article{Nellist1994,
  year = {1994},
  title = {Beyond the conventional information limit: the relevant coherence function},
  pages = {61-74},
  journal = {Ultramicroscopy},
  volume = {54},
  author = {Nellist, P.D. and Rodenburg, J.M.}
}
@article{Maragos1989,
  number = {7},
  year = {1989},
  title = {Pattern Spectrum and Multiscale Shape Representation},
  pages = {701--716},
  journal = {IEEE Transactions on Pattern Analysis and Machine Intelligence},
  volume = {11},
  author = {Maragos, P.}
}
@article{DeMoment1989,
  number = {12},
  month = {December},
  year = {1989},
  title = {Image Reconstruction and Restoration: Overview of Common Estimation Structures and Problems},
  pages = {2024--2036},
  journal = {IEEE Transactions on Acoustics, Speech, and Signal Processing},
  volume = {37},
  author = {DeMoment, G.}
}
@article{Maragos1986,
  number = {5},
  year = {1986},
  title = {Morphological Skeleton Representation and Coding of Binary Images},
  pages = {1228-1244},
  journal = {IEEE Transactions on Acoustics, Speech, and Signal Processing},
  volume = {34},
  author = {Maragos, P. and Schafer, R. W.}
}
@article{GRADALT,
  year = {1986},
  title = {A Note on the Gradient of a Multi-Image},
  pages = {166--125},
  journal = {Computer Vision, Graphics, and Image Processing},
  volume = {33},
  author = {S. di Zeno}
}
@phdthesis{Ecker2004,
  month = {September},
  year = {2004},
  title = {Conformations of single polymer chains on surfaces},
  address = {Berlin},
  school = {Humboldt-Universit{\"a}t zu Berlin},
  author = {Ecker, C.}
}
@article{Haider2000,
  year = {2000},
  title = {Upper limits for the residual aberrations of a high-resolution aberration-corrected {STEM}},
  pages = {163-175},
  journal = {Ultramicroscopy},
  volume = {81},
  author = {Haider, M. and Uhlemann, S. and Zach, J.}
}
@article{Breen2000,
  year = {2000},
  title = {Mathematical Morphology: A Useful Set of Tools for Image Analysis},
  pages = {105--120},
  journal = {Statistics and Computing},
  volume = {10},
  author = {Breen, E.J. and Jones, R. and Talbot, H.}
}
@article{Mucke2004,
  number = {5},
  year = {2004},
  title = {Assessing the Flexibility of Intermediate Filaments by Atomic Force Microscopy},
  pages = {1241-1250},
  journal = {Journal of Molecular Biology},
  volume = {335},
  author = {{M\"ucke}, N. and Kreplak, L. and Krimse, R. and Wedig, T. and Herrmann, H. and Aebi, U. and Langowski, J.}
}
@article{Kusumi1993,
  year = {1993},
  title = {Confined Lateral Diffusion of Membrane Receptors as Studied by Single Particle Tracking (Nanovid Microscopy)},
  pages = {2021-2040},
  journal = {Biophysical Journal},
  volume = {65},
  author = {Kusumi, A. and Sako, Y. and Yamamoto, M.}
}
@article{Tarabusi1999,
  month = {February},
  year = {1999},
  title = {Characterization of the Range of the Radon Transform on Homogeneous Trees},
  pages = {11--17},
  journal = {Electronic Research Announcements of the American Mathematical Society},
  volume = {5},
  annote = {key_radon},
  author = {Tarabusi, E.C. and Cohen, J.M. and Colonna, F.}
}
@article{Dugelay1995,
  year = {1995},
  title = {Differential methods for the identification of 2D and 3D motion models in image sequences },
  pages = {105--127},
  journal = {Signal Processing: Image Communication},
  volume = {7},
  author = {Dugelay, J.L. and Sanson, H.}
}
@article{Gryczynski1995,
  number = {1},
  year = {1995},
  title = {Three-photon induced fluorescence of 2,5-diphenyloxazole with a femtosecond {Ti:sapphire} laser},
  pages = {30-35},
  journal = {Chemical Physics Letters},
  volume = {245},
  author = {Gryczynski, I. and Malak, H. and Lakowicz, J.R.}
}
@article{Fernandez2006a,
  number = {3},
  year = {2006},
  title = {Strategies for structural determination of biological specimens},
  pages = {84-94},
  journal = {IEEE Signal Processing Magazine},
  volume = {23},
  author = {Fernandez, J.-J. and Sorzano, C.O.S. and Marabini, R. and Carazo, J.-M.}
}
@article{Immerkaer1996,
  number = {2},
  year = {1996},
  title = {Fast Noise Variance Estimation},
  pages = {300-302},
  journal = {Computer Vision and Image Understanding},
  volume = {64},
  author = {{Immerk\aer}, J.}
}
@article{Bazin1965,
  month = {August},
  year = {1965},
  title = {Off-line Global Approach to Pattern Recognition for Bubble Chamber Pictures},
  pages = {291--295},
  journal = {IEEE Transactions on Nuclear Science},
  volume = {12},
  author = {Bazin, M.J. and Benoit, J.W.}
}
@article{Lenz1987a,
  year = {1987},
  title = {Rotation-Invariant Operators and Scale-Space Filtering},
  pages = {151--154},
  journal = {Pattern Recognition Letters},
  volume = {6},
  author = {Lenz, R.}
}
@article{Miller1953,
  year = {1953},
  title = {A Production of Amino Acids Under Possible Primitive Earth Conditions},
  pages = {528--529},
  journal = {Science},
  volume = {117},
  author = {Miller, S.L.}
}
@article{Thapa1997,
  number = {1},
  month = {January/February},
  year = {1997},
  title = {Semi-automatic Analysis of Rock Fracture Orientations From Borehole Wall Images},
  pages = {129--137},
  journal = {Geophysics},
  volume = {62},
  author = {Thapa, B.B. and Hughett, P. and Karasaki, K.}
}
@phdthesis{Xu1996,
  year = {1996},
  title = {Motion and Optical Flow in Computer Vision},
  address = {{Link\"oping}, Sweden},
  school = {{Link\"oping} University},
  author = {Xu, S.}
}
@misc{VedelJensen2000,
  month = {May 20--25},
  year = {2000},
  title = {Stereology and Geometric Tomography},
  howpublished = {Summer School, Sandbjerg Manor, Denmark},
  author = {Vedel Jensen, E.B.}
}
@article{Pauwels1995,
  number = {7},
  month = {July},
  year = {1995},
  title = {An Extended Class of Scale-Invariant and Recursive Scale Space Filters},
  pages = {691--701},
  journal = {IEEE Transactions on Pattern Analysis and Machine Intelligence},
  volume = {17},
  author = {Pauwels, E.J. and Gool, L.J. van and Fiddelaers, P. and Moons, T.}
}
@inproceedings{Goldfarb1986,
  year = {1986},
  title = {Metric Data Models and Associative Memories},
  booktitle = {IASTED/AFCET International Symposium on Robotics and Artificial Intelligence, University Paul Sabatier, Toulouse},
  pages = {53--73},
  volume = {3},
  author = {Goldfarb, L.}
}
@article{Goldfarb1984,
  number = {5},
  year = {1984},
  title = {A Unified Approach to Pattern Recognition},
  pages = {575--582},
  journal = {Pattern Recognition},
  volume = {17},
  author = {Goldfarb, L.}
}
@article{Silcox1992,
  year = {1992},
  title = {Resolution limits in annular dark field {STEM}},
  pages = {173-186},
  journal = {Ultramicroscopy},
  volume = {47},
  author = {Silcox, J. and Xu, P. and Loane, R.F.}
}
@article{Blair1996,
  number = {B9},
  year = {1996},
  title = {Using Two-Point Correlation Functions to Characterize Microgeometry and Estimate Permeabilities of Sandstones and Porous Glass},
  pages = {20359--20375},
  journal = {Journal of Geophysical Research},
  volume = {101},
  author = {Blair, S.C. and Berge, P.A. and Berryman, J.G.}
}
@article{Rieger2001a,
  number = {7},
  year = {2002},
  title = {Curvature of n-dimensional Space Curves in Grey-Value Images},
  pages = {738--745},
  journal = {IEEE Transactions on Image Processing},
  volume = {11},
  author = {Rieger, B. and Vliet, L.J. van}
}
@article{Deegan1997,
  year = {1997},
  title = {Capillary flow as the cause of ring stains from dried liquid drops},
  pages = {827--829},
  journal = {Nature},
  volume = {389},
  author = {Deegan, R.D. and Bakajin, O. and Dupont, T.F. and Huber, G. and Nagel, S.R. and Witten, T.A.}
}
@article{Biemond1990,
  number = {5},
  month = {May},
  year = {1990},
  title = {Iterative Methods for Image Deblurring},
  pages = {856--883},
  journal = {Proceedings of the IEEE},
  volume = {78},
  author = {Biemond, J. and Lagendijk, R.L. and Mersereau, R.M.}
}
@article{Jones2005,
  number = {4},
  year = {2005},
  title = {Measuring Forces between Protein Fibers by Microscopy},
  pages = {2433-2441},
  journal = {Biophysical Journal},
  volume = {88},
  author = {Jones, C.W. and Wang, J.C. and Briehl, R.W. and Turner, M.S.}
}
@article{Jares-Erijman2003,
  number = {7},
  year = {2003},
  title = {{FRET} imaging},
  pages = {1138-1395},
  journal = {Nature Biotechnology},
  volume = {21},
  author = {Jares-Erijman, E.A. and Jovin, T.M.}
}
@article{Jares-Erijman2006,
  year = {2006},
  title = {Imaging molecular interactions in living cells by {FRET} microscopy},
  journal = {Current Opinion in Chemical Biology},
  author = {Jares-Erijman, E.A. and Jovin, T.M.}
}
@inproceedings{Sorensen1988,
  month = {April},
  year = {1988},
  title = {Efficient Computation of the Short-Time {FFT}},
  booktitle = {Proceedings of the IEEE International Conference on Acoustics, Speech, and Signal Processing, (New York, U.S.A.)},
  pages = {1894--1897},
  annote = {key_fft},
  author = {Sorensen, H.V. and Burrus, C.S.}
}
@article{Bonnet2000,
  year = {2000},
  title = {Artificial Intelligence and Pattern Recognition Techniques in Microscope Image Processing and Analysis},
  journal = {Advances in Imaging and Electron Physics},
  volume = {114},
  author = {Bonnet, {No\"el}}
}
@article{Sukanya2000,
  number = {3},
  month = {July},
  year = {2000},
  title = {Multiscale Image Analysis through the Surface-shape Operator},
  pages = {305--316},
  journal = {Journal of Electronic Imaging},
  volume = {9},
  author = {Sukanya, P. and Takamatsu, R. and Sato, M.}
}
@article{Sorensen1987,
  number = {6},
  month = {June},
  year = {1987},
  title = {Real-Valued Fast {Fourier} Transform Algorithms},
  pages = {849--863},
  journal = {IEEE Transactions on Acoustics, Speech, and Signal Processing},
  volume = {35},
  annote = {key_fft},
  author = {Sorensen, H.V. and Jones, D.L. and Heideman, M.T. and Burrus, C.S.}
}
@article{Moon1996,
  number = {6},
  month = {November},
  year = {1996},
  title = {The Expectation-Maximization Algorithm},
  pages = {47--60},
  journal = {IEEE Signal Processing Magazine},
  volume = {13},
  author = {Moon, T.K.}
}
@article{Noble1988,
  number = {2},
  month = {May},
  year = {1988},
  title = {Finding Corners},
  pages = {121--128},
  journal = {Image and Vision Computing},
  volume = {6},
  author = {Noble, A.}
}
@book{Barham2001,
  year = {2001},
  title = {The Science of Cooking},
  address = {Berlin, Heidelberg, New York},
  publisher = {Springer},
  author = {Barham, P.}
}
@article{Bleau1992,
  number = {2},
  month = {September},
  year = {1992},
  title = {A New Set of Fast Algorithms for Mathematical Morphology, I. Idempotent Geodesic Transforms},
  pages = {178--209},
  journal = {CVGIP: Image Understanding},
  volume = {56},
  author = {Bleau, A. and Guise, J. de and LeBlanc, A.-R.}
}
@article{Iverson1995,
  number = {10},
  month = {October},
  year = {1995},
  title = {Logical/Linear Operators for Image Curves},
  pages = {982--996},
  journal = {IEEE Transactions on Pattern Analysis and Machine Intelligence},
  volume = {17},
  author = {Iverson, L.A. and Zucker, S.W.}
}
@inproceedings{Tretiak1984,
  year = {1984},
  title = {Velocity estimation for mimage sequences with second order differential operators},
  booktitle = {Int. Conf. on Pattern Recognition (Montreal, Canada)},
  pages = {20--22},
  publisher = {IEEE Computer Society Press, Los Alamitos, USA},
  author = {Tretiak, O. and Pastor, L.}
}
@book{Dudgeon1984,
  year = {1984},
  title = {Multidimensional Digital Signal Processing},
  publisher = {Prentice-Hall},
  author = {Dudgeon, D.E. and Merserau, R.M.}
}
@phdthesis{Iverson1994,
  year = {1994},
  title = {Toward Discrete Geometric Models for Early Vision},
  address = {{Montr\'eal}, Canada},
  school = {McGill University},
  author = {Iverson, L.A.}
}
@article{Potter2004,
  year = {2004},
  title = {Robotic grid loading system for a transmission electron microscope},
  pages = {431-440},
  journal = {Journal of Structural Biology},
  volume = {146},
  author = {Potter, C.S. and Pulokas, J. and Smith, P. and Suloway, C. and Carragher, B.}
}
@book{Kohonen1995,
  series = {Springer Series in Information Sciences},
  year = {1995},
  title = {Self-Organizing Maps},
  volume = {30},
  publisher = {Springer-Verlag},
  author = {Kohonen, T.}
}
@article{Qian1999,
  year = {1999},
  title = {Quantitative Study of Polymer Conformation and Dynamics by Single-Particle Tracking},
  pages = {1598-1805},
  journal = {Biophysical Journal},
  volume = {78},
  author = {Qian, H. and Elson, E.L.}
}
@article{Bennett1999,
  number = {7},
  month = {July},
  year = {1999},
  title = {A Method to Detect and Characterize Ellipses using the Hough Transform},
  pages = {652--657},
  journal = {IEEE Transactions on Pattern Analysis and Machine Intelligence},
  volume = {21},
  annote = {key_radon},
  author = {Bennett, N. and Burridge, R. and Saito, N.}
}
@inproceedings{Faas2003,
  series = {LNCS 2749},
  month = {June 29 -July 2},
  year = {2003},
  title = {3D-Orientation space; filters and sampling},
  booktitle = {SCIA'03, Proceedings of the 13th Scandinavian Conference on Image Analysis ({G\"oteborg}, Sweden)},
  pages = {36-42},
  address = {Berlin},
  publisher = {Springer-Verlag},
  author = {Faas, F.G.A. and Vliet, L.J. van}
}
@article{Qian1991,
  year = {1991},
  title = {Single Particle Tracking; Analysis of diffusion flow in two-dimensional systems},
  pages = {910-921},
  journal = {Biophysical Journal},
  volume = {60},
  author = {Qian, H. and Sheetz, M.P. and Elson, E.L.}
}
@article{Mallat1992a,
  number = {2},
  month = {March},
  year = {1992},
  title = {Singularity Detection and Processing with Wavelets},
  pages = {617--643},
  journal = {IEEE Transactions on Information Theory},
  volume = {38},
  author = {Mallat, S.G. and Hwang, W.L.}
}
@article{Qian1994,
  number = {10},
  month = {October},
  year = {1994},
  title = {Self-Sorting In-Place {FFT} Algorithm with Minimum Working Space},
  pages = {2835--2836},
  journal = {IEEE Transactions on Signal Processing},
  volume = {42},
  annote = {key_fft},
  author = {Qian, Z. and Lu, C. and An, M. and Tolimieri, R.}
}
@inproceedings{Williams1998,
  series = {Proceedings of SPIE},
  year = {1998},
  title = {Back-Illuminated {CCD} Imagers for High Information Content Digital Photography},
  author = {Williams, G.M. Jr and Marsh, H.H. and Hinds, M.}
}
@article{Ragnemalm1992,
  number = {3},
  month = {November},
  year = {1992},
  title = {Neighborhoods for Distance Transformation Using Ordered Propagation},
  pages = {399--409},
  journal = {CVGIP: Image Understanding},
  volume = {56},
  author = {Ragnemalm, I.R.}
}
@techreport{Andersson1999,
  year = {1999},
  title = {Filter Networks},
  institution = {{Link\"oping} University},
  author = {Andersson, M. and Wiklund, J. and Knutsson, H.}
}
@techreport{Andersson1998,
  year = {1998},
  title = {Sequential Filter Trees for Efficient 2{D}, 3{D} and 4{D} Orientation Estimation},
  institution = {{Link\"oping} University},
  author = {Andersson, M. and Wiklund, J. and Knutsson, H.}
}
@article{Duits2004,
  number = {3},
  year = {2004},
  title = {On the Axioms of Scale Space Theory},
  pages = {267-298},
  journal = {Journal of Mathematical Imaging and Vision},
  volume = {20},
  author = {Duits, R. and Florak, L.M.J. and Graaf, J. de and Haar Romey, B.M. ter}
}
@article{Louverdis2002,
  year = {2002},
  title = {A New Approach to Morphological Color Image Processing},
  pages = {1733-1741},
  journal = {Pattern Recognition},
  volume = {35},
  author = {Louverdis, G. and Vardavoulia, M.I. and Andreadis, I. and Tsalides, Ph.}
}
@article{Grunewald2003a,
  year = {2003},
  title = {Three-Dimensional Structure of Herpes Simplex Virus from Cryo-Electron Tomography},
  pages = {1396-1398},
  journal = {Science},
  volume = {302},
  author = {{Gr\"unewald}, K. and Desai, P. and Winkler, D.C. and Heymann, J.B. and Belnap, D. and Baumeister, W. and Steven, A.C.}
}
@article{Jamitzky2001,
  number = {1-2},
  year = {2001},
  title = {Scaling-index method as an image processing tool in scanning-probe microscopy},
  pages = {241-246},
  journal = {Ultramicroscopy},
  volume = {86},
  author = {Jamitzky, F. and Stark, R.W. and Bunk, W. and Thalhammer, S. and {R\"ath}, C. and Aschenbrenner, T. and Morfill, G.E. and Heckl, W.M.}
}
@phdthesis{Andersson1992,
  year = {1992},
  title = {Controllable Multidimensional Filters and Models in Low Level Computer Vision},
  address = {{Link\"oping, Sweden}},
  school = {{Link\"oping University}},
  author = {Andersson, M.T.}
}
@inproceedings{Ye1997,
  month = {June 15-19},
  year = {1997},
  title = {Automatic High Resolution Sedimentary Dip Detection on Borehole Imagery},
  booktitle = {SPWLA 38th Annual Logging Symposium},
  author = {Ye, S. and Rabiller, P. and Keskes, N.}
}
@article{Shannon1949,
  number = {1},
  year = {1949},
  title = {Communication in the Presence of Noise},
  pages = {10--21},
  note = {[reprinted in: Proceedings of the IEEE, vol. 86, no. 2, pp. 447-457, February 1998]},
  journal = {Proceedings of the IRE},
  volume = {37},
  author = {Shannon, C.E.}
}
@article{Peters2003,
  year = {2001},
  title = {Trafficking of prion proteins through a novel caveolae-mediated endosomal pathway},
  pages = {703-717},
  journal = {Journal of Cell Biology},
  volume = {162},
  author = {Peters, P.J. and Vey, M. and Donselaar, E. van and Mironov, A. Jr. and Erpel, S. and Peretx, D. and Lexlerc, E. and DeArmond, S.J. and Burton, D.R. and Williamson, R.A. and Prusiner, S.B.}
}
@article{Shannon1948,
  month = {July, October},
  year = {1948},
  title = {A Mathematical Theory of Communication},
  pages = {379--423, 623--656},
  journal = {The Bell System Technical Journal},
  volume = {27},
  author = {Shannon, C.E.}
}
@article{Robinson2004,
  number = {15},
  year = {2004},
  title = {Efficient morphological reconstruction: a downhill filter},
  pages = {1759-1767},
  journal = {Pattern Recognition Letters},
  volume = {25},
  author = {Robinson, K. and Whelan, P.F.}
}
@article{Cherny1999,
  number = {4},
  year = {1999},
  title = {{DNA} Bending Due to Specific p53 and p53 Core Domain-{DNA} Interactions Visualized by Electron Microscopy},
  pages = {1015-1026},
  journal = {Journal of Molecular Biology},
  volume = {294},
  author = {Cherny, D.I. and Striker, G. and Subramaniam, V. and Jett, S.D. and Pale\v{c}ek, E. and Jovin, T.M.}
}
@inproceedings{Rieger2001,
  month = {May 30 -June 1},
  year = {2001},
  title = {Estimation of Curvature of n-dimensional Space Curves in Grey-value Images},
  booktitle = {Proc. ASCI 2001, 7th Annual Conf. of the Advanced School for Computing and Imaging},
  pages = {436--442},
  editor = {Lagendijk, R. and Pimentel, A. and Wilkinson, M.},
  address = {Delft},
  author = {Rieger, B. and Vliet, L.J. van},
  organization = {ASCI}
}
@inproceedings{Rieger2003,
  series = {LNCS 2749},
  month = {June 29 -July 2},
  year = {2003},
  title = {Estimation of curvature based shape properties of surfaces in 3D grey-value images},
  booktitle = {SCIA'03, Proceedings of the 13th Scandinavian Conference on Image Analysis ({G\"oteborg}, Sweden) },
  pages = {262-267},
  editor = {{Big\"un}, J. and Gustavsson, T.},
  address = {Berlin},
  publisher = {Springer-Verlag},
  author = {Rieger, B. and Vliet, L.J. van and Verbeek, P.W.}
}
@article{Borgefors1986,
  year = {1986},
  title = {Distance transformations in digital images},
  pages = {344--371},
  journal = {Computer Vision, Graphics and Image Processing },
  volume = {34},
  author = {Borgefors, G.}
}
@article{Wiener1949,
  year = {1949},
  title = {Extrapolation, Interpolation and Smoothing of stationary Time Series},
  journal = {Cambridge, MA : M.I.T. Press},
  author = {Wiener, N.}
}
@article{Borgefors1984,
  year = {1984},
  title = {Distance transformations in arbitrary dimensions},
  pages = {321-345},
  journal = {Computer Vision, Graphics and Image Processing },
  volume = {27},
  author = {Borgefors, G.}
}
@article{Dougherty2001,
  year = {2001},
  title = {Optimal Conjunctive Granulometric Bandpass Filters},
  pages = {39--51},
  journal = {Journal of Mathematical Imaging and Vision},
  volume = {14},
  author = {Dougherty, Edward R.}
}
@article{Pei2001,
  number = {11},
  year = {2001},
  title = {Efficient Implementation of Quaternion Fourier Transform, Convolution, and Correlation by 2D Complex FFT},
  pages = {2783--2797},
  journal = {IEEE Transactions on Signal Processing},
  volume = {49},
  annote = {key_fft},
  author = {Pei, S.-C. and Ding, J.-J. and Chang, J.-H.}
}
@book{Scheck1999,
  year = {1999},
  title = {Mechanics: From {N}ewton's Law to Deterministic Chaos},
  address = {Berlin},
  publisher = {Springer},
  author = {F. Scheck}
}
@article{Gordon2004,
  number = {17},
  year = {2004},
  title = {Single-molecule high-resolution imaging with photobleaching},
  pages = {6462-6465},
  journal = {Proceedings of the National Academy of Sciences of the United States of America},
  volume = {101},
  author = {Gordon, M.P. and Ha, T. and Selvin, P.R.}
}
@inproceedings{Koenderink2002,
  series = {Lecture Notes in Computer Science},
  year = {2002},
  title = {Image Processing Done Right},
  booktitle = {Proceedings of the ECCV 2002},
  pages = {158--172},
  editor = {Heyden, A.},
  volume = {2350},
  publisher = {Springer-Verlag},
  author = {Koenderink, J.J. and Doorn, A.J. van}
}
@article{Huang1979,
  number = {1},
  month = {February},
  year = {1979},
  title = {A Fast Two-Dimensional Median Filtering Algorithm},
  pages = {13--18},
  journal = {IEEE Transactions on Acoustics, Speech, and Signal Processing},
  volume = {27},
  author = {Huang, T.S. and Yang, G.J. and Tang, G.Y.}
}
@misc{LevitzXXXX,
  title = {Evaluation of 3D Structural Properties of Porous Materials from 2D Sections: Morphology and Chord Length Distribution Functions},
  howpublished = {www},
  author = {Levitz, P.}
}
@inproceedings{Vliet1988a,
  year = {1988},
  title = {An edge detection model based on nonlinear Laplace filtering},
  booktitle = {Pattern Recognition and Artificial Intelligence},
  pages = {63--73},
  editor = {Gelsema, E.S. and Kanal L.N.},
  address = {North-Holland},
  publisher = {Elsevier Science Publishers B.V.},
  author = {Vliet, L.J. van and Young, I.T. and Beckers, A.L.D.}
}
@article{Hansen2001,
  year = {2001},
  title = {Nonparametric Estimation of the Chord Length Distribution},
  journal = {Advances in Applied Probability},
  volume = {33},
  author = {Hansen, M.B. and Zwet, E.W. van}
}
@article{Baddeley1997,
  year = {1997},
  title = {Kaplan-Meier Estimators for Interpoint Distance Distributions for Spatial Point Processes},
  pages = {263--292},
  journal = {Annals of Statistics 25},
  volume = {25},
  author = {Baddeley, A.J. and Gill, R.D.}
}
@inproceedings{Vliet1995a,
  month = {June},
  year = {1995},
  title = {Estimators for Orientation and Anisotropy in Digitized Images},
  booktitle = {ASCI'95, Proceedings of the First Annual Conference of the Advanced School for Computing and Imaging},
  pages = {442--450},
  editor = {van Katwijk, J. and Gerbrands, J.J. and van Steen, M.R. and Tonino, J.F.M.},
  address = {Heijen, The Netherlands},
  author = {Vliet, L.J. van and Verbeek, P.W.}
}
@article{Maintz1998,
  number = {1},
  year = {1998},
  title = {A survey of medical image registration},
  pages = {1-37},
  journal = {Medical Image Analysis},
  volume = {1},
  author = {Maintz, J.B.A. and Viergever, M.A.}
}
@book{Barrett1981,
  year = {1981},
  title = {Radiological Imaging; The Theory of Image Formation, Detection, and Processing},
  annote = {key_radon},
  publisher = {Academic Press},
  author = {Barrett, H.H. and Swindell, W.}
}
@book{Honerkamp1998,
  year = {1998},
  title = {Statistical Physics: An Advanced Approach with Applications},
  publisher = {Springer-Verlag},
  author = {Honerkamp, J.}
}
@article{Maintz1996,
  number = {4},
  year = {1996},
  title = {Evaluation of ridge seeking operators for multimodality medical image matching},
  pages = {353--365},
  journal = {IEEE Transactions on Pattern Analysis and Machine Intelligence},
  volume = {18},
  author = {Maintz, J.B.A. and Elsen, P.A. van den and Viergever, M.A.}
}
@book{Hyvarinen2001,
  year = {2001},
  title = {Independant Component Analysis},
  address = {New York},
  publisher = {Wiley Interscience},
  author = {{Hyv\"arinen}, A. and Karhumen, J. and Oja, E.}
}
@techreport{Almansa1998,
  year = {1998},
  title = {Fingerprint Enhancement by Shape Adaptation of Scale-Space Operators with Automatic Scale Selection},
  annote = {Partial document},
  institution = {University of the Republic of Uruguay},
  author = {Almansa, A. and Lindeberg, T.}
}
@article{Hofmann1984,
  number = {3},
  year = {1984},
  title = {Localization of flexible sites in thread-like molecules from electron micrographs. Comparison of interstitial, basement membrane and intima collagens},
  pages = {325-343},
  journal = {Journal of Molecular Biology},
  volume = {172},
  author = {Hofmann, H. and Voss, T. and {K\"uhn}, K. and Engel, J.}
}
@inproceedings{Aguado1996,
  month = {16--19 September},
  year = {1996},
  title = {Improving Parameter Space Decomposition for the Generalised {Hough} Transform},
  booktitle = {International Conference on Image Processing},
  pages = {627--630},
  volume = {3},
  author = {Aguado, A.S. and Montiel, M.E. and Nixon, M.S.}
}
@article{Roberts2001,
  number = {2},
  month = {February},
  year = {2001},
  title = {Curvature attributes and their application to 3D interpreted horizons},
  pages = {85-100},
  journal = {First Break},
  volume = {19},
  author = {Roberts, A.}
}
@inproceedings{Vliet1993akort,
  year = {1993},
  title = {Curvature and Bending Energy in Digitized 2D and 3D Images },
  booktitle = {SCIA'93},
  pages = {1403--1410 },
  address = {{Troms\o }, Norway},
  author = {Vliet, L.J. van and Verbeek, P.W. }
}
@article{Koenderink1992b,
  number = {4},
  year = {1992},
  title = {Second-order optic flow},
  pages = {530-538},
  journal = {Journal of the Optical Society of America A},
  volume = {9},
  author = {Koenderink, J.J. and Doorn, A.J. van}
}
@book{Lakowicz1999,
  edition = {2nd},
  year = {1999},
  title = {Principles of Fluorescence Spectroscopy},
  address = {New York},
  publisher = {Kluwer Academic Press},
  author = {Lakowicz, J.R.}
}
@article{Cardoso1998,
  number = {10},
  year = {1998},
  title = {Blind signal separation: statistical principles},
  pages = {2009-2025},
  journal = {Proceedings of the IEEE},
  volume = {86},
  author = {Cardoso, J.-F.}
}
@article{Koenderink1992a,
  number = {8},
  year = {1992},
  title = {Surface shape and curvature scales},
  pages = {557--565},
  journal = {Image and Vision Computing},
  volume = {10},
  author = {Koenderink, J.J. and Doorn, A.J. van}
}
@article{Kornprobst1999,
  year = {1999},
  title = {Image Sequence Analysis via Partial Differential Equations},
  pages = {5--26},
  journal = {Journal of Mathematical Imaging and Vision},
  volume = {11},
  author = {Kornprobst, P. and Sand, S. and Deriche, R. and Aubert, G.}
}
@article{Shevelev1998,
  year = {1998},
  title = {Second-order features extraction in the cat visual cortex: selective and invariant sensitivity of neurons to the shape and orientation of crosses and corners},
  pages = {195-204},
  journal = {BioSystems},
  volume = {48},
  author = {Shevelev, I.A.}
}
@article{Bacia2003,
  number = {1},
  year = {2003},
  title = {A dynamic view of cellular processes by in vivo fluorescence auto- and cross-correlation spectroscopy},
  pages = {74-85},
  journal = {Methods},
  volume = {29},
  author = {Bacia, K. and Schwille, P.}
}
@article{Yuille1986,
  number = {1},
  month = {January},
  year = {1986},
  title = {Scaling theorems for zero crossings},
  pages = {15--25},
  journal = {IEEE Transactions on Pattern Recognition and Machine Intelligence},
  volume = {8},
  author = {Yuille, A.L. and Poggio, T.}
}
@article{Volkmer2000,
  number = {3},
  year = {2000},
  title = {One- and two-photon excited fluorescence lifetimes and anisotropy decays of green fluorescent proteins},
  pages = {1589-1598},
  journal = {Biophysical Journal},
  volume = {78},
  author = {Volkmer, A. and Subramaniam, V. and Birch, D.J. and Jovin, T.M.}
}
@article{Bigelow2003,
  number = {9},
  month = {May},
  year = {2003},
  title = {Confocal fluorescence spectroscopy and anisotropy imaging system},
  pages = {695-697},
  journal = {Optics Letters},
  volume = {28},
  author = {Bigelow, C.E. and Conover, D.L. and Foster, T.H.}
}
@inproceedings{Coeurjolly2001,
  series = {Lecture Notes on Computer Science},
  month = {May},
  year = {2001},
  title = {Discrete Curvature Based on Osculating Circle Estimation},
  booktitle = {Visual Form 2001},
  pages = {303--312},
  editor = {Arcelli, C. and Cordella, L.P. and Sanniti di Baja, G. },
  volume = {2059},
  address = {Capri, Italy},
  publisher = {Springer-Verlag},
  author = {Coeurjolly, D. and Miguet, S. and Tougne, L.}
}
@book{Kak1988,
  year = {1988},
  title = {Principles of Computerized Tomographic Imaging},
  publisher = {IEEE Press},
  author = {Kak, A. C. and Slaney, M.}
}
@inproceedings{Cao1999,
  series = {Lecture Notes on Computer Science},
  month = {September},
  year = {1999},
  title = {Morphological Scale Space and Mathematical Morphology},
  booktitle = {Scale-Space Theories in Computer Vision (Second International Conference, Scale-Space'99, Corfu, Greece)},
  pages = {164--174},
  editor = {Nielsen, Mads and Johansen, Peter and Olsen, Ole F. and Weickert, Joachim},
  volume = {1682},
  address = {Berlin Heidelberg},
  publisher = {Springer-Verlag},
  author = {Cao, {Fr\'ed\'eric}}
}
@book{Leibovic1990,
  year = {1990},
  title = {Science of Vision},
  publisher = {Springer-Verlag},
  author = {Leibovic (ed), K.N.}
}
@inbook{Hediger2004,
  series = {Methods in Enzymology},
  year = {2004},
  title = {Methods for Visualizing Chromatin Dynamics in Living Yeast},
  volume = {375},
  chapter = {22},
  publisher = {Elsevier Academic Press},
  author = {Hediger, F. and Taddei, A. and Neumann, F.R. and Gasser, S.M.}
}
@article{Axelrod2001,
  year = {2001},
  title = {Total Internal Reflection Fluorescence Microscopy in Cell Biology},
  pages = {764-774},
  journal = {Traffic},
  volume = {2},
  author = {Axelrod, D.}
}
@article{Kuwahara1980,
  year = {1980},
  title = {Image enhancement and left ventricular contour extraction techniques applied to radioisotope angiocardiograms},
  pages = {107-119},
  journal = {Audiomedica},
  volume = {3},
  author = {Kuwahara, M. and Hachimura, K. and Kinoshita, M.}
}
@inproceedings{Whitworth1999,
  year = {1999},
  title = {The imaging and measurement of bubbles in bread doughs},
  booktitle = {Bubbles In Food},
  pages = {221-231},
  editor = {Campbell, G.M. and Webb, C. and Pandiella, S.S.},
  address = {St. Paul, USA},
  publisher = {Eagan Press},
  author = {Whitworth, M.B. and Alava, J.M.}
}
@article{Daugman1988,
  number = {7},
  year = {1988},
  title = {Pattern and motion vision without Laplacian zero-crossings},
  pages = {1142--1148},
  journal = {Journal of the Optical Society of America A},
  volume = {5},
  author = {Daugman, J.G.}
}
@book{Rutishauer1990,
  year = {1990},
  title = {Lectures on numerical mathematics},
  publisher = {{Birkh\"auser}},
  author = {Rutishauer, H.}
}
@article{Nagel1983,
  year = {1983},
  title = {Displacement vectors derived from second-order intensity variations in image sequences},
  pages = {85-117},
  journal = {Computer Graphics and Image Processing},
  volume = {21},
  author = {Nagel, H.H.}
}
@misc{BaddeleyXXXX,
  title = {Spatial Sampling and Censoring},
  howpublished = {Some chapter. From www},
  author = {Baddeley, A.}
}
@article{Nagel1986,
  year = {1986},
  title = {An investigation of smoothness constraints for the estimation of displacement vector fields form image sequences},
  pages = {168-176},
  journal = {IEEE Transactions of Pattern Recognition and Machine Intelligence},
  volume = {8},
  author = {Nagel, H.H. and Enkelmann, W.}
}
@article{Daugman1985,
  number = {7},
  month = {July},
  year = {1985},
  title = {Uncertainty Relation for Resolution in Space, Spatial Frequency, and Orientation Optimized by Two-dimensional Visual Cortical Filters},
  pages = {1160--1169},
  journal = {Journal of the Optical Society of America A},
  volume = {2},
  author = {Daugman, J.G.}
}
@article{Sorzano2004,
  year = {2004},
  title = {{XMIPP:} a new generation of an open-source image processing package for electron microscopy},
  pages = {194-204},
  journal = {Journal of Structural Biology},
  volume = {148},
  author = {Sorzano, C.O.S. and Marabini, R. and Vel\'azquez-Muriel, J. and Bilbao-Castro, J.R. and Scherees, S.H.W. and Carazo, J.M. and Pascual-Montano, A.}
}
@article{Sorzano2001,
  year = {2001},
  title = {The Effect of Overabundant Projection Directions on {3D} Reconstruction Algorithms},
  pages = {108-118},
  journal = {Journal of Structural Biology},
  volume = {133},
  author = {Sorzano, C.O.S. and Marabini, R. and Boisset, N. and Rietzel, E. and {Schr\"oder}, R. and Herman, G.T. and Carazo, J.M.}
}
@inproceedings{Kerbyson1995,
  month = {4--6 July},
  year = {1995},
  title = {Circle Detection using {Hough} Transform Filters},
  booktitle = {Image Processing and Its Applications},
  pages = {370--374},
  author = {Kerbyson, D.J. and Atherton, T.J.}
}
@article{Meyer2004,
  year = {2004},
  title = {A new method for the determination of the wave aberration function for high-resolution {TEM}. {2. Measurement} of the antisymmetric aberrations},
  pages = {115-123},
  journal = {Ultramicroscopy},
  volume = {99},
  author = {Meyer, R.R. and Kirkland, A.I. and Saxton, W.O.}
}
@article{Lin1999,
  year = {1999},
  title = {The Refined Crystal Structure of Cowpea Mosaic Virus at 2.8 Resolution},
  pages = {20-34},
  journal = {Virology},
  volume = {265},
  author = {Lin, T. and Chen, Z. and Usha, R. and Stauffacher, C.V. and Dai, J.-B. and Schmidt, T. and Johnson, J.E.}
}
@book{Mitra2000,
  year = {2000},
  title = {Nonlinear Image Processing},
  publisher = {Academic Press},
  author = {Mitra (Ed), S. and Sicuranza (Ed), G.}
}
@book{HandbookCP1980,
  edition = {60th},
  year = {1980},
  title = {Handbook of Chemistry and Physics},
  editor = {Lide, D.R.},
  publisher = {CRC Press}
}
@article{Olsen1994,
  number = {8},
  month = {August},
  year = {1994},
  title = {Wavelet Localization of the {R}adon Transform},
  pages = {2055--2067},
  journal = {IEEE Transactions on Signal Processing},
  volume = {42},
  author = {Olsen, T. and DeStefano, J.}
}
@inproceedings{Wijk2004,
  year = {2004},
  title = {On Normalized Convolution to Measure Curvature Features for Automatic Polyp Detection},
  booktitle = {LNCS 3216, MICCAI'04},
  pages = {200-208},
  editor = {Barillot, C. and Haynor, D.R. and Hellier, P.},
  author = {Wijk, C. van and Truyen, R. and Gelder, R.E. van and Vliet, L.J. van and Vos, F.M.}
}
@article{Aitken1995,
  number = {4},
  year = {1995},
  title = {A Comparison of Rotational Representation in Structure and Motion Estimation for Maneuvering Objects},
  pages = {516--520},
  journal = {IEEE Transactions on Image Processing},
  volume = {4},
  author = {Aitken, V.C. and Schwartz, H.M.}
}
@article{Barber1996,
  number = {4},
  month = {December},
  year = {1996},
  title = {The Quickhull Algorithm for Convex Hulls},
  pages = {469--483},
  journal = {ACM Transactions on Mathematical Software},
  volume = {22},
  author = {Barber, C.B. and Dobkin, D.P. and Huhdanpaa, H.}
}
@book{Wilson1984a,
  year = {1984},
  title = {Theory and Practice of Scanning Optical Microscopy},
  address = {London,New York},
  annote = {ph2341},
  publisher = {Academic Press},
  author = {Wilson, T. and Sheppard, C.J.R.}
}
@misc{Zach2001,
  year = {2001},
  title = {Method for detecting geometrical-optical aberrations},
  howpublished = {WO 01.56057},
  author = {Zach, J.}
}
@article{Lee2001,
  number = {16},
  month = {July},
  year = {2001},
  title = {Neural Synergy in Visual Grouping: When Good Continuation Meets Common Fate},
  pages = {2057--2064},
  journal = {Vision Research},
  volume = {41},
  author = {Lee, S.-H. and Blake, R.}
}
@article{Lichte1996,
  year = {1996},
  title = {Electron holography: optimum position of the biprism in the electron microscope},
  pages = {89-109},
  journal = {Ultramicroscopy},
  volume = {64},
  author = {Lichte, H.}
}
@article{Lee2005,
  number = {4},
  year = {2005},
  title = {Accurate {FRET} Measurements within Single Diffusing Biomolecules Using Alternating-Laser Excitation},
  pages = {2939-2953},
  journal = {Biophysical Journal},
  volume = {88},
  author = {Lee, N.K. and Kapanidis, A.N. and Wang, Y. and Michalet, X. and Mukhopadhyay, J. and Ebright, R.H. and Weiss, S.}
}
@misc{Verbeek1999,
  year = {1999},
  note = {The GST as a projection operator},
  howpublished = {private communications},
  author = {Verbeek, P.W.}
}
@article{Cuisenaire1999,
  number = {2},
  year = {1999},
  title = {Fast Euclidean distance transformation by propagation using multiple neighborhoods},
  pages = {163-172},
  journal = { Computer Vision and Image Understanding},
  volume = {76},
  author = {Cuisenaire, O. and Macq, B.}
}
@inproceedings{Verbeek1995,
  month = {June 6-9},
  year = {1995},
  title = {Approximate Analytic Paraboloid Dilation},
  booktitle = {9th Scandinavian Conference on Image Analysis (Uppsala, Sweden)},
  pages = {95--102},
  editor = {Borgefors, G.},
  volume = {1},
  author = {Verbeek, P.W. and Vliet, L.J. van}
}
@inproceedings{Verbeek1998,
  month = {17-20 August},
  year = {1998},
  title = {Improved Curvature and Anisotropy Estimation for Curved Line Bundles},
  booktitle = {ICPR'98, Proc. 14th Int. Conference on Pattern Recognition},
  pages = {528--533},
  editor = {Jain, A.K. and Venkatesh, S. and Lovell, B.C.},
  publisher = {IEEE Computer Society Press, Los Alamitos},
  author = {Verbeek, P.W. and van Vliet, L.J. and van de Weijer, J.}
}
@article{Verbeek1990,
  year = {1990},
  title = {Shading from shape, the eikonal equation solved by grey-weighted distance transform},
  pages = {681--690},
  journal = {Pattern Recognition Letters},
  volume = {11},
  author = {Verbeek, P.W. and Verwer, B.J.H}
}
@misc{Verbeek1996,
  year = {1996},
  title = {Angular Deconvolution},
  howpublished = {Internal Communication},
  author = {Verbeek, P.W.}
}
@article{Verbeek1994,
  number = {7},
  year = {1994},
  title = {On the location error of curved edges in low-pass filtered {2-D} and {3-D} images},
  pages = {726--733},
  journal = {IEEE Transactions on Pattern Analysis and Machine Intelligence},
  volume = {16},
  author = {Verbeek, P.W. and Vliet, L.J. van}
}
@article{Verbeek1993,
  number = {1},
  year = {1993},
  title = {Estimators of {2D} edge length and position, {3D} surface area and position in sampled grey-valued images},
  pages = {46--61},
  journal = {BioImaging},
  volume = {1},
  author = {Verbeek, P.W. and Vliet, L.J. van}
}
@inproceedings{Verbeek1992,
  month = {August 30-September 3},
  year = {1992},
  title = {Line and Edge Detection by Symmetry Filters},
  booktitle = {Proc. 11th IAPR Int. Conf. on Pattern Recognition (ICPR11, The Hague, The Netherlands)},
  pages = {749--753},
  volume = {III},
  publisher = {IEEE Computer Society Press, Los Alamitos, USA},
  author = {Verbeek, P.W. and Vliet, L.J. van}
}
@article{Griffith1973,
  number = {4},
  month = {April},
  year = {1973},
  title = {Edge Detection in Simple Scenes Using A Priori Information},
  pages = {371--381},
  journal = {IEEE Transactions on Computers},
  volume = {22},
  author = {Griffith, A.K.}
}
@article{Chermant2001,
  year = {2001},
  title = {Some Fields of Applications of Automatic Image Analysis in Civil Engineering},
  pages = {157--169},
  journal = {Cement {\&} Concrete Composites},
  volume = {23},
  author = {Chermant, J.-L. and Chermant, L. and Coster, M. and Dequiedt, A.-S. and Redon, C.}
}
@article{Thrift1983,
  number = {3},
  year = {1983},
  title = {Approximating Point-Set Images by Line Segments Using a Variation of the {H}ough Transform},
  pages = {383--394},
  journal = {Computer Vision, Graphics and Image Processing},
  volume = {21},
  annote = {key_radon},
  author = {Thrift, P.R. and Dunn, S.M.}
}
@misc{Rull1993,
  year = {1993},
  title = {{BARRY}: An Autonomous Train-Spotter},
  author = {Rull, P.H.}
}
@article{Schellman1980a,
  number = {3},
  year = {1980},
  title = {The flexibility of {DNA : II. Spontaneous} and ligand induced distortions},
  pages = {329-337},
  journal = {Biophysical Chemistry},
  volume = {11},
  author = {Schellman, J.A.}
}
@article{Tang2001,
  number = {8},
  year = {2001},
  title = {N-dimensional tensor voting and application to epipolar geometry estimation},
  pages = {829 -844},
  journal = {IEEE Transactions on Pattern Analysis and Machine Intelligence},
  volume = {23},
  author = {Tang, Chi-Keung and Medioni, G. and Lee, Mi-Suen}
}
@article{Park1996,
  number = {11},
  year = {1996},
  title = {Scale-Space Using Mathematical Morphology},
  pages = {1121--1126},
  journal = {IEEE Transactions on Pattern Analysis and Machine Intelligence},
  volume = {18},
  author = {Park, K.-R. and Lee, C.-N.}
}
@book{Haykin1999,
  edition = {second},
  year = {1999},
  title = {Neural Networks, a comprehensive foundation},
  publisher = {Prentice-Hall},
  author = {Haykin, S.}
}
@inproceedings{Faugeras1992,
  series = {Lecture Notes in Computer Science 588},
  month = {May},
  year = {1992},
  title = {What Can Be Seen in Three Dimensions with an Uncalibrated Stereo Rig},
  booktitle = {Second European Conference on Computer Vision},
  pages = {563--578},
  editor = {Sandini, G.},
  address = {Santa Margherita Ligure, Italy},
  publisher = {Springer},
  author = {Faugeras, O.D.}
}
@article{Dequiedt2001,
  year = {2001},
  title = {Study of Phase Dispersion in Concrete by Image Analysis},
  pages = {215--226},
  journal = {Cement \& Concrete Composites},
  volume = {23},
  author = {Dequiedt, A.-S. and Coster, M. and Chermant, L. and Chermant, J.-L.}
}
@article{Tang2002,
  number = {6},
  year = {2002},
  title = {Curvature-Augmented Tensor Voting for Shape Interference from Noisy 3D Data},
  pages = {858--864},
  journal = {IEEE Transactions on Pattern Analysis and Machine Intelligence},
  volume = {24},
  author = {Tang, C.-K. and Medioni, G.}
}
@inproceedings{Hartley1992a,
  series = {Lecture Notes in Computer Science 588},
  month = {May},
  year = {1992},
  title = {Estimation of Relative Camera Positions for Uncalibrated Cameras},
  booktitle = {Second European Conference on Computer Vision},
  pages = {579--587},
  editor = {Sandini, G.},
  address = {Santa Margherita Ligure, Italy},
  publisher = {Springer},
  author = {Hartley, R.I.}
}
@article{Dalen2002,
  month = {November},
  year = {2002},
  title = {Determination of the Water Droplet Size Distribution of Fat Spreads using Confocal Scanning Laser Microscopy},
  pages = {116--133},
  journal = {Journal of Microscopy},
  volume = {208 Pt. 2},
  author = {Dalen, G. van}
}
@article{Bergsma2001,
  number = {4},
  year = {2001},
  title = {Velocity Estimation of Spots in 3D Confocal Images Sequences of Living Cells},
  pages = {261--272},
  journal = {Cytometry},
  volume = {43},
  author = {Bergsma, C.B.J. and Streekstra, G.J. and Smeulders, A.W.M. and Manders, E.M.M.}
}
@article{Florack1999,
  number = {2/3},
  year = {1999},
  title = {Pseudo-linear Scale-space Theory},
  pages = {247--259},
  journal = {International Journal of Computer Vision},
  volume = {31},
  author = {Florack, L.M.J. and Maas, R. and Niessen, W.J.}
}
@phdthesis{Florack1993,
  year = {1993},
  title = {The Syntactical Structure of Scalar Images},
  school = {University of Utrecht, The Netherlands},
  author = {Florack, L.M.J.}
}
@article{Welch1967,
  year = {1967},
  title = {The use of fast Fourier Transform for the estimation of power spectra: A method based on time averaging over short, modified periodograms},
  pages = {70-73},
  journal = {IEEE Transactions on Audio and Electroacoustics},
  volume = {15},
  author = {Welch, P.}
}
@article{Florack1998,
  number = {3},
  year = {1998},
  title = {The Intrinsic Structure of Optic Flow Incorporating Measurement Duality},
  pages = {263--286},
  journal = {International Journal of Computer Vision},
  volume = {27},
  author = {Florack, L.M.J. and Niessen, W.J. and Nielsen, M.}
}
@article{Florack1992,
  number = {6},
  month = {July},
  year = {1992},
  title = {Scale and the Differential Structure of Images},
  pages = {376--388},
  journal = {Image and Vision Computing},
  volume = {10},
  author = {Florack, L.M.J. and Haar Romeny, B.M. ter and Koenderink, J.J. and Viergever, M.A.}
}
@article{Florack1994,
  number = {4},
  month = {December},
  year = {1994},
  title = {Linear Scale-Space},
  pages = {325--351},
  journal = {Journal of Mathematical Imaging and Vision},
  volume = {4},
  author = {Florack, L.M.J. and Haar Romeny, B.M. ter and Koenderink, J.J. and Viergever, M.A.}
}
@book{Florack1997,
  year = {1997},
  title = {Image Structure},
  publisher = {Kluwer Academic Publishers},
  author = {Florack, L.M.J.}
}
@article{Kim1990,
  number = {2},
  year = {1990},
  title = {Shape Description of Biological Objects via Stereo Light Microscopy},
  pages = {475--489},
  journal = {IEEE Transactions on Systems},
  volume = {20},
  author = {Kim, N.H. and Bovik, A.C. and Aggarwal, S.J.}
}
@article{Borgefors1996,
  number = {3},
  year = {1996},
  title = {On digital distance transforms in three dimensions},
  pages = {344-371},
  journal = {Computer Vision and Image Understanding},
  volume = {64},
  author = {Borgefors, G.}
}
@article{Komenda2001,
  number = {2--3},
  year = {2001},
  title = {Automatic Recognition of Complex Microstructures using the Image Classifier},
  pages = {87--92},
  journal = {Materials Characterization},
  volume = {46},
  author = {Komenda, J.}
}
@article{Vetterli1984,
  year = {1984},
  title = {Simple {FFT} and {DCT} Algorithms with Reduced Number of Operations},
  pages = {267--278},
  journal = {Signal Processing},
  volume = {6},
  annote = {key_fft},
  author = {Vetterli, M. and Nussbaumer, H.J.}
}
@article{Vetterli1986,
  number = {3},
  year = {1986},
  title = {Filter Banks Allowing Perfect Reconstruction},
  pages = {219--244},
  journal = {Signal Processing},
  volume = {10},
  author = {Vetterli, M.}
}
@article{Florack1996,
  year = {1996},
  title = {The {Gaussian} Scale-Space Paradigm and the Multiscale Local Jet},
  pages = {61--75},
  journal = {International Journal of Computer Vision},
  volume = {18},
  author = {Florack, L.M.J. and Haar Romeny, B.M. ter and Viergever, M.A. and Koenderink, J.J.}
}
@phdthesis{Molenaar2003,
  month = {June},
  year = {2003},
  title = {Methods for molecular analysis in living cells},
  address = {Leiden, The Netherlands},
  school = {Leiden University Medical Center},
  author = {Molenaar, C.}
}
@inproceedings{Leavers1990,
  year = {1990},
  title = {The Dynamic Generalized {H}ough transform},
  booktitle = {Computer Vision -- ECCV90. Proceedings, 1990},
  pages = {592--594},
  editor = {O. Faugeras},
  publisher = {Springer-Verlag},
  author = {Leavers, V.F.}
}
@book{Leavers1992,
  year = {1992},
  title = {Shape Detection in Computer Vision Using the {H}ough Transform},
  address = {London},
  publisher = {Springer-Verlag},
  author = {Leavers, V.F.}
}
@article{Morgan2002,
  year = {2002},
  title = {Structure of the Mammalian Ribosome-Channel Complex at 17 Resolution},
  pages = {871-886},
  journal = {Journal of Molecular Biology},
  volume = {324},
  author = {Morgan, D.G. and Mnntret, J.-F. and Neuhof, A. and Rapoport, T.A. and Akey, C.W.}
}
@article{Su2003,
  year = {2003},
  title = {High resolution EELS using monochromator and high performance spectrometer: comparison of $V_2O_5$ {ELNES} with {NEXAFS} and band structure calculations},
  pages = {235-238},
  journal = {Micron},
  volume = {34},
  author = {Su, D.S. and Zandbergen, H.W. and Tiemeijer, P.C. and Kothleitner, G. and {H\"avecker}, M. and {H\'ebert}, C. and Knop-Gericke, A. and Freitag, B.H. and Hofer, F. and {Schl\"ogl}, R.}
}
@article{Thirion1995,
  number = {2},
  year = {1995},
  title = {Computing the differential characteristics of isointensity surfaces},
  pages = {190--202},
  journal = {Computer Vision and Image Understanding},
  volume = {61},
  author = {Thirion, J.P. and Gourdon, A.}
}
@article{Rao1992,
  number = {7},
  month = {July},
  year = {1992},
  title = {Computerized Flow Field Analysis: Oriented Texture Fields},
  pages = {693--709},
  journal = {IEEE Transactions on Pattern Analysis and Machine Intelligence},
  volume = {14},
  author = {Rao, A.R. and Jain, R.C.}
}
@article{Potter1999,
  year = {1999},
  title = {Leginon: a system for fully automated acquisition of 1000 electron micrographs a day},
  pages = {153-161},
  journal = {Ultramicroscopy},
  volume = {77},
  author = {Potter, C.S. and Chu, H. and Frey, B. and Green, C. and Kisseberth, N. and Madden, T.J. and Miller, K.L. and Nahrstedt, K. and Pulokas, J. and Reilein, A. and Tcheng, D. and Weber, D. and Carragher, B.}
}
@article{Ferraro1988,
  number = {5},
  month = {May},
  year = {1988},
  title = {Relationship between Integral Transform Invariances and {Lie} Group Theory},
  pages = {738--742},
  journal = {Journal of the Optical Society of America A},
  volume = {5},
  author = {Ferraro, M. and Caelli, T.M.}
}
@article{Rao1991,
  number = {2},
  month = {March},
  year = {1991},
  title = {Computing Oriented Texture Fields},
  pages = {157--185},
  journal = {CVGIP: Graphical Models and Image Processing},
  volume = {53},
  author = {Rao, A.R. and Schunck, B.G.}
}
@article{Gaspar1997,
  year = {1997},
  title = {Partially Folded States of the Capsid Protein of Cowpea Severe Mosaic Virus in the Disassembly Pathway},
  pages = {456-466},
  journal = {Journal of Molecular Biology},
  volume = {273},
  author = {Gaspar, L.P. and Johnson, J.E. and Silva, J.L. and Poian, A.T. da}
}
@article{Rieger2004,
  number = {6},
  year = {2004},
  title = {A systematic approach to {nD} orientation representation},
  pages = {453-459},
  journal = {Image and Vision Computing},
  volume = {22},
  author = {Rieger, B. and Vliet, L.J. van}
}
@book{Papoulis1977,
  year = {1977},
  title = {Signal Analysis},
  address = {New York},
  publisher = {McGraw-Hill},
  author = {Papoulis, A.}
}
@article{Hanbury2001,
  number = {12},
  month = {December},
  year = {2001},
  title = {Morphological Operators on the Unit Circle},
  pages = {1842--1850},
  journal = {IEEE Transactions on Image Processing},
  volume = {10},
  author = {Hanbury, Allan G. and Serra, Jean}
}
@inbook{Porat1994a,
  year = {1994},
  title = {Digital Signal Processing of Random Signals: Theory and Methods},
  chapter = {11.4},
  publisher = {Prentice Hall},
  author = {Porat, B.}
}
@article{Villasenor1987,
  month = {December},
  year = {1987},
  title = {Optical Phase Obtained by Analogue Hartley Transformation},
  pages = {735--737},
  journal = {Nature},
  volume = {330},
  author = {Villasenor, J. and Bracewell, R.N.}
}
@article{Lacey1998,
  number = {5},
  year = {1998},
  title = {A Multi-Stage Approach to the Dense Estimation of Disparity from Stereo {SEM} Images},
  pages = {373--383},
  journal = {Image and Vision Computing},
  volume = {16},
  author = {Lacey, A.J. and Thacker, N.A. and Crossley, S. and Yates, R.B.}
}
@article{Sengupta2001,
  year = {2001},
  title = {Visualization of protein {S1} within the {30S} ribosomal subunit and its interaction with messenger {RNA}},
  pages = {11991-11996},
  journal = {Proceedings of the National Academy of Sciences of the United States of America},
  volume = {98},
  author = {Sengupta, J. and Agrawal, R.K. and Frank, J.}
}
@article{Domer2003,
  number = {10},
  year = {2003},
  title = {High-speed transmission electron microscope},
  pages = {4369-4372},
  journal = {Review of Scientific Instruments},
  volume = {74},
  author = {{D\"omer}, H. and Bostanjoglo, O.}
}
@inproceedings{Lacey1996,
  year = {1996},
  title = {Surface Approximation from Industrial {SEM} Images},
  booktitle = {Proceedings of the British Machine Vision Conference},
  address = {Edinburgh, Scotland},
  author = {Lacey, A.J. and Thacker, N.A. and Yates, R.B.},
  organization = {University of Edinburgh}
}
@article{Kimia1992,
  year = {1992},
  title = {On the Evolution of Curves via a Function of Curvature. I. The Classical Case},
  pages = {438--458},
  journal = {Journal of Mathematical Analysis and Applications},
  volume = {163},
  author = {Kimia, B. and Tannenbaum, A. and Zucker, S.W.}
}
@unpublished{Vliet1998b,
  title = {Adaptive Filtering. From Scaleable Elliptic, and Banana to Leech Filters},
  author = {Vliet, L.J. van}
}
@article{Giro2004,
  number = {4},
  year = {2004},
  title = {Single Molecule Studies of {RNA} Secondary Structure: {AFM} of {TYMV} Viral {RNA}},
  pages = {235-245},
  journal = {Microscopy Research and Technique},
  volume = {65},
  author = {Giro, A. and Bergia, A. and Zuccheri, G. and Bink, H.H.J. and Pleij, C.W.A. and Samori, B.}
}
@inbook{Vliet1998a,
  edition = {2nd},
  year = {1998},
  title = {Cell Biology},
  pages = {109-120},
  editor = {Celis, J.E.},
  volume = {III},
  address = {New York},
  chapter = {Digital Fluorescence Imaging Using Cooled {CCD} Array Cameras},
  publisher = {Academic Press},
  author = {Vliet, L.J. van and Sudar, D. and Young, I.T.}
}
@unpublished{Vliet1998c,
  title = {Detection of End-points},
  author = {Vliet, L.J. van}
}
@article{Pulokas1999,
  year = {1999},
  title = {Improving the positional accuracy of the goniometer on the {Philips CM} series {TEM}},
  pages = {250-256},
  journal = {Journal of Structural Biology},
  volume = {128},
  author = {Pulokas, J. and Green, C. and Kisseberth, N. and Potter, C.S. and Carragher, B.}
}
@article{Ficz2005,
  number = {17},
  year = {2006},
  title = {Polycomb group complexes exchange rapidly in living {Drosophila}},
  pages = {3964-3976},
  journal = {Development},
  volume = {132},
  author = {Ficz, G. and Heintzmann, R. and Arndt-Jovin, D.J.}
}
@article{Thovert1993,
  month = {April},
  year = {1993},
  title = {Computerized Characterization of the Geometry of Real Porous Media: their Discretization, Analysis and Interpretation},
  pages = {65--79},
  journal = {Journal of Microscopy},
  volume = {170, Pt 1},
  author = {Thovert, J.F. and Salles, J. and Adler, P.M.}
}
@book{Kincaid1991,
  year = {1991},
  title = {Numerical analysis; mathematics of scientific computing},
  address = {Brooks/Cole},
  publisher = {Pacific Grove},
  author = {Kincaid,D.}
}
@article{Netten1994,
  year = {1994},
  title = {A fast scanner for fluorescence microscopy using a {2-D CCD} amd time delayed integration},
  pages = {184-192},
  journal = {Bioimaging},
  volume = {2},
  author = {Netten, H. and Vliet, L.J. van and Boddeke, F.R. and Jong, P. de and Young, I.T.}
}
@article{Loncaric1998,
  number = {8},
  year = {1998},
  title = {A Survey of Shape Analysis Techniques},
  pages = {983--1001},
  journal = {Pattern Recognition},
  volume = {31},
  author = {Loncaric, S.}
}
@article{Malladi1995,
  number = {2},
  month = {February},
  year = {1995},
  title = {Shape Modeling with Front Propagation: A Level Set Approach},
  pages = {158--175},
  journal = {IEEE Transactions on Pattern Analysis and Machine Intelligence},
  volume = {17},
  author = {Malladi, R. and Sethian, J.A. and Vemuri, B.C.}
}
@book{Bronstein1999,
  edition = {4th},
  year = {1999},
  title = {Taschenbuch der Mathematik},
  address = {Thun, Frankfurt (Main)},
  publisher = {Verlag Harri Deutsch},
  author = {Bronstein, I. N. and Semendjajew, K. A. and Musiol, G. and {M\"uhlig}, H.}
}
@article{Kundur1996,
  number = {3},
  month = {May},
  year = {1996},
  title = {Blind Image Deconvolution},
  pages = {43--64},
  journal = {IEEE Signal Processing Magazine},
  volume = {13},
  author = {Kundur, D. and Hatzinakos, D.}
}
@article{Levi1970,
  number = {1},
  month = {August},
  year = {1970},
  title = {A grey-weighted skeleton},
  pages = {62-91},
  journal = {Information and Control},
  volume = {17},
  author = {Levi, G. and Montanari, U.}
}
@book{Press1992,
  edition = {2},
  year = {1992},
  title = {Numerical Recipes in C: The Art of Scientific Computing},
  address = {Cambridge},
  publisher = {Cambridge University Press},
  author = {Press, W.H. and Teukolsky, S.A. and Vetterling, W.T. and Flannery, B.P.}
}
@article{Luengo2005,
  number = {12},
  year = {2005},
  title = {The Generalized Radon Transform: Sampling, Accuracy and Memory Considerations},
  pages = {2494-2505},
  journal = {Pattern Recognition},
  volume = {38},
  author = {Luengo Hendriks, C.L. and Ginkel, M. van and Verbeek, P.W. and Vliet, L.J. van}
}
@inproceedings{Lambert2000,
  year = {2000},
  title = {Filtering and Segmentation: the Specificity of Color Images},
  booktitle = {International Conference on Color in Graphics and Image Processing CGIP'2000},
  author = {Lambert, P. and Macaire, L.}
}
@article{Rivetti1998,
  number = {1},
  year = {1998},
  title = {Polymer chain statistics and conformational analysis of {DNA} molecules with bends or sections of different flexibility},
  pages = {41-59},
  journal = {Journal of Molecular Biology},
  volume = {280},
  author = {Rivetti, C. and Walker, C. and Bustamante, C.}
}
@inproceedings{Luengo2000,
  series = {Proc. SPIE Electronic Imaging 2000 Conf.},
  year = {2000},
  title = {Improving resolution to reduce aliasing in an undersampled image sequence},
  booktitle = {Sensors and Camera Systems for Sensors and Camera Systems for Scientific, Industrial, and Digital Photography Applications},
  pages = {2134--222},
  editor = {Blouke, M. M. and Williams, G.M. and Sampat, N. and Yeh, T.},
  volume = {3965},
  address = {San Jose},
  author = {Luengo Hendriks, C.L. and Vliet, L.J. van}
}
@inproceedings{Luengo2003,
  series = {Lecture Notes on Computer Science},
  year = {2003},
  title = {Basic Morphological Operations, Band-Limited Images and Sampling},
  booktitle = {Scale Space Methods in Computer Vision, Proceedings of the Fourth International Conference, Scale-Space 2003},
  pages = {313-324},
  editor = {Griffin, L.D. and Lillholm, M.},
  volume = {2695},
  address = {Berlin},
  publisher = {Springer-Verlag},
  author = {Luengo Hendriks, C.L. and Vliet, L.J. van}
}
@article{Rivetti1996,
  year = {1996},
  title = {Scanning Force Microscopy of {DNA} Deposited onto Mica: Equilibration versus Kinetic Trapping Studied by Statistical Polymer Chain Analysis},
  pages = {919-932},
  journal = {Journal of Molecular Biology},
  volume = {264},
  author = {Rivetti, C. and Guthold, M. and Bustamante, C.}
}
@article{Kroustrup1988,
  month = {February},
  year = {1988},
  title = {Stereological Analysis of Three-Dimensional Structure Organization of Surfaces in Multiphase Specimens: Statistical Methods and Model-Inferences},
  pages = {135--152},
  journal = {Journal of Microscopy},
  volume = {149, Pt 2},
  author = {Kroustrup, J.P. and Gundersen, H.J.G. and V,h, M.}
}
@article{Saxl1993,
  month = {April},
  year = {1993},
  title = {Contact Distances and Random Free Paths},
  pages = {53--64},
  journal = {Journal of Microscopy},
  volume = {170, Pt 1},
  author = {Saxl, I.}
}
@article{Hildreth1984,
  year = {1984},
  title = {The computation of the velocity field},
  pages = {189-220},
  journal = {Proceedings of the Royal Society of London B},
  volume = {221},
  author = {Hildreth, E.C.}
}
@article{Summerscales2001,
  month = {February},
  year = {2001},
  title = {Voronoi Cells, Fractal Dimensions and Fibre Composites},
  pages = {153--162},
  journal = {Journal of Microscopy},
  volume = {201, Pt 2},
  author = {Summerscales, J. and Guild, F.J. and Pearce, N.R.L. and Russell, P.M.}
}
@article{Ruiz2003,
  year = {2003},
  title = {The 10.8- structure of Saccharomyces cerevisiae phosphofructokinase determined by cryoelectron microscopy: localization of putative fructose 6-phosphate binding sites},
  pages = {124-134},
  journal = {Journal of Structural Biology},
  volume = {143},
  author = {Ruiz, T. and {Koppenschl\"ager}, G. and Radermacher, M.}
}
@article{Lagerholm2006,
  number = {10},
  year = {2006},
  title = {Analysis method for measuring submicroscopic distances with blinking Quantum Dots},
  pages = {3050-3060},
  journal = {Biophysical Journal},
  volume = {91},
  author = {Lagerholm, B.C. and Averett, L. and Weinreb, G.E. and Jacobson, K. and Thompson, N.L.}
}
@article{Berney2003,
  number = {6},
  year = {2003},
  title = {{FRET} or no {FRET}: A Quantitative Comparison},
  pages = {3992-4010},
  journal = {Biophysical Journal},
  volume = {84},
  author = {Berney, C. and Danuser, G.}
}
@article{Harrigan1984,
  year = {1984},
  title = {Characterization of Microstructural Anisotropy in Orthotropic Materials Using a Second Rank Tensor},
  pages = {761--767},
  journal = {Journal of Materials Science},
  volume = {19},
  author = {Harrigan, T.P. and Mann, R.W.}
}
@article{Mironov2003,
  year = {2003},
  title = {{ER-to-Golgi} Carriers Arise through Direct En Bloc Protrusion and Multistage Maturation of Specialized {ER} Exit Domains},
  pages = {583-594},
  journal = {Developmental Cell},
  volume = {5},
  author = {Mironov, A.A. and Mironov, A.A.Jr. and Beznoussekno, G.V. and Trucco, A. and Lupetti, P. and Smith, J.D. and Geerts, W.J.C. and Koster, A.J. and Burger, K.N.J. and Martone, M.E. and Deerinck, T.J. and Ellisman, M.H. and Luini, A.}
}
@book{Frankel1997,
  year = {1997},
  title = {The Geometry of Physics},
  address = {Cambridge},
  publisher = {Cambridge University Press},
  author = {T. Frankel}
}
@article{Shaner2005,
  year = {2005},
  title = {A guide to choosing fluorescent proteins},
  pages = {905-909},
  journal = {Nature Methods},
  volume = {2},
  author = {Shaner, N.C. and Steinbach, P.A. and Tsien, R.Y.}
}
@inproceedings{Lozier1994,
  series = {Proceedings of Symposia in Applied Mathematics},
  month = {December},
  year = {1994},
  title = {Numerical Evaluation of Special Functions},
  booktitle = {Mathematics of Computation 1943--1993: A Half-Century of Computational Mathematics},
  pages = {79--125},
  note = {{\tt http://math.nist.gov/nesf/}},
  editor = {Gautschi, W.},
  volume = {48},
  author = {Lozier, D.W. and Olver, F.W.J.},
  organization = {American Mathematical Society}
}
@inbook{Simmonds1982a,
  year = {1982},
  title = {A Brief on Tensor Analysis},
  chapter = {1,2},
  publisher = {Spring-Verlag},
  author = {Simmonds, J.G.}
}
@article{Schoenle2002,
  number = {10},
  year = {2002},
  title = {Calculation of vectorial three-dimensional transfer functions in large angle focusing systems},
  pages = {2121-2126},
  journal = {Journal of the Optical Society of America A},
  volume = {19},
  author = {{Sch\"onle}, A. and Hell, S.W.}
}
@phdthesis{Kempen1999a,
  year = {1999},
  title = {Image Restoration in Fluorescence Microscopy},
  address = {Delft, The Netherlands},
  school = {Delft University of Technology},
  author = {Kempen, G.M.P. van}
}
@article{Min1995,
  year = {1995},
  title = {Comparison of three-dimensional imaging properties between two-photon and single-photon fluorescence microscopy},
  pages = {128--137},
  journal = {Journal of Microscopy},
  volume = {177},
  author = {Min, G. and Sheppard, C.J.R.}
}
@article{Min1990,
  year = {1990},
  title = {Image formation in two-photon fluorescence microscopy},
  pages = {104--106},
  journal = {Optik},
  volume = {86},
  author = {Min, G. and Sheppard, C.J.R.}
}
@phdthesis{Karlholm1998,
  year = {1998},
  title = {Local Signal Models for Image Sequence Analysis},
  address = {{Link\"oping}, Sweden},
  school = {{Link\"oping} University},
  author = {Karlholm, J.}
}
@article{Kimoto2005,
  year = {2005},
  title = {Advantages of a monochromator for bandgap measurements using electron energy-loss spectroscopy},
  pages = {185-189},
  journal = {Micron},
  volume = {36},
  author = {Kimoto, K. and Kothleitner, G. and Grogger, W. and Matsui, Y. and Hofer, F.}
}
@book{Mallat2001,
  edition = {2nd edition},
  year = {1999},
  title = {A wavelet tour of signal processing},
  address = {New York},
  publisher = {John Wiley \& Sons},
  author = {Mallat, S.G.}
}
@book{Walter1994,
  edition = {3},
  year = {1994},
  title = {{Einf\"uhrung in die Theorie der Distributionen}},
  publisher = {Spektrum Akademischer Verlag},
  author = {Walter, W.}
}
@misc{GinkelWWWqqnvphbv2001,
  title = {http://www.ph.tn.tudelft.nl/\char126michael/qqnvphnv.html},
  key = {ZZZZ}
}
@article{Cucchiara1998,
  number = {7},
  month = {July},
  year = {1998},
  title = {The Vector-Gradient Hough Transform},
  pages = {746--750},
  journal = {IEEE Transactions on Pattern Recognition and Machine Intelligence},
  volume = {20},
  annote = {key_radon},
  author = {Cucchiara, R. and Filicori, F.}
}
@inproceedings{Mullikien1994,
  month = {February 9-10},
  year = {1994},
  title = {Methods for {CCD} camera characterization},
  booktitle = {SPIE Proceedings},
  pages = {73-84},
  editor = {Titus, H.C. and Waks, A.},
  volume = {2173},
  address = {San Jose, CA},
  author = {Mullikien, J.C. and Vliet, L.J. van and Netten, H. and Boddeke, F.R. and Feltz, G.W. van der and Young, I.T.}
}
@techreport{Verbeek1982,
  year = {1982},
  title = {Space Invariant Image Operations Constructed from Local Direction Detection and Shift Invariant Filters},
  address = {Pattern Recognition Group},
  institution = {Delft University of Technology},
  author = {Verbeek, P.W.}
}
@inproceedings{Verbeek1986,
  year = {1986},
  title = {Collision Avoidance and Path Finding through Constrained Distance Transformation in Robot State Space},
  booktitle = {Preprints Intelligent Autonomous Systems (Amsterdam, December 8-11)},
  pages = {634--641},
  author = {Verbeek, P.W. and Dorst, L. and Verwer, B.J.H. and Groen, F.C.A.}
}
@article{Verbeek1985,
  year = {1985},
  title = {A Class of Sampling-error Free Measures in Oversampled Band-Limited Images},
  pages = {287--292},
  journal = {Pattern Recognition Letters},
  volume = {3},
  author = {Verbeek, P.W.}
}
@article{Verbeek1988,
  number = {3},
  year = {1988},
  title = {Low-level Image Processing by Max-Min Filters},
  pages = {249--258},
  journal = {Signal Processing},
  volume = {15},
  author = {Verbeek, P.W. and Vrooman, H.A. and Vliet, L.J. van}
}
@techreport{Verbeek2000,
  year = {2000},
  title = {Subspaces of Generalised Projection Operators},
  address = {Pattern Recognition Group},
  institution = {Delft University of Technology},
  author = {Verbeek, P.W.}
}
@inproceedings{Verbeek2003,
  series = {LNCS 2756},
  month = {August 25-27},
  year = {2003},
  title = {The {D}-dimensional inverse vector-gradient operator and its application for scale free image enhancement},
  booktitle = {10th International Conference on Computer Analysis of Images and Patterns (Groningen, The Netherlands) },
  pages = {738-745},
  editor = {Petkov, N. and Westenberg, M.A.},
  address = {Berlin},
  publisher = {Springer},
  author = {Verbeek, P.W. and Dijk, J.}
}
@article{Verbeek1989,
  year = {1989},
  title = {{2-D} Adaptive Smoothing by {3-D} Distance Transformation},
  pages = {53--65},
  journal = {Pattern Recognition Letters},
  volume = {9},
  author = {Verbeek, P.W. and Verwer, B.J.H.}
}
@article{Manders1996,
  number = {1},
  year = {1996},
  title = {Largest contour segmentation: A tool for the localization of spots in confocal images},
  pages = {15-21},
  journal = {Cytometry Part A},
  volume = {23},
  author = {Manders, E.M.M. and Hoebe, R. and Strackee, J. and Vossepoel, A.M. and Aten, J.A.}
}
@phdthesis{Boomgaard1992,
  year = {1992},
  title = {Mathematical Morphology: Extensions Towards Computer Vision},
  address = {Amsterdam},
  school = {University of Amsterdam},
  author = {Boomgaard, R. van den}
}
@article{Boomgaard1999,
  year = {1999},
  title = {Affine invariant deformation curves a tool for shape characterization},
  pages = {375--380},
  journal = {Image and Vision Computing},
  volume = {17},
  author = {Boomgaard, R. van den}
}
@article{Bos1992,
  number = {1},
  year = {1992},
  title = {Ultimate resolution: a mathematical framework},
  pages = {298-306},
  journal = {Ultramicroscopy},
  volume = {47},
  author = {Bos, A. van den}
}
@article{Boomgaard1994,
  number = {11},
  year = {1994},
  title = {The morphological structure of images: The differential equations of morphological scale-space},
  pages = {1101--1113},
  journal = {IEEE Transactions on Pattern Analysis and Machine Intelligence},
  volume = {16},
  author = {Boomgaard, R. van den and Smeulders, A.}
}
@article{Manders1993,
  number = {3},
  year = {1993},
  title = {Measurement of co-localization of objects in dual-colour confocal images},
  pages = {375-382},
  journal = {Journal of Microscopy},
  volume = {169},
  author = {Manders, E.M.M. and Verbeek, F.J. and Aten, J.A.}
}
@misc{Dijkstra1982,
  month = {August 11},
  year = {1982},
  title = {Why Numbering Should Start at Zero},
  howpublished = {PDF file},
  author = {Dijkstra, E.W.}
}
@misc{DelftXXXX,
  title = {Magische Vierkanten},
  howpublished = {uit ``Spelen met Puzzels''},
  author = {Delft, P. van and Botermans,J.}
}
@article{Mayall1990,
  number = {1},
  year = {1990},
  title = {Experience with the {Athena} Semi-Automated Karyotyping System},
  pages = {59--72},
  journal = {Cytometry},
  volume = {11},
  author = {Mayall, B.H. and Tucker, J.D. and Christensen, M.L. and Vliet, L.J. van and Young, I.T.}
}
@article{Schoenberg1930,
  year = {1930},
  title = {{\"Uber} Variationsvermindernde Lineare Transformationen},
  pages = {321--328},
  journal = {Mathematische Zeitschrift},
  volume = {32},
  author = {Schoenberg, I.}
}
@book{Rade1999,
  edition = {4th},
  year = {1999},
  title = {Mathematical Handbook for Science and Engineering},
  publisher = {Springer Verlag},
  author = {{R\aa de}, L. and Westergren, B.}
}
@article{Blostein1989,
  number = {12},
  month = {December},
  year = {1989},
  title = {Shape from Texture: Integrating Texture-Element Extraction and Surface Estimation},
  pages = {1233--1251},
  journal = {IEEE Transactions on Pattern Analysis and Machine Intelligence},
  volume = {11},
  author = {Blostein, D. and Ahuja, N.}
}
@inproceedings{Hartley1992,
  month = {15--18 June},
  year = {1992},
  title = {Stereo from Uncalibrated Cameras},
  booktitle = {Proceedings of the IEEE Conference on Computer Vision and Pattern Recognition - CVPR'92},
  pages = {761--764},
  address = {Urbana-Champaign, USA},
  author = {Hartley, R. and Gupta, R. and Chang, T.}
}
@article{Patwardhan2002,
  number = {1},
  year = {2002},
  title = {Coherent, non-planar illumination of a defocused specimen: consequences for transmission electron microscopy},
  pages = {4-12},
  journal = {Optik},
  volume = {13},
  author = {Patwardhan, A.}
}
@article{Kybic2002a,
  number = {8},
  year = {2002},
  title = {Generalized sampling: A variational approach - Part {II}: Applications},
  pages = {1977--1985},
  journal = {IEEE Transactions on Signal Processing},
  volume = {50},
  author = {Kybic, J. and Blu, T. and Unser, M.}
}
@inproceedings{Cooper2003,
  series = {LNCS 2749},
  month = {June 29 -July 2},
  year = {2003},
  title = {Estimating Motion in Ultrasound Images of the Small Bowel: Optical Flow without Image Structure},
  booktitle = {SCIA'03, Proceedings of the 13th Scandinavian Conference on Image Analysis ({G\"oteborg}, Sweden) },
  pages = {571-578},
  editor = {{Big\"un}, J. and Gustavsson, T.},
  address = {Berlin},
  publisher = {Springer-Verlag},
  author = {Cooper, D.H. and Madsen, B.R. and Graham, J.}
}
@article{Weijer2001,
  number = {9},
  year = {2001},
  title = {Curvature estimation in oriented patterns using curvilinear models applied to gradient vector fields},
  pages = {1035 -1042},
  journal = {IEEE Transactions on Pattern Analysis and Machine Intelligence},
  volume = {23},
  author = {Weijer, J. van de and Vliet, L.J. van and Verbeek, P.W. and Ginkel, M. van}
}
@article{Weijer2005,
  number = {4},
  year = {2005},
  title = {Edge and Corner Detection by Photometric Quasi-Invariants},
  pages = {625-630},
  journal = {IEEE Transactions on Pattern Analysis and Machine Intelligence},
  volume = {27},
  author = {Weijer, J. van de and Vliet, L.J. van and Verbeek, P.W. and Ginkel, M. van }
}
@article{Unsalan2001,
  number = {1},
  year = {2001},
  title = {Conversions between Parametric and Implicit Forms Using Polar/Spherical Coordinate Representations},
  pages = {1--25},
  journal = {Computer Vision and Image Understanding},
  volume = {81},
  author = {{\"Unsalan}, C. and {Er\c{c}il}, A.}
}
@article{Aguado2000a,
  number = {1995},
  year = {2000},
  title = {On the Intimate Relationship between the Principle of Duality and the {Hough} Transform},
  pages = {503--526},
  journal = {Proceedings of the Royal Society London A},
  volume = {456},
  author = {Aguado, A.S. and Montiel, E. and Nixon, M.S.}
}
@article{Unser1999,
  month = {November},
  year = {1999},
  title = {Splines: A Perfect Fit for Signal and Image Processing},
  pages = {22--38},
  journal = {IEEE Signal Processing Magazine},
  author = {Unser, Michael}
}
@article{Haussecker2001,
  number = {6},
  month = {June},
  year = {2001},
  title = {Computing Optical Flow with Physical Models of Brightness Variation},
  pages = {661--673},
  journal = {IEEE Transactions on Pattern Analysis and Machine Intelligence},
  volume = {23},
  author = {Haussecker, H.W. and Fleet, D.J.}
}
@article{Unser1995,
  number = {10},
  year = {1995},
  title = {Convolution-based interpolation for fast, high-quality rotation of images},
  pages = {1371-1381},
  journal = {IEEE Transactions on Image Processing},
  volume = {4},
  author = {Unser, M. and Thevenaz, P. and Yaroslavsky, L.}
}
@article{Duncan1991,
  number = {3},
  year = {1991},
  title = {A bending energy model for measurement of cardiac shape deformaty},
  pages = {307--319},
  journal = {IEEE Transactions on Medical Imaging},
  volume = {10},
  author = {Duncan, J.S. and Lee, F.A. and Smeulders, A.W.M. and Zaret, B.L.}
}
@article{Unser1991,
  number = {3},
  month = {March},
  year = {1991},
  title = {Fast {B}-Spline Transform for Continuous Image Representation and Interpolation},
  pages = {277--285},
  journal = {IEEE Transactions on Pattern Analysis and Machine Intelligence},
  volume = {13},
  author = {Unser, M. and Aldroubi, A. and Eden, M.}
}
@article{Whitaker1993,
  number = {1},
  month = {January},
  year = {1993},
  title = {A Multi-Scale Approach to Nonuniform Diffusion},
  pages = {99--110},
  journal = {CVGIP Image Understanding},
  volume = {57},
  author = {Whitaker, R.T. and Pizer, S.M.}
}
@article{Unser1993,
  number = {2},
  month = {February},
  year = {1993},
  title = {{B}-Spline Signal Processing: Part {I} - Theory},
  pages = {821--833},
  journal = {IEEE Transactions on Signal Processing},
  volume = {41},
  author = {Unser, Michael and Aldroubi, Akram and Eden, Murray}
}
@article{Vries2004,
  number = {4},
  year = {2004},
  title = {Patterned Electroplating of Micrometer Scale Magnetic Structures on Glass Substrates},
  pages = {391-395},
  journal = {Journal of Microelectromechanical Systems},
  volume = {13},
  author = {Vries, A.H.B. de and Kanger, J.S. and Krenn, B.E. and Driel, R. van}
}
@article{Vries2005,
  number = {3},
  year = {2005},
  title = {Micro Magnetic Tweezers for Nanomanipulation Inside Live Cells},
  pages = {2137-2144},
  journal = {Biophysical Journal},
  volume = {88},
  author = {Vries, A.H.B. de and Krenn, B.E. and Driel, R. van and Kanger, J.S.}
}
@article{Sheppard1988,
  number = {2},
  year = {1988},
  title = {Super-resolution in confocal microscopy},
  pages = {53-54},
  journal = {Optik},
  volume = {80},
  author = {Sheppard, C.J.R.}
}
@article{Kippenberg2011,
  year = {2011},
  title = {Microresonator-Based Optical Frequency Combs},
  pages = {555-560},
  journal = {Science},
  volume = {332},
  author = {Kippenberg, T.J. and Holzwarth, R. and Diddams, S.A.}
}
@misc{DIPlib,
  year = {1995},
  title = {{DIPlib}: a scientific image processing library},
  note = {Pattern Recognition Group, Department of Applied Physics, Delft University of Technology, {\tt http://www.qi.tnw.tudelft.nl/DIPlib}},
  author = {Ginkel, M. van and Kempen, G.M.P. van and Luengo Hendriks, C.L. and Rieger, B. and Vliet, L.J. van}
}
@article{Michielsen2000,
  year = {2000},
  title = {Morphological Image Analysis},
  pages = {94--103},
  journal = {Computer Physics Communications},
  volume = {132},
  author = {Michielsen, K. and De Raedt, H.}
}
@article{Heertje1997,
  number = {2},
  year = {1997},
  title = {Vet Zonder Vet},
  pages = {30--40},
  journal = {Natuur en Techniek},
  volume = {65},
  author = {Heertje, I.}
}
@inproceedings{Tomasi1998a,
  month = {January 4-7},
  year = {1988},
  title = {Bilateral Filtering for Gray and Color Images},
  booktitle = { Proceedings of the Sixth International Conference on Computer Vision, ICCV'98 (Bombay, India)},
  pages = {836-846},
  publisher = {Narosa Publishing House},
  author = {Tomasi, C. and Manduchi, R.}
}
@book{Jain1989,
  year = {1989},
  title = {Fundamentals of Digital Image Processing},
  publisher = {Prentice-Hall},
  author = {Jain, A.K.}
}
@article{Thompson2002,
  year = {2002},
  title = {Precise Nanometer Localization Analysis for Individual Fluorescent Probes},
  pages = {2775-2783},
  journal = {Biophysical Journal},
  volume = {82},
  author = {Thompson, R.E. and Larson, D.R. and Webb, W.W.}
}
@techreport{Pizer1990,
  year = {1990},
  title = {Toward Interactive Object Definition in 3D Scalar Images},
  note = {TR90-034},
  institution = {University of North Carolina, U.S.A.},
  author = {Pizer, S.M. and Cullip, T.J. and Fredericksen, R.E.}
}
@article{Taton2001,
  year = {2001},
  title = {Two-color labeling of oligonucleotide arrays via size-selctive scattering of nanoparticles},
  pages = {5164-5165},
  journal = {Journal of the American Chemical Society},
  volume = {123},
  author = {Taton, T.A. and Mirkin, C.A. and Lestinger, R.L.}
}
@article{Orr1993,
  number = {1},
  month = {January},
  year = {1993},
  title = {The Order of Computation for Finite Discrete Gabor Transforms},
  pages = {122--130},
  journal = {IEEE Transactions on Signal Processing},
  volume = {41},
  author = {Orr, R.S.}
}
@article{Marfurt1998,
  number = {4},
  month = {July-August},
  year = {1998},
  title = {3-D Seismic Attributes using a Semblance-based coherency algorithm},
  pages = {1150--1165},
  journal = {Geophysics},
  volume = {63},
  author = {Marfurt, K.J. and Kirlin, R.L. and Farmer, S.L. and Bahorich, M.S.}
}
@inproceedings{Witkin1983,
  month = {October},
  year = {1983},
  title = {Scale Space Filtering},
  booktitle = {Proceedings of the International Conference on Artificial Intelligence},
  pages = {1019--1023},
  address = {Karlsruhe, Germany},
  author = {Witkin, A.}
}
@article{Doel2001,
  number = {25},
  year = {2001},
  title = {Temporal phase unwrapping algorithm for dynamic interference pattern analysis in interference-contrast microscopy},
  pages = {4487--4500},
  journal = {Applied Optics},
  volume = {40},
  author = {Doel, L.R. van den and Vliet, L.J. van}
}
@inproceedings{Zucker1999,
  month = {June 7-11},
  year = {1999},
  title = {Complexity and Confusion in Computational Vision},
  booktitle = {SCIA'99 the 11th Scandinavian Conference on Image Analysis (Kangerlussuaq, Greenland)},
  pages = {1--10},
  author = {Zucker, S.W.}
}
@article{HelOr1998,
  year = {1998},
  title = {Canonical Decomposition of Steerable Functions},
  pages = {83--95},
  journal = {Journal of Mathematical Imaging and Vision},
  volume = {9},
  author = {Hel-Or, Y. and Teo, P.C.}
}
@phdthesis{Doel2002,
  year = {2002},
  title = {Quantitative Microscopic Techniques for Monitoring Dynamic Processes in Microarrays},
  address = {Delft, The Netherlands},
  school = {Delft University of Technology},
  author = {Doel, L.R. van den}
}
@article{Fredrich1997,
  number = {3-4},
  year = {1997},
  title = {Statistical Characterization of the Three-dimensional Microgeometry of Porous Media and Correlation with Macroscopic Transport Properties},
  pages = {Paper No. 85},
  journal = {Int. J. Roch Mech. \& Min. Sci.},
  volume = {34},
  author = {Fredrich, J.T. and Lindquist, W.B.}
}
@article{Fredrich1999,
  number = {7},
  year = {1999},
  title = {3D Imaging of Porous Media using Laser Scanning Confocal Microscopy with Application to Microscale Transport Processes},
  pages = {551--561},
  journal = {Physics and Chemistry of the Earth (A)},
  volume = {24},
  author = {Fredrich, J.T.}
}
@book{Duda2001,
  edition = {second},
  year = {2001},
  title = {Pattern Classification},
  publisher = {John Wiley \& Sons},
  author = {Duda, R.O. and Hart, P.E. and Stork, D.G.}
}
@article{Fredrich1995,
  month = {April},
  year = {1995},
  title = {Imaging the Pore Structure of Geomaterials},
  pages = {276--279},
  journal = {Science},
  volume = {268},
  author = {Fredrich, J.T. and {Men\'endez}, B. and Wong, T.F.}
}
@article{Whitehouse1974a,
  year = {1974},
  title = {Scanning Electron Microscope Studies of Trabecular Bone in the Proximal End of the Human Femur},
  pages = {417--444},
  journal = {J. Anatomy},
  volume = {118},
  author = {Whitehouse, W.J. and Dyson, E.D.}
}
@inproceedings{Beucher1982,
  year = {1982},
  title = {Watersheds of Functions and Picture Segmentation},
  booktitle = {IEEE International Conference on Acoustics, Speech, and Signal Processing},
  pages = {1928-1931},
  author = {Beucher, S.}
}
@article{Booth2000,
  number = {1},
  year = {2000},
  title = {Strategies for the compensation of specimen-induced spherical aberration in confocal microscopy of skin},
  pages = {68-74},
  journal = {Journal of Microscopy},
  volume = {200},
  author = {Booth, M.J. and Wilson, T.}
}
@article{Redon1998,
  month = {September},
  year = {1998},
  title = {Assessment of Fibre Orientation in Reinforced Concrete using {Fourier} Image Transform},
  pages = {258--265},
  journal = {Journal of Microscopy},
  volume = {191 Pt 3},
  author = {Redon, C. and Chermant, L. and Chermant, J.-L. and Coster, M.}
}
@article{Booth2004,
  year = {2004},
  title = {A 9 single particle reconstruction from {CCD} captured images on a 200 {kV} electron cryomicroscope},
  pages = {116-127},
  journal = {Journal of Structural Biology},
  volume = {147},
  author = {Booth, C.R. and Jiang, W. and Baker, M.L. and Zhou, Z.H. and Ludtke, S.J. and Chiu, W.}
}
@article{Booth2002,
  number = {9},
  year = {2002},
  title = {Adaptive aberration correction in a confocal microscope},
  pages = {5788-5792},
  journal = {Proceedings of the National Academy of Sciences of the United States of America},
  volume = {99},
  author = {Booth, M.J. and Neil, M.A.A. and Juskaitis, R. and Wilson, T.}
}
@article{Jakobsen2000,
  number = {6},
  month = {November/December},
  year = {2000},
  title = {Anisotropic approximations for mudrocks: a seismic laboratory study},
  pages = {1711--1725},
  journal = {Geophysics},
  volume = {65},
  author = {Jakobsen, M. and Johansen, T.A.}
}
@article{Kiryati1991a,
  number = {6},
  month = {June},
  year = {1991},
  title = {On Navigating between Friends and Foes},
  pages = {602--606},
  journal = {IEEE Transactions on Pattern Analysis and Machine Intelligence},
  volume = {13},
  annote = {key_radon},
  author = {Kiryati, N. and Bruckstein, A.M.}
}
@article{Gustafsson1999,
  number = {1},
  year = {1999},
  title = {{I$^5$M}: {3D} widefield light microscopy with better than 100 nm axial resolution},
  pages = {10-16},
  journal = {Journal of Microscopy},
  volume = {195},
  author = {Gustafsson, M.G.L. and Agard, D.A. and Sedat, J.W.}
}
@book{Lovell1999,
  year = {1999},
  title = {Borehole imaging: Applications and case histories, Geological Society special publication, no. 159},
  publisher = {Geological Society, London},
  author = {Lovell, M. and Williamson, G. and Harvey, P.}
}
@article{Faydi2001a,
  year = {2001},
  title = {Experimental Study and Modeling of the Ice Crystal Morphology of Model Standard Ice Cream. Part {II}: Heat Transfer Data and Texture Modeling},
  pages = {293--300},
  journal = {Journal of Food Engineering},
  volume = {48},
  author = {Faydi, E. and Andrieu, J. and Laurent, P. and Peczalski, R.}
}
@article{Kitchen1982,
  number = {2},
  year = {1982},
  title = {Gray-Level Corner Detection},
  pages = {95--102},
  journal = {Pattern Recognition Letters},
  volume = {1},
  author = {Kitchen, L. and Rosenfeld, A.}
}
@inbook{Digabel1978,
  year = {1978},
  title = {Quantitative Analysis of Microstructures in Materials Sciences, Biology and Medicine},
  pages = {85-99},
  editor = {Chermant, J. L.},
  address = {Stuttgart},
  chapter = {Iterative Algorithms},
  publisher = {Dr. Rieder-Verlag},
  author = {Digabel, H. and {Lantu\'ejoul}, C.}
}
@article{Leung2000,
  number = {12},
  month = {December},
  year = {2000},
  title = {Clustering by Scale-space Filtering},
  pages = {1396--1410},
  journal = {IEEE Transactions on Pattern Analysis and Machine Intelligence},
  volume = {22},
  author = {Leung, Y. and Zhang, J.S. and Xu, Z.B.}
}
@article{Tomasi1998,
  number = {3},
  month = {March},
  year = {1998},
  title = {Stereo Matching as a Nearest-Neighbor Problem},
  pages = {333--340},
  journal = {IEEE Transactions on Pattern Analysis and Machine Intelligence},
  volume = {20},
  author = {Tomasi, C. and Manduchi, R.}
}
@article{Shi1996,
  number = {2},
  year = {1996},
  title = {Statistical mechanics of the extensible and shearable elastic rod and of {DNA}},
  pages = {714-731},
  journal = {The Journal of Chemical Physics},
  volume = {105},
  author = {Shi, Y. and He, S. and Hearst, J.E.}
}
@article{Schwertner2004,
  number = {26},
  year = {2004},
  title = {Characterizing specimen induced aberrations for high NA adaptive optical microscopy},
  pages = {6540-6552},
  journal = {Optics Express},
  volume = {12},
  author = {Schwertner, M. and Booth, M.J. and Wilson, T.}
}
@article{Ville1948,
  number = {1},
  year = {1948},
  title = {{Th\'eorie} et Applications de la Notion de Signal Analytique},
  pages = {61--74},
  journal = {Cables et Transmission},
  volume = {{2A}},
  author = {Ville, J.}
}
@article{Good1958,
  year = {1958},
  title = {The Interaction Algorithm and Practical {Fourier} Analysis},
  pages = {361--372},
  note = {Addendum in vol B. 22, 1960, pp. 372-375},
  journal = {J. Roy. Statist. Soc. Ser. B},
  volume = {B. 20},
  annote = {key_fft},
  author = {Good, I.J.}
}
@article{Digman2005a,
  year = {2005},
  title = {Measuring Fast Dynamics in Solutions and Cells with a Laser Scanning Microscope},
  pages = {1317-1327},
  journal = {Biophysical Journal},
  volume = {89},
  author = {Digman, M.A. and Brown, C.M. and Sengupta, P. and Wiseman, P.W. and Howritz, A.R. and Grattown, E.}
}
@article{Kiryati1992,
  number = {4},
  month = {April},
  year = {1992},
  title = {What 's in a Set of Points?},
  pages = {496--500},
  journal = {IEEE Transactions on Pattern Analysis and Machine Intelligence},
  volume = {14},
  annote = {key_radon},
  author = {Kiryati, N. and Bruckstein, A.M.}
}
@inbook{Rosenfeld1969_Hough,
  year = {1969},
  title = {Picture Processing by Computer},
  pages = {151--153},
  note = {Section 8.4.e. Coordinate Conversion},
  chapter = {8. Picture Segmentation},
  publisher = {Academic Press},
  author = {Rosenfeld, A.}
}
@article{Kiryati1991,
  number = {3},
  month = {May},
  year = {1991},
  title = {Antialiasing the {H}ough transform},
  pages = {213--222},
  journal = {CVGIP: Graphical Models and Image Processing},
  volume = {53},
  annote = {key_radon},
  author = {Kiryati, N. and Bruckstein, A.M.}
}
@article{Randen1999,
  number = {4},
  month = {April},
  year = {1999},
  title = {Filtering for Texture Classification: A Comparative Study},
  pages = {291--310},
  journal = {IEEE Transactions on Pattern Analysis and Machine Intelligence},
  volume = {21},
  author = {Randen, T. and {Hus\oe y}, H.}
}
@article{Birk1979,
  number = {2},
  month = {April},
  year = {1979},
  title = {Image Feature Extraction Using Diameter-Limited Gradient Direction Histograms},
  pages = {228--235},
  journal = {IEEE Transactions on Pattern Analysis and Machine Intelligence},
  volume = {1},
  author = {Birk, J. and Kelley, R. and Chen, N. and Wilson, L.}
}
@article{Betzig2006,
  year = {2006},
  title = {Imaging Intracellular Fluorescent Proteins at Nanometer Resolution},
  pages = {1643-1645},
  journal = {Science},
  volume = {313},
  author = {Betzig, E. and Patterson, G.H. and Sougrat, R. and Lindwasser, O.W. and Olenych, S. and Bonifacino, J.S. and Davidson, M.W. and Lippincott-Schwartz, J. and Hess, H.F.}
}
@article{Lopez2000,
  year = {2000},
  title = {Multilocal Creaseness Based on the Level-Set Extrinsic Curvature},
  pages = {111--144},
  journal = {Computer Vision and Image Understanding},
  volume = {77},
  author = {{L\'opez}, A.M. and Lloret, D. and Serrat, J. and Villanueva, J.J.}
}
@book{Stoker1969,
  year = {1969},
  title = {Differential Geometry},
  publisher = {John Wiley and Sons, Inc},
  author = {Stoker, J.J.}
}
@article{Robinson2004a,
  number = {9},
  year = {2004},
  title = {Fundamental performance limits in image registration},
  pages = {1185-1199},
  journal = {IEEE Transactions on Image Processing},
  volume = {13},
  author = {Robinson, M.D. and Milanfar, P.}
}
@article{Frontali1988,
  number = {8},
  year = {1988},
  title = {Excluded-volume effect on the bidimensional conformation of {DNA} molecules adsorbed to protein films},
  pages = {1329-1331},
  journal = {Biopolymers},
  volume = {27},
  author = {Frontali, C.}
}
@article{Veen1981,
  year = {1981},
  title = {Discretization Error in the {H}ough transform},
  pages = {137--145},
  journal = {Pattern Recognition},
  volume = {14},
  annote = {key_radon},
  author = {Veen, T.M. van and Groen, F.C.A.}
}
@article{Eberly1991a,
  number = {6},
  month = {November},
  year = {1991},
  title = {On Gray Scale Image Measurements. {II}. Surface Area and Volume},
  pages = {550--562},
  journal = {CVGIP: Graphical Models and Image Processing},
  volume = {53},
  author = {Eberly, D. and Lancaster, J. and Alyassin, A.}
}
@article{Stowell1998,
  year = {1998},
  title = {Macromolecular structure determination by electron microscopy: new advances and recent results},
  pages = {595-600},
  journal = {Current Opinion Structural Biology},
  volume = {8},
  author = {Stowell, M.H.B. and Miyazawa, A. and Unwin, N.}
}
@article{Yang1997,
  number = {2},
  month = {March},
  year = {1997},
  title = {Fast Computation of Three-Dimensional Geometric Moments Using a Discrete Divergence Theorem and a Generalization to Higher Dimensions},
  pages = {97--108},
  journal = {Graphical Models and Image Processing},
  volume = {59},
  author = {Yang, L. and Albregtsen, F. and Taxt, T.}
}
@article{Jovin2003,
  year = {2003},
  title = {Quantum dots finally come of age},
  pages = {32-33},
  journal = {Nature Biotechnology},
  volume = {21},
  author = {Jovin, T.M.}
}
@article{Ioannidis2000,
  year = {2000},
  title = {On the Geometry and Topology of 3D Stochastic Porous Media},
  pages = {323--334},
  journal = {Journal of Colloid and Interface Science},
  volume = {229},
  author = {Ioannidis, M.A. and Chatzis, I.}
}
@article{Srinivasa1996,
  number = {8},
  year = {1996},
  title = {A FFT-based technique for translation, rotation and scale-invariant image registration},
  pages = {1266-1271},
  journal = {IEEE Transactions on Image Processing},
  volume = {5},
  author = {Srinivasa Reddy, B. and Chatterji, B.N.}
}
@article{Zheng1995,
  year = {1995},
  title = {Automatic feature point extraction and tracking in image sequences for arbitrary camera motion},
  pages = {31--76},
  journal = {International Journal of Computer Vision},
  volume = {15},
  author = {Zheng, Q. and Chellappa, R.}
}
@article{Mattfeldt1993,
  month = {August},
  year = {1993},
  title = {Second-order Stereology of Benign and Malignant Alterations of the Human Mammary Gland},
  pages = {143--151},
  journal = {Journal of Microscopy},
  volume = {171, Pr 2},
  author = {Mattfeldt, T. and Frey, H. and Rose, C.}
}
@book{Campbell2001a,
  year = {2001},
  title = {Exploring the Nanoworld with {LEGO} bricks},
  editor = {Campbell, D.J.}
}
@article{Murk2003,
  number = {23},
  year = {2003},
  title = {Endosomal compartmentalization in three dimensions: Implications for membrane fusion},
  pages = {13332-13337},
  journal = {Proceedings of the National Academy of Sciences of the United States of America},
  volume = {100},
  author = {Murk, J.L.A.N. and Humbel, B.M. and Ziese, U. and Griffith, J.M. and Posthuma, G. and Slot, J.W. and Koster, A.J. and Verkleij, A.J. and Geuze, H.J. and Kleijmeer, M.J.}
}
@article{Chiuso2002,
  number = {4},
  year = {2002},
  title = {Structure from motion causally integrated over time},
  pages = {523--535},
  journal = {IEEE Transactions on Pattern Analysis and Machine Intelligence},
  volume = {24},
  author = {Chiuso, A. and Favaro, P. and Hailin Jin and Soatto, S. }
}
@misc{Atherton1993,
  year = {1993},
  title = {Using Phase to Represent Radius in the Coherent Circle {Hough} Transform},
  howpublished = {IEE Colloquium on {Hough} Transforms},
  author = {Atherton, T.J. and Kerbyson, D.J.}
}
@article{Lidke2005a,
  year = {2005},
  title = {Reaching out for signals: filopodia sense {EGF} and respond by directed retrograde transport of activated receptors},
  pages = {619-626},
  journal = {Journal of Cell Biology},
  volume = {170},
  author = {Lidke, D.S. and Lidke, K.A. and Rieger, B. and Jovin, T.M. and Arndt-Jovin, D.J.}
}
@article{Squire2000,
  number = {3},
  year = {2000},
  title = { Invariant Signatures: Characterizing Contours by their Departures from Invariance},
  pages = {284--316},
  journal = {Computer Vision and Image Understanding},
  volume = {77},
  author = {Squire, D. and Caelli, T.}
}
@article{Lidke2005b,
  number = {18},
  year = {2005},
  title = {Superresolution by localization of quantum dots using blinking statistics},
  pages = {7052-7062},
  journal = {Optics Express},
  volume = {13},
  author = {Lidke, K.A. and Rieger, B. and Jovin, T.M. and Heintzmann, R.}
}
@article{Rosenfeld1968,
  number = {1},
  month = {july},
  year = {1968},
  title = {Distance functions on digital pictures},
  pages = {33-61},
  journal = {Pattern Recognition},
  volume = {1},
  author = {Rosenfeld, A. and Pfaltz, J.L.}
}
@article{Garini1999,
  number = {3},
  year = {1999},
  title = {Signal to Noise Analysis of Multiple Color Fluorescence Imaging Microscopy},
  pages = {214-226},
  journal = {Cytometry},
  volume = {35},
  author = {Garini, Y. and Bar-Am, G.I. and Cabib, D. and Katzir, N.}
}
@article{Yuen1997,
  number = {6},
  year = {1997},
  title = {An Investigation of the Nature of Parameterization for the {Hough} Transform},
  pages = {1009--1040},
  journal = {Pattern Recognition},
  volume = {30},
  author = {Yuen, S.Y. and Ma, C.H.}
}
@inproceedings{Niessen1994,
  year = {1994},
  title = {Nonlinear Diffusion of Scalar Images using Well-Posed Differential Operators},
  booktitle = {CVPR'94 (Seattle, U.S.A.)},
  pages = {92--97},
  author = {Niessen, W.J. and Haar Romeny, B.M. ter and Florack, L.M.J. and Salden, A.H. and Viergever, M.A.}
}
@book{Rosenfeld1969,
  year = {1969},
  title = {Picture Processing by Computer},
  publisher = {Academic Press},
  author = {Rosenfeld, A.}
}
@article{Besl1992,
  number = {2},
  year = {1992},
  title = {A method for registration of {3-D} shapes},
  pages = {239-256},
  journal = {IEEE Transactions on Pattern Analysis and Machine Intelligence},
  volume = {14},
  author = {Besl, P.J. and McKay, N.D.}
}
@article{Neher2004a,
  number = {1},
  year = {2004},
  title = {Optimizing imaging parameters for the separation of multiple labels in a fluorescence image},
  pages = {46-62},
  journal = {Journal of Microscopy},
  volume = {213},
  author = {Neher, R.A. and Neher, E.}
}
@article{Kempen1997,
  number = {3},
  year = {1997},
  title = {A Quantitative Comparison of Image Restoration Methods for Confocal Microscopy},
  pages = {354--365},
  journal = {Journal of Microscopy},
  volume = {185},
  author = {Kempen, G.M.P. van and Vliet, L.J. van and Verveer, P.J. and Voort, H.T.M. van der}
}
@article{Walters1987,
  year = {1987},
  title = {Selection of Image Primitives for General-Purpose Visual Processing},
  pages = {261--298},
  journal = {Computer Vision, Graphics, and Image Processing},
  volume = {37},
  author = {Walters, D.}
}
@article{Heintzmann2001,
  year = {2001},
  title = {A dual path programmable array microscope ({PAM}): simultaneous acquisition of conjugate and non-conjugate images},
  pages = {119-135},
  journal = {Journal of Microscopy},
  volume = {204},
  author = {Heintzmann, R. and Hanley, Q.S. and Ardent-Jovin, D.J. and Jovin, T.M.}
}
@inproceedings{Kempen1999,
  month = {June 7-11},
  year = {1999},
  title = {The Application of a Local Dimensionality Estimator to the Analysis of 3D Microscopic Network Structures},
  booktitle = {SCIA'99, Proc. 11th Scandinavian Conference on Image Analysis (Kangerlussuaq, Greenland)},
  pages = {447--455},
  author = {Kempen, G.M.P. van and Brink, N. van den and Vliet, L.J. van and Ginkel, M. van and Verbeek, P.W.}
}
@manual{Ieee1985,
  year = {1985},
  title = {{IEEE} Standard for Binary Floating-Point Arithmetic},
  note = {Std. 754-1985},
  address = {Standards Committee of the {IEEE} Computer Society},
  author = {IEEE}
}
@article{Cairney2001,
  month = {February},
  year = {2001},
  title = {Microstructural Analysis of a FeAl/quasicrystal-based composite prepared using a focused ion beam miller},
  pages = {201--211},
  journal = {Journal of Microscopy},
  volume = {201, Pt 2},
  author = {Cairney, J.M. and Munroe, P.R. and Sordelet, D.J.}
}
@article{Chen1994,
  number = {9},
  year = {1994},
  title = {Segmentation and Association Among Lines and Junctions for a Line Image},
  pages = {1135--1157},
  journal = {Pattern Recognition},
  volume = {27},
  author = {Chen, Y.S.}
}
@inproceedings{Hurley1999,
  year = {1999},
  title = {Force Field Energy Functionals for Image Feature Extraction},
  booktitle = {10th British Machine Vision Conference},
  pages = {604--613},
  editor = {Pridmore, T. and Elliman, D.},
  volume = {2},
  author = {Hurley, D.J. and Nixon, M.S. and Carter, J.N.}
}
@book{Kay1993,
  year = {1993},
  title = {Fundamentals of Statistical Processing: Estimation Theory},
  address = {New Jersey},
  publisher = {Prentice Hall},
  author = {Kay, S.M.}
}
@article{Chen1993,
  number = {6},
  year = {1993},
  title = {An Improved Line Continuation Model in Human Visual Perception},
  pages = {825--842},
  journal = {Pattern Recognition},
  volume = {26},
  author = {Chen,Y.S. and Chang, S.L. and Hsu, W.H.}
}
@article{Goldberg1991,
  number = {1},
  year = {1991},
  title = {What Every Computer Scientist Should Know about Floating-Point Arithmetic},
  pages = {5--48},
  journal = {ACM Computing Surveys},
  volume = {23},
  author = {Goldberg, D.}
}
@article{Mancini2000,
  year = {2000},
  title = {Supplanting crystallography or supplementing microscopy? A combined approach to the study of an enveloped virus},
  pages = {1278-1287},
  journal = {Acta Crystallographica Section D},
  volume = {56},
  author = {Mancini, E.J. and Fuller, S.D.}
}
@inproceedings{Aguado1997,
  month = {12--15 October},
  year = {1997},
  title = {Arbitrary Shape {Hough} Transform by Invariant Geometric Features},
  booktitle = {International Conference on Systems, Man and Cybernetics},
  pages = {2661--2665},
  volume = {3},
  author = {Aguado, A.S. and Montiel, M.E. and Nixon, M.S.},
  organization = {IEEE}
}
@inproceedings{Granlund1997,
  series = {Lecture Notes on Computer Science},
  year = {1997},
  title = {From Multidimensional Signals to the Generation of Responses},
  booktitle = {Algebraic Frames for the Perception-Action Cycle (AFPAC 1997)},
  editor = {Sommer, G. and Koenderink, J.J.},
  volume = {1315},
  address = {Kiel, Germany},
  publisher = {Springer-Verlag},
  author = {Granlund, G.H.}
}
@article{Smit1998,
  number = {3},
  month = {September},
  year = {1998},
  title = {Star Length Distribution: a Volume-Based Concept for the Characterization of Structural Anisotropy},
  pages = {249--257},
  journal = {Journal of Microscopy},
  volume = {191},
  author = {Smit, Th.H. and Schneider, E. and Odgaard, A.}
}
@book{Granlund1995,
  year = {1995},
  title = {Signal processing for computer vision},
  address = {Boston/Dordrecht/London},
  publisher = {Kluwer Academic Publishers},
  author = {Granlund, G.H. and Knutsson, H.}
}
@mastersthesis{Brink1999,
  year = {1999},
  title = {Three Dimensional Image Analysis of Microstructures in Microscopical Images},
  address = {Delft, The Netherlands},
  school = {Delft University of Technology},
  author = {Brink, N. van den}
}
@article{Acton2000a,
  year = {2000},
  title = {Area Operators for Edge Detection},
  pages = {771--777},
  journal = {Pattern Recognition Letters},
  volume = {21},
  author = {Acton, Scott T. and Mukherjee, Dipti Prasad}
}
@article{Forster2005,
  number = {13},
  year = {2005},
  title = {Retrovirus envelope protein complex structure in situ studied by cryo-electron tomography},
  pages = {4729-4734},
  journal = {Proceedings of the National Academy of Sciences of the United States of America},
  volume = {102},
  author = {{F\"orster},F. and Medalia, O. and Zauberman, N. and Baumeiser, W. and Fass, D.}
}
@article{Mardia1999,
  year = {1999},
  title = {Estimation of torsion},
  pages = {373--381},
  journal = {Journal of Applied Statistics},
  volume = {26},
  author = {Mardia, K.V. and Morris, R.J. and Walder, A.N. and Koenderink, J.J}
}
@article{Torr1997,
  number = {8},
  year = {1997},
  title = {Robust Parameterization and Computation of the Trifocal Tensor},
  pages = {591--605},
  journal = {Image and Vision Computing},
  volume = {15},
  author = {Torr, P.H.S. and Zisserman, A.}
}
@article{Richards1959,
  number = {1274},
  year = {1959},
  title = {Electromagnetic Diffraction in Optical Systems. {II.} Structure of the Image Field in an Aplanatic System},
  pages = {358-379},
  journal = {Proceedings of the Royal Society of London A},
  volume = {253},
  author = {Richards, B. and Wolf, E.}
}
@incollection{Yuille1988,
  year = {1988},
  title = {Scaling and fingerprint theorems for zero-crossings},
  booktitle = {Advances in computer vision, volume 2},
  pages = {47--78},
  editor = {Christopher Brown},
  chapter = {2},
  publisher = {Lawrence Erlbaum Associates, Inc},
  author = {Yuille, A.L. and Poggio, T.}
}
@article{Zucker1985,
  year = {1985},
  title = {Early Orientation Selection: Tangent Fields and the Dimensionality of Their Support},
  pages = {74--103},
  journal = {Computer Vision, Graphics, and Image Processing},
  volume = {32},
  author = {Zucker, S.W.}
}
@article{Zucker1981,
  number = {3},
  year = {1981},
  title = {A 3-D edge operator},
  pages = {324--331},
  journal = {IEEE Transactions on Pattern Analysis and Machine Intelligence},
  volume = {3},
  author = {Zucker, S.W. and Hummel, R.A.}
}
@article{Kurdy1989,
  number = {2},
  year = {1989},
  title = {Directional Mathematical morphology Operations},
  pages = {473--480},
  journal = {Acta. Stereology},
  volume = {8},
  author = {Kurdy, M.B. and Jeulin, D.}
}
@article{Post2005,
  number = {2},
  year = {2005},
  title = {One- and two-photon photoactivation of a {paGFP}-fusion protein in live {Drosophila} embryos},
  pages = {325-330},
  journal = {FEBS Letters},
  volume = {579},
  author = {Post, J.N. and Lidke, K.A. and Rieger, B. and Arndt-Jovin, D.J.}
}
@article{Bitter2001,
  number = {3},
  month = {July--September},
  year = {2001},
  title = {Penalized-Distance Volumetric Skeleton Algorithm},
  pages = {195--205},
  journal = {IEEE Transactions on Visualization and Computer Graphics},
  volume = {7},
  author = {Bitter, I. and Kaufman, A.E.}
}
@article{Jeulin2001,
  year = {2001},
  title = {Gypsum Morphological Analysis and Modeling},
  pages = {299--311},
  journal = {Cement {\&} Concrete Composites},
  volume = {23},
  author = {Jeulin, D. and Monnaie, P. and P?onnet, F.}
}
@article{OConner1999,
  number = {7},
  year = {1999},
  title = {Microscale Flow Modeling in Geologic Materials},
  pages = {611--616},
  journal = {Phys. Chem. Earth (A)},
  volume = {24},
  author = {O'Conner, R.M. and Fredrich, J.T.}
}
@inproceedings{Bluestein1968,
  year = {1968},
  title = {A Linear Filtering Approach to the Computation of the Discrete {Fourier} Transform},
  booktitle = {Northeast Electronics Res. and Eng. Meeting Record},
  pages = {218--129},
  volume = {10},
  annote = {key_fft},
  author = {Bluestein, L.I.}
}
@article{Thust1996a,
  year = {1996},
  title = {Focal-series reconstruction in {HRTEM}: simulation studies on non-peridc objects},
  pages = {211-230},
  journal = {Ultramicroscopy},
  volume = {64},
  author = {Thust, A. and Coene, W.M.J. and Beeck, M. op de and Dyck, D. van}
}
@book{Valeur2002,
  year = {2002},
  title = {Molecular Fluorescence},
  address = {Weinheim},
  publisher = {Wiley-VCH},
  author = {Valeur, B.}
}
@article{Hiraoka1992,
  number = {6},
  year = {1992},
  title = {Temporal and Spatial Coordination of Chromosome Movement, Spindle Formation, and Nuclear Envelope Breakdown During Prometaphase in Drosophila melanogaster Embryos},
  pages = {2815-2828},
  journal = {The Journal of Cell Biology},
  volume = {111},
  author = {Hiraoka, Y. and Agard, D.A. and Sedat, J.W.}
}
@article{Heeger1988,
  year = {1988},
  title = {Optical flow from spatio-temporal filters},
  pages = {279--302},
  journal = {International Journal of Computer Vision},
  volume = {1},
  author = {Heeger, D.J..}
}
@article{Cox1999,
  number = {9},
  month = {September},
  year = {1999},
  title = {Two- and Three-Dimensional Image Rotation Using the {FFT}},
  pages = {1297--1299},
  journal = {IEEE Transactions on Image Processing},
  volume = {8},
  annote = {key_fft},
  author = {Cox, R.W. and Raoqiong, T.}
}
@article{Parent1989,
  number = {8},
  month = {August},
  year = {1989},
  title = {Trace Inference, Curvature Consistency, and Curve Detection},
  pages = {823--839},
  journal = {IEEE Transactions on Pattern Recognition and Machine Intelligence},
  volume = {11},
  author = {Parent, P. and Zucker, S.W.}
}
@article{Ludtke2001,
  year = {2001},
  title = {A 11.5 single particle reconstruction of {GroEL} using {EMAN}},
  pages = {253-262},
  journal = {Journal of Molecular Biology},
  volume = {314},
  author = {Ludtke, S.J. and Jakana, J. and Song, J.-L. and Chuang, D.T. and Chiu, W.}
}
@article{Niessen1997,
  number = {2},
  year = {1997},
  title = {A multiscale approach to image sequence analysis},
  pages = {259-268},
  journal = {Computer Vision and Image Understanding},
  volume = {65},
  author = {Niessen, W.J. and Duncan, J.S. and Nielsen, M. and Florack, L.M.J. and Haar Romeny, B.M. ter and Viergever, M.A.}
}
@article{Hirsh1976,
  number = {2},
  year = {1976},
  title = {High resolution electron microscopic studies of genetic regulation},
  pages = {471-490},
  journal = {Journal of Molecular Biology},
  volume = {108},
  author = {Hirsh, J. and Schleif, R.}
}
@article{Gemkow2001,
  year = {2001},
  title = {Develpoment regulation of {DNA}-topoisomerases during Drosophila embryogenesis},
  pages = {114-121},
  journal = {Experimental Cell Research},
  volume = {262},
  author = {Gemkow, M.J. and Dichter, J. and Ardent-Jovin, D.J.}
}
@book{Grivet1965,
  year = {1965},
  title = {Electron Optics},
  note = {Copy Peter Tiemeijer},
  address = {London},
  publisher = {Pergamon Press},
  author = {Grivet, P.}
}
@inproceedings{Forstner1987,
  month = {June},
  year = {1987},
  title = {A Fast Operator for Detection and Precise Location of Distinct Points, Corners and Centres of Circular Features},
  booktitle = {ISPRS Intercommission Workshop (Interlaken)},
  pages = {149--155},
  annote = {Not in collection},
  author = {{F\"orstner}, W. and {G\"ulch}, E.}
}
@article{Squire2004,
  number = {1},
  year = {2004},
  title = {Red-edge anisotropy microscopy enables dynamic imaging of homo-{FRET} between fluorescent proteins in cells},
  pages = {62-69},
  journal = {Journal of Structural Biology},
  volume = {147},
  author = {Squire, A. and Verveer, P.J. and Rocks, O. and Bastiaens, P.I.H.}
}
@phdthesis{Westin1994,
  year = {1994},
  title = {A Tensor Framework for Multidimensional Signal Processing},
  address = {{Link\"oping, Sweden}},
  school = {{Link\"oping University}},
  author = {Westin, C.F.}
}
@inproceedings{Matheron2002,
  year = {2002},
  title = {The Birth of Mathematical Morphology},
  booktitle = {Mathematical Morphology, Proceedings of the VI International Symposium ISMM, Sydney, April 2002},
  editor = {Talbot, H. and Beare, R.},
  address = {Collingwood, Australia},
  publisher = {CSIRO Publishing},
  author = {Matheron, G. and Serra, J.}
}
@article{Gauch1993,
  number = {6},
  month = {June},
  year = {1993},
  title = {Multiresolution Analysis of Ridges and Valleys in Grey-Scale Images},
  pages = {635--646},
  journal = {IEEE Transactions on Pattern Analysis and Machine Analysis},
  volume = {15},
  author = {Gauch, J.M. and Pizer, S.M.}
}
@article{Dellby2001,
  number = {3},
  year = {2001},
  title = {Progress in aberration-corrected scanning transmission electron microscopy},
  pages = {177-185},
  journal = {Journal of Electron Microscopy},
  volume = {50},
  author = {Bellby, N. and Krinvanek, O.L. and Nellist, P.D. and Batson, P.E. and Lupini, A.R.}
}
@inproceedings{Westin1992,
  series = {LNCS 588},
  year = {1992},
  title = {The {M\"obius} Strip Parameterization for Line Extraction},
  booktitle = {Computer Vision -- ECCV92. Proceedings, 1992},
  pages = {33--38},
  editor = {Sandini, G.},
  volume = {588},
  address = {Heidelberg},
  publisher = {Springer-Verlag},
  author = {Westin, C.-F. and Knutsson, H.},
  organization = {Springer}
}
@article{Gauch1993a,
  number = {8},
  month = {August},
  year = {1993},
  title = {The Intensity Axis of Symmetry and its Application to Image Segmentation},
  pages = {753--770},
  journal = {IEEE Transactions on Pattern Analysis and Machine Intelligence},
  volume = {15},
  author = {Gauch, J.M. and Pizer, S.M.}
}
@article{Bruun1978,
  number = {1},
  month = {February},
  year = {1978},
  title = {z-Transform {DFT} Filters and {FFT}'s},
  pages = {56--63},
  journal = {IEEE Transactions on Acoustics, Speech, and Signal Processing},
  volume = {26},
  annote = {key_fft},
  author = {Bruun, G.}
}
@article{Cheng1992,
  number = {4},
  year = {1992},
  title = {An Adaptive Morphological Filter for Image Processing},
  pages = {533-539},
  journal = {IEEE Transactions on Image Processing},
  volume = {1},
  author = {Cheng, F. and Venetsanopoulos, A. N.}
}
@article{Rockmore2000,
  number = {1},
  month = {January/February},
  year = {2000},
  title = {The {FFT} -- An Algorithm the Whole Family Can Use},
  pages = {60--64},
  journal = {Computing in Science \& Engineering},
  volume = {2},
  author = {Rockmore, D.}
}
@book{Porat1994,
  year = {1994},
  title = {Digital Signal Processing of Random Signals},
  publisher = {Prentice Hall},
  author = {Porat, B.}
}
@inproceedings{Knutsson1981a,
  year = {1981},
  title = {Anisotropic Filtering Controlled by Image Content},
  booktitle = {Proceedings of the 2nd Scandinavian Conference on Image Analysis (Finland)},
  author = {Knutsson, H. and Wilson, R. and Granlund, G.H.}
}
@book{Chung1974,
  edition = {second},
  year = {1974},
  title = {Elementary Probability Theory with Stochastic Processes},
  publisher = {Springer Verlag},
  author = {Chung, K.L.}
}
@inproceedings{Barman1991a,
  year = {1991},
  title = {Estimation of velocity, acceleration and disparity in time sequences},
  booktitle = {Proc. Conf. Pattern Recognition ICPR'91},
  pages = {44-51},
  author = {{B\aa rman}, H. and Haglund, L. and Granlund, G. H. and Knutsson, H.}
}
@article{Gui2000,
  number = {1},
  year = {2000},
  title = {A comparative study of the MQD method and several correlation-based PIV evaluation algorithms},
  pages = {36-44},
  journal = {Experiments in Fluids},
  volume = {28},
  author = {Gui, L. and Merzkirch, W.}
}
@article{Li1994,
  number = {8},
  year = {1994},
  title = {Nonlinear Diffusion with Multiple Edginess Thresholds},
  pages = {1029--1037},
  journal = {Pattern Recognition},
  volume = {27},
  author = {Li, X. and Chen, T.}
}
@article{Canny1986,
  number = {6},
  month = {November},
  year = {1986},
  title = {A Computational Approach to Edge Detection},
  pages = {679--697},
  journal = {IEEE Transactions on Pattern Analysis and Machine Intelligence},
  volume = {8},
  author = {Canny, J.}
}
@article{Rodrigo2004a,
  number = {19},
  year = {2005},
  title = {Real-time three-dimensional optical micromanipulation of multiple particles and living cells},
  pages = {2270-2273},
  journal = {Optics Letters},
  volume = {29},
  author = {Rodrigo, P.J. and Daria, V.R. and {Gl\"uckstad}, J.}
}
@inproceedings{Bracewell1984,
  month = {August},
  year = {1984},
  title = {The Fast {H}artley Transform},
  booktitle = {Proc. IEEE},
  pages = {1010--1018},
  annote = {key_fft},
  author = {Bracewell, R.N.}
}
@article{Coggins1985,
  year = {1985},
  title = {A Spatial Filtering Approach to Texture Analysis},
  pages = {195--203},
  journal = {Pattern Recognition Letters},
  volume = {3},
  author = {Coggins, J.M. and Jain, A.K.}
}
@inproceedings{Li1998,
  series = {Computational Imaging and Vision},
  year = {1998},
  title = {Generation of the {Euclidean} Skeleton by a Bisector Decision Rule on a Two-Shortest-Vector Distance Map},
  booktitle = {Mathematical Morphology and its Applications to Image and Signal Processing},
  pages = {151--158},
  editor = {Heijmans, H.J.A.M. and Roerdink, J.B.T.M.},
  volume = {12},
  publisher = {Kluwer, Dordrecht},
  author = {Li, H. and Vossepoel, A.M.}
}
@article{Horbelt2002,
  number = {4},
  month = {April},
  year = {2002},
  title = {Discretization of the Radon Transform and of its Inverse by Spline Convolutions},
  pages = {363--376},
  journal = {IEEE Transactions on Medical Imaging},
  volume = {21},
  author = {Horbelt, Stefan and Liebling, Michael and Unser, Michael}
}
@article{Bracewell1983,
  number = {12},
  month = {December},
  year = {1983},
  title = {Discrete {H}artley Transform},
  pages = {1832--1835},
  journal = {J. Opt. Soc. Am.},
  volume = {73},
  annote = {key_fft},
  author = {Bracewell, R.N.}
}
@article{Duda1972,
  number = {1},
  year = {1972},
  title = {Use of the {Hough} Transformation to Detect Lines and Curves in Pictures},
  pages = {11--15},
  journal = {Communications of the ACM},
  volume = {15},
  author = {Duda, R.O. and Hart, P.E.}
}
@article{Hopt2001,
  number = {4},
  month = {April},
  year = {2001},
  title = {Highly Nonlinear Photodamage in Two-Photon Fluorescence Microscopy},
  pages = {2029-2036},
  journal = {Biophysical Journal},
  volume = {80},
  author = {Hopt, A. and Neher, E.}
}
@article{Jensen2000,
  year = {2000},
  title = {Defocus-gradient corrected back-projection},
  pages = {57-64},
  journal = {Ultramicroscopy},
  volume = {84},
  author = {Jensen, G.J. and Kornberg, R.D.}
}
@article{Sanz1989,
  number = {7},
  month = {July},
  year = {1989},
  title = {Image Representation by Sign Information},
  pages = {729--738},
  journal = {IEEE Transactions on Pattern Analysis and Machine Intelligence},
  volume = {11},
  author = {Sanz, J.L.C. and Huang, T.T.}
}
@article{Batson2003,
  year = {2003},
  title = {Aberration correction results in the {IBM STEM} instrument},
  pages = {239-249},
  journal = {Ultramicroscopy},
  volume = {96},
  author = {Batson, P.E.}
}
@article{Dorst2000,
  number = {2},
  month = {February},
  year = {2000},
  title = {The Support Cone: A Representational Tool for the Analysis of Boundaries and Their Interactions},
  pages = {174--178},
  journal = {IEEE Transactions on Pattern Analysis and Machine Intelligence},
  volume = {22},
  author = {Dorst, L. and Boomgaard, R. van den}
}
@article{Torre1986,
  number = {2},
  month = {March},
  year = {1986},
  title = {On Edge Detection},
  pages = {1986},
  journal = {IEEE Transactions on Pattern Analysis and Machine Intelligence},
  volume = {8},
  author = {Torre, V. and Poggio, T.A.}
}
@article{Montanari1968,
  number = {4},
  year = {1968},
  title = {A Method for Obtaining Skeletons Using a Quasi-Euclidean Distance.},
  pages = {600-624},
  journal = {Journal of the Association for Computing Machinery},
  volume = {15},
  author = {Montanari,U.}
}
@inproceedings{Anwander2000,
  year = {2000},
  title = {Segmentation of Crystals in Microscopic Images using Multi-scale Color Gradient (MCG)},
  booktitle = {International Conference on Color in Graphics and Image Processing CGIP2000},
  author = {Anwander, A. and Neyran, B. and Baskurt, A.}
}
@inproceedings{Ginkel1997a,
  month = {June 2-4},
  year = {1997},
  title = {Multi-Orientation Estimation: Selectivity and Localization},
  booktitle = {Proceedings of the 3rd Annual Conference of the Advanced School for Computing and Imaging (Heijen, The Netherlands)},
  pages = {99--105},
  editor = {Bal, H.E. and Corporaal, H. and Jonker, P.P. and Tonino, J.F.M.},
  author = {Ginkel, M. van and Verbeek, P.W. and van Vliet, L.J.}
}
@article{Chen1989,
  number = {5},
  year = {1989},
  title = {An Interpretive Model of Line Continuation in Human Visual Perception},
  pages = {619--639},
  journal = {Pattern Recognition},
  volume = {22},
  author = {Chen, Y.S. and Hsu, W.H.}
}
@inproceedings{Ehrich1978,
  year = {1978},
  title = {Elements of a structural model of texture},
  booktitle = {Proceedings of PRIP},
  pages = {319--326},
  author = {Ehrich, R.W. and Lai, P.F.}
}
@misc{Lasenby1999,
  year = {1999},
  title = {A Lecture Course in Geometric Algebra},
  howpublished = {{\tt http://www.mrao.cam.ac.uk/~clifford/ptIIIcourse/course99/}, Geometric Algebra Research Group, Cambridge University},
  author = {Lasenby, A. and Doran, C.}
}
@inproceedings{Beaudet1978,
  year = {1978},
  title = {Rotationally Invariant Image Operators},
  booktitle = {International Joint Conference on Pattern Recognition},
  pages = {579--583},
  author = {Beaudet, P.R.}
}
@article{Yildiz2003,
  year = {2003},
  title = {Myosin V Walks Hand-Over-Hand: Single Fluorophore Imaging with 1.5 nm localization},
  pages = {2061-2066},
  journal = {Science},
  volume = {300},
  author = {Yildiz, A. and Forkey, J.N. and McKinney, S.A. and Ha, T. and Goldman, Y.E. and Selvin, P.R.}
}
@article{ArndtJovin2006,
  year = {2006},
  title = {Quantum dots shed light on processes in living cells},
  pages = {1-3},
  journal = {SPIE Newsroom},
  volume = {DOI: 10.1117/2.1200605.0228},
  author = {Arndt-Jovin, D.J. and Lidke, D.S. and Lidke, K.A. and Rieger, B. and Jovin, T.M.}
}
@article{Westerweel2000,
  number = {7},
  year = {2000},
  title = {Theoretical analysis of the measurement precision in particle image velocimetry},
  pages = {S3-S12},
  journal = {Experiments in Fluids },
  volume = {29},
  author = {Westerweel, J.}
}
@article{Schenkeveld1997,
  number = {1},
  year = {1997},
  title = {Simulations of Measurements of Fluorescene Lifetimes Using Noise-Modulated Light},
  pages = {55-58},
  journal = {Journal of Fluorescence},
  volume = {7},
  author = {Schenkeveld, V.M.E. and Young, I.T.}
}
@article{Calabi1998,
  number = {2},
  year = {1998},
  title = {Differential and Numerically Invariant Signature Curves Applied to Object Recognition},
  pages = {107--135},
  journal = {International Journal of Computer Vision},
  volume = {26},
  author = {Calabi, E. and Olver, P.J. and Shakiban, C. and Tannenbaum, A. and Haker, S.}
}
@article{Barth1993,
  number = {6},
  year = {1993},
  title = {Image Encoding, Labeling, and Reconstruction from Differential Geometry},
  pages = {428--446},
  journal = {Graphical Models and Image Processing},
  volume = {55},
  author = {Barth, E. and Caelli, T. and Zetzsche, C.}
}
@book{Milnor1965,
  year = {1965},
  title = {Topology from the differentiable viewpoint},
  address = {Princeton, New Jersey},
  publisher = {Princeton University Press},
  author = {Milnor, J.W.}
}
@article{Mirza1993,
  number = {1},
  month = {February},
  year = {1993},
  title = {Performance Evaluation of a Class of {M}-Estimators for Surface Parameter Estimation in Noisy Range Data},
  pages = {75--85},
  journal = {IEEE Transactions on Robotics and Automation},
  volume = {9},
  author = {Mirza, M.J. and Boyer, K.L.}
}
@article{Brockett1994,
  number = {12},
  year = {1994},
  title = {Evolution Equations for Continuous-Scale Morphological Filtering},
  pages = {3377-3386},
  journal = {IEEE Transactions on Signal Processing},
  volume = {42},
  author = {Brockett, R. W. and Maragos, P.}
}
@inproceedings{Brockett1992,
  year = {1992},
  title = {Evolution Equations for Continuous-Scale Morphology},
  booktitle = {IEEE International Conference on Acoustics, Speech and Signal Processing},
  pages = {125-128},
  volume = {3},
  author = {Brockett, R. W. and Maragos, P.}
}
@article{Clapp2004,
  year = {2004},
  title = {Fluorescence Resonance Energy Transfer Between Quantum Dot Donors and Dye-Labeled Protein Acceptors},
  pages = {301-310},
  journal = {Journal of the American Chemical Society},
  volume = {126},
  author = {Clapp, A.R. and Medintz, I.L. and Mauro, J.M. and Fisher, B.R. and Bawendi, M.G. and Mattoussi, H.}
}
@article{Chen1995,
  number = {3},
  year = {1995},
  title = {Recursive Erosion, Dilation, Opening, and Closing Transforms},
  pages = {335-346},
  journal = {IEEE Transactions on Image Processing},
  volume = {4},
  author = {Chen, S. and Haralick, R.M.}
}
@article{Curtis1987,
  number = {1},
  month = {January},
  year = {1987},
  title = {Reconstruction of Multidimensional Signals from Zero Crossings},
  pages = {221--231},
  journal = {Journal of the Optical Society of America A},
  volume = {4},
  author = {Curtis, S.R. and Oppenheim, A.V.}
}
@article{Rattey1981,
  number = {5},
  month = {October},
  year = {1981},
  title = {Sampling the 2-{D} {R}adon Transform},
  pages = {994--1002},
  journal = {IEEE Transactions on Acoustics, Speech and Signal Processing},
  volume = {29},
  annote = {key_radon},
  author = {Rattey, P.A. and Lindgren, A.G.}
}
@article{Pluim2003,
  year = {2003},
  title = {Mutual-Information-based registration of medical images: a survey},
  pages = {986-1004},
  journal = {IEEE Transactions on Medical Imaging},
  volume = {22},
  author = {Pluim, J.P.W. and Maintz, J.B.A. and Viergever, M.A.}
}
@article{Volkmann2003,
  number = {6},
  year = {2003},
  title = {Myosin isoforms show unique conformations in the actin-bound state},
  pages = {3227-3232},
  journal = {Proceedings of the National Academy of Sciences of the United States of America},
  volume = {100},
  author = {Volkmann, N. and Ouyang, G. and Trybus, K.M. and DeRosier, D.J. and Lowey, S. and Hanein, D.}
}
@article{Pham2006,
  year = {2006},
  title = { Robust fusion of irregularly sampled data using adaptive normalized convolution},
  pages = {1-12},
  journal = {EURASIP Journal on Applied Signal Processing},
  volume = { },
  author = {Pham, T.Q. and Vliet, L.J. van and Schutte, K.}
}
@article{Hoyer2004,
  number = {1},
  year = {2004},
  title = {Rapid self-assembly of $\alpha$-synuclein observed by in situ atomic force microscopy},
  pages = {127-139},
  journal = {Journal of Molecular Biology},
  volume = {340},
  author = {Hoyer, W. and Cherny, D.I. and Subramaniam, V. and Jovin, T.M.}
}
@inproceedings{Pham2005,
  series = {Proceedings of SPIE Defense \& Security},
  month = {March 29-30},
  year = {2005},
  title = {Performance of optimal registration estimators},
  booktitle = {Visual Information Processing XIV},
  pages = {133-144},
  editor = {Rahman, Z. and Schowengerdt, R.A. and Reichenbach, S.E.},
  volume = {5817},
  address = {Orlando, USA},
  author = {Pham, T.Q. and Bezuijen, M. and Vliet, L.J. van and Schutte, K. and Luengo Hendriks, C.L.}
}
@article{Harada2005,
  number = {1},
  year = {2005},
  title = {Optical system for double-biprism electron holography},
  pages = {19-27},
  journal = {Journal of Electron Microscopy},
  volume = {54},
  author = {Harada, K. and Akashi, T. and Togawa, Y. and Matsuda, T. and Tonomura, A.}
}
@inproceedings{Pham2003,
  series = {LNCS 2749 },
  month = {June 29 -July 2 },
  year = {2003},
  title = {Normalized averaging using adaptive applicability functions with applications in image reconstruction from sparsely and randomly sampled data},
  booktitle = {SCIA'03, Proceedings of the 13th Scandinavian Conference on Image Analysis ({G\"oteborg}, Sweden) },
  pages = {485-492},
  editor = {{Big\"un}, J. and Gustavsson, T. },
  address = {Berlin},
  publisher = {Springer-Verlag },
  author = {Pham, T.Q. and Vliet, L.J. van}
}
@article{Scharcanski2000,
  number = {5},
  month = {October},
  year = {2000},
  title = {Stochastic Texture Image Estimators for Local Spatial Anisotropy and Its Variability},
  pages = {971--979},
  journal = {IEEE Transactions on Instrumentation and Measurement},
  volume = {49},
  author = {Scharcanski, J. and Dodson, C.T.J.}
}
@article{Ballard1983,
  number = {6},
  year = {1983},
  title = {Viewer Independent Shape Recognition},
  pages = {653--660},
  journal = {IEEE Transactions on Pattern Analysis and Machine Intelligence},
  volume = {5},
  annote = {key_radon},
  author = {Ballard, D.H. and Sabbah, D.}
}
@incollection{Alvarez1994,
  year = {1994},
  title = {Morphological Approach to Multi-scale Analysis: From Principles to Equations},
  booktitle = {Geometry-Driven Diffusion in Computer Vision},
  editor = {Viergever, M. A.},
  address = {Dordrecht},
  publisher = {Kluwer Academic Publishers},
  author = {Alvarez, L. and Morel, J.-M.}
}
@inproceedings{Diehl1989,
  year = {1989},
  title = {Planar motion estimation with a fast converging algorithm},
  booktitle = {Proc. 8th Int. Conf. Pattern Recognition, ICPR'86},
  pages = {1099--1102},
  address = {Paris, France},
  author = {Diehl, N. and Burkhardt, H.}
}
@article{Dirks1999,
  number = {3-4},
  year = {1999},
  title = {Synthesis, processing, and transport of {RNA} within the three-dimensional context of the cell nucleus},
  pages = {191-201},
  journal = {Crit Rev Eukaryot Gene Expr},
  volume = {9},
  author = {Dirks, R.W. and Hattinger, C.M. and Molenaar, C. and Snaar, S.P.}
}
@phdthesis{Kirchgessner2003,
  month = {April},
  year = {2003},
  title = {Extraktion Physiologischer Koordinatensysteme von Pflanzenwurzeln und {-Bl\"attern} aus Bildsequenzen},
  address = {Heidelberg, Germany},
  school = {Ruprechts-Karls-{Universit\"at} University},
  author = {Kirchgessner, N.}
}
@article{Vandergheynst2002,
  number = {4},
  month = {April},
  year = {2002},
  title = {Directional Dyadic Wavelet Transforms: Design and Algorithms},
  pages = {363--372},
  journal = {IEEE Transactions on Image Processing},
  volume = {11},
  author = {Vandergheynst, P. and Gobbers, J.-F.}
}
@article{Meyer2002,
  year = {2002},
  title = {A new method for the determination of the wave aberration function for high resolution {TEM} {1. Measurement} of the symmetric aberrations},
  pages = {89-109},
  journal = {Ultramicroscopy},
  volume = {92},
  author = {Meyer, R.R. and Kirkland, A.I. and Saxton, W.O.}
}
@article{Kubitscheck2000,
  month = {April},
  year = {2000},
  title = {Imaging and Tracking of Single {GFP} Molecules in Solution},
  pages = {2170-2179},
  journal = {Biophysical Journal},
  volume = {78},
  author = {Kubitscheck, U. and {K\"uckmann}, O. and Kues, T. and Peters, R.}
}
@inproceedings{Harris1988,
  month = {31 August--2 September},
  year = {1988},
  title = {A Combined Corner and Edge Detector},
  booktitle = {Proceedings of the fourth Alvey Vision Conference},
  pages = {147--151},
  author = {Harris, C. and Stephens, M.},
  organization = {University of Manchester}
}
@inproceedings{Harris1987,
  year = {1987},
  title = {Determination of Ego-Motion from Matched Points},
  booktitle = {Proceedings of the Alvey Vision Conference},
  annote = {Not in collection},
  author = {Harris, C.G.}
}
@article{Muller2001,
  number = {3},
  year = {2001},
  title = {Optimizing the environment for sub-0.2 nm scanning transmission electron microscopy},
  pages = {219-226},
  journal = {Journal of Electron Microscopy},
  volume = {50},
  author = {Muller, D.A. and Grazul, J.}
}
@misc{Mathematica,
  year = {1998},
  title = {Mathematica 4},
  note = {{\tt www.wolfram.com}},
  author = {Wolfram Research}
}
@article{Leis2006,
  number = {3},
  year = {2006},
  title = {The essential role of digital signal processing in automated tomography},
  pages = {95-103},
  journal = {IEEE Signal Processing Magazine},
  volume = {23},
  author = {Leis, A.P. and Beck, M. and Gruska, M. and Best, C. and Hegerl, R. and Baumeister, W. and Leis, J.W.}
}
@article{Kube1996,
  number = {10},
  month = {October},
  year = {1996},
  title = {Scale-space Properties of Quadratic Feature Detectors},
  pages = {987--999},
  journal = {IEEE Transactions on Pattern Analysis and Machine Intelligence},
  volume = {18},
  author = {Kube, P. and Perona, P.}
}
@article{Bluestein1970,
  number = {4},
  month = {December},
  year = {1970},
  title = {A Linear Filtering Approach to the Computation of Discrete {Fourier} Transform},
  pages = {451--455},
  journal = {IEEE Transactions on Audio and Electroacoustics},
  volume = {18},
  annote = {key_fft},
  author = {Bluestein, L.I.}
}
@article{Danielsson1980,
  year = {1980},
  title = {Euclidean Distance Mapping},
  pages = {227--248},
  journal = {Computer Graphics and Image Processing},
  volume = {14},
  author = {Danielsson, P.-E.}
}
@article{Molenaar2003a,
  number = {24},
  year = {2003},
  title = {Visualizing telomere dynamics in living mammalian cells using {PNA} probes},
  pages = {6631-6641},
  journal = {The EMBO Journal},
  volume = {22},
  author = {Molenaar, C. and Wiesmeijer, K. and Verwoerd, N.P. and Khazen, S. and Eils, R. and Tanke, H.J. and Dirks, R.W.}
}
@article{Rieger2004d,
  number = {3},
  year = {2004},
  title = {Diffusion of microspheres in sealed and open microarrays},
  pages = {218-225},
  journal = {Microscopy Research and Technique},
  volume = {65},
  author = {Rieger, B. and Dietrich, H.R.C. and Doel, L.R. van den and Vliet, L.J. van}
}
@phdthesis{Rieger2004a,
  year = {2004},
  title = {Structure from Motion in nD Image Analysis},
  note = {digital version available:\\\ {\small\tt http://www.ph.tn.tudelft.nl/Publications/PHDTheses/BRieger/thesis_rieger.html}},
  address = {Delft, The Netherlands},
  school = {Delft University of Technology},
  author = {Rieger, B.}
}
@misc{Krivanek2003,
  year = {2003},
  title = {Autoadjusting charged-particle probe-forming apparatus},
  howpublished = {US6552340},
  author = {Krivanek, O.L. and Dellby, N. and Lupini, A.R.}
}
@article{Royer2000,
  year = {2000},
  title = {Structural hierarchy in erythrocruorin, the giant respiratory assemblage of annelids},
  pages = {7107-7111},
  journal = {Biochemistry},
  volume = {97},
  author = {Royer, W.E. Jr. and Strand, K. and Heel, M. van and Hendrickson, W.A. }
}
@article{Rieger2004b,
  number = {8},
  year = {2004},
  title = {On curvature estimation of iso-surfaces in {3D} gray-value images and the computation of shape descriptors},
  pages = {1088-1094},
  journal = {IEEE Transactions on Pattern Recognition and Machine Intelligence},
  volume = {26},
  author = {Rieger, B. and Timmermans, F.J. and Vliet, L.J. van and Verbeek, P.W.}
}
@article{Desbat1993,
  year = {1993},
  title = {Efficient Sampling on Coarse Grids in Tomography},
  pages = {251--269},
  journal = {Inverse Problems},
  volume = {9},
  annote = {key_radon},
  author = {Desbat, L.}
}
@article{Goldman2002,
  year = {2002},
  title = {A new window on the cell's inner workings},
  pages = {1155-1156},
  journal = {Science},
  volume = {298},
  author = {Goldmann, E.}
}
@misc{WeickertYYYY,
  title = {On the History of Gaussian Scale-Space Axiomatics},
  annote = {Chapter 4 from something},
  author = {Weickert, J. and Ishikawa, S. and Imiya, A.}
}
@article{DorphPetersen2000,
  month = {November},
  year = {2000},
  title = {Non-Uniform Systematic Sampling in Stereology},
  pages = {148--157},
  journal = {Journal of Microscopy},
  volume = {200, Pt 2},
  author = {Dorph-Petersen, K.-A. and Gundersen, H.J.G. and Jensen, E.B.V.}
}
@article{Fernandez1997,
  year = {1997},
  title = {A spectral estimation approach to contrast transfer function detection in electron microscopy},
  pages = {267-295},
  journal = {Ultramicroscopy},
  volume = {68},
  author = {Feranandez, J.J. and Sanjurjo, J.R. and Carazo, J.-M.}
}
@inproceedings{Bakker2001a,
  month = {May 30-june 1},
  year = {2001},
  title = {Analysis and detection of 3-D curvilinear structures},
  booktitle = {ASCI'01 (Heijen, The Netherlands)},
  pages = {35--40},
  editor = {Vliet, L.J. van and Heijnsdijk, J.W.K. and Kielmann, T. and Knijnenburg, P.M.W.},
  author = {Bakker, P. and Verbeek, P.W. and Vliet, L.J. van},
  organization = {ASCI}
}
@article{Rodrigo2004,
  number = {7},
  year = {2004},
  title = {Real-time interactive optical micromanipulation of a mixture of high- and low-index particles},
  pages = {1417-1425},
  journal = {Optics Express},
  volume = {12},
  author = {Rodrigo, P.J. and Daria, V.R. and {Gl\"uckstad}, J.}
}
@unpublished{Verbeek2001a,
  title = {Continuous Cube to Cube Mappings as Analytic 3{D} Look-up Tables for {RGB} Color Rendering},
  author = {Verbeek, P.W.}
}
@article{Rodrigo2005,
  number = {7},
  year = {2005},
  title = {Four-dimensional optical manipulation of colloidal particles},
  pages = {074103},
  journal = {Applied Physics Letters},
  volume = {86},
  author = {Rodrigo, P.J. and Daria, V.R. and {Gl\"uckstad}, J.}
}
@inproceedings{Niblack1988,
  month = {June},
  year = {1988},
  title = {On Improving the Accuracy of the {H}ough Transform: Theory, Simulations, and Experiments},
  booktitle = {Proceedings of the IEEE Computer Society Conference CVPR (Ann-Arbor)},
  pages = {574--579},
  annote = {key_radon},
  author = {Niblack, W. and Petkovic, D.}
}
@article{Gautier2001,
  number = {6},
  year = {2001},
  title = {Homo-{FRET} Microscopy in Living Cells to Measure Monomer-Dimer Transition of {GFP}-Tagged Proteins},
  pages = {3000-3008},
  journal = {Biophysical Journal},
  volume = {80},
  author = {Gautier, I. and Tramier, C. and Coppey, J. and Pansu, R.B. and Nicolas, J-C. and Kemnitz, K. and Coppey-Moisan, M.}
}
@inproceedings{Nystrom2001,
  series = {Lecture Notes on Computer Science},
  year = {2001},
  title = {Curve Skeletonization by Junction Detection in Surface Skeletons},
  booktitle = {IWVF4, 4th International Workshop on Visual Form},
  pages = {229--238},
  editor = {Arcelli, C. and Cordella, L.P. and Sanniti di Baja, G.},
  volume = {2059},
  publisher = {Springer-Verlag},
  author = {{Nystr\"om}, I. and Sanniti di Baja, G. and Svensson, S.}
}
@article{Cianci2004,
  number = {2},
  year = {2004},
  title = {Saturation Modified Point Spread Functions in Two-Photon Microscopy},
  pages = {135-141},
  journal = {Microscopy Research and Technique},
  volume = {64},
  author = {Cianci, G.C. and Wu, J. and Berland, K.M.}
}
@article{Good1971,
  number = {3},
  month = {March},
  year = {1971},
  title = {The Relationship Between two Fast {Fourier} Transforms},
  pages = {310--317},
  journal = {IEEE Transactions on Computers},
  volume = {C-20},
  annote = {key_fft},
  author = {Good, I.J.}
}
@manual{Ieee1987,
  year = {1987},
  title = {{IEEE} Standard for Radix-Independent Floating-Point Arithmetic},
  note = {Std. 854-1987},
  address = {Technical Committee on Microprocessors and Microcomputers of the {IEEE} Computer Society},
  author = {IEEE}
}
@book{Spivak1979,
  year = {1979},
  title = {A Comprehensive Introduction to Differential Geometry},
  volume = {2},
  address = {Berkley},
  publisher = {Publish or Perish},
  author = {M. Spivak}
}
@inproceedings{Paeth1986,
  year = {1986},
  title = {A Fast Algorithm for General Raster Rotation},
  booktitle = {Graphics Interface '86},
  pages = {77--81},
  editor = {Green, M.},
  author = {Paeth, A.W.}
}
@article{Dong1998,
  year = {1998},
  title = {Particle Polymorphism Caused by Deletion of a Peptide Molecular Switch in a Quasiequivalent Icosahedral Virus},
  pages = {6024-6033},
  note = {Ultramicroscopy},
  journal = {Journal of Virology},
  volume = {72},
  author = {Dong, X.F. and Natarajan, P. and Tihova, M. and Johnson, J.E. and Schneemann, A.}
}
@phdthesis{Barman1991,
  year = {1991},
  title = {Hierarchical Curvature Estimation in Computer Vision},
  school = {{Link\"oping} University, Sweden},
  author = {{B\aa rman}, H.}
}
@article{Zetzsche1991,
  year = {1991},
  title = {Direct detection of flow discontinuities by 3D curvature operators},
  pages = {771--779},
  journal = {Pattern Recognition Letters},
  volume = {12},
  author = {Zetzsche, C. and Barth, E.}
}
@inproceedings{Barman1990,
  year = {1990},
  title = {Estimation of Curvature in 3-{D} Images Using Tensor Field Filtering},
  booktitle = {Computer Vision -- ECCV90. Proceedings, 1990},
  pages = {563--565},
  editor = {O. Faugeras},
  publisher = {Springer-Verlag},
  author = {{B\aa rman}, H. and Granlund, G. H. and Knutsson, H.}
}
@article{Minkowski1903,
  year = {1903},
  title = {Volumen und {Oberfl\"achen}},
  pages = {447--495},
  journal = {Mathematische Annalen},
  author = {Minkowski, H.}
}
@book{Foley1996,
  edition = {2},
  year = {1996},
  title = {Computer graphics, principles and practice},
  address = {London},
  publisher = {Addison-Wesley},
  author = {Foley, J.D. and Dam, A. van and Feiner, S.K. and Hughes, J.F.}
}
@book{Boyce1986,
  edition = {fourth},
  year = {1986},
  title = {Elementary differential equations and boundary value problems},
  publisher = {John Wiley \& sons},
  author = {Boyce, W.E. and DiPrima, R.C.}
}
@article{Cranage1988,
  number = {726},
  year = {1988},
  title = {Ring Artifacts in {X}-Ray Computed Tomography},
  pages = {529--529},
  journal = {British Journal of Radiology},
  volume = {61},
  author = {Cranage, R.W. and Tofts, P.S.}
}
@inproceedings{Luengo2001,
  series = {Lecture Notes on Computer Science},
  year = {2001},
  title = {Segmentation-Free Estimation of Length Distributions Using Sieves and RIA Morphology},
  booktitle = {Proc. Third International Conference on Scale-Space},
  pages = {389--406},
  editor = {Kerckhove, M.},
  volume = {2106},
  address = {Vancouver, Canada},
  publisher = {Springer-Verlag},
  author = {Luengo Hendriks, C.L. and Vliet, L.J. van}
}
@article{Hillyard1993,
  year = {1993},
  title = {Thickness effects in {ADF STEM} zone axis images},
  pages = {325-334 },
  journal = {Ultramicroscopy},
  volume = {52},
  author = {Hillyard, J. and Silcox, J.}
}
@phdthesis{Aronsson2002,
  year = {2002},
  title = {On 3D Fibre Measurement of Digitized Paper},
  address = {Uppsala, Sweden},
  school = {Swedish University of Agricultural Science},
  author = {Aronsson, M.}
}
@inbook{Berkner1995,
  year = {1995},
  title = {Visualisierung - Dynamik und {Komplexit\"at}},
  chapter = {Eine lokale Charakterisierung von Kanten basierend auf Skalierungseigenschaften von Wavelet-Transformation},
  publisher = {Tagungsband Bremen},
  author = {Berkner, K. and Evertsz, C.J.G. and Berghorn, W.}
}
@article{Martens1997,
  number = {8},
  month = {August},
  year = {1997},
  title = {Local Orientation Analysis in Images by Means of the Hermite Transform},
  pages = {1103--1116},
  journal = {IEEE Transactions on Image Processing},
  volume = {6},
  author = {Martens, J.B.}
}
@inproceedings{Wheeler2000,
  year = {2000},
  title = {Processing Color and Complex Data using Mathematical Morphology},
  booktitle = {Proceedings of the IEEE, National Aerospace and Electronics Conference},
  pages = {618-624},
  volume = {1},
  address = {Berlin},
  author = {Wheeler, M. and Zmuda, M. A.}
}
@article{Svensson2002,
  year = {2002},
  title = {Distance transforms in 3D using four different weights},
  pages = {1407--1418},
  journal = {Pattern Recognition Letters},
  volume = {23},
  author = {Svensson, S. and Borgefors, G.}
}
@article{Mattheyses2004,
  number = {4},
  year = {2004},
  title = {Polarized Fluorescence Resonance Energy Transfer Microscopy},
  pages = {2787-2797},
  journal = {Biophysical Journal},
  volume = {87},
  author = {Mattheyses, A.L. and Hoppe, A.D. and Axelrod, D.}
}
@phdthesis{Verveer1998b,
  year = {1998},
  title = {Computational and Optical Methods for Improving Resolution and Signal Quality in Fluorescence Microscopy},
  type = {Thesis},
  address = {Delft, The Netherlands},
  school = {Technische Universiteit Delft},
  author = {Verveer, P.J.}
}
@inproceedings{Illers2004a,
  year = {2004},
  title = {Measurement of correlated noise in images of computed radiography systems and its influence on the detective quantum efficiency},
  booktitle = {Proceedings of SPIE},
  address = {San Diego, California, USA},
  author = {Illers, H. and Broucke, D. van den and Buhr, E.}
}
@article{Verveer1998a,
  number = {26},
  year = {1998},
  title = {Improved Restoration from Multiple Images of a Single Object: Application to Fluorescence Microscopy},
  pages = {6240-6239},
  journal = {Applied Optics},
  volume = {37},
  author = {Verveer, P.J. and Jovin, T.M.}
}
@book{Serra1988,
  year = {1988},
  title = {Image Analysis and Mathematical Morphology, Volume 2: Theoretical Advances},
  editor = {Serra, J.},
  address = {London},
  publisher = {Academic Press}
}
@article{Chen2000,
  number = {5},
  month = {May},
  year = {2000},
  title = {Orientation Space Filtering for Multiple Orientation Line Segmentation},
  pages = {417--429},
  journal = {Pattern Analysis and Machine Intelligence},
  volume = {22},
  author = {Chen, J. and Sato, Y. and Tamura, S.}
}
@article{Hestenes1994a,
  number = {1},
  year = {1994},
  title = {Invariant Body Kinematics: {II}. Reaching and Neurogeometry},
  pages = {79--88},
  journal = {Neural Networks},
  volume = {7},
  author = {Hestenes, D.}
}
@article{Zemlin2002,
  year = {2002},
  title = {Diffractogram tableaux by mouse click},
  pages = {77-82},
  journal = {Ultramicroscopy},
  volume = {93},
  author = {Zemlin, J. and Zemlin, F.}
}
@inproceedings{Papoulis1976,
  month = {August},
  year = {1976},
  title = {Topics in Signal Analysis},
  booktitle = {International Conference on Information Sciences and Systems},
  pages = {247--249},
  address = {Patras, Greece},
  author = {Papoulis, A.}
}
@techreport{Calway1991,
  month = {September},
  year = {1991},
  title = {Incorporating Orientation Selectivity in Wavelet Transforms for Multiresolution {Fourier} Analysis of Images},
  note = {LiTH-ISY-I-1243},
  institution = {{Link\"oping University}},
  author = {Calway, A.}
}
@article{Esa2000,
  number = {2},
  year = {2000},
  title = {Three-dimensional spectral precision distance microscopy of chromatin nanostructures after triple-colour {DNA} labelling: a study of the {BCR} region on chromosome 22 and the {Philadelphia} chromosome},
  pages = {96-105},
  journal = {Journal of Microscopy},
  volume = {199},
  author = {Esa, A. and Edelmann, P. and Kreth, G. and Trakhtenbrot, L. and Amariglio, N. and Rechavi, G. and Hausmann, M. and Cremer, C.}
}
@article{Greenspan1992,
  number = {11},
  month = {November},
  year = {1992},
  title = {Projection-based Approach to Image Analysis: Pattern Recognition and Representation in the Position-Orientation Space},
  pages = {1105--1110},
  journal = {IEEE Transactions on Pattern Analysis and Machine Intelligence},
  volume = {14},
  author = {Greenspan, H. and Porat, M. and Zeevi, Y.Y.}
}
@article{Nakagawa1978,
  number = {8},
  year = {1978},
  title = {A Note on the Use of Local Min and Max Operations in Digital Picture Processing},
  pages = {3},
  journal = {IEEE Transactions on Systems, Man and Cybernetics},
  volume = {8},
  author = {Nakagawa, Y. and Rosenfeld, A.}
}
@article{Lenz1987,
  number = {2},
  year = {1987},
  title = {Optimal Filters for the Detection of Linear Patterns in 2-{D} and Higher Dimensional Images},
  pages = {163--172},
  journal = {Pattern Recognition},
  volume = {20},
  author = {Lenz, R.}
}
@book{Oppenheim1983,
  year = {1983},
  title = {Signals and Systems},
  address = {London},
  publisher = {Prentice-Hall International},
  author = {Oppenheim, A.V. and Willsky, A.S. and Young, I.T.}
}
@article{Abels2005,
  year = {2005},
  title = {Single-Molecule Measurements of the Persistence Length of Double-Stranded {RNA}},
  pages = {2737-2744},
  journal = {Biophysical Journal},
  volume = {88},
  author = {Abels, J.A. and Moreno-Herreo, F. and Heijden, T. van der and Dekker, C. and Dekker, N.H.}
}
@inproceedings{Breton1996kort,
  year = {1996},
  title = {Shadows and Shading Flow Fields },
  booktitle = {CVPR'96 },
  pages = {782--789},
  author = {Breton, P. and Zucker, S.W. }
}
@book{Tukey1977,
  year = {1977},
  title = {Exploratory Data Analysis},
  address = {Reading, Massachusetts},
  publisher = {Addison-Wesley},
  author = {Tukey, J. W.}
}
@article{Rotem1986,
  number = {5},
  month = {October},
  year = {1986},
  title = {Image Reconstruction from Zero Crossings},
  pages = {1269--1277},
  journal = {IEEE Transactions on Acoustics, Speech, and Signal Processing},
  volume = {34},
  author = {Rotem, D. and Zeevi, Y.Y.}
}
@article{Vigneau2000,
  year = {2000},
  title = {Number of Particles for the Determination of Size Distribution from Microscopic Images},
  pages = {243--250},
  journal = {Powder Technology},
  volume = {107},
  author = {Vigneau, E. and Loisel, C. and Devaux, M.F. and Cantoni, P.}
}
@article{Ammouche2001,
  year = {2001},
  title = {Image Analysis for the Automated Study of Microcracks in Concrete},
  pages = {267--278},
  journal = {Cement \& Concrete Composites},
  volume = {23},
  author = {Ammouche, A. and Riss, J. and Breysse, D. and Marchand, J.}
}
@article{Vincent1991,
  number = {6},
  month = {June},
  year = {1991},
  title = {Watersheds in Digital Spaces: An Efficient Algorithm Based on Immersion Simulations},
  pages = {583--598},
  journal = {IEEE Transactions on Pattern Analysis and Machine Intelligence},
  volume = {13},
  author = {Vincent, L. and Soille, P.}
}
@unpublished{Verbeek2002,
  title = {De Relatie van {L}arkin, {B}one and {O}ldfield (2001) en Felsberg en Sommer (2001) met het vectorgradient verhaal (PWV, submitted to ICPR2002)},
  author = {Verbeek, P.W.}
}
@article{Vincent1993,
  number = {2},
  month = {April},
  year = {1993},
  title = {Morphological Grayscale Reconstruction in Image Analysis: Applications and Efficient Algorithms},
  pages = {176--201},
  journal = {IEEE Transactions on Image Processing},
  volume = {2},
  author = {Vincent, L.}
}
@article{Gadella1997,
  number = {1},
  year = {1997},
  title = {Fast algorithms for the analysis of single and double exponential decay curves with a background term. Application to time-resolved imaging microscopy},
  pages = {19-39},
  journal = {Bioimaging},
  volume = {5},
  author = {Gadella, T.W.J. jr. and Jovin, T.M.}
}
@article{Gadella1995,
  number = {6},
  year = {1995},
  title = {Oligomerization of Epidermal Growth Factor Receptors on {A431} Cells Studied by Time-resolved Fluorescence Imaging Microscopy. {A} Stereochemical Model for Tyrosine Kinase Receptor Activation},
  pages = {1543-1558},
  journal = {Journal of Cell Biology},
  volume = {129},
  author = {Gadella, T.W.J. jr. and Jovin, T.M.}
}
@book{Matheron1975,
  year = {1975},
  title = {Random Sets and Integral Geometry},
  address = {New York},
  publisher = {Wiley},
  author = {Matheron, G.}
}
@book{Weisstein1999,
  year = {1999},
  title = {Concise Encyclopedia of Mathematics},
  publisher = {CRC},
  author = {Weisstein, E.W.}
}
@article{Gadella1994,
  number = {3},
  year = {1994},
  title = {Fluorescence lifetime imaging microscopy: Pixel-by-pixel analysis of phase-modulation data},
  pages = {139-159},
  journal = {Bioimaging},
  volume = {2},
  author = {Gadella, T.W.J. jr. and Clegg, R.M. and Jovin, T.M.}
}
@article{Kratky1949,
  year = {1949},
  title = {{R\"ontgenuntersuchungen gel\"oster Fadenmolek\"ule}},
  pages = {1106-1124},
  journal = {Rec. Trav. Chim. Pays-Bas Belg},
  volume = {68},
  author = {Kratky, O. and Porod, G.}
}
@article{Maragos1996,
  number = {6},
  year = {1996},
  title = {Differential Morphology and Image Processing},
  pages = {922-937},
  journal = {IEEE Transactions on Image Processing},
  volume = {5},
  author = {Maragos, Petros}
}
@inproceedings{Leavers2000,
  month = {September 3-7},
  year = {2000},
  title = {Analysis of Wear Particles Using the Radon Transform},
  booktitle = {ICPR15, Proc. 15th Int. Conference on Pattern Recognition (Barcelona, Spain)},
  pages = {764--766},
  editor = {Sanfeliu, A. and Villanueva, J.J. and Vanrell, M. and Alquezar, R. and Huang, T. and Serra, J. },
  annote = {key_radon},
  publisher = {IEEE Computer Society Press, Los Alamitos },
  author = {Leavers, V.F.}
}
@article{Cosgriff2005,
  year = {2005},
  title = {The spatial resolution of imaging using core-loss spectroscopy in the scanning transmission electron microscope},
  pages = {317-326},
  journal = {Ultramicroscopy},
  volume = {102},
  author = {Cosgriff, E.C. and Oxley, M.P. and Allen, L.J. and Pennycock, S.J.}
}
@phdthesis{Freeman1992,
  year = {1992},
  title = {Steerable Filters and Local Analysis of Image Structure},
  school = {Massachusetts Institute of Technology},
  author = {Freeman, W.T.}
}
@article{Freeman1991,
  number = {9},
  month = {September},
  year = {1991},
  title = {The Design and Use of Steerable Filters},
  pages = {891--906},
  journal = {IEEE Transactions on Pattern Analysis and Machine Intelligence},
  volume = {13},
  author = {Freeman, W.T. and Adelson, E.H.}
}
@inproceedings{Lindeberg1993a,
  month = {May},
  year = {1993},
  title = {On Scale Selection for Differential Operators},
  booktitle = {Proc. 8th Scandinavian Conference on Image Analysis ({Troms\o} Norway)},
  pages = {857--866},
  author = {Lindeberg, T.}
}
@inproceedings{Lindeberg1993b,
  year = {1993},
  title = {Shape from texture from a multi-scale perspective},
  booktitle = {Proceeding of the 4th International Conference on Computer Vision},
  address = {Berlin, Germany},
  author = {Lindeberg, T. and {G\aa rding}, J.}
}
@misc{DIPimage,
  year = {1999},
  title = {{DIPimage}: a scientific image processing toolbox for {MATLAB}},
  note = {Delft University of Technology, {\tt http://www.qi.tnw.tudelft.nl/DIPlib}},
  author = {Luengo Hendriks, C.L. and Rieger, B. and Ginkel, M. van and Kempen, G.M.P. van and Vliet, L.J. van}
}
@inproceedings{Yu1998,
  month = {June 23-25},
  year = {1998},
  title = {Rotated Wedge Averaging Method for Junction Characterization},
  booktitle = {Proc. Computer Society Conference on Computer Vision and Pattern Recognition, CVPR'98, Santa Barbara, USA},
  pages = {390--395},
  author = {Yu, W. and Daniilidis, K. and Sommer, G.}
}
@book{Klotzek,
  year = {1994},
  title = {{Einf\"uhrung} in die Differentialgeometrie},
  address = {Thun, Frankfurt am Main},
  publisher = {Verlag Harri Deutsch},
  author = {Benno Klotzek}
}
@article{Sprague2005,
  number = {2},
  year = {2005},
  title = {{FRAP} analysis of binding: proper and fitting},
  pages = {84-91},
  journal = {Trends in Cell Biology},
  volume = {15},
  author = {Sprague, B.L. and McNally, J.G.}
}
@article{Maragos1994,
  number = {1},
  year = {1994},
  title = {Morphological Systems: Slope Transforms and Max-Min Difference and Differential Equations},
  pages = {57-77},
  journal = {Signal Processing},
  volume = {38},
  author = {Maragos, Petros}
}
@article{Sprague2004,
  month = {June},
  year = {2004},
  title = {Analysis of Binding Reactions by Fluorescence Recovery after Photobleaching},
  pages = {3473-3495},
  journal = {Biophysical Journal},
  volume = {86},
  author = {Sprague, B.L. and Pego, R.L. and Stavreva, D.A. and McNally, J.G.}
}
@phdthesis{Westerweel1993,
  year = {1993},
  title = {Digital particle image velocimetry - theory and application},
  address = {Delft, The Netherlands},
  school = {Delft University of Technology},
  author = {Westerweel, J.}
}
@article{Marek2005,
  number = {2},
  year = {2005},
  title = {Interactive Measurement and Characterization of {DNA} Molecules by Analysis of {AFM} Images},
  pages = {87-93},
  journal = {Cytometry Part A},
  volume = {63},
  author = {Marek, J. and Demj\'enov\'a and Tomori, Z. and Jan\'a\v{c}ek, J. and Zolotov\'a, I. and Valle, F. and Farve, M. and Dietler, G.}
}
@book{Smith2000,
  edition = {thrid},
  year = {2000},
  title = {Modern Optical Engenering},
  address = {New York},
  publisher = {McGraw-Hill},
  author = {Smith, W.J.}
}
@article{Nirmal1996,
  number = {6603},
  year = {1996},
  title = {Fluorescience intermittency in single cadmium selenide nanocrystals},
  pages = {802-805},
  journal = {Nature},
  volume = {383},
  author = {Nirmal, M. and Dabbausi, B.O. and Bawendi, M.G. and Macklin, J.J. and Trautman, J.K. and Harris, T.D. and Brus, L.E.}
}
@article{Grillo2006,
  year = {2006},
  title = {A novel method for focus assessment in atomic resolution {STEM HAADF} experiments},
  pages = {603-613},
  journal = {Ultramicrosocpy},
  volume = {106},
  author = {Grillo, V. and Carlino, E.}
}
@article{Heine1961,
  number = {1},
  year = {1961},
  title = {Eine verfeinerte {Theorie} der {R\"ontgenkleinwinkelstreuung} des {verkn\"auelten} {Fadenmolek\"uls} und ihre {Anwendung} auf {Cellulosenitrat} in {L\"o}sung},
  pages = {682-726},
  journal = {Macromolecular Chemistry and Physics},
  volume = {44},
  author = {Heine, S. von and Kratky, O. and Porod, G. and Schmitz, P.J.}
}
@incollection{Hilditch1969,
  year = {1969},
  title = {Linear skeletons from square cupboards},
  booktitle = {Machine Intelligence},
  pages = {404--420},
  editor = {{Meltzer B. and Mitchie D.}},
  publisher = {University Press Edinburgh},
  author = {Hilditch, C.J.}
}
@article{Subramaniam2003,
  year = {2003},
  title = {Photophysics of green and red fluorescent proteins: some implications for quantitative microscopy},
  pages = {178-201},
  journal = {Methods in Enzymology.},
  volume = {360},
  author = {Subramaniam, V. and Hanley, Q.S. and Clayton, A.H.A. and Jovin, T.M.}
}
@article{Brink1998a,
  year = {1998},
  title = {Evaluation of charing on macromolecules in electron mircoscopy},
  pages = {41-52},
  journal = {Ultamicroscopy},
  volume = {72},
  author = {Brink, J. and Sherman, M.B. and Berrniman, J. and Chiu, W.}
}
@inproceedings{Ginkel1997,
  month = {June 9-11},
  year = {1997},
  title = {Orientation Selectivity for Orientation Estimation},
  booktitle = {Proceedings of the 10th Scandinavian Conference on Image Analysis (Lappeenranta, Finland)},
  pages = {533--537},
  volume = {I},
  author = {Ginkel, M. van and Verbeek, P.W. and Vliet, L.J. van}
}
@mastersthesis{Ginkel1995,
  month = {August},
  year = {1995},
  title = {Diffusion Generated Scale-space for Blob Analysis},
  address = {Delft, The Netherlands},
  school = {Delft University of Technology},
  author = {Ginkel, M. van}
}
@inproceedings{Ginkel1998,
  month = {June 9-11},
  year = {1998},
  title = {Curvature Estimation for Overlapping Curved Patterns using Orientation Space},
  booktitle = {Proceedings of the third annual conference of the Advanced School for Computing and Imaging (Lommel, Belgium)},
  pages = {173--178},
  editor = {Haar Romeny, B. ter and Epema, D.H.J. and Tonino, J.F.M.},
  author = {Ginkel, M. van and Verbeek, P.W. and van Vliet, L.J.}
}
@inproceedings{Ginkel1999,
  month = {June 7-11},
  year = {1999},
  title = {Curvature Estimation from Orientation Fields},
  booktitle = {SCIA'99, Proc. 11th Scandinavian Conference on Image Analysis (Kangerlussuaq, Greenland)},
  pages = {545--551},
  editor = {Ersboll, B.K. and Johansen, P.},
  author = {Ginkel, M. van and Weijer, J. van de and Verbeek, P.W. and Vliet, L.J. van},
  organization = {Pattern Recognition Society of Denmark, Lyngby}
}
@inproceedings{Bakker1999a,
  year = {1999},
  title = {Edge preserving orientation adaptive filtering},
  booktitle = {ASCI'99, Proc. 5th Annual Conference of the Advanced School for C omputing and Imaging (Heijen, The Netherlands)},
  pages = {207--213},
  editor = {Boasson, M. and Kaandorp, J.A. and Tonino, J.F.M. and Vosselman, M.G.},
  author = {Bakker, P. and Verbeek, P.W. and Vliet, L.J. van},
  organization = {ASCI, Delft}
}
@article{Mecke1996,
  number = {5},
  month = {May},
  year = {1996},
  title = {Morphological Characterization of Patterns in Reaction-Diffusion Systems},
  pages = {4794--4800},
  journal = {Physical Review {E}},
  volume = {53},
  author = {Mecke, K.R.}
}
@article{Lawton1992,
  number = {3},
  month = {July},
  year = {1992},
  title = {Multidimensional Chirp Algorithms for Computing {Fourier} Transforms},
  pages = {429--431},
  journal = {IEEE Transactions on Image Processing},
  volume = {1},
  annote = {key_fft},
  author = {Lawton, W.M.}
}
@article{Pratt1972,
  year = {1972},
  title = {Generalized {Wiener} filtering computation techniques},
  pages = {297--303},
  journal = {IEEE Trans. Comput.},
  volume = {C-21},
  author = {Pratt, W.K.}
}
@article{Zhu2004,
  year = {2004},
  title = {Automatic particle selection: results of a comparative study},
  pages = {3-14},
  journal = {Journal of Structural Biology},
  volume = {145},
  author = {Zhu, Y. and Carragher, B. and Glaeser, R.M. and Fellmann, D. and Bajaj, C. and Bern, M. and Mouche, F. and Haas, F. de and Hall, R.J. and Kriegman, D.J. and Ludtke, S.J. and Mallick, S.P. and Penczek, P.A. and Roseman, A.M. and Sigworth, F.J. and Volkmann, N. and Potter, C.S.}
}
@article{Breen1996a,
  number = {3},
  year = {1996},
  title = {Attribute Openings, Thinnings, and Granulometries},
  pages = {377-389},
  journal = {Computer Vision and Image Understanding},
  volume = {64},
  author = {Breen, E. J. and Jones, R.}
}
@article{Funaro2003,
  number = {4},
  year = {2003},
  title = {Independent component analysis for artefact separation in astrophysical images},
  pages = {469-478},
  journal = {Neural Networks},
  volume = {16},
  author = {Funaro, M. and Oja, E. and Valpula, H.}
}
@article{Lehmann1997,
  year = {1997},
  title = {A Simple Parametric Equation for Pseudocoloring Grey Scale Images Keeping their Original Brightness Progression},
  pages = {251--257},
  journal = {Image and Vision Computing},
  volume = {15},
  author = {Lehmann, T.M. and Kaser, A. and Repges, R.}
}
@inproceedings{Michaelis1994,
  month = {May},
  year = {1994},
  title = {Junction Classification by Multiple Orientation Detection},
  booktitle = {ECCV'94, Third European Conference on Computer Vision},
  pages = {101--108},
  editor = {Eklundh, Jan-Olof},
  address = {Stockholm, Sweden},
  author = {Michaelis, M. and Sommer, G.}
}
@article{Ginneken2000,
  number = {2},
  year = {2000},
  title = {Applications of Locally Orderless Images},
  pages = {196--208},
  journal = {Journal of Visual Communication and Image Representation},
  volume = {11},
  author = {Ginneken, B. van and Haar Romeny, B.M. ter}
}
@article{Michaelis1995,
  year = {1995},
  title = {A Lie Group Approach to Steerable Filters},
  pages = {1165--1174},
  journal = {Pattern Recognition Letters},
  volume = {16},
  author = {Michaelis, M. and Sommer, G.}
}
@article{Brink1998,
  number = {1},
  year = {1998},
  title = {Reduction of charging in protein electron cryomicroscopy},
  pages = {67-73},
  journal = {Journal of Microscopy},
  volume = {191},
  author = {Brink, J. and Gross, H. and Tittmann, P. and Sherman, M.B. and Chiu, W.}
}
@article{Cowley1986,
  year = {1966},
  title = {Greatly defocused, point-projection, off-axis electron holographyy},
  pages = {133-147},
  journal = {Ultramicroscopy},
  volume = {63},
  author = {Cowley, J.M. and Mankos, M. and Scheinfein, M.R.}
}
@article{Hutchison2005,
  year = {2005},
  title = {A versatile double aberration-corrected, energy filtered {HREM/STEM} for materials science},
  pages = {7-15},
  journal = {Ultramicroscopy},
  volume = {103},
  author = {Hutchison, J.L. and Titchmarsh, J.M. and Cockayne, D.J.H. and Doole, R.C. and Hetherington, C.J.D. and Kirkland, A.I. and Sawada, H.}
}
@article{Bergholm1987,
  number = {6},
  month = {November},
  year = {1987},
  title = {Edge Focusing},
  pages = {726--741},
  journal = {IEEE Transactions on Pattern Analysis and Machine Intelligence},
  volume = {9},
  author = {Bergholm, F.}
}
@article{Axelrod1989,
  year = {1989},
  title = {Fluorescence Polarization Microscopy},
  pages = {333-352},
  journal = {Methods in Cell Biology},
  volume = {30},
  author = {Axelrod, D.}
}
@article{Heideman1992,
  number = {1},
  month = {January},
  year = {1992},
  title = {Computation of an Odd-Length DCT from a Real-Valued DFT of the Same Length},
  pages = {54--61},
  journal = {IEEE Transactions on Signal Processing},
  volume = {40},
  annote = {key_fft},
  author = {Heideman, M.T.}
}
@article{Nagao1979,
  year = {1979},
  title = {Edge Preserving Smoothing},
  pages = {394--407},
  journal = {Computer Graphics and Image Processing},
  volume = {9},
  author = {Nagao, M. and Matsuyama, T.}
}
@article{Aguado2000,
  number = {1},
  year = {2000},
  title = {Bias Error Analysis of the Generalised {Hough} Transform},
  pages = {25--42},
  journal = {Journal of Mathematical Imaging and Vision},
  volume = {12},
  author = {Aguado, A.S. and Montiel, E. and Nixon, M.S.}
}
@article{Lin2000,
  month = {221-231},
  year = {2000},
  title = {Pore Structure and network analysis of filter cake},
  journal = {Chemical Engineering Journal},
  volume = {80},
  author = {Lin, C.L. and Miller, J.D.}
}
@phdthesis{Lin2003,
  year = {2003},
  title = {Enhancement, Extraction, and Visualization of {3D} Volume Data},
  school = {{Link\"oping University}, Sweden},
  author = {Lin, Q.}
}
@article{Jackway1996,
  number = {1},
  month = {January},
  year = {1996},
  title = {Scale-Space Properties of the Multiscale Morphological Dilation-Erosion},
  pages = {38--51},
  journal = {IEEE Transactions on Pattern Analysis and Machine Intelligence},
  volume = {18},
  author = {Jackway, Paul T. and Deriche, Mohamed}
}
@article{Sederberg1984,
  number = {1},
  year = {1984},
  title = {Implicit Representation of Parametric Curves and Surfaces},
  pages = {72--84},
  journal = {Computer Vision, Graphics, and Image Processing},
  volume = {28},
  author = {Sederberg, T.W. and Anderson, D.C. and Goldman, R.N.}
}
@article{Jackway1998,
  number = {3},
  year = {1998},
  title = {On the Scale-Space Theorem of Chen and Yan},
  pages = {351-352},
  journal = {IEEE Transactions on Pattern Analysis and Machine Intelligence},
  volume = {20},
  author = {Jackway, Paul T.}
}
@article{Zimmermann2002,
  number = {2},
  year = {2002},
  title = {Spectral imaging and linear un-mixing enables improved {FRET} effciency with a novel {GFP2-YFP FRET} pair},
  pages = {245-249},
  journal = {FEBS Letters},
  volume = {531},
  author = {Zimmermann, T. and Rietdorf, J. and Girod, A. and Georget, V. and Pepperkok, R.}
}
@article{Zimmermann2003,
  number = {1},
  year = {2003},
  title = {Spectral imaging and its application in live cell microscopy},
  pages = {87-92},
  journal = {FEBS Letters},
  volume = {546},
  author = {Zimmermann, T. and Rietdorf, J. and Pepperkok, R.}
}
@article{Fischl1999,
  number = {NO. 1},
  year = {1999},
  title = {Adaptive Nonlocal Filtering: A Fast Alternative to Anisotropic Diffusion for Image Enhancement},
  journal = {IEEE Transactions on Pattern Analysis and Machine Intelligence},
  volume = {VOL. 21},
  author = {Fischl, B. and Schwartz, E.L.}
}
@article{Reed1990,
  number = {1},
  month = {January},
  year = {1990},
  title = {Segmentation of Textured Images and Gestalt Organization Using Spatial/Spatial-Frequency Representations},
  pages = {1--12},
  journal = {IEEE Transactions on Pattern Analysis and Machine Intelligence},
  volume = {12},
  author = {Reed, T.R. and Wechsler, H.}
}
@article{Reed1999,
  month = {August},
  year = {1999},
  title = {Stereological Estimation of Covariance using Linear Dipole Probes},
  pages = {96--103},
  journal = {Journal of Microscopy},
  volume = {195, Pt 2},
  author = {Reed, M.G. and Howard, C.V.}
}
@article{Hell1994a,
  number = {11},
  year = {1994},
  title = {Breaking the diffraction limit resolution by stimulated emission: stimulated-emission-depletion microscopy},
  pages = {780-783},
  journal = {Optics Letters},
  volume = {19},
  author = {Hell, S.W. and Wichmann, J.}
}
@article{Nicholson2001,
  year = {2001},
  title = {Review: Automatic Particle Detection in Electron Microscopy},
  pages = {90-101},
  journal = {Journal of Structural Biology},
  volume = {133},
  author = {Nicholson, W.V. and Glaser, R.M.}
}
@inproceedings{Glas2001,
  series = {Lecture Notes on Computer Science},
  year = {2001},
  title = {Assessment of Center of Rotation of the Glenohumeral Joint by a Modified {H}ough Transform},
  booktitle = {4th International Conference on Medical Image Computing and Computer-Assisted Intervention - MICCAI 2001, Utrecht, The Netherlands},
  editor = {Niessen, W.J. and Viergever, M.A.},
  volume = {2208},
  annote = {key_radon},
  author = {Glas, M. van der and Vos, F.M. and Vossepoel, A.M.}
}
@article{Danielsson2001,
  year = {2001},
  title = {Efficient Detection of Second-Degree Variations in {2D} and {3D} Images},
  pages = {255--305},
  journal = {Journal of Visual Communication and Image Representation},
  volume = {12},
  author = {Danielsson, P.-E. and Lin, Q. and Ye, Q.-Z.}
}
@article{Dirac1927,
  year = {1927},
  title = {The Physical Interpretation of the Quantum Dynamics},
  pages = {621-641},
  journal = {Proceedings of the Royal Society of London},
  volume = {A113},
  author = {Dirac, P.}
}
@techreport{Danielsson2000,
  month = {October},
  year = {2000},
  title = {A New Shape Space for Second Order 3D-Variations},
  note = {LiTH-ISY-R-2299},
  institution = {{Link\"oping} University, Sweden},
  author = {Danielsson,P.-E. and Lin, Q.}
}
@article{Otten1993,
  year = {1993},
  title = {High-resolution imaging on a field emission {TEM}},
  pages = {77-91},
  journal = {Ultramicroscopy},
  volume = {48},
  author = {Otten, M.T. and Coene, W.M.J.}
}
@article{Nelson2006,
  year = {2006},
  title = {Tethered Particle Motion as a Diagnostic of {DNA} Tether Length},
  journal = {Journal of Physical Chemistry B},
  author = {Nelson, P.C. and Zurla, C. and Brogioli, D. and Beausang, J.F. and Finzi, L. and Dunlap, D.}
}
@article{Ballester2001,
  number = {8},
  month = {August},
  year = {2001},
  title = {Filling-In by Joint Interpolation of Vector Fields and Gray Levels},
  pages = {1200-1211},
  journal = {IEEE Transactions on Image Processing},
  volume = {10},
  author = {Ballerster, C. and Bertalmio, M. and Caselles, V. and Sapiro, G. and Verdera, J.}
}
@inbook{Kohonen1995a,
  series = {Springer Series in Information Sciences},
  year = {1995},
  title = {Self-Organizing Maps},
  volume = {30},
  chapter = {5.8--5.10},
  publisher = {Springer-Verlag},
  author = {Kohonen, T.}
}
@article{Saff1997,
  number = {1},
  year = {1997},
  title = {Distributing Many Points on a Sphere},
  pages = {5--11},
  journal = {the Mathematical Intelligencer},
  volume = {19},
  author = {Saff, E.B. and Kuijlaars, A.B.J.}
}
@article{Johansen2000,
  number = {3},
  year = {2000},
  title = {Branch Points in One-Dimensional {Gaussian} Scale Space},
  pages = {193--203},
  journal = {Journal of Mathematical Imaging and Vision},
  volume = {13},
  author = {Johansen, P. and Nielsen, M. and Olsen, O.F.}
}
@techreport{Lieshout1997,
  year = {1997},
  title = {Size Distributions in Stochastic Geometry},
  note = {PNA-R9715},
  institution = {CWI, Amsterdam},
  author = {Lieshout, M.N.M. van}
}
@article{Raven1998,
  number = {8},
  year = {1998},
  title = {Numerical Removal of Ring Artefacts in Microtomography},
  pages = {2978--2980},
  journal = {Review of Scientific Instruments},
  volume = {69},
  author = {Raven, C.}
}
@book{Spivak1965,
  year = {1965},
  title = {Calculus on Manifolds},
  address = {Cambridge, MA},
  publisher = {Perseus Books},
  author = {Spivak, M.}
}
@article{Prabhat2004,
  number = {4},
  year = {2004},
  title = {Simultaneous imaging of different focal planes in fluorescence microscopy for the study of cellular dynamics in three dimensions},
  pages = {237-242},
  journal = {IEEE Transactions on Nanobioscience},
  volume = {3},
  author = {Prabhat, P. and Ram, S. and Ward, E.S. and Ober, R.J.}
}
@article{Meijster2002,
  number = {4},
  month = {April},
  year = {2002},
  title = {A Comparison of Algorithms for Connected Set Openings and Closings},
  pages = {484--494},
  journal = {IEEE Transactions on Pattern Analysis and Machine Intelligence},
  volume = {24},
  author = {Meijster, Arnold and Wilkinson, Michael H.F.}
}
@article{Venkatesh1990,
  month = {May},
  year = {1990},
  title = {On the Classification of Image Features},
  pages = {339--349},
  journal = {Pattern Recognition Letters},
  volume = {11},
  author = {Venkatesh, S. and Owens, R.}
}
@article{Nummiaro2002,
  number = {1},
  year = {2003},
  title = {An Adaptive Color-Based Particle Filter},
  pages = {99-110},
  journal = {Image and Vision Computing},
  volume = {21},
  author = {Nummiaro, K. and Koller-Meier, E. and Gool, L. van}
}
@mastersthesis{Asselt1997,
  year = {1997},
  title = {Line and Edge Characterisation Using Mallat Wavelets},
  address = {Delft},
  school = {Pattern Recognition Group, Faculty of Applied Physics, Delft University of Technology},
  author = {Asselt, R.J. van}
}
@article{Grecco2005,
  number = {3},
  year = {2004},
  title = {Ensemble and single particle photophysical properties (two-photon excitation, anisotropy, {FRET}, lifetime, spectral conversion) of commercial quantum dots in solution and in live cells},
  pages = {169-179},
  journal = {Microscopy Research and Technique},
  volume = {65},
  author = {Grecco, H. and Lidke, K.A. and Heintzmann, R. and Lidke, D.S. and Spagnuolo, C. and Martinez, O.E. and Jares-Erijman, E.A. and Jovin, T.M.}
}
@article{Goshtasby1994,
  number = {4},
  month = {May},
  year = {1994},
  title = {On Edge Focusing},
  pages = {247--256},
  journal = {Image and Vision Computing},
  volume = {12},
  author = {Goshtasby, A.}
}
@article{Kadyrov2001,
  number = {8},
  year = {2001},
  title = {The Trace transform and its applications },
  journal = {IEEE Transactions on Pattern Analysis and Machine Intelligence},
  volume = {23},
  annote = {key_radon},
  author = {Kadyrov, A. and Petrou, M. }
}
@misc{Vliet2003,
  month = {May},
  year = {2003},
  howpublished = {private communications},
  author = {Vliet, L.J. van and Rieger, B.}
}
@article{Harscher1996,
  year = {1996},
  title = {Experimental study of amplitude and phase detection limits in electron holography},
  pages = {57-66},
  journal = {Ultramicroscopy},
  volume = {64},
  author = {Harscher, A. and Lichte, H.}
}
@inproceedings{Vliet2004,
  month = {Cambridge, UK, August 23-26},
  year = {2004},
  title = {Robust Local Max-Min Filters by Normalized Power-Weighted Filtering},
  booktitle = {ICPR17, Proceedings 17th International Conference on Pattern Recognition},
  pages = {696-699},
  editor = {Kittler,J. and Petrou, M. and Nixon, M.},
  address = {Los Alamitos},
  publisher = {IEEE Computer Society Press},
  author = {Vliet, L.J. van}
}
@inproceedings{Knutsson1983b,
  month = {October},
  year = {1983},
  title = {Texture Analysis using Two-Dimensional Quadrature Filters},
  booktitle = {IEEE Computer Society Workshop on Computer Architecture for Pattern Analysis and Image Database Management},
  address = {Pasadena},
  author = {Knutsson, H. and Granlund, G.H.}
}
@article{Knutsson1983a,
  number = {3},
  month = {March},
  year = {1983},
  title = {Anisotropic Non-Stationary Image Estimation and its Applications --- {P}art {II}: {P}redictive Image Coding},
  pages = {398--406},
  journal = {IEEE Transactions on Communications},
  volume = {31},
  author = {Knutsson, H. and Wilson, R. and Granlund, G.H.}
}
@article{Vakman1996,
  number = {4},
  month = {April},
  year = {1996},
  title = {On the Analytic Signal, the {Teager--Kaiser} Energy Algorithm, and Other Methods for Defining Amplitude and Frequency},
  pages = {791--797},
  journal = {IEEE Transactions on Signal Processing},
  volume = {44},
  author = {Vakman, D.}
}
@article{Jepson1991,
  number = {5},
  month = {October},
  year = {1991},
  title = {Phase Singularities in Scale-space},
  pages = {338--343},
  journal = {Image and Vision Computing},
  volume = {9},
  author = {Jepson, A.D. and Fleet, D.J.}
}
@article{Hanley1999,
  number = {53},
  year = {1999},
  title = {Spectral imaging in a programmable array microscope by Hadamard transform fluorescence spectroscopy},
  pages = {1-10},
  journal = {Applied Spectroscopy},
  author = {Hanley, Q.S. and Verveer, P.J. and Jovin, T.M.}
}
@inproceedings{Jepson1990,
  year = {1990},
  title = {Scale-Space Singularities},
  booktitle = {Computer Vision -- ECCV90. Proceedings, 1990},
  pages = {50--55},
  editor = {O. Faugeras},
  publisher = {Springer-Verlag},
  author = {Jepson, A.D. and Fleet, D.J.}
}
@article{Jones1996,
  number = {10},
  year = {1996},
  title = {Periodic Lines: Definition, Cascades, and Application to Granulometries},
  pages = {1057--1063},
  journal = {Pattern Recognition Letters},
  volume = {17},
  author = {Jones, Ronald and Soille, Pierre}
}
@inproceedings{Rutovitz1968,
  year = {1968},
  title = {Datastructures for operations on digital images},
  booktitle = {Pictorial Pattern Recognition},
  pages = {105--133},
  editor = {Cheng, G.C. and Ledley, R.S. and Pollock, D.K. and Rosenfeld, A.},
  address = {Washington, DC},
  publisher = {Thompson},
  author = {Rutovitz, D.}
}
@inproceedings{Lucas1981,
  month = {August},
  year = {1981},
  title = { An Iterative Image Registration Technique with an Application to Stereo Vision},
  booktitle = {Proceedings of the Seventh Int. Conf. on Artificial Intelligence},
  pages = {674--679},
  editor = {P.J. Hayes},
  address = {Vancouver, B.C., Canada},
  publisher = {William Kaufmann},
  author = {Lucas, B.D. and Kanade, T.}
}
@phdthesis{Toft1996,
  month = {June},
  year = {1996},
  title = {The Radon Transform - Theory and Implementation},
  address = {Department of Mathematical Modeling, Denmark},
  annote = {key_radon},
  school = {Technical University of Denmark},
  author = {Toft, P.}
}
@article{Sapiro1993,
  number = {9},
  year = {1993},
  title = {Implementing Continuous-Scale Morphology via Curve Evolution},
  pages = {1363--1372},
  journal = {Pattern Recognition},
  volume = {26},
  author = {Sapiro, G. and Kimmel, R. and Shaked, D. and Kimia, B. and Bruckstein, A.M.}
}
@article{Kanmani1993,
  month = {April},
  year = {1993},
  title = {On the Computation of the Minkowski Dimension using Morphological Operations},
  pages = {81--85},
  journal = {Journal of Microscopy},
  volume = {170, Pt 1},
  author = {Kanmani, S. and Babu Rao, C. and Raj, B.}
}
@article{Zhao2004,
  year = {2004},
  title = {Morphological variation of individual Escherichia coli {50S} ribosomal subunits in situ, as revealed by cryo-electron tomography},
  pages = {190-201},
  journal = {Experimental Cell Research},
  volume = {300},
  author = {Zhao, Q. and {\"Ofverstedt}, L.-G. and Skoglund, U. and Isaksson, L.A.}
}
@article{Yeong1988a,
  number = {1},
  month = {July},
  year = {1998},
  title = {Reconstructing random media. {II}. Three-dimensional media from two-dimensional cuts},
  journal = {Physical Review E},
  volume = {58},
  author = {Yeong, C.L.Y. and Torquato, S.}
}
@article{Geraets1998,
  number = {2},
  year = {1998},
  title = {The Radiographic Trabecular Pattern of Hips in Patients with Hip Fractures and in Elderly Control Subjects},
  pages = {165--173},
  journal = {Bone},
  volume = {22},
  author = {Geraets, W.G.M. and Stelt, P.F. van der and Lips, P. and Ginkel, F.C. van}
}
@article{Rodriguez2000,
  year = {2000},
  title = {Origins of Illusory Percepts in Digital Images},
  pages = {2007--2017},
  journal = {Pattern Recognition},
  volume = {33},
  author = {Rodriguez-Sanchez, R. and Garcia, J.A. and Fdez-Valdivia, J. and Fdez-Valdivia, X.R.}
}
@book{Lenz1990,
  year = {1990},
  title = {Group Theoretical Methods in Image Processing},
  publisher = {Springer-Verlag},
  author = {Lenz, R.}
}
@phdthesis{Geraets1994,
  year = {1994},
  title = {Computer Aided Analysis of the Radiographic Trabecular Pattern},
  address = {Amsterdam, The Netherlands},
  school = {Vrije Universiteit Amsterdam},
  author = {Geraets, W.G.M.}
}
@article{Grossmann1984,
  year = {1984},
  title = {Decomposition of {Hardy} functions into square integrable wavelets of constant shape},
  pages = {723--736},
  journal = {SIAM Journal of Mathematics},
  volume = {15},
  author = {Grossmann, A. and Morlet, J.}
}
@misc{Poynton1999,
  year = {1999},
  title = {Frequently Asked Questions about Color},
  howpublished = {{\tt http://www.inforamp.net/~poynton}},
  author = {Poynton, C.}
}
@book{Matheron1967,
  year = {1967},
  title = {Elements pour une Theorie des Milieux Poreux},
  address = {Paris},
  publisher = {Masson},
  author = {Matheron, G.}
}
@article{Xu2003,
  number = {5},
  year = {2003},
  title = {Curvature Computations of 2-manifolds in $\sR^k$},
  pages = {681 -- 688},
  journal = {Journal of Computational Mathematics},
  volume = {21},
  author = {Xu, G. and Bajaj, C.L.}
}
@article{Xu2001,
  number = {9},
  year = {2001},
  title = {Efficient morphological shape representation with overlapping disk components },
  pages = {1346 -1356},
  journal = {IEEE Transactions on Image Processing},
  volume = {10},
  author = {Xu, J.}
}
@article{Wilson1984,
  number = {6},
  month = {November},
  year = {1984},
  title = {The Uncertainty Principle in Image Processing},
  pages = {758--767},
  journal = {IEEE Transactions on Pattern Analysis and Machine Intelligence},
  volume = {6},
  author = {Wilson, R. and Granlund, G.H.}
}
@article{Daniels1952,
  year = {1952},
  title = {The statistical theory of stiff chains},
  pages = {290-311},
  journal = {Proceedings of the Royal Society Edinburgh A},
  volume = {63},
  author = {Daniels, H.E.}
}
@article{Wilson1988,
  number = {2},
  month = {March/April},
  year = {1988},
  title = {Uncertainty and Inference in the Visual System},
  pages = {305--312},
  journal = {IEEE Transactions on Systems, Man and Cybernetics},
  volume = {18},
  author = {Wilson, R. and H. Knutsson, H.}
}
@article{Axelrod1976,
  year = {1976},
  title = {Mobility measurement by analysis of fluorescence photobleaching recovery kinetics},
  pages = {1055-1069},
  journal = {Biophysical Journal},
  volume = {16},
  author = {Axelrod, D. and Koppel, D.E. and Schlesinger, J. and Elson, E. and Webb, W.W.}
}
@article{Benes2000,
  month = {October},
  year = {2000},
  title = {Stereological Estimation of Integral Mixed Curvature with Application},
  pages = {26--31},
  journal = {Journal of Microscopy},
  volume = {200, Pt 1},
  author = {Bene{\v s}, V. and Hlawiczkov? M. and Volen?, K.}
}
@inproceedings{Bertalmio2000,
  month = {July},
  year = {2000},
  title = {Image Inpainting},
  booktitle = {Proceedings of SIGGRAPH},
  address = {New Orleans, USA},
  author = {Bertalmio, M. and Sapiro, G. and Caselles, V. and Ballester, C.}
}
@article{Axelrod1979,
  year = {1979},
  title = {Carbocyanine dye orientation in red cell membrane studied by microscopic fluorescence polarization},
  pages = {557-574},
  journal = {Biophysical Journal},
  volume = {26},
  author = {Axelrod, D.}
}
@article{Tang1998,
  number = {11},
  year = {1998},
  title = {Inference of Integrated Surface, Curve, and Junction Descriptions From Sparse 3D Data},
  pages = {1206--1223},
  journal = {IEEE Transactions on Pattern Analysis and Machine Intelligence},
  volume = {20},
  author = {Tang, C.K. and Medioni, G.}
}
@book{Fukunaga1972,
  year = {1972},
  title = {Introduction to Statistical Pattern Recognition},
  address = {New York},
  publisher = {Academic Press},
  author = {Fukunaga, K.}
}
@article{Ahmed1974,
  month = {January},
  year = {1974},
  title = {Discrete cosine transform},
  pages = {88--93},
  journal = {IEEE Transactions on Computers},
  volume = {23},
  annote = {key_fft},
  author = {Ahmed, N. and Natarajan, T. and Rao, K.R.}
}
@article{Topf2005,
  year = {2005},
  title = {Structural characterization of components of protein assemblies 3 by comparative modeling and electron cryo-microscopy},
  pages = {191-203},
  journal = {Journal of Structural Biology},
  volume = {149},
  author = {Topf, M. and Baker, M.L. and John, B. and Chiu, W. and Sali, A.}
}
@book{Born1959,
  edition = {6th},
  year = {1980, 1977},
  title = {Principles of Optics},
  publisher = {Pergamon Press},
  author = {Born, M. and Wolf, E.}
}
@book{Landau1969,
  edition = {second},
  year = {1969},
  title = {Statistical Physics, Part 1},
  publisher = {Pergamon Press},
  author = {Landau, L.D. and Lifshitz,E.M.}
}
@article{Deegan2000,
  number = {1},
  year = {2000},
  title = {Contact line deposits in an evaporating drop},
  pages = {756--765},
  journal = {Physical Review E},
  volume = {62},
  author = {Deegan, R.D. and Bakajin, O. and Dupont, T.F. and Huber, G. and Nagel, S.R. and Witten, T.A.}
}
@article{Abbe1873,
  year = {1873},
  title = {{Beitr\"age} zur {T}heorie des {M}ikroskopes und der mikroskopischen {W}ahrnehmung},
  pages = {413-468},
  journal = {Arch Mikrosk Anat},
  volume = {9},
  author = {Abbe, E.}
}
@article{Rocheleau2003,
  year = {2003},
  title = {Intrasequence {GFP} in Class {I MHC} Molecules, a Rigid Probe for Fluorescence Anisotropy Measurements of the Membrane Environment},
  pages = {4078-4086},
  journal = {Biophysical Journal},
  volume = {84},
  author = {Rocheleau, J.V. and Edidin, M. and Piston, D.W.}
}
@article{Hyvarinen1999,
  number = {3},
  year = {1999},
  title = {Fast and Robust Fixed-Point Algorithms for Independent Component Analysis},
  pages = {626-634},
  journal = {IEEE Transactions on Neural Networks},
  volume = {10},
  author = {{Hyv\"arinen}, A.}
}
@article{Hell1995,
  number = {2},
  year = {1995},
  title = {Two- and multiphoton detection as an imaging mode and means of increasing the resolution in far-field light microscopy: a study based on photon-optics},
  pages = {64-69},
  journal = {Bioimaging},
  volume = {3},
  author = {Hell, S.W. and Soukka, J. and {H\"anninen}, P.E.}
}
@article{Hell1994,
  number = {11},
  year = {1994},
  title = {Measurement of the 4pi-confocal point spread function proves 75 nm axial resolution},
  pages = {1335-1337},
  journal = {Applied Physics Letter},
  volume = {64},
  author = {Hell, S.W. and Lindek, S. and Cremer, C. and Stelzer, E.H.K.}
}
@article{Hell1993,
  number = {3},
  year = {1993},
  title = {Aberrations in confocal fluorescence microscopy induced by mismatching in refractive index},
  pages = {391--405},
  journal = {Journal of Microscopy},
  volume = {169},
  author = {Hell, S.W. and Reiner, G. and Cremer, C. and Stelzer, E.H.K.}
}
@article{Yin1994,
  year = {1994},
  title = {Tethered particle motion method for studying transcript elongation by a single {RNA} Polymerase Molecule},
  pages = {2468-2478},
  journal = {Biophysical Journal},
  volume = {67},
  author = {Yin, H. and Landick, R. and Gelles, J.}
}
@article{Chen1994a,
  number = {12},
  year = {1994},
  title = {Symmetric phase only matched filtering of {Fourier-Mellin} transforms for image registration and recognition},
  pages = {1156--1168},
  journal = {IEEE Transactions on Pattern Analysis and Machine Intelligence},
  volume = {16},
  author = {Chen, Q. and Defrise, M. and Deconinck, F.}
}
@inproceedings{Boomgaard2001,
  series = {Lecture Notes on Computer Science},
  year = {2001},
  title = {Gaussian Convolutions (Numerical Approximations Based on Interpolation)},
  booktitle = {Proceedings Third International Conference on Scale-Space},
  pages = {205--214},
  editor = {Kerckhove, M.},
  volume = {2106},
  address = {Vancouver, Canada},
  publisher = {Springer-Verlag},
  author = {Boomgaard, R. van den and Weij, R. van der}
}
@inproceedings{Boomgaard2002,
  month = {August 11-15},
  year = {2002},
  title = {On the equivalence of local-mode finding, robust estimation and mean-shift analysis as used in early vision tasks},
  booktitle = {ICPR 2002, International Conference on Pattern Recognition},
  editor = {Kasturi, R. and Laurendeau, D. and Suen, C.},
  author = {Boomgaard, R. van den and Weijer, J. van de},
  organization = {IEEE Computer Society}
}
@phdthesis{Lindeberg1991,
  year = {1991},
  title = {Discrete Scale-Space Theory and the Scale-Space Primal Sketch},
  school = {Royal Institute of Technology Stockholm, Sweden},
  author = {Lindeberg, T.}
}
@article{Cohen2002,
  number = {6},
  month = {June},
  year = {2002},
  title = {The {Gaussian} Watermarking Game},
  pages = {1639--1667},
  journal = {IEEE Transactions on Information Theory},
  volume = {48},
  author = {Cohen, A.S. and Lapidoth, A.}
}
@article{Lindeberg1993,
  year = {1993},
  title = {Discrete Derivative Approximations with Scale-space Properties: A Basis for Low-level Feature Extraction},
  pages = {349--376},
  journal = {Journal of Mathematical Imaging and Vision},
  volume = {3},
  author = {Lindeberg, T.}
}
@inbook{Davis1971,
  series = {Methods in Enzymology},
  year = {1971},
  title = {Electron microscope heteroduplex methods for mapping regions of base sequence homology in nucleic acids},
  pages = {413-428},
  editor = {Grossman, L. and Moldave, K.},
  volume = {21D},
  address = {London},
  publisher = {Academic Press},
  author = {Davis, R.W. and Simon, M. and Davidson, N.}
}
@article{Cohen2005,
  number = {6},
  year = {2005},
  title = {The history of noise},
  pages = {20-45},
  journal = { IEEE Signal Processing Magazine},
  volume = {22},
  author = {Cohen, L.}
}
@article{Lindeberg1998,
  number = {2},
  year = {1998},
  title = {Feature Detection with Automatic Scale Selection},
  pages = {79--116},
  journal = {International Journal of Computer Vision},
  volume = {30},
  author = {Lindeberg, T.}
}
@article{Owens1994,
  month = {January},
  year = {1994},
  title = {Feature-free Images},
  pages = {35--44},
  journal = {Pattern Recognition Letters},
  volume = {15},
  author = {Owens, R.A.}
}
@article{Lumia1983,
  year = {1983},
  title = {A New Connected Components Algorithm for Virtual Memory Computers},
  pages = {287--300},
  journal = {Computer Vision, Graphics, and Image Processing},
  volume = {22},
  author = {Lumia, R. and Shapiro, L. and Zuniga, O.}
}
@book{Stoyan1985,
  edition = {second},
  year = {1985, 1995},
  title = {Stochastic Geometry and its Applications},
  publisher = {John Wiley \& Sons, inc},
  author = {Stoyan, D. and Kendall, W.S. and Mecke, J.}
}
@article{Patterson1997,
  number = {5},
  year = {1997},
  title = {Use of green fluorescent protein and its mutants in quantitative fluorescence microscopy},
  pages = {2782-2790},
  journal = {Biophysical Journal},
  volume = {73},
  author = {Patterson, G.H. and Knobel, S.M. and Sharif, W.D. and Kain, S.R. and Piston, D.W.}
}
@inproceedings{Felsberg2001a,
  year = {2001},
  title = {Scale Adaptive Filtering Derived from the {Laplace} Equation},
  booktitle = {DAGM Symposium},
  note = {extended version.},
  address = {{M\"unchen}, Germany},
  author = {Felsberg, M. and Sommer, G.}
}
@techreport{Oktem2001,
  year = {2001},
  title = {A short overview of the {COMET} (COnstrained Maximum Entropy Tomography) methodology for solving inverse problems},
  institution = {KTH, Sweden},
  author = {{\"Oktem}, O.}
}
@phdthesis{Ellenberger2000,
  year = {2000},
  title = {Influence of defocus on measurements in microscope images },
  type = {Thesis},
  address = {The Netherlands},
  school = {Technische Universiteit Delft},
  author = {Ellenberger, S.L.}
}
@book{Poularikas1996,
  year = {1996},
  title = {The Transforms and Applications Handbook},
  publisher = {CRC Press},
  author = {Poularikas (ed), A.D.}
}
@article{Fleet1990,
  year = {1990},
  title = {Computation of component image velocity from local phase information},
  pages = {77-104},
  journal = {International Journal of Computer Vision},
  volume = {5},
  author = {Fleet, D.J. and Jepson, A.D.}
}
@inproceedings{Soille1998,
  year = {1998},
  title = {Image Structure Orientation using Mathematical Morphology},
  booktitle = {Proceedings of the 14th IAPR International Conference on Pattern Recognition},
  pages = {1467-1469},
  editor = {Jain, A. K. and Venkatesh, S. and Lovell, B. C.},
  volume = {1},
  address = {Los Alamitos},
  author = {Soille, P. and Talbot, H.},
  organization = {IEEE Computer Society Press}
}
@article{Einstein1905a,
  year = {1905},
  title = {{Zur Elektro}dynamik bewegter {K\"orper}},
  pages = {891-921},
  journal = {Annalen der Physik},
  volume = {17},
  author = {Einstein, A.}
}
@article{Einstein1905b,
  year = {1905},
  title = {Ist die {Tr\"agheit} eines {K\"orpers} von seinem {Energieinhalt} {abh\"angig?}},
  pages = {639-641},
  journal = {Annalen der Physik},
  volume = {18},
  author = {Einstein, A.}
}
@book{Soille1999,
  year = {1999},
  title = {Morphological Image Analysis. Principles and Applications},
  publisher = {Springer-Verlag},
  author = {Soille, P.}
}
@inproceedings{Knutsson1981,
  month = {August},
  year = {1981},
  title = {Anisotropic Filtering Operations for Image Enhancement and their Relation to the Visual System},
  booktitle = {Proceedings of {IEEE} Computer Society Conference on Pattern Recognition and Image Processing},
  address = {Dallas, Texas},
  author = {Knutsson , H. and Wilson, R. G. and Granlund, G. H.}
}
@article{Soille1996,
  number = {5},
  year = {1996},
  title = {Recursive Implementation of Erosions and Dilations Along Discrete Lines at Arbitrary Angles},
  pages = {562-567},
  journal = {IEEE Transactions on Pattern Analysis and Machine Intelligence},
  volume = {18},
  author = {Soille, P. and Breen, E. J. and Jones, R.}
}
@inproceedings{Spies2003,
  series = {LNCS 2749},
  month = {June 29 -July 2},
  year = {2003},
  title = {Two-Dimensional Channel Representation for Multiple Velocities},
  booktitle = {SCIA'03, Proceedings of the 13th Scandinavian Conference on Image Analysis ({G\"oteborg}, Sweden) },
  pages = {356-362},
  editor = {{Big\"un}, J. and Gustavsson, T.},
  address = {Berlin},
  publisher = {Springer-Verlag},
  author = {Spies, H. and Forssen, P.E.}
}
@phdthesis{Spies2001,
  month = {July},
  year = {2001},
  title = {Analysing Dynamic Processes in Range Data Sequences},
  address = {Heidelberg, Germany},
  school = {Ruprechts-Karls-{Universit\"at} University},
  author = {Spies, H.}
}
@article{Shapiro1978a,
  year = {1978},
  title = {Properties of Transforms for the Detection of Curves in Noisy Pictures},
  pages = {219--236},
  journal = {Computer Graphics and Image Processing},
  volume = {8},
  annote = {key_radon},
  author = {Shapiro, S.D.}
}
@article{Schellman1980,
  number = {3},
  year = {1980},
  title = {The flexibility of {DNA : I. Thermal} fluctuations},
  pages = {321-328},
  journal = {Biophysical Chemistry},
  volume = {11},
  author = {Schellman, J.A.}
}
@article{Klein1972,
  number = {2},
  year = {1972},
  title = {The Texture Analyzer},
  pages = {349--356},
  journal = {Journal of Microscopy},
  volume = {95},
  author = {Klein, J.-C. and Serra, J.}
}
@article{Toffoli1997,
  number = {2},
  month = {March},
  year = {1997},
  title = {Three-Dimensional Rotations by Three Shears},
  pages = {89--95},
  journal = {Graphical Models and Image Processing},
  volume = {59},
  author = {Toffoli, T.}
}
@article{Sato2000,
  number = {2},
  month = {April--June},
  year = {2000},
  title = {Tissue Classification Based on 3{D} Local Intensity Structures for Volume Rendering},
  pages = {160--179},
  journal = {IEEE Transactions on Visualization and Computer Graphics},
  volume = {6},
  author = {Sato, Y. and Westin, C.-F. and Bhalerao, A. and Nakajima, S. and Shiraga, N. and Tamura, S. and Kikinus, R.}
}
@article{Kappers1996,
  number = {2},
  year = {1996},
  title = {Detection of divergence in optical flow fields},
  pages = {227-235},
  journal = {Journal of the Optical Society of America A},
  volume = {13},
  author = {Kappers, A.M.L. and Pas, S.F. te and Koenderink, J.J. and Doorn, A.J van}
}
@article{Graham1997,
  year = {1997},
  title = {Detergent Foam Images as Analogue/Digital Model Fluids. 2. Investigation of Neighborship Partition of the Radial Distribution Function},
  pages = {11212--11220},
  journal = {Journal of Physical Chemistry B},
  volume = {101},
  author = {Graham, D.J. and Magdalinos, P. and Pimentel, D.}
}
@article{Siegmund1995,
  year = {1995},
  title = {Testing for a signal with unknown location and scale in a stationary Gaussian random field},
  pages = {608--639},
  journal = {Annals of Statistics},
  volume = {23},
  author = {Siegmund,D.O. and Worsley, K.J.}
}
@article{Zitova2003,
  number = {11},
  year = {2003},
  title = {Image registration methods: a survey},
  pages = {977-1000},
  journal = {Image and Vision Computing},
  volume = {21},
  author = {{Zitov\'a}, B. and Flusser, J.}
}
@article{Balzarini2001,
  year = {2001},
  title = {Quantification and Description of Fracture Network by {MRI} Image Analysis},
  pages = {539--541},
  journal = {Magnetic Resonance Imaging},
  volume = {19},
  author = {Balzarini, M. and Nicula, S. and Mattiello, D. and Aliverti, E.}
}
@article{Watson1994,
  number = {1},
  year = {1994},
  title = {Image Compression Using the Discrete Cosine Transform},
  pages = {81--88},
  journal = {The Mathematica Journal},
  volume = {4},
  author = {Watson, A.B.}
}
@article{Bradley2005,
  year = {2005},
  title = {An Astronomical 2175 \AA Feature in Interplanetary Dust Particles},
  pages = {244-},
  journal = {Science},
  volume = {307},
  author = {Bradley, J. and Dai Rong, Z. and Erni, R. and Browning, N. and Graham, G. and Weber, P. and Smith, J. and Hutcheon, I. and Ishii, H. and Bajt, S. and Floss, C. and Stadermann, F. and Sandford, S.}
}
@article{Coene1996,
  year = {1996},
  title = {Maximum-likelihood method for focus-variation image reconstruction in high resolution transmission electron microscopy},
  pages = {109-135},
  journal = {Ultramicroscopy},
  volume = {64},
  author = {Coene, W.M.J. and Thust, A. and Beeck, M. op de and Dyck, D. van}
}
@article{Bradley2004,
  year = {2004},
  title = {An analytical superstem for extraterrestrial materials research},
  journal = {Lunar and Panetary Science},
  volume = {35},
  author = {Bradley, J.P. and Dia, Z.R. and Wall, M. and Erni, R. and Browning, N.}
}
@article{Morrone1987,
  month = {December},
  year = {1987},
  title = {Feature Detection from Local Energy},
  pages = {303--313},
  journal = {Pattern Recognition Letters},
  volume = {6},
  author = {Morrone, M.C. and Owens, R.A.}
}
@inproceedings{Illers2004,
  number = {1},
  year = {2004},
  title = {Measurement of the Detective Quantum Efficiency (DQE) of digital X-ray imaging devices according to the standard IEC 62220-1},
  booktitle = {SPIE Proceedings},
  pages = {177-187},
  volume = {5368},
  address = {Bellingham, Washington, USA},
  author = {Illers, H. and Buhr, E. and Bergmann, D. and Hoeschen, C.}
}
@article{Princen1994,
  number = {4},
  month = {April},
  year = {1994},
  title = {Hypothesis Testing: A Framework for Analyzing and Optimizing {Hough} Transform Performance},
  pages = {329--341},
  journal = {IEEE Transactions on Pattern Analysis and Machine Intelligence},
  volume = {16},
  author = {Princen, J. and Illingworth, J. and Kittler, J.}
}
@phdthesis{Bakker2002,
  year = {2002},
  title = {Image structure analysis for seismic interpretation},
  address = {The Netherlands},
  school = {Delft University of Technology},
  author = {Bakker, P.}
}
@article{Saxton1997,
  year = {1997},
  title = {Single-particle tracking: the distribution of diffusion coefficients},
  pages = {1744-1753},
  journal = {Biophysical Journal},
  volume = {72},
  author = {Saxton, M.J.}
}
@article{Princen1992,
  year = {1992},
  title = {A Formal Definition of the {Hough} Transform: Properties and Relationships},
  pages = {153--168},
  journal = {Journal of Mathematical Imaging and Vision},
  volume = {1},
  author = {Princen, J. and Illingworth, J. and Kittler, J.}
}
@inproceedings{Bakker2001,
  month = {July 9-12},
  year = {2001},
  title = {Confidence and curvature estimation of curvilinear structures in {3-D}},
  booktitle = {ICCV'01 (Vancouver, Canada)},
  pages = {139--144},
  volume = {II},
  author = {Bakker, P. and Verbeek, P.W. and Vliet, L.J. van},
  organization = {IEEE}
}
@book{Constantinescu1974,
  year = {1974},
  title = {Distributionen und ihre Anwendung in der Physik},
  address = {Stuttgart},
  publisher = {Teubner},
  author = {Constantinescu, F.}
}
@book{Chung2001,
  edition = {third},
  year = {2001 (1968)},
  title = {A Course in Probability Theory},
  publisher = {Academic Press},
  author = {Chung, K.L.}
}
@phdthesis{BOOMGAARD1992chap3,
  year = {1992},
  title = {Mathematical Morphology: Extensions Towards Computer Vision},
  note = {Chapter 3, Dimensional Decomposition of Structuring Functions},
  school = {University of Amsterdam},
  author = {Boomgaard, R. van den}
}
@article{Mindell2003,
  year = {2003},
  title = {Accurate determination of local defocus and specimen tilt in electron microscopy},
  pages = {334-347},
  journal = {Journal of Structural Biology},
  volume = {142},
  author = {Mindell, J.A. and Grigorieff, N.}
}
@article{Chung2000,
  number = {9},
  month = {September},
  year = {2000},
  title = {On the Level Lines and Geometry of Vector-valued Images},
  pages = {241--243},
  journal = {IEEE Signal Processing Letters},
  volume = {7},
  author = {Chung, D.H. and Sapiro, G.}
}
@article{Pei1997,
  month = {November},
  year = {1997},
  title = {An Introduction to Discrete Finite Frames},
  pages = {84--96},
  journal = {Signal Processing Magazine},
  author = {Pei, S.-C. and Yeh, M.-H.}
}
@article{Rooms2005,
  number = {1},
  year = {2005},
  title = {Simultaneous degradation estimation and restoration of confocal images and performance evaluation by colocalization analysis},
  pages = {22-36},
  journal = {Journal of Microscopy},
  volume = {218},
  author = {Rooms, F. and Philips, W. and Lidke, D.S.}
}
@article{Pei1994,
  number = {8},
  year = {1994},
  title = {Using moments to acquire the motion Parameters of a deformable object without correspondence },
  pages = {475--485},
  journal = {Image and Vision Computing},
  volume = {12},
  author = {Pei, S.-C. and Liou, L.-G.}
}
@techreport{TEAMReport2000,
  year = {2000},
  author = {Material Science Division Argonne National Laboratory}
}
@inproceedings{Felsberg2002,
  series = {Lecture Notes in Computer Science},
  year = {2002},
  title = {Image Features Based on a New Approach to {2D} Rotation Invariant Quadrature Filters},
  booktitle = {ECCV 2002 (Copenhagen, Denmark)},
  pages = {369--383},
  editor = {Heyden, A. and Sparr, G. and Nielsen, M. and Johansen, P.},
  volume = {2350},
  publisher = {Springer Verlag},
  author = {Felsberg, M. and Sommer, G.}
}
@article{Parida1998,
  number = {7},
  month = {July},
  year = {1998},
  title = {Junctions: Detection, Classification, and Reconstruction},
  pages = {687--698},
  journal = {IEEE Transactions on Pattern Recognition and Machine Intelligence},
  volume = {20},
  author = {Parida, L. and Geiger, D. and Hummel, R.}
}
@inproceedings{Felsberg2000,
  year = {2000},
  title = {Structure Multivector for Local Analysis of Images},
  booktitle = {Proc. Dagstuhl Workshop on Theoretical Foundations of Computer Vision},
  author = {Felsberg, M. and Sommer, G.}
}
@article{Felsberg2001,
  number = {12},
  year = {2001},
  title = {The Monogenic Signal},
  pages = {3136--3144},
  journal = {IEEE Transactions on Signal Processing},
  volume = {49},
  author = {Felsberg, M. and Sommer, G.}
}
@article{Felsberg2004,
  number = {1},
  year = {2004},
  title = {The Monogenic Scale-Space: A Unifying Approach to Phase-Based Image Processing in Scale-Space},
  pages = {5--26},
  journal = {Journal of Mathematical Imaging and Vision},
  volume = {21},
  author = {Felsberg, M. and Sommer, G.}
}
@article{Stoger-Pollach2006,
  year = {2006},
  title = {Cerenkov losses: A limit for bandgap determination and {Kramers-Kronig} analysis},
  pages = {396-402},
  journal = {Micron},
  volume = {37},
  author = {{St\"oger-Pollach}, M. and Franco, H. and Schattschneider, P. and Lazar, S. and Schaffer, B. and Grogger, W. and Zandbergen, H.W.}
}
@article{Dekker1997,
  number = {3},
  year = {1997},
  title = {Resolution: a survey},
  pages = {547-557},
  journal = {Journal of the Optical Society of America A},
  volume = {14},
  author = {Dekker, A.J. den and Bos, A. van den}
}
@article{Porod1953,
  number = {2},
  year = {1953},
  title = {X-ray and light scattering by chain molecules in solution},
  pages = {157-166},
  journal = {Journal of Polymer Science},
  volume = {10},
  author = {Porod, G.}
}
@article{Wong1992,
  year = {1992},
  title = {Measurement of spherical aberration in {STEM}},
  pages = {139-150},
  journal = {Ultramicroscopy},
  volume = {40},
  author = {Wong, K. and Kirkland, E. and Xu, P. and Loane, R. and Silcox, J.}
}
@techreport{Cozman1997,
  year = {1997},
  title = {An Informal Introduction to Quasi-{Bayesian} Theory (and Lower Probability, Lower Expectations, Choquet Capacities, Robust {Bayesian} Methods, etc\dots) for {AI}},
  note = {CMU-RI-TR-97-24},
  address = {Pittsburgh, USA},
  institution = {The Robotics Institute, Carnegie Mellon University},
  author = {Cozman, F.}
}
@article{Dekker1999,
  number = {1},
  year = {1999},
  title = {How to optimize the design of a quantitative {HREM} experiment so as to attain the highest precision},
  pages = {95-104},
  journal = {Journal of Microscopy},
  volume = {194},
  author = {Dekker, A.J. den and Sijbers, J. and Dyck, D. van}
}
@article{Zhang2003,
  year = {2003},
  title = {Automated image acquisition and processing using a new generation of {4Kx4K CCD} cameras for cryo electron microscopic studies of macromolecular assemblies},
  pages = {135-144},
  journal = {Journal of Structural Biology},
  volume = {143},
  author = {Zhang, P. and Borgnia, M.J. and Mooney, P. and Shi, D. and Pan, M. and O'Herron, P. and Mao, A. and Brogan, D. and Milne, J.L.S. and Subramaniam, S.}
}
@article{Zhang2001,
  number = {5},
  month = {May},
  year = {2001},
  title = {Image Sequence Segmentation Using 3-D Structure Tensor and Curve Evolution},
  pages = {629--641},
  journal = {IEEE Transactions on Circuits and Systems for Video Technology},
  volume = {11},
  author = {Zhang, J. and Gao, J. and Liu, W.}
}
@article{Kutka1996,
  number = {1},
  month = {February},
  year = {1996},
  title = {Extraction of Line Properties Based on Direction Fields},
  pages = {51--58},
  journal = {IEEE Transactions on Medical Imaging},
  volume = {15},
  author = {Kutka, R. and Stier, S.}
}
@article{Adams1993,
  number = {5},
  year = {1993},
  title = {Radial Decomposition of Discs and Spheres},
  pages = {325--332},
  journal = {CVGIP: Graphical Models and Image Processing},
  volume = {55},
  author = {Adams, R.}
}
@inproceedings{Gilles1985,
  year = {1985},
  title = {Universal Computer Program for Seeking of a Collision Free Path for an Industrial Robot},
  booktitle = {Proceedings of the 15th ISIR Conference (Tokyo)},
  author = {Gilles, W.}
}
@article{Rushing2001,
  number = {8},
  year = {2001},
  title = {Using association rules as texture features},
  pages = {845 -858},
  journal = {IEEE Transactions on Pattern Analysis and Machine Intelligence},
  volume = {23},
  author = {Rushing, J.A. and Ranganath, H.S. and Hinke, T.H. and Graves, S.J.}
}
@article{Jonge2004,
  year = {2004},
  title = {Carbon nanotube electron sources and applications},
  pages = {2239-2266},
  journal = {Philosophical Transactions of the Royal Society of London A},
  volume = {362},
  author = {Jong, N. de and Bonard, J.M.}
}
@article{Mullikin1992,
  number = {6},
  year = {1992},
  title = {The vector distance transform in two and three dimensions},
  pages = {526-535},
  journal = {Graphical Models and Image Processing},
  volume = {54},
  author = {Mullikin, J.C.}
}
@article{Hermans1952,
  number = {11},
  year = {1952},
  title = {The statistics of stiff chains, with applications to light scattering},
  pages = {951-971},
  journal = {Physica},
  volume = {18},
  author = {Hermans, J.J. and Ullman, R.}
}
@article{Kram1993,
  year = {1993},
  title = {Localization of branching enzyme in potato tuber cells with the use of immunoelectron microscopy},
  pages = {237-243},
  journal = {Plant Physiology},
  volume = {101},
  author = {Kram, A.M. and Oostergetel, G.T. and Bruggen, E.F.J. van}
}
@article{Daubechies1986,
  year = {1986},
  title = {Painless nonorthogonal expansions},
  pages = {1271--1283},
  journal = {J. Math. Phys.},
  volume = {27},
  author = {Daubechies, I. and Grossmann, A. and Meyer, Y.}
}
@book{Misner1999,
  year = {1999},
  title = {Gravitation},
  address = {New York},
  publisher = {W.H. Freeman and Company},
  author = {Misner, C.W. and Thorne, K.S. and Wheeler, J.A.}
}
@book{Abramowitz1973,
  year = {1973},
  title = {Handbook of Mathematical Functions},
  publisher = {Dover Publications},
  author = {Abramowitz, M. and Stegun, I.A.}
}
@article{CLIF1,
  year = {1993},
  title = {Imaginary Numbers are not Real - the Geometric Algebra of Spacetime.},
  pages = {1775},
  journal = {Found. Phys.},
  volume = {23},
  author = {Gull, S. and Lasenby, A. and Doran, C.}
}
@book{Young1983,
  year = {1983},
  title = {Signals and Systems},
  publisher = {Prentice-Hall},
  author = {Oppenheim, A.V. and Willsky, A.S. and Young, I.T.}
}
@article{Elder1999,
  number = {2/3},
  year = {1999},
  title = {Are Edges Incomplete?},
  pages = {97--122},
  journal = {International Journal of Computer Vision},
  volume = {34},
  author = {Elder, J.H.}
}
@article{Sole2001,
  year = {2001},
  title = {Crease Enhancement Diffusion},
  pages = {241--248},
  journal = {Computer Vision and Image Understanding},
  volume = {84},
  author = {{Sol\'e}, A.F. and {L\'opez}, A. and Sapiro, G.}
}
@article{Elder1998,
  number = {7},
  year = {1998},
  title = {Local scale control for edge detection and blur estimation},
  pages = {699--716},
  journal = {IEEE Transactions on Pattern Analysis and Machine Intelligence},
  volume = {20},
  author = {Elder, J.H. and Zucker, S.W.}
}
@book{Vladimirov1986,
  year = {1986},
  title = {A Collection of Problems on the Equations of Mathematical Physics},
  address = {Heildelberg},
  publisher = {Springer},
  author = {Vladimirov, S.V.}
}
@inproceedings{Elder1996,
  year = {1996},
  title = {Scale Space Localization, Blur and Contour-based Image Coding},
  booktitle = {Proceedings of the IEEE Conference on Computer Vision and Pattern Recognition},
  pages = {27--34},
  address = {San Francisco, USA},
  author = {Elder, J. and Zucker, S.}
}
@article{Young1977,
  number = {7},
  year = {1977},
  title = {Proof without Prejudice: Use of the {Kolmogorov-Smirnov} Test for the Analysis of Histograms from Flow Systems and Other Sources},
  pages = {935--941},
  journal = {Journal of Histochemistry and Cytochemistry},
  volume = {25},
  author = {Young, I.T.}
}
@article{Young1974,
  number = {4},
  month = {August},
  year = {1974},
  title = {An Analysis Technique for Biological Shape {I}},
  pages = {357--370},
  journal = {Information and Control},
  volume = {25},
  author = {Young, I.T. and Walker, J.E. and Bowie, J.E.}
}
@article{Ebeling1993,
  number = {1},
  month = {January},
  year = {1993},
  title = {Detecting Structure in Two Dimensions Combining Voronoi Tessellation and Percolation},
  pages = {704--710},
  journal = {Physical Review E},
  volume = {47},
  author = {Ebeling, H. and Wiedemann, G.}
}
@article{Goutsias2000,
  year = {2000},
  title = {Fundamenta Morphologicae Mathematicae},
  pages = {1--31},
  journal = {Fundamenta Informaticae},
  volume = {41},
  author = {Goutsias, John and Heijmans, Henk J.A.M.}
}
@article{Winkler2003,
  year = {2003},
  title = {Focus gradient correction applied to tilt series image data used in electron tomography},
  pages = {24-32},
  journal = {Journal of Structural Biology},
  volume = {143},
  author = {Winkler, H. and Taylor, K.A.}
}
@article{Winkler2006,
  year = {2006},
  title = {Accurate marker-free alignment with simultaneous geometry determination and reconstruction of tilt series in electron tomography},
  pages = {240-254},
  journal = {Ultramicroscopy},
  volume = {106},
  author = {Winkler, H. and Taylor, K.A.}
}
@article{Shapiro1975,
  year = {1975},
  title = {Transformations for the Computer Detection of Curves in Noisy Pictures},
  pages = {328--338},
  journal = {Computer Graphics and Image Processing},
  volume = {4},
  annote = {key_radon},
  author = {Shapiro, S.D.}
}
@article{Weickert2001,
  number = {3},
  year = {2001},
  title = {Variational Optic Flow Computation with a Spatio-Temporal Smoothness Constraint},
  pages = {245 - 255},
  journal = {Journal of Mathematical Imaging and Vision},
  volume = {14},
  author = {Weickert, J. and {Sch\"orr}, C.}
}
@article{Heintzmann2003a,
  number = {7},
  year = {2003},
  title = {Saturated patterned excitation microscopy with two-dimensional excitation patterns},
  pages = {283-291},
  journal = {Micron},
  volume = {34},
  author = {Heintzmann, R.}
}
@article{Shapiro1978,
  year = {1978},
  title = {Feature Space Transforms for Curve Detection},
  pages = {129--143},
  journal = {Pattern Recognition},
  volume = {10},
  annote = {key_radon},
  author = {Shapiro, S.D.}
}
@article{Verbeek1994kort,
  number = {7},
  year = {1994},
  title = {On the location error of curved edges in low-pass filtered {2-D} and {3-D} images },
  pages = {726--733},
  journal = {PAMI},
  volume = {16},
  author = {Verbeek, P.W. and Vliet, L.J. van }
}
@inproceedings{Thevenaz2000,
  year = {2000},
  title = {Image Interpolation and Resampling},
  booktitle = {Handbook of Medical Image Processing},
  editor = {Bankman, I.},
  publisher = {Academic Press},
  author = {Th\'evenaz, P. and Blu, T. and Unser M.}
}
@article{Guessoum1986,
  number = {4},
  month = {August},
  year = {1986},
  title = {Fast Algorithms for the Multidimensional Discrete {Fourier} Transform},
  pages = {937--943},
  journal = {IEEE Transactions on Acoustics, Speech and Signal Processing},
  volume = {34},
  annote = {key_fft},
  author = {Guessoum, A. and Merserau, R.M.}
}
@phdthesis{Vrooman1991,
  year = {1991},
  title = {Quantitative analysis of interferograms},
  address = {Delft, the Netherlands},
  school = {Delft University of Technology},
  author = {Vrooman, H.A.}
}
@article{Levi2005,
  number = {4},
  year = {2005},
  title = {{3-D} Particle Tracking in a Two-Photon Microscope: Application to the Study of Molecular Dynamics in Cells},
  pages = {2919-2929},
  journal = {Biophysical Journal},
  volume = {88},
  author = {Levi, V. and Ruan, Q.Q. and Grattown, E.}
}
@book{Bernerian1992,
  year = {1992},
  title = {Linear Algebra},
  address = {Oxford},
  publisher = {Oxford},
  author = {Berberian, S.K.}
}
@misc{Zach2003,
  year = {2003},
  title = {Method for detecting geometrical-optical aberrations},
  howpublished = {US2003/0001102},
  author = {Zach, J.}
}
@book{Heijmans1994,
  series = {Advances in Electronics and Electron Physics},
  year = {1994},
  title = {Morphological Image Operators},
  editor = {Hawkes, P.W. and Kazan, B.},
  volume = {25},
  address = {San Diego},
  publisher = {Academic Press},
  author = {Heijmans, H.J.A.M.}
}
@article{Zemlin1978,
  year = {1978},
  title = {Coma-free alignment of high resolution electron microscopes with the aid of optical diffratctorgrams},
  pages = {49-60},
  journal = {Ultramicroscopy},
  volume = {3},
  author = {Zemlin, F. and Weiss, K. and Schiske, P. and Kunath, W. and Herrmann, K.-H.}
}
@article{Goetcherian1980,
  year = {1980},
  title = {From Binary to Grey Tone Image Processing Using Fuzzy Logic Concepts},
  pages = {7-15},
  journal = {Pattern Recognition},
  volume = {12},
  author = {Goetcherian, V.}
}
@inbook{Rao2002,
  year = {2002},
  title = {Encyclopedia of Imaging Science and Technology},
  pages = {1444--1450},
  editor = {Hornak, J.P.},
  volume = {2},
  chapter = {Wavelet Transforms},
  publisher = {John Wiley\&Sons},
  author = {Rao, R.}
}
@book{Jahne2002,
  year = {2002},
  title = {Digital Image Processing},
  address = {Berlin},
  publisher = {Springer-Verlag},
  author = {{J\"ahne}, B.}
}
@misc{Kahan1995,
  year = {1995},
  title = {The Baleful Effect of Computer Benchmarks upon Applied Mathematics, Physics and Chemistry},
  howpublished = {Mathematics Dept., and Elect. Eng. \& Computer Sci. Dept., University of California, USA},
  author = {Kahan, W.}
}
@article{You1996,
  number = {2},
  month = {February},
  year = {1996},
  title = {Ringing Reduction in Image Restoration by Orientation-Selective Regularization},
  pages = {29--31},
  journal = {IEEE Signal Processing Letters},
  volume = {3},
  author = {You, Y.-L. and Kaveh, M.}
}
@article{Luengo2005a,
  number = {11},
  year = {2005},
  title = {Using Line Segments as Structuring Elements for Sampling-Invariant Measurements},
  pages = {1826-1831},
  journal = {IEEE Transactions on Pattern Analysis and Machine Intelligence},
  volume = {27},
  author = {Luengo Hendriks, C.L. and Vliet, L.J. van}
}
@mastersthesis{Luengo1998,
  year = {1998},
  title = {Improved Resolution in Infrared Imaging Using randomly Shifted Images},
  address = {Delft},
  school = {Pattern Recognition Group, Faculty of Applied Sciences, Delft University of Technology},
  author = {Luengo Hendriks, C.L.}
}
@article{Gatica2001,
  number = {9},
  year = {2001},
  title = {Extensive partition operators, gray-level connected operators, and region merging/classification segmentation algorithms: theoretical links },
  pages = {1332 -1345},
  journal = {IEEE Transactions on Image Processing},
  volume = {10},
  author = {Gatica-Perez, D. and Gu, C. and Sun, M.-T. and Ruiz-Correa, S.}
}
@article{Keil1996,
  number = {10},
  month = {May},
  year = {1996},
  title = {Modelling of Phenomena within Catalyst Particles},
  pages = {1543--1567},
  journal = {Chemical Engineering Science},
  volume = {51},
  author = {Keil, F.J.}
}
@misc{Tolimieri2000,
  year = {2000},
  title = {Lesser Known {FFT} Algorithms},
  note = {20th Century Harmonic Analysis -- A Celebration, NATO Advanced Study Institute},
  annote = {key_fft},
  author = {Tolimieri, R. and An, M.}
}
@inproceedings{Felsberg2000a,
  year = {2000},
  title = {The Multidimensional Isotropic Generalization of Quadrature Filters in Geometric Algebra},
  booktitle = {2nd International Workshop on Algebraic Frames for the Perception-Action Cycle, AFPAC 2000, Kiel, Germany},
  pages = {175--185},
  publisher = {Springer Verlag},
  author = {Felsberg, M. and Sommer, G.}
}
@incollection{Young1998,
  year = {1998},
  title = {Image Processing Fundamentals },
  booktitle = {The Digital Signal Processing handbook},
  editor = {Madisetti, V.K. and Williams, D.B.},
  chapter = {51},
  publisher = {IEEE Press and CRC Press },
  author = {Young, I.T. and Gerbrands, J.J. and Vliet, L.J. van }
}
@article{Jeulin2000,
  year = {2000},
  title = {Random Texture Models for Material Structures},
  pages = {121--132},
  journal = {Statistics and Computing},
  volume = {10},
  author = {Jeulin, D.}
}
@inproceedings{Young1993,
  month = {May 25-28},
  year = {1993},
  title = {Depth-of-focus in microscopy },
  booktitle = {SCIA'93, Proceedings of the 8th Scandinavian Conference on Image Analysis},
  pages = {493-498},
  editor = {{H\o gda}, K. A. and Braathen, B. and Heia, K.},
  address = {{Troms\o} Norway},
  publisher = {Norwegian Society for Image Processing and Pattern Recognition},
  author = {Young, I.T. and Zagers, R. and Vliet, L.J. van and Mullikin, J. and Boddeke, F.R. and Netten, H.}
}
@article{HaarRomeny1994,
  number = {6},
  year = {1994},
  title = {Higher order differential structure of images},
  pages = {317-325},
  journal = {Image and Vision Computing},
  volume = {12},
  author = {Haar Romeny, B.M. ter and Florack, L.M.J. and Salden, A.H. and Viergever, M.A.}
}
@article{Haider1998,
  year = {1998},
  title = {A spherical-aberration-corrected 200 {kV} transmission electron microscope},
  pages = {53-60},
  journal = {Ultramicroscopy},
  volume = {75},
  author = {Haider, M. and Rose, H. and Uhlemann, S. and Schwan, E. and Kabius, B. and Urban, K.}
}
@article{Young1995,
  number = {2},
  year = {1995},
  title = {Recursive implementation of the {G}aussian filter},
  pages = {139--151},
  journal = {Signal Processing},
  volume = {44},
  author = {Young, I.T. and Vliet, L.J. van}
}
@article{Young1996,
  number = {1},
  year = {1996},
  title = {Quantitative Microscopy},
  pages = {59-66},
  journal = {IEEE Engineering in Medicine and Biology},
  volume = {15},
  author = {Young, I.T.}
}
@article{Milne2002,
  year = {2002},
  title = {Molecular architecture and mechanism of an icosahedral pyruvate dehydrogenase complex: a multifunctional catalytic machine},
  pages = {5587-5598},
  journal = {EMBO Journal},
  volume = {21},
  author = {Milne, J.L.S. and Shi, D. and Rosenthal, P.B. and Sunshine, J.S. and Domingo, G.J. and Wu, X. and Brooks, B.R. and Perham, R.N. and Henderson, R. and Subramaniam, S.}
}
@incollection{Ginkel2001a,
  year = {2001},
  title = {Applications of Image Analysis in Orientation Space},
  booktitle = {Fourth Quinqennial Review 1996-2001 of the Dutch Society for Pattern Recognition and Image Processing},
  pages = {365--380},
  editor = {Vossepoel, A.M. and Vos, F.M.},
  author = {Ginkel, M. van and Vliet, L.J. van and Verbeek, P.W.}
}
@book{Schone1990,
  year = {1990},
  title = {Differentialgeometrie},
  address = {Leipzig},
  publisher = {Teubner},
  author = {W. {Sch\"one}}
}
@article{Nickell2004,
  number = {3},
  year = {2004},
  title = {{TOM} software toolbox: acquisition and analysis for electron tomography},
  pages = {227-234},
  journal = {Journal of Strcutural Biology},
  volume = {149},
  author = {Nickell, S. and {F\"orster}, F. and Linaroudis, A. and Net, W. del and Beck, F. and Hegerl, R. and Baumeister, W. and Plizko, J.M.}
}
@inproceedings{Kaltenbacher1996,
  year = {1996},
  title = {High resolution infrared image reconstruction using multiple, low resolution, aliased frames},
  booktitle = {SPIE Proceedings},
  pages = {142-152},
  volume = {2751},
  author = {Kaltenbacher, E.A. and Hardie, R.C.}
}
@article{Yaroslavsky2003,
  number = {20},
  year = {2003},
  title = {Boundary effect free and adaptive discrete signal sinc-interpolation algorithms for signal and image resampling},
  pages = {4166-4175},
  journal = {Applied Optics},
  volume = {42},
  author = {Yaroslavsky, L.}
}
@article{Yeong1998,
  number = {1},
  month = {January},
  year = {1998},
  title = {Reconstructing random media},
  journal = {Physical review E},
  volume = {57},
  author = {Yeong, C.L.Y. and Torquato, S.}
}
@inproceedings{Leonardis1992,
  series = {Lecture Notes in Computer Science 588},
  month = {May},
  year = {1992},
  title = {Finding Parametric Curves in an Image},
  booktitle = {Second European Conference on Computer Vision},
  pages = {653--657},
  editor = {Sandini, G.},
  address = {Santa Margherita Ligure, Italy},
  publisher = {Springer},
  author = {Leonardis, A. and Bajcsy, R.}
}
@article{Wallrabe2005,
  number = {1},
  year = {2005},
  title = {Imaging protein molecules using FRET and FLIM microscopy},
  pages = {19-27},
  journal = {Current Opinion in Biotechnology},
  volume = {16},
  author = {Wallrabe, H. and Periasamy, A.}
}
@article{Barron1994,
  number = {1},
  year = {1994},
  title = {Performance of optical flow techniques},
  pages = {43--77},
  journal = {International Journal of Computer Vision},
  volume = {12},
  author = {Barron, J.L. and Fleet, D.J. and Beauchemin, S.}
}
@book{Bronstein2000,
  year = {2000},
  title = {Taschenbuch der Mathematik},
  publisher = {Verlag Harri Deutsch},
  author = {Bronstein, I.N. and Semendjajew, K.A. and Musiol, G. and {M\"uhlig}, H.}
}
@article{Martin2001,
  year = {2001},
  title = {Combined {EM/X}-Ray Imaging Yields a Quasi-Atomic Model of the Adenovirus-Related Bacteriophage {PRD1} and Shows Key Capsid and Membrane Interactions},
  pages = {917-930},
  journal = {Structure},
  volume = {9},
  author = {Martin, C. san and Burnett, R.M. and Hass, F. de and Heinkel, R. and Rutten, T. and Fuller, S.D. and Butcher, S.J. and Bamford, D.H.}
}
@article{Cowley1969,
  number = {2},
  year = {1969},
  title = {Image contrast in a transmission scanning electron microscope},
  pages = {58-59},
  journal = {Applied Physics Letters},
  volume = {15},
  author = {Cowley, J.M.}
}
@article{Rivetti2001,
  number = {1-2},
  year = {2001},
  title = {Accurate length determination of {DNA} molecules visualized by atomic force microscopy: evidence for a partial {B-} to {A-form} transition on mica},
  pages = {55-66},
  journal = {Ultramicroscopy},
  volume = {87},
  author = {Rivetti, C. and Codeluppi, S.}
}
@article{Aert2004,
  year = {2004},
  title = {How to optimize the experimental design of quantitative atomic resolution {TEM} experiments?},
  pages = {425-429},
  journal = {Micron},
  volume = {35},
  author = {Aert, S. van and Dekker, A.J. den and Dyck, D. van}
}
@book{Fraleigh1994,
  edition = {5th},
  year = {1994},
  title = {A First Course in Abstract Algebra},
  publisher = {Addison-Wesley},
  author = {Fraleigh, J.B.}
}
@article{Duffin1952,
  month = {March},
  year = {1952},
  title = {A Class of Nonharmonic {Fourier} Series},
  pages = {341--366},
  journal = {Transactions of the American Mathematical Society},
  volume = {72},
  author = {Duffin, R.J. and Schaeffer, A.C.}
}
@article{Aert2002,
  year = {2002},
  title = {High-resolution electron microscopy and electron tomography: resolution versus precision},
  pages = {21-33},
  journal = {Journal of Structural Biology},
  volume = {138},
  author = {Aert, S. van and Dekker, A.J. den and Dyck, D. van and Bos, A. van den}
}
@article{Cootes2001,
  number = {6},
  month = {June},
  year = {2001},
  title = {Active Appearance Models},
  pages = {681--685},
  journal = {IEEE Transactions on Pattern Analysis and Machine Intelligence},
  volume = {23},
  author = {Cootes, T.F. and Edwards, G.J. and Taylor, C.J.}
}
@article{Hilfer1991,
  number = {1},
  month = {July},
  year = {1991},
  title = {Geometric and Dielectric Characterization of Porous Media},
  pages = {60--75},
  journal = {Physical Review B},
  volume = {44},
  author = {Hilfer, R.}
}
@article{Hilfer1992,
  number = {13},
  month = {April},
  year = {1992},
  title = {Local-Porosity Theory for Flow in Porous Media},
  pages = {7115--7121},
  journal = {Physical Review B},
  volume = {45},
  author = {Hilfer, R.}
}
@article{Rieger2004c,
  year = {2004},
  title = {Alignment of the Cell Nucleus From Labeled Proteins Only for {4D} In Vivo Imaging},
  pages = {142-150},
  journal = {Microscopy Research and Technique},
  volume = {64},
  author = {Rieger, B. and Molenaar, C. and Dirks, R.W. and Vliet, L.J.}
}
@unpublished{VerbeekXXXX,
  title = {Line and Edge Detection by Symmetry Filters},
  author = {Verbeek, P.W.}
}
@article{Heertje1998,
  number = {31},
  year = {1998},
  title = {Liquid Crystalline Phases in the Structuring of Food Products},
  pages = {387--396},
  journal = {Lebensmittel-Wissenschaft und Technologie},
  author = {Heertje, I. and Roijers, E.C. and Hendrikx, H.A.C.M.}
}
@article{Ritchie1974,
  number = {7},
  month = {July},
  year = {1974},
  title = {The {UNIX} Time-Sharing System},
  pages = {365--375},
  journal = {Communications of the {ACM}},
  volume = {17},
  author = {Ritchie, D.M. and Thompson, K.}
}
@inproceedings{Blanc1995,
  year = {1995},
  title = {{X}-Splines: A Spline Model Designed for the End-User},
  booktitle = {Proceedings of SIGGRAPH},
  pages = {377--386},
  author = {Blanc, C. and Schlick, C.}
}
@article{Zwiggelaar1999,
  number = {1},
  year = {1999},
  title = {Model-based Detection of Spiculated Lesions in Mammograms},
  pages = {39-62},
  journal = {Medical Image Analysis},
  volume = {3},
  author = {Zwiggelaar, R. and Parr, T. and Schumm, J.E. and Hutt, I.W. and Taylor, C.J. and Astley, S.M. and Boggis, R.M.}
}
@article{Pothuaud2000,
  month = {August},
  year = {2000},
  title = {A New Method for Three-Dimensional Skeleton Graph Analysis of Porous Media: Application to Trabecular Bone Microarchitecture},
  pages = {149--161},
  journal = {Journal of Microscopy},
  volume = {199, Pt 2},
  author = {Pothuaud, L. and Porion, P. and Lespessailles, E. and Benhamou, C.L. and Levitz, P.}
}
@inproceedings{Zwiggelaar1998,
  series = {Lecture Notes in Computer Science},
  year = {1998},
  title = {Abnormal Masses in Mammograms: Detection Using Scale-Orientation Signatures},
  booktitle = {Medical Image Computing and Computer-Assisted Intervention - MICCAI'98, Proc. 1st Int. Conf. (Cambridge, MA, USA, Oct.11-13)},
  volume = {1496},
  address = {Berlin},
  publisher = {Springer Verlag},
  author = {Zwiggelaar, R. and Taylor, C.J.}
}
@article{Besag1974,
  year = {1974},
  title = {Spatial Interaction and the Statistical Analysis of Lattice Systems},
  pages = {192--236},
  journal = {Journal of the Royal Statistical Society, Series B},
  volume = {36},
  author = {Besag, J.E.}
}
@inproceedings{SHORTGlas2001,
  series = {Lecture Notes on Computer Science},
  year = {2001},
  title = {Assessment of Center of Rotation of the Glenohumeral Joint by a Modified {H}ough Transform},
  volume = {2208},
  author = {Glas, M. van der and Vos, F.M. and Vossepoel, A.M.}
}
@article{Liang2002,
  year = {2002},
  title = {{IMIRS}: a high-resolution 3D reconstruction pachage integrated with a relational image database},
  pages = {292-304},
  journal = {Journal of Structural Biology},
  volume = {137},
  author = {Liang, Y. and Ke, E.Y. and Zhou, Z.H.}
}
@article{Wang2005,
  year = {2005},
  title = {An iterative Fourier-Bessel algorithm for reconstruction of helical structures with severe Bessel overlap},
  pages = {65-78},
  journal = {Journal of Structural Biology},
  volume = {149},
  author = {Wang, H.-W. and Nogales, E.}
}
@article{Milanfar1999,
  number = {9},
  year = {1999},
  title = {A Model of the Effect on Image Motion in the Radon Transform Domain},
  pages = {1276--1281},
  journal = {IEEE Transaction on Image Processing},
  volume = {8},
  annote = {key_radon},
  author = {P. Milanfar}
}
@article{Lee1997,
  number = {5},
  month = {May},
  year = {1997},
  title = {Adaptive Basis Matrix for the Morphological Function Processing Opening and Closing},
  pages = {769--774},
  journal = {IEEE Transactions on Image Processing},
  volume = {6},
  author = {Lee, Kyung-Hoon and Morales, Aldo and Ko, Sung-Jea}
}
@article{DeRosier2000,
  number = {2},
  year = {2000},
  title = {Correction of high-resolution data for curvature of the {Ewald} sphere},
  pages = {83-98},
  journal = {Ultramicrosocpy},
  volume = {81},
  author = {DeRosier, D.J.}
}
@article{Jansen1993,
  year = {1993},
  title = {Analysis of Grey Level Histograms by using Statistical Methods for Mixtures of Distributions},
  pages = {585--590},
  journal = {Pattern Recognition Letters},
  volume = {14},
  author = {Jansen, R.C. and Reinink, K. and Heijden, G.W.A.M. van der}
}
@article{Lee1999,
  number = {1},
  month = {October},
  year = {1999},
  title = {Grouping ., -, {$\rightarrow$}, ?, into Regions, Curves, and Junctions},
  pages = {54--69},
  journal = {Computer Vision and Image Understanding},
  volume = {76},
  author = {Lee, M.S. and Medioni, G.}
}
@article{Schellman1995,
  number = {1},
  year = {1995},
  title = {Static contributions to the persistence length of {DNA} and dynamic contributions to {DNA} curvature},
  pages = {95-114},
  journal = {Biophysical Chemistry},
  volume = {55},
  author = {Schellman, J.A. and Harvey, S.C.}
}
@article{Bigun1994a,
  number = {1},
  month = {January},
  year = {1994},
  title = {{N}-folded Symmetries by Complex Moments in {Gabor} Space and their Application to Unsupervised Texture Segmentation},
  pages = {80--87},
  journal = {IEEE Transactions on Pattern Analysis and Machine Intelligence},
  volume = {16},
  author = {{Big\"un}, J. and Hans du Buf, J.M.}
}
@inproceedings{Danielsson1980a,
  month = {December},
  year = {1980},
  title = {Rotation-Invariant Linear Operators with Directional Response},
  booktitle = {Proceedings of the 5th international conference on Pattern Recognition (Miami Beach, Florida)},
  pages = {1171--1176},
  volume = {2},
  author = {Danielsson, P.-E.}
}
@article{Heintzmann2003,
  number = {7},
  year = {2003},
  title = {On resolution enhancement by subtraction of confocal signals taken at different pinhole sizes},
  pages = {293-300},
  journal = {Micron},
  volume = {34},
  author = {Heintzmann, R. and Sarafis, V. and Munroe, P. and Nailon, J. and Hanley, Q.S. and Jovin, T.M.}
}
@article{Arnison2002,
  year = {2002},
  title = {A 3D vectorial optical transfer function suitable for arbitrary pupil functions},
  pages = {53-63},
  journal = {Optics Communications},
  volume = {211},
  author = {Arnison, M.R. and Sheppard, C.J.R.}
}
@article{Heintzmann2002,
  number = {8},
  year = {2002},
  title = {Saturated patterned excitation microscopy concept for optical resolution improvement},
  pages = {1599-1609},
  journal = {Journal of Optical Society of America A},
  volume = {19},
  author = {Heintzmann, R. and Jovin, T.M. and Cremer, C.}
}
@inproceedings{Yu2000,
  year = {2000},
  title = {A New 3{D} Orientation Steerable Filter},
  booktitle = {Symposium {f\"ur} Mustererkennung, DAGM 2000, Kiel, Germany},
  pages = {203--212},
  publisher = {Springer Verlag},
  author = {Yu, W. and Daniilidis, K. and Sommer, G.}
}
@article{Yu2001,
  number = {2},
  month = {February},
  year = {2001},
  title = {Approximate Orientation Steerability Based on Angular Gaussians},
  pages = {193--205},
  journal = {IEEE Transactions on Image Processing},
  volume = {10},
  author = {Yu, W. and Daniilidis, K. and Sommer, G.}
}
@inbook{Arnison2003,
  series = {Optical imaging and microscopy - Techniques and Advanced Systems},
  year = {2003},
  title = {Wavefront Coding Fluorescence Microscopy Using High Aperture Lenses},
  editor = {{T\"or\"ork}, P. and Kao, F.J.},
  address = {Heidelberg, },
  publisher = {Springer-Verlag},
  author = {Arnison, M.R. and Cogswell, C.J. and Sheppard, C.J.R. and {T\"or\"ork}, P.}
}
@article{Heintzmann2004,
  year = {2004},
  title = {Double-pass Fourier transform imaging spectroscopy},
  pages = {753-763},
  journal = {Optics Express},
  volume = {12},
  author = {Heintzmann, R. and Lidke, K.A. and Jovin, T.M.}
}
@article{Yu2003,
  number = {5},
  year = {2003},
  title = {Three Dimensional Orientation Signatures with Conic Kernel Filtering for Multiple Motion Analysis},
  pages = {447--458},
  journal = {Image and Vision Computing},
  volume = {21},
  author = {Yu, W. and Sommer, G. and Daniilidis, K.}
}
@article{Hyun2000,
  year = {2000},
  title = {On the Level Lines and Geometry of Vector Valued Images},
  pages = {241--243},
  journal = {IEEE Signal Processing Letters},
  volume = {7},
  author = {Hyun Chung, D. and Sapiro, G.}
}
@article{Schellman1974,
  number = {1},
  year = {1974},
  title = {Flexibility of {DNA}},
  pages = {217-226},
  journal = {Biopolymers},
  volume = {13},
  author = {Schellman, J.A.}
}
@article{Mastronarde1997,
  year = {1997},
  title = {Dual-Axis Tomography: An Approach with Alignment Methods That Preserve Resolution},
  pages = {343-352},
  journal = {Journal of Structural Biology},
  volume = {120},
  author = {Mastronarde, D.N.}
}
@article{Verveer2000,
  year = {2000},
  title = {Global Analysis of Fluorescence Lifetime Imaging Microscopy Data},
  pages = {2127-2137},
  journal = {Biophysical Journal},
  volume = {78},
  author = {Verveer, P.J. and Squire, A. and Bastiaens, P.I.H.}
}
@article{Hermann1993,
  month = {April},
  year = {1993},
  title = {Determination of Microstructural Parameters of Random Spatial Surface Fractals by Measuring Chord Length Distributions},
  pages = {87--93},
  journal = {Journal of Microscopy},
  volume = {170, Pt 1},
  author = {Hermann, H. and Ohser, J.}
}
@article{Kuwahara1976,
  year = {1976},
  title = {Processing of RI-angiocardiographic images},
  pages = {187-203},
  journal = {Digital Processing of Biomedical Images},
  author = {Kuwahara, M. and Hachimura, K. and Eiho, S. and Kinoshita, M.}
}
@article{Luo1998,
  number = {4},
  year = {1998},
  title = {Iterative Multilevel Thresholding and Splitting for Three-Dimensional Segmentation of Live Cell Nuclei Using Laser Scanning Confocal Microscopy},
  pages = {151--162},
  journal = {Journal of Computer-Assisted Microscopy},
  volume = {10},
  author = {Luo, D. and Barker, J. and McGrath, J.C. and Daly, C.J.}
}
@article{Jaffer1993,
  month = {September},
  year = {1993},
  title = {Algebra and the Lambda Calculus},
  pages = {36--40},
  journal = {Dr. Dobbs's Journal},
  author = {Jaffer, A.}
}
@book{Stoecker2000,
  edition = {4},
  year = {2000},
  title = {Taschenbuch der {Physik}},
  address = {Frankfurt (Main)},
  publisher = {Verlag Harri Deutsch},
  author = {{St\"ocker}, H.}
}
@article{Mouche2001,
  year = {2001},
  title = {Lumbricus terrestris Hemoglobin - The Architecture of Linker Chains and Structural Variation of the Central Toroid},
  pages = {176-192},
  journal = {Journal of Structural Biology},
  volume = {133},
  author = {Mouche, F. and Boisset, N. and Penczek, P.A.}
}
@article{Mouche2003,
  year = {2003},
  title = {Automated three-dimensional reconstruction of keyhole limpet hemocyanin type 1},
  pages = {301-312},
  journal = {Journal of Structural Biology},
  volume = {144},
  author = {Mouche, F. and Zhu, Y. and Pulokas, J. and Potter, C.S. and Carragher, B.}
}
@article{Knuth1987,
  number = {4},
  month = {October},
  year = {1987},
  title = {Digital Halftones by Dot Diffusion},
  pages = {245--273},
  journal = {ACM Transactions on Graphics},
  volume = {6},
  author = {Knuth, D.E.}
}
@article{Scharstein2002,
  number = {1},
  month = {April-June},
  year = {2002},
  title = {A Taxonomy and Evaluation of Dense Two-Frame Stereo Correspondence Algorithms},
  pages = {7--42},
  journal = {International Journal of Computer Vision},
  volume = {47},
  author = {Scharstein, D. and Szeliski, R.}
}
@article{Teuner1995,
  number = {6},
  month = {June},
  year = {1995},
  title = {Unsupervised Texture Segmentation of Images Using Tuned Matched Gabor Filters},
  pages = {863--870},
  journal = {IEEE Transactions on Image Processing},
  volume = {4},
  author = {Teuner, A. and Pichler, O. and Hosticka, B.J.}
}
@article{Kubitscheck2002,
  number = {5-6},
  year = {2002},
  title = {Single Protein Molecules Visualized and Tracked in the Interior of Eukaryotic Cells},
  pages = {267-274},
  journal = {Single Molecule},
  volume = {3},
  author = {Kubitscheck, U.}
}
@article{Wigner1932,
  number = {5},
  month = {June},
  year = {1932},
  title = {On the Quantum Correction For Thermodynamic Equilibrium},
  pages = {749--759},
  journal = {Physical Review},
  volume = {40},
  author = {Wigner, E.}
}
@phdthesis{Gokstorp1995,
  year = {1995},
  title = {Depth Computation in Robot Vision},
  address = {{Link\"oping}, Sweden},
  school = {{Link\"oping} University},
  author = {{G\"okstorp}, M.}
}
@article{Zuccheri2001,
  number = {6},
  year = {2001},
  title = {Mapping the intrinsic curvature and flexibility along the {DNA} chain},
  pages = {3074-3079},
  journal = {Proceedings of the National Academy of Sciences of the United States of America},
  volume = {98},
  author = {Zuccheri, G. and Scipioni, A. and Cavaliere, V. and Gargiulo, G. and Sanits, P. de and Samori, B. }
}
@article{Singleton1969,
  number = {2},
  month = {June},
  year = {1969},
  title = {An Algorithm for Computing the Mixed Radix Fast {Fourier} Transform},
  pages = {93--103},
  journal = {IEEE Transactions on Audio and Electroacoustics},
  volume = {17},
  annote = {key_fft},
  author = {Singleton, R.C.}
}
@article{Daubechies1990,
  number = {5},
  month = {September},
  year = {1990},
  title = {The Wavelet Transform, Time-Frequency Localization and Signal Analysis},
  pages = {961--1005},
  journal = {IEEE Transactions on Information Theory},
  volume = {36},
  author = {Daubechies, I.}
}
@inproceedings{Dubowy2005,
  series = {IEEE International Conference on Image Processing},
  year = {2005},
  title = {An approach to the correction of distance-dependent defocus in electron microscopic reconstruction},
  pages = {748-751},
  volume = {3},
  author = {Dubowy, J.N. and Herman, G.T.}
}
@article{Whittaker1934,
  year = {1934},
  title = {On Lidstone's Series and Two-point Expansions of Analytic Functions},
  pages = {451--469},
  journal = {Proceedings London Math. Soc. (2)},
  volume = {36},
  author = {Whittaker, J.M.}
}
@article{Unser2000,
  number = {4},
  month = {April},
  year = {2000},
  title = {Sampling -- 50 Years after {Shannon}},
  pages = {569--587},
  journal = {Proceedings of the IEEE},
  volume = {88},
  author = {Unser, M.}
}
@article{Edelman1999,
  number = {3},
  year = {1999},
  title = {The Future Fast {Fourier} Transform?},
  pages = {1094--1114},
  journal = {SIAM Journal on Scientific Computing},
  volume = {20},
  annote = {key_fft},
  author = {Edelman, A. and McCorquodale, P. and Toledo, S.}
}
@book{Jahne1997a,
  year = {1997},
  title = {Practical handbook on Image Processing for Scientific Applications},
  publisher = {CRC Press},
  author = {{J\"ahne}, B.}
}
@article{Brox2006,
  year = {2006},
  title = {Nonlinear structure tensor},
  pages = {41-55},
  journal = {Image and Vision Computing},
  volume = {24},
  author = {Brox, T. and Weickert, J. and Burgeth, B. and Mrazek, P.}
}
@article{Zheng2004,
  year = {2004},
  title = {An improved strategy for automated electron microscopic tomography},
  pages = {91-101},
  journal = {Journal of Structural Biology},
  volume = {147},
  author = {Zheng, Q.S. and Braunfeld, M.B. and Sedat, J.W. and Agard, D.A.}
}
@article{Chepic1990,
  number = {3},
  year = {1990},
  title = {Auger ionization of semiconductor quantum drops in a glass matrix},
  pages = {113-127},
  journal = {Journal of Luminescence},
  volume = {47},
  author = {Chepic, D.I. and Efros, A.L. and Ekimov, A.I. and Ivanov, M.G. and Kharchenko, V.A. and Kudriavtsev, I.A. and Yazeva, T.V.}
}
@article{Frenken1993,
  year = {1993},
  title = {Thermal Roughening Investigated by Scanning Tunnelling Microscopy},
  pages = {27--36},
  journal = {Faraday Discussions},
  volume = {95},
  author = {Frenken, J.W.M. and Kuipers, L. and Sanders, J.B.}
}
@article{Hilton1995,
  number = {8},
  year = {1995},
  title = {Statistics of surface curvature estimates},
  pages = {1201--1221},
  journal = {Pattern Recognition},
  volume = {28},
  author = {Hilton, A. and Illingworth, J. and Windeatt, T.}
}
@article{Voort1995,
  year = {1995},
  title = {Restoration of confocal images for quantitative image analysis},
  pages = {165--181},
  journal = {J. Microscopy},
  volume = {178},
  author = {T.M. van der Voort and K.C. Strassers}
}
@article{Schatzman1996,
  number = {3},
  month = {March},
  year = {1996},
  title = {Index Mappings for the Fast {Fourier} Transform},
  pages = {717--719},
  journal = {IEEE Transactions on Signal Processing},
  volume = {44},
  annote = {key_fft},
  author = {Schatzman, J.C.}
}
@misc{WeickertXXXX,
  title = {Nonlinear Diffusion Scale-Spaces},
  author = {Weickert, J.}
}
@book{Reimer1997,
  edition = {4th},
  year = {1997},
  title = {Transition Electron Microscopy},
  note = {sold out, reprint 2006},
  address = {Berlin},
  publisher = {Springer Verlag},
  author = {Reimer, L.}
}
@article{Fukano2003,
  number = {19},
  year = {2003},
  title = {Whole-Field Fluorescence Microscope with Digital Micromirror Device: Imaging of Biological Samples},
  pages = {4119-4124},
  journal = {Applied Optics},
  volume = {42},
  author = {Fukano, T. and Miyawaki, A.}
}
@article{Lifshitz1990,
  number = {6},
  month = {June},
  year = {1990},
  title = {A Multiresolution Hierarchical Approach to Image Segmentation Based on Intensity Extrema},
  pages = {529--540},
  journal = {IEEE Transactions on Pattern Analysis and Machine Intelligence},
  volume = {12},
  author = {Lifshitz, L.M. and Pizer, S.M.}
}
@article{Zenzo1986,
  year = {1986},
  title = {A Note on the Gradient of a Multi-Image},
  pages = {116--125},
  journal = {Computer Vision, Graphics and Image Processing},
  volume = {33},
  author = {Zenzo, S. di}
}
@article{Ranson2001,
  year = {2001},
  title = {{ATP}-Bound States of {GroEL} Captured by Cryo-Electron Microscopy},
  pages = {869-879},
  journal = {Cell},
  volume = {107},
  author = {Ranson, N.A. and Farr, G.W. and Roseman, A.M. and Gowen, B. and Fenton, W.A. and Horwich, A.L. and Saibil, H.R.}
}
@article{Fukano2004,
  year = {2004},
  title = {Similar diffusibility of membrane proteins across the axon-soma and dendrite-soma boundaries revealed by a novel {FRAP} technique},
  pages = {12-18},
  journal = {Journal of Structural Biology},
  volume = {147},
  author = {Fukano, T. and Hama, H. and Miyawaki, A.}
}
@article{Pape1999,
  number = {5},
  month = {September/October},
  year = {1999},
  title = {Permeability prediction based on fractal pore-space geometry},
  pages = {1447--1460},
  journal = {Geophysics},
  volume = {64},
  author = {Pape, H. and Clauser, C. and Iffland, J.}
}
@article{Ritchie1984,
  number = {6},
  month = {October},
  year = {1984},
  title = {The Evolution of the Unix Time-sharing System},
  pages = {1577-1593},
  journal = {{AT\&T} Bell Laboratories Technical Journal},
  volume = {63},
  author = {Ritchie, D.M.}
}
@article{Streekstra2001,
  number = {3},
  year = {2001},
  title = {Scale dependent differential geometry for the measurement of center line and diameter in 3d curvilinear structures},
  pages = {177-189},
  journal = {International Journal of Computer Vision},
  volume = {42},
  author = {Streekstra, G.J. and Boomgaard, R. van den and Smeulders, A.W.M.}
}
@article{Jares-Erijman1996,
  number = {3},
  year = {1996},
  title = {Determination of DNA Helical Handedness by Fluorescence Resonance Energy Transfer},
  pages = {597-617},
  journal = {Journal of Molecular Biology},
  volume = {257},
  author = {Jares-Erijman, E.A. and Jovin, T.M.}
}
@article{Dologlou1991,
  number = {7},
  month = {July},
  year = {1991},
  title = {Physical Interpretation of Signal Reconstruction from Reduced Rank Matrices},
  pages = {1681--1682},
  journal = {IEEE Transactions on Signal Processing},
  volume = {39},
  author = {Dologlou, I. and Carayannis, G.}
}
@article{Dologlou1996,
  number = {2},
  year = {1996},
  title = {Projection-based Rank Reduction Algorithms for Multichannel Modeling and Image Compression},
  pages = {97--109},
  journal = {Signal Processing},
  volume = {48},
  author = {Dologlou, I. and Pesquet, J.-C. and Skowronski, J.}
}
@article{Sethi1987,
  year = {1987},
  title = {Finding trajectories of feature points in monocular image sequences},
  pages = {56--73},
  journal = {IEEE Transactions on Pattern Analysis and Machine Intelligence},
  volume = {9},
  author = {Sethi, I.K. and Jain, R. }
}
@phdthesis{Whitaker1993a,
  year = {1993},
  title = {Geometry-Limited Diffusion},
  school = {The University of North Carolina, Chapel Hill, North Carolina},
  author = {Whitaker, R.T.}
}
@article{Unser1995a,
  number = {3},
  year = {1995},
  title = {Enlargement or reduction of digital images with minimum loss of information},
  pages = {247-258},
  journal = {IEEE Transactions on Image Processing},
  volume = {4},
  author = {Unser, Michael and Aldroubi, Akram and Eden, Murray}
}
@article{Hubel1962,
  year = {1962},
  title = {Receptive fields, binocular interaction and functional architecture in the cat's visual cortex},
  pages = {106-154},
  journal = {The Journal of Physiology},
  volume = {160},
  author = {Hubel, D.H. and Wiesel, T.N.}
}
@article{Young1985,
  year = {1985},
  title = {Estimation of Sampling Errors},
  pages = {273--275},
  journal = {Cytometry},
  volume = {6},
  author = {Young, I.T.}
}
@phdthesis{Nordberg1994a,
  year = {1994},
  title = {Signal Representation and Processing using Operator Groups},
  address = {{Link\"oping}, Sweden},
  school = {{Link\"oping University}},
  author = {Nordberg, K.}
}
@article{Young1988,
  number = {4},
  year = {1988},
  title = {Sampling Density and Quantitative Microscopy},
  pages = {269--275},
  journal = {Analytic and Quantitative Cytology Histology},
  volume = {10},
  author = {Young, I.T.}
}
@article{Alvarez1992,
  number = {3},
  month = {June},
  year = {1992},
  title = {Image selective smoothing and edge detection by nonlinear diffusion {II}},
  pages = {845--866},
  journal = {SIAM J. Numer. Anal.},
  volume = {29},
  author = {Alvarez, L. and Lions, P. and Morel, J.}
}
@article{Deriche1990,
  number = {1},
  month = {January},
  year = {1990},
  title = {Fast Algorithms for Low-Level Vision},
  pages = {78--87},
  journal = {IEEE Transactions on Pattern Analysis and Machine Intelligence},
  volume = {12},
  author = {Deriche, R.}
}
@article{Sartor2001,
  number = {2},
  year = {2001},
  title = {Morphological Operations on Color Images},
  pages = {548-559},
  journal = {Journal of Electronic Imaging},
  volume = {10},
  author = {Sartor, L. J. and Weeks, A. R.}
}
@article{Rohr1997,
  year = {1997},
  title = {On 3D Differential Operators for Detecting Point Landmarks},
  pages = {219--233},
  journal = {Image and Vision Computing},
  volume = {15},
  author = {Rohr, K.}
}
@inproceedings{Luengo1999,
  year = {1999},
  title = {Resolution Enhancement of a Sequence of Undersampled Shifted Images},
  booktitle = {ASCI'99, Proc. 5th Annual Conference of the Advanced School for Computing and Imaging (Heijen, The Netherlands)},
  pages = {95--102},
  editor = {Boasson, M. and Kaandorp, J.A. and Tonino, J.F.M. and Vosselman, M.G.},
  author = {Luengo Hendriks, C.L. and Vliet, L.J. van},
  organization = {ASCI, Delft}
}
@article{Sandberg2003,
  year = {2003},
  title = {A fast reconstruction algorithm for electron microscope tomography},
  pages = {61-72},
  journal = {Journal of Structural Biology},
  volume = {144},
  author = {Sandberg, K. and Mastronarde, D.N. and Beylkin, G.}
}
@article{Grigorieff1998,
  year = {1998},
  title = {Three-dimensional Structure of Bovine {NADH}:Ubiquinone Oxidoreductase (Complex {I}) at {22\AA} in Ice},
  pages = {1033-1046},
  journal = {Journal of Molecular Biology},
  volume = {277},
  author = {Grigorieff, N.}
}
@inproceedings{Smith1984,
  month = {March},
  year = {1984},
  title = {A Procedure for Designing Exact Reconstruction Filter Banks for Tree Structured Sub-Band Coders},
  booktitle = {Proceedings of the IEEE International Conference on Acoustics, Speech, and Signal Processing},
  pages = {27.1.1--27.1.4},
  address = {San Diego, U.S.A.},
  author = {Smith, M.J. and Barnwell, T.P.}
}
@article{Santos2000,
  number = {17},
  year = {2000},
  title = {Model-based resolution - applying the theory in quantitative microscopy},
  pages = {2948-2958},
  journal = {Applied Optics},
  volume = {39},
  author = {Santos, A. and Young, I.T.}
}
@article{Vossepoel1988,
  year = {1988},
  title = {A note on distance transformations in digital images},
  pages = {88-97},
  journal = {Computer Vision, Graphics, and Image Processing},
  volume = {43},
  author = {Vossepoel, A.M.}
}
@article{Garboczi1995,
  number = {1},
  month = {July},
  year = {1995},
  title = {Geometrical percolation threshold of overlapping ellipsoids},
  journal = {Physical Review E},
  volume = {52},
  author = {Garboczi, E.J. and Snyder, K.A. and Douglas, J.F. and Thorpe, M.F.}
}
@article{Wu2000,
  number = {24},
  year = {2000},
  title = {Picometer Accuracy in Measuring Lattice Displacements Across Planar Faults by Interferometry in Coherent Electron Diffraction},
  pages = {5126-5129},
  journal = {Physical Review Letters},
  volume = {85},
  author = {Wu, L. and Zhu, Y. and Tafto, J.}
}
@article{Vossepoel1982,
  year = {1982},
  title = {Vector code probability and metrication error in the representation of straight lines of finite length},
  pages = {347-364},
  journal = {Computer Graphics and Image Processing},
  volume = {20},
  author = {Vossepoel, A.M. and Smeulders, A.W.M.}
}
@article{Lazar2003,
  year = {2003},
  title = {Materials science applications of {HREELS} in near edge structure analysis and low-energy loss spectroscopy},
  pages = {533-546},
  journal = {Ultramicroscopy},
  volume = {96},
  author = {Lazar, S. and Botton, G.A. and Wu, M.-Y. and Tichelaar, F.D. and Zandbergen, H.W.}
}
@article{Muller1995,
  year = {1995},
  title = {Delocalization in inelastic scattering},
  pages = {195-213},
  journal = {Ultramicroscopy},
  volume = {59},
  author = {Muller, D.A. and Silcox, J.}
}
@mastersthesis{Brusse1995,
  month = {August},
  year = {1995},
  title = {Quantitative structuuranalyse van aardlagen op basis van boorgatbeelden},
  note = {in {D}utch},
  school = {Delft University of Technology},
  author = {Brusse, H.}
}
@book{JAEHNE,
  year = {1997},
  title = {Practical Handbook on Image Processing for Scientific Applications},
  address = {New York},
  publisher = {CRC Press},
  author = {{J\"ahne}, B.}
}
@article{Lazar2004,
  year = {2004},
  title = {Investigation of hexagonal and cubic {GaN} by high-resolution electron energy-loss spectroscopy and density functional theory},
  pages = {249-257},
  journal = {Ultramicroscopy},
  volume = {98},
  author = {Lazar, S. and {H\'ebert}, C. and Zandbergen, H.W.}
}
@article{Huang1998,
  year = {1998},
  title = {The Empirical Mode Decomposition and the {Hilbert} Spectrum for Nonlinear and Non-stationary Time Series Analysis},
  pages = {903--995},
  journal = {Proceedings of the Royal Society of London A},
  volume = {454},
  author = {Huang, N.E. and Shen, Z. and Long, S.R. and Wu, M.C. and Shih, H.H. and Zheng, Q. and Yen, N.-C. and Tung, C.C. and Liu, H.H.}
}
@article{Huang1995,
  number = {1},
  month = {February},
  year = {1995},
  title = {Motion Estimation method using a 3D steerable filter},
  pages = {21--32},
  journal = {Image and Vision Computing},
  volume = {13},
  author = {Huang, C.-L. and Chen, Y.-T.}
}
@article{Peh2002,
  number = {10},
  year = {2002},
  title = {Synergizing spatial and temporal texture},
  pages = {1179--1191},
  journal = {IEEE Transactions on Image Processing},
  volume = {11},
  author = {Peh, C.-H. and Loong-Fah Cheong}
}
@article{Lee1983,
  year = {1983},
  title = {Digital Image Smoothing and the Sigma Filter},
  pages = {255--270},
  journal = {Computer Vision, Graphics, and Image Processing},
  volume = {24},
  author = {Lee, J.-S.}
}
@inproceedings{Buhr2003,
  month = {16-18 February},
  year = {2003},
  title = {Simple method for modulation transfer function determination of digital imaging detectors from edge images},
  booktitle = {Proceedings of SPIE},
  volume = {5030,3},
  address = {San Diego, California, USA},
  author = {Buhr, E. and {G\"unther}-Kohfahl, S. and Neitzel, U.}
}
@inproceedings{Lee1984,
  year = {1984},
  title = {{FCT} - a fast cosine transform},
  booktitle = {Proc. IEEE ICASSP},
  pages = {28A.3.1-28A.3.4},
  annote = {key_fft},
  author = {Lee, B.G.}
}
@article{Feret1931,
  year = {1931},
  title = {La Grosseur des Grains},
  journal = {Assoc. Intern. Essais Math. 2D, Zurich},
  author = {Feret, L.R.}
}
@article{Bunt2004,
  year = {2004},
  title = {Visualization of Molecular Activities Inside Living Cells with Fluorescent Labels},
  pages = {205-280},
  journal = {International Review of Cytology},
  volume = {237},
  author = {Bunt, G. and Wouters, F.S.}
}
@article{Vaidyanathan1987,
  number = {3},
  month = {July},
  year = {1987},
  title = {Quadrature Mirror Filter Banks, M-Band Extensions and Perfect-Reconstruction Techniques},
  pages = {4--20},
  journal = {IEEE Acoustics, Speech, and Signal Processing Magazine},
  volume = {4},
  author = {Vaidyanathan, P.P.}
}
@inproceedings{Knutsson2003,
  series = {LNCS 2749},
  month = {June 29 -July 2},
  year = {2003},
  title = {Loglets: Generalized Quadrature and Phase for Local Spatio-Temporal Structure Estimation},
  booktitle = {SCIA'03, Proceedings of the 13th Scandinavian Conference on Image Analysis ({G\"oteborg}, Sweden) },
  pages = {741-748},
  editor = {{Big\"un}, J. and Gustavsson, T.},
  address = {Berlin},
  publisher = {Springer-Verlag},
  author = {Knutsson, H. and Anderson, M.}
}
@article{Mokhtarian1992,
  number = {8},
  month = {August},
  year = {1992},
  title = {A Theory of Multiscale, Curvature-Based Shape Representation for Planar Curves},
  pages = {789--805},
  journal = {IEEE Transactions on Pattern Analysis and Machine Analysis},
  volume = {14},
  author = {Mokhtarian, F. and Machworth, A.K.}
}
@article{Lin1986,
  year = {1986},
  title = {Calibration of the operating parameters for an {HB5 STEM} instrument},
  pages = {31-42},
  journal = {Ultramicroscopy},
  volume = {19},
  author = {Lin, J.A. and Cowley, J.M.}
}
@article{Zack1977,
  number = {7},
  year = {1977},
  title = {Automatic Measurement of Sister Chromatid Exchange Frequency},
  pages = {741--753},
  journal = {Journal of Histochemistry and Cytochemistry},
  volume = {25},
  author = {Zack, G.W. and Rogers, W.E. and Latt, S.A.}
}
@article{Bewersdorf2006,
  year = {2006},
  title = {Comparison of {I$^5$M} and {4Pi}-microscopy},
  pages = {105-117},
  journal = {Journal of Microscopy},
  volume = {222},
  author = {Bewersdorf, J. and Schmidt, R. and Hell, S.W.}
}
@inproceedings{Leung1998,
  month = {June},
  year = {1998},
  title = {Contour Continuity in Region Based Image Segmentation},
  booktitle = {5th. Euro. Conf. Computer Vision, Freiburg, Germany },
  author = {Leung, T. and Malik, J.}
}
@article{Kempen2000,
  number = {3},
  year = {2000},
  title = {Background estimation in nonlinear image restoration},
  pages = {425-434},
  journal = {Journal of the Optical Society of America},
  volume = {17},
  author = {Kempen, G.M.P. van and Vliet, L.J. van}
}
@article{Nellist2004,
  year = {2004},
  title = {Direct Sub-Angstrom Imaging of a Crystal Lattice},
  pages = {1741},
  journal = {Science},
  volume = {305},
  author = {Nellist, P.D. and Chisholm, M.F. and Dellby, N. and Krivanek, O.L. and Murfitt, M.F. and Szilagyi, Z.S. and Lupini, A.R. and Borisevick, A. and Sides, W.H. jr. and Pennycook, S.J. }
}
@article{Liu1997,
  number = {8},
  year = {1997},
  title = {Dimension Estimation of Discrete-Time Fractional Brownian Motion with Application to Image Texture Classification},
  pages = {1176-1184},
  journal = {IEEE Transaction on Image Processing},
  volume = {6},
  author = {S-C. Liu and S. Chang}
}
@article{Keenan2004,
  number = {3},
  year = {2004},
  title = {Accounting for Poisson noise in the multivariate analysis of {ToF-SIMS} spectrum images},
  pages = {203-212},
  journal = {Surface and Interface Analysis},
  volume = {36},
  author = {Keenan, M.R. and Kotula, P.G.}
}
@book{Gelfand1964,
  year = {1964},
  title = {Generalized Functions. Volume 1, Properties and Operations},
  publisher = {Academic Press},
  author = {{Gel'fand}, I.M. and Shilov, G.E.}
}
@book{Gelfand1966,
  year = {1966},
  title = {Generalized Functions. Volume 5, Integral Geometry and Representation Theory},
  publisher = {Academic Press},
  author = {{Gel'fand}, I.M. and Graev, M.I. and Vilenkin, N.Ya.}
}
@techreport{Lindeberg1998b,
  number = {ISRN KTH/NA/P-98/14-SE},
  month = {August},
  year = {1998},
  title = {Principles for Automatic Scale Selection},
  address = {Stockholm, Sweden},
  institution = {Computational Vision and Active Perception Laboratory, Royal Institute of Technology},
  author = {Lindeberg, T.}
}
@article{Lindeberg1998a,
  number = {2},
  year = {1998},
  title = {Edge Detection and Ridge Detection with Automatic Scale Selection},
  pages = {117--154},
  journal = {International Journal of Computer Vision},
  volume = {30},
  author = {Lindeberg, T.}
}
@article{Koenderink1999,
  number = {2/3},
  year = {1999},
  title = {The Structure of Locally Orderless Images},
  pages = {159--168},
  journal = {International Journal of Computer Vision},
  volume = {31},
  author = {Koenderink, J.J. and Doorn, A.J. van}
}
@inproceedings{Kalitzin1997,
  series = {Lecture Notes in Computer Science},
  month = {July},
  year = {1997},
  title = {Invertible Orientation Bundles on 2D Scalar Images},
  booktitle = {Proceedings of the First International Conference on Scale-Space Theory in Computer Vision},
  pages = {77--88},
  publisher = {Springer-Verlag},
  author = {Kalitzin, S.N. and ter Haar Romeny, B.M. and Viergever, M.A.}
}
@article{Koenderink1992,
  number = {6},
  month = {June},
  year = {1992},
  title = {Generic Neighborhood Operators},
  pages = {597--605},
  journal = {IEEE Transactions on Pattern Analysis and Machine Intelligence},
  volume = {14},
  author = {Koenderink, J.J. and Doorn, A.J. van}
}
@article{Koenderink1990,
  year = {1990},
  title = {Receptive Field Families},
  pages = {291--297},
  journal = {Biological Cybernetics},
  volume = {63},
  author = {Koenderink, J.J. and Doorn, A.J. van}
}
@inproceedings{Haussecker1996,
  series = {Proceedings in Artificial Intelligence 3},
  month = {November 18--19},
  year = {1996},
  title = {A Tensor Approach for Local Structure Analysis in Multi-Dimensional Images},
  booktitle = {Proceedings 3D Image Analysis and Synthesis},
  pages = {171--178},
  editor = {Girod, B. and Niemann, H. and Seidel, H.-P.},
  author = {{Hau\ss ecker}, H. and {J\"ahne}, B.},
  organization = {{Universit\"at} Erlangen-{N\"urnberg}}
}
@article{Kalitzin1999,
  number = {2/3},
  year = {1999},
  title = {Invertible Apertured Orientation filters in Image Analysis},
  pages = {145--158},
  journal = {International Journal of Computer Vision},
  volume = {31},
  author = {Kalitzin, S.N. and Haar Romeny, B. ter and Viergever, M.A.}
}
@inproceedings{Haussecker1997,
  series = {Informatik Aktuell},
  month = {September 15-17},
  year = {1997},
  title = {A tensor approach for precise computation of dense displacement vector fields},
  booktitle = {Proc. Mustererkennung 1997 (Braunschweig, Germany)},
  pages = {199--208},
  editor = {Paulus, E. and Wahl, F.M.},
  publisher = {Springer},
  author = {{Hau\ss ecker}, H. and {J\"ahne}, B.}
}
@inproceedings{Vliet1993a,
  year = {1993},
  title = {Curvature and Bending Energy in Digitized 2D and 3D Images},
  booktitle = {8th Scandinavian Conference on Image Analysis, {Troms\o } Norway},
  pages = {1403--1410},
  author = {Vliet, L.J. van and Verbeek, P.W.}
}
@article{Cam1994,
  number = {3},
  year = {1994},
  title = {Conformational Analysis of a 139 Base-pair {DNA} Fragment Containing a Single-stranded Break and Its Interaction with {Human Poly(ADP-ribose)} Polymerase},
  pages = {1062-1071},
  journal = {Journal of Molecular Biology},
  volume = {235},
  author = {Cam, E. le and Fack, F. and Menissier-de Murcia, J. and Cognet, J.A.H. and Barbin, A. and Sarantoglou, V. and Revet, B. and Delain, E. and Murcia, G. de}
}
@article{Digman2005,
  year = {2005},
  title = {Fluctuation correlation spectroscopy with a laser-scanning microscope: exploiting the hidden time structure},
  journal = {Biophysical Journal - Biophysical Letters},
  author = {Digman, M.A. and Sengupta, P. and Wiseman, P.W. and Brown, C.M. and Howritz, A.R. and Grattown, E.}
}
@article{Bangham1996a,
  number = {5},
  year = {1996},
  title = {Scale-Space From Nonlinear Filters},
  pages = {520--528},
  journal = {IEEE Transactions on Pattern Analysis and Machine Intelligence},
  volume = {18},
  author = {Bangham, J.A. and Ling, P.D. and Harvey, R.}
}
@article{Talbot2000,
  month = {December},
  year = {2000},
  title = {Image Analysis of Insulation Mineral Fibres},
  pages = {251--268},
  journal = {Journal of Microscopy},
  volume = {200, Pt 3},
  author = {Talbot, H. and Lee, T. and Jeulin, D. and Hanton, D. and Hobbs, L.W.}
}
@article{Dietrich2004,
  number = {14},
  year = {2004},
  title = {Nanoarrays: A Method for Performing Enzymatic Assays},
  pages = {4112-4117},
  journal = {Analytical Chemistry},
  volume = {76},
  author = {Dietrich, H.R.C. and Knoll, J. and Doel, L.R. van den and Dedem, G.W.K. van and Daran-Lapujade, P.A.S. and Vliet, L.J. van and Moerman, R. and Pronk, J.R. and Young, I.T.}
}
@inproceedings{Laptev2003,
  series = {Lecture Notes on Computer Science },
  year = {2003},
  title = {Interest point detection and scale-selection in space-time},
  booktitle = {Proceedings of the fourth Int. Conf. on Scale Space},
  pages = {372-387},
  editor = {Griffin, L.D. and Lillholm, M.},
  volume = {2695},
  address = {Isle of Skye, United Kingdom},
  author = {Laptev, I. and Lindeberg, T.}
}
@article{Thomson1982,
  number = {9},
  month = {September},
  year = {1982},
  title = {Spectrum Estimation and Harmonic Analysis},
  pages = {1055--1096},
  journal = {Proceedings of the IEEE},
  volume = {70},
  author = {Thomson, D.J.}
}
@misc{Dorst1999a,
  year = {1999},
  title = {{Clifford} Algebra: a Practical Tool for Efficient Geometrical Representation},
  note = {Tutorial presentation},
  author = {Dorst, L.}
}
@phdthesis{Hansen1995,
  year = {1995},
  title = {Spatial Statistics for Network Structures in Processed Milk},
  address = {Copenhagen, Denmark},
  school = {The Royal Veterinary and Agricultural University Copenhagen},
  author = {Hansen, M.B.}
}
@article{Hansen1999,
  number = {1},
  year = {1999},
  title = {First Contact Distributions for Spatial Patterns: Regularity and Estimation},
  pages = {15--33},
  journal = {Advances in Applied Probability},
  volume = {31},
  author = {Hansen, M.B. and Baddeley, A.J. and Gill, R.D.}
}
@article{Stockman1977,
  number = {11},
  year = {1977},
  title = {Equivalence of {Hough} Curve Detection to Template Matching},
  pages = {820--822},
  journal = {Communications of the {ACM}},
  volume = {20},
  annote = {key_radon},
  author = {Stockman, G.C. and Agrawala, A.K.}
}
@article{Li1994a,
  number = {12},
  year = {1994},
  title = {Approximation of an Arbitrary Filter and its Recursive Implementation},
  pages = {1767--1774},
  journal = {Pattern Recognition},
  volume = {27},
  author = {Li, B.C. and Ma, S.D.}
}
@article{Endres1997,
  number = {1},
  month = {January/February},
  year = {1997},
  title = {Incorporating Pore Geometry and Fluid Pressure Communication into Modeling the Elastic Behavior of Porous Rocks},
  pages = {106--117},
  journal = {Geophysics},
  volume = {62},
  author = {Endres, A.L. and Knight, R.J.}
}
@article{Hansen1997,
  number = {3},
  year = {1997},
  title = {Understanding the {Hough} Transform: {Hough} Cell Support and its Utilization},
  pages = {205--218},
  journal = {Image and Vision Computing},
  volume = {15},
  author = {Hansen, K. and Andersen, J.D.}
}
@article{Maxwell1870,
  number = {269},
  year = {1870},
  title = {On Hills and Dales},
  pages = {421--427},
  journal = {The London, Edinburgh, and Dublin Philosophical Magazine and Journal of Science},
  volume = {40},
  author = {Maxwell, J.C.}
}
@article{Qian2000,
  year = {2000},
  title = {Single-Particle Tracking: Brownian Dynamics of Viscoelastic Materials},
  pages = {137-143},
  journal = {Biophysical Journal},
  volume = {79},
  author = {Qian, H. and Elson, E.L.}
}
@article{Jain2000,
  number = {1},
  year = {2000},
  title = {Statistical Pattern Recognition: A Review},
  pages = {4--37},
  journal = {IEEE Transactions on Pattern Analysis and Machine Intelligence},
  volume = {22},
  author = {Jain, A.K. and Duin, R.P.W. and Mao, J.}
}
@article{Watson1953,
  number = {4356},
  month = {April},
  year = {1953},
  title = {Molecular Structure of Nucleic Acids},
  pages = {737--738},
  journal = {Nature},
  volume = {171},
  author = {Watson, J.D. and Crick, F.H.C.}
}
@inproceedings{Knutsson1989kort,
  year = {1989},
  title = {Representing Local Structure Using Tensors },
  booktitle = {SCIA'89},
  pages = {244--251},
  author = {Knutsson, H.}
}
@article{Chadoeuf2000,
  month = {October},
  year = {2000},
  title = {Testing Local Dependence of Spatial Structures on Images},
  pages = {32--41},
  journal = {Journal of Microscopy},
  volume = {200, Pt 1},
  author = {Chadoeuf, J. and Brix, A. and Pierret, A. and Allard, D.}
}
@article{Brock2003,
  year = {2003},
  title = {Quantitative image analysis of cellular protein translocation induced by magnetic microspheres: Application to the EGF receptor},
  pages = {1-11},
  journal = {Cytometry Part A},
  volume = {52A},
  author = {Brock, R. and Jovin, T.M. }
}
@article{Costes2004,
  year = {2004},
  title = {Automatic and Quantitative Measurement of Protein-Protein Colocalization in Live Cells},
  pages = {3993-4003},
  journal = {Biophysical Journal},
  volume = {86},
  author = {Costes, S.V. and Daelemans, D. and Cho, E.H. and Dobbin, Z. and Pavlakis, G. and Lockett, S.}
}
@article{Zhou2003,
  year = {2003},
  title = {Cytoplasmic Ployhedrosis Virus Structure at 8 by Electron Cryomicroscopy: Structural Basis of Capsid Stability and {mRNA} Processing Regulation},
  pages = {651-663},
  journal = {Structure},
  volume = {1},
  author = {Zhou, Z.H. and Zhang, H. and Jakana, J. and Lu, X.-Y. and Zhang, J.-Q.}
}
@article{Zhou2000,
  year = {2000},
  title = {Seeing the Herpesvirus Capsid at 8.5},
  pages = {877-880},
  journal = {Science},
  volume = {288},
  author = {Zhou, Z.H. and Dougherty, M. Jakana, J. and He, J. and Rixon, F.J. and Chiu, W.}
}
@article{Zhou2001,
  number = {26},
  year = {2001},
  title = {The remarkable structural and functional organization of the eukaryotic pyruvate dehydrogenase complexes},
  pages = {14802-14807},
  journal = {Proceedings of the National Academy of Sciences of the United States of America},
  volume = {98},
  author = {Zhou, Z.H. and McCarthy, D.B. and O'Conor, C.M. and Reed, L.J. and Stoops, J.K.}
}
@article{Medintz2004,
  year = {2004},
  title = {Reversible Modulation of Quantum Dot Photoluminescence Using a Protein- Bound Photochromic Fluorescence Resonance Energy Transfer Acceptor},
  pages = {30-31},
  journal = {Journal of the American Chemical Society},
  volume = {126},
  author = {Medintz, I.L. and Trammell, S.A. and Mattoussi, H. and Mauro, J.M.}
}
@article{Cherny2005,
  number = {3},
  year = {2005},
  title = {Sequestering of p53 into {DNA}-protein filaments revealed by electron microscopy},
  pages = {261-271},
  journal = {Biophysical Chemistry},
  volume = {114},
  author = {Cherny, D.I. and Brzdov4, M. and Pale\v{c}ek, J. and Pale\v{c}ek, E. and Jovin, T.M.}
}
@article{Cherny2004,
  number = {4},
  year = {2004},
  title = {Double-stranded {DNA} stimulates the fibrillation of $\alpha$-synuclein in vitro and is associated with the mature fibrils: An electron microscopy study},
  pages = {929-938},
  journal = {Journal of Molecular Biology},
  volume = {344},
  author = {Cherny, D.I. and Hoyer, W. and Subramaniam, V. and Jovin, T.M.}
}
@article{Cherny2001,
  number = {2},
  year = {2001},
  title = {Electron and scanning force microscopy studies of alterations in supercoiled {DNA} tertiary structure},
  pages = {295-307},
  journal = {Journal of Molecular Biology},
  volume = {313},
  author = {Cherny, D.I. and Jovin, T.M.}
}
@article{Comer1999,
  number = {3},
  year = {1999},
  title = {Morphological Operations for Color Image Processing},
  pages = {279-189},
  journal = {Journal of Electronic Imaging},
  volume = {8},
  author = {Comer, M. L. and Delp, E. J.}
}
@inproceedings{Farnebaeck2000,
  month = {September},
  year = {2000},
  title = {Fast and {A}ccurate {M}otion {E}stimation using {O}rientation {T}ensors and {P}arametric {M}otion {M}odels},
  booktitle = {Proceedings of 15th International Conference on Pattern Recognition},
  pages = {135--139},
  volume = {1},
  address = {Barcelona, Spain},
  annote = {Also as Technical Report LiTH-ISY-R-2254},
  author = {G. {Farneb\"ack}},
  organization = {IAPR}
}
@inproceedings{Farnebaeck2003,
  series = {LNCS 2749},
  month = {June 29 -July 2},
  year = {2003},
  title = {Two-Frame Motion Estimation Based on Polynomial Expansion},
  booktitle = {SCIA'03, Proceedings of the 13th Scandinavian Conference on Image Analysis ({G\"oteborg}, Sweden) },
  pages = {363-370},
  editor = {{Big\"un}, J. and Gustavsson, T.},
  address = {Berlin},
  publisher = {Springer-Verlag},
  author = {{Farneb\"ack}, G.}
}
@article{Freitag2005,
  year = {2005},
  title = {Breaking the spherical and chromatic aberration barrier in transmission electron microscopy},
  pages = {209-214},
  journal = {Ultramicroscopy},
  volume = {102},
  author = {Freitag, B. and Kujawa, S. and Mul, P.M. and Ringnalda, J. and Tiemeijer, P.C.}
}
@article{Lidke2005,
  number = {9},
  year = {2005},
  title = {The role of photon statistics in fluorescence anisotropy imaging},
  pages = {1237-1245},
  journal = {IEEE Transactions on Image Processing},
  volume = {14},
  author = {Lidke, K.A. and Rieger, B. and Lidke, D.S. and Jovin, T.M.}
}
@article{Lidke2003,
  number = {5},
  year = {2003},
  title = {Imaging molecular interactions in cells by dynamic and static fluorescence anisotropy ({rFLIM} and {emFRET})},
  pages = {1020-1027},
  journal = {Biochemical Society Transactions},
  volume = {31},
  author = {Lidke, D.S. and Nagy, P. and Barisas, B.G. and Heintzmann, R. and Post, J.N. and Lidke, K.A. and Clayton, A.H.A. and Arndt-Jovin, D.J. and Jovin, T.M.}
}
@article{Lidke2004,
  number = {2},
  year = {2004},
  title = {Quantum dot ligands provide new insights into {erbB/HER} receptor-mediated signal transduction},
  pages = {198-203},
  journal = {Nature Biotechnology},
  volume = {22},
  author = {Lidke, D.S. and Nagy, P. and Heintzmann, R. and Arndt-Jovin, D.J. and Post, J.N. and Grecco, H. and Jares-Erijman, E.A. and Jovin, T.M.}
}
@article{Dubuc2001a,
  number = {1--2},
  year = {2001},
  title = {Complexity, Confusion, and Perceptual Grouping. Part {II}: Mapping Complexity},
  pages = {83--116},
  journal = {Journal of Mathematical Imaging and Vision},
  volume = {15},
  author = {Dubuc, B. and Zucker, S.W.}
}
@article{Larkin2001a,
  number = {8},
  month = {August},
  year = {2001},
  title = {Natural Demodulation of Two-Dimensional Fringe Patterns. {II}. Stationary Phase Analysis of the Spiral Phase Quadrature Transform},
  pages = {1871--1881},
  journal = {Journal of the Optical Society of America A},
  volume = {18},
  author = {Larkin, K.G.}
}
@article{Salden1998,
  year = {1998},
  title = {Differential Integral Geometry of Linear Scale-Space},
  pages = {5--27},
  journal = {Journal of Mathematical Imaging and Vision},
  volume = {9},
  author = {Salden, A.H. and ter Haar Romeny, B.M. and Viergever, M.A. }
}
@misc{Lehar1994,
  year = {1994},
  title = {Harmonic Resonance in Visual Perception Suggests a Novel Form of Neural Communication},
  note = {Rejected. Department of Cognitive and Neural Systems, Center for Adaptive Systems, Boston, U.S.A.},
  author = {Lehar, S.}
}
@techreport{Luengo2003d,
  month = {May},
  year = {2003},
  title = {Underestimation of the Radius in the Radon Transform for Circles and Spheres},
  note = {Technical Report PH-2003-02},
  institution = {Pattern Recognition Group, Delft University of Technology},
  author = {Luengo Hendriks, C.L. and Ginkel, M. van and Vliet, L.J. van}
}
@inproceedings{Luengo2003c,
  series = {Lecture Notes on Computer Science},
  year = {2003},
  title = {Discrete Morphology with Line Structuring Elements},
  booktitle = {Computer Analysis of Images and Patterns, Proceedings of the Tenth International Conference, {\footnotesize CAIP} 2003},
  pages = {722-729},
  editor = {Petkov, N. and Westenberg, M.A.},
  volume = {2756},
  address = {Berlin},
  publisher = {Springer-Verlag},
  author = {Luengo Hendriks, C.L. and Vliet, L.J. van}
}
@article{Stark1996,
  year = {1996},
  title = {Electron radiation damage to protein crystals of bacteriorhodopsin at different temperatures},
  pages = {75-70},
  journal = {Ultramicroscopy},
  volume = {63},
  author = {Stark, H. and Zemlin, F. and Boettcher, C.}
}
@inproceedings{Luengo2003b,
  series = {Lecture Notes on Computer Science},
  year = {2003},
  title = {The Generalized Radon Transform: Sampling and Memory Considerations},
  booktitle = {Computer Analysis of Images and Patterns, Proceedings of the Tenth International Conference, {\footnotesize CAIP} 2003},
  pages = {681-688},
  editor = {Petkov, N. and Westenberg, M.A.},
  volume = {2756},
  address = {Berlin},
  publisher = {Springer-Verlag},
  author = {Luengo Hendriks, C.L. and Ginkel, M. van and Verbeek, P.W. and Vliet, L.J. van}
}
@article{Cariolaro1998,
  number = {12},
  month = {December},
  year = {1998},
  title = {A Unified Framework for the Fractional {Fourier} Transform},
  pages = {3206--3219},
  journal = {IEEE Transactions on Signal Processing},
  volume = {46},
  author = {Cariolaro, G. and Erseghe, T. and Kraniauskas, P. and Laurenti, N.}
}
@article{Chen1977,
  number = {9},
  month = {September},
  year = {1977},
  title = {A Fast Computational Algorithm for the Discrete Cosine Transform},
  pages = {1004--1009},
  journal = {IEEE Transactions on Communications},
  volume = {25},
  annote = {key_fft},
  author = {Chen, W.-H. and Harrison Smith, C. and Fralick, S.C.}
}
@article{Beckers1990,
  year = {1990},
  title = {The Probability of a Random Straight Line in Two and Three Dimensions},
  pages = {233--240},
  journal = {Pattern Recognition Letters},
  volume = {11},
  author = {Beckers, A.L.D. and Smeulders, A.W.M.}
}
@article{Aert2002a,
  year = {2002},
  title = {Optimal experimental design of {STEM} measurement of atom column positions},
  pages = {273-289},
  journal = {Ultramicroscopy},
  volume = {90},
  author = {Aert, S. van and Dekker, A.J. den and Dyck, D. van and Bos, A. van den}
}
@article{Mallat1989,
  number = {7},
  month = {July},
  year = {1989},
  title = {A Theory for Multiresolution Signal Decomposition: The Wavelet Representation},
  pages = {674--693},
  journal = {IEEE Transaction on Pattern Analysis and Machine Intelligence},
  volume = {11},
  author = {Mallat, S.G.}
}
@book{Ripley1988,
  year = {1988},
  title = {Statistical Inference for Spatial Processes},
  publisher = {Cambridge University Press},
  author = {Ripley, B.D.}
}
@book{Landau1959,
  edition = {first},
  year = {1959},
  title = {Theory of Elasticity},
  publisher = {Pergamon Press},
  author = {Landau, L.D. and Lifshitz, E.M.}
}
@article{Oudejans2000,
  year = {2000},
  title = {Errors in judging 'offside' in football},
  pages = {33},
  journal = {Nature},
  volume = {404},
  author = {Oudejans, R.R.D. and Verheijen, R. and Bakker, F.C. and Gerrits, J.C. and Steinbrcker, M. and Beek, P.J.}
}
@article{Kubinova2001,
  number = {6},
  year = {2001},
  title = {Confocal Microscopy and Stereology: Estimating Volume, Number, Surface Area and Length by Virtual Test Probes Applied to Three-Dimensional Images},
  pages = {425--435},
  journal = {Microscopy Research and Technique},
  volume = {53},
  author = {Kubinova, L. and Janacek, J.}
}
@article{Duynhoven2003,
  number = {4},
  year = {2003},
  title = {Quantitative Assessment of Gas Cell Development during the Proofing of Dough by Magnetic Resonance Imaging and Image Analysis},
  pages = {360-369},
  journal = {Cereal Chemistry},
  volume = {80},
  author = {Duynhoven, P.M. van and Kempen, G.M.P. van and Sluis, R. van and Rieger, B. and Weegels, P. and Vliet, L.J. van and Nicolay, K.}
}
@misc{DMD,
  title = {www.dlp.com},
  author = {Texas Instruments Technology}
}
@article{Merlin1975,
  month = {January},
  year = {1975},
  title = {A Parallel Mechanism for Detecting Curves in Pictures},
  pages = {96--98},
  journal = {IEEE Transactions on Computers},
  volume = {24},
  author = {Merlin, P.M. and Farber, D.J.}
}
@inproceedings{Meyer1999,
  series = {Lecture Notes on Computer Science},
  month = {September},
  year = {1999},
  title = {Multiscale Morphological Segmentations Based on Watershed, Flooding, and Eikonal PDE},
  booktitle = {Scale-Space Theories in Computer Vision (Second International Conference, Scale-Space'99, Corfu, Greece)},
  pages = {351--362},
  editor = {Nielsen, Mads and Johansen, Peter and Olsen, Ole F. and Weickert, Joachim},
  volume = {1682},
  address = {Berlin Heidelberg},
  publisher = {Springer-Verlag},
  author = {Meyer, Fernand and Maragos, Petros}
}
@article{Borgefors2003,
  number = {1},
  year = {2003},
  title = {Weighted Digital Distance Transforms in Four Dimensions},
  pages = {161--176},
  journal = {Discrete Applied Mathematics},
  volume = {125},
  author = {Borgefors, G.}
}
@incollection{Proesmans1994,
  year = {1994},
  title = {Coupled geometry-driven diffusion equations for low-level vision},
  booktitle = {Geometry-driven diffusion in computer vision},
  pages = {191--228},
  editor = {Ter Haar Romeny B.M.},
  chapter = {9},
  publisher = {Kluwer Academic Publishers},
  author = {Proesmans, M. and Pauwels, P. and van Gool, L.}
}
@article{Smith1997,
  number = {1},
  year = {1997},
  title = {SUSAN - A New Approach to Low Level Image Processing},
  pages = {45--78},
  journal = {International Journal of Computer Vision},
  volume = {23},
  author = {Smith, S.M., Brady J.M.}
}
@article{Catte1992,
  number = {1},
  month = {February},
  year = {1992},
  title = {Image selective smoothing and edge detection by nonlinear diffusion},
  pages = {182--193},
  journal = {SIAM J. Numer. Anal.},
  volume = {29},
  author = {{Catt\'e}, F. and Lions, P. and Morel, J. and Coll, T.}
}
@article{Radon1917,
  year = {1917},
  title = {{\"Uber} die {B}estimmung von {F}unktionen durch ihre {I}ntegralwerte {l\"angs} gewisser {M}annigfaltigkeiten},
  pages = {262--277},
  journal = {Berichte {S\"achsische} Akademie der Wissenschaften, Leipzig, Mathematisch-Physikalische Klasse},
  volume = {69},
  author = {Radon, J.}
}
@techreport{MuntheKaas1995,
  year = {1995},
  title = {Coordinate Free Numerics. Part 1: How to Avoid Index Wrestling in Tensor Computations},
  institution = {Department of Informatics, University of Bergen, Norway},
  author = {Munthe-Kaas, H. and Haveraaen, M.}
}
@inproceedings{Ginkel1999kort,
  year = {1999},
  title = {Curvature Estimation from Orientation Fields },
  booktitle = {SCIA'99 },
  pages = {545--551 },
  editor = {Ersboll, B.K. and Johansen, P. },
  publisher = {Pattern Recognition Society of Denmark},
  author = {Ginkel, M. van and Weijer, J. van de and Verbeek, P.W. and Vliet, L.J. van }
}
@article{Squire1999,
  year = {1999},
  title = {Three Dimensional Image Restoration in Fluorescence Lifetime Imaging Microscopy},
  pages = {36--49},
  journal = {Journal of Microscopy},
  volume = {193},
  author = {Squire, A. and Bastiaens, P.I.H.}
}
@article{Larkin2005,
  number = {20},
  year = {2005},
  title = {Uniform estimation of orientation using local and nonlocal {2-D} energy operators},
  pages = {8097-8121},
  journal = {Optics Express},
  volume = {13},
  author = {Larkin, K.G.}
}
@article{Babaud1986,
  number = {1},
  month = {January},
  year = {1986},
  title = {Uniqueness of the {G}aussian Kernel for Scale-Space Filtering},
  pages = {26--33},
  journal = {IEEE Transactions on Pattern Recognition and Machine Intelligence},
  volume = {8},
  author = {Babaud, J. and Witkin, A.P. and Baudin, M. and Duda, R.O.}
}
@article{Grossman1984,
  number = {4},
  month = {July},
  year = {1984},
  title = {Decomposition of {Hardy} Functions into Square Integrable Wavelets of Constant Shape},
  pages = {723--736},
  journal = {{SIAM} Journal on Mathematical Analysis},
  volume = {15},
  author = {Grossman, A. and Morlet, J.}
}
@article{OlivoMarin2002,
  number = {9},
  month = {September},
  year = {2002},
  title = {Extraction of Spots in Biological Images using Multiscale Products},
  pages = {1989--1996},
  journal = {Pattern Recognition},
  volume = {35},
  author = {Olivo-Marin, J.-C.}
}
@article{Larkin2001,
  number = {8},
  month = {August},
  year = {2001},
  title = {Natural Demodulation of Two-Dimensional Fringe Patterns. {I}. General Background of the Spiral Phase Quadrature Transform},
  pages = {1862--1870},
  journal = {Journal of the Optical Society of America A},
  volume = {18},
  author = {Larkin, K.G. and Bone, D.J. and Oldfield, M.A.}
}
@article{Nakajima2003,
  year = {2003},
  title = {Physics-based flow estimation of fluids},
  pages = {1203-1212},
  journal = {Pattern Recognition},
  volume = {36},
  author = {Nakajima, Y. and Inomata, H. and Nogawa, H. and Sato, Y. and Tamura, S. and Okazaki, K. and Torii, S.}
}
@article{Garini2005,
  number = {1},
  year = {2005},
  title = {From micro to nano: recent advances in high-resolution microscopy},
  pages = {3-12},
  journal = {Current Opinion in Biotechnology},
  volume = {16},
  author = {Garini, Y. and Vermolen, B.J. and Young, I.T.}
}
@article{Duhamel1990,
  year = {1990},
  title = {Fast {F}ourier transforms: a tutorial review and a state of the art},
  pages = {259--299},
  journal = {Signal Processing},
  volume = {19},
  annote = {key_fft},
  author = {Duhamel. P. and Vetterli, M.}
}
@article{Martinez2004,
  year = {2004},
  title = {Design of {Wien} filters with high resolution},
  pages = {105-114},
  journal = {Ultramicroscopy},
  volume = {100},
  author = {Martinez, G. and Tsuno, K.}
}
@inproceedings{Tanaka1986,
  year = {1986},
  title = {A Rotation Method for Raster Image Using Skew Transformation},
  booktitle = {CVPR'86, IEEE Conference on Computer Vision and Pattern Recognition},
  pages = {272--277},
  author = {Tanaka, A. and Kameyama, M. and Kazama, S. and Watanabe, O.}
}
@article{Nyquist1928,
  year = {1928},
  title = {Certain Topics in Telegraph Transmission Theory},
  pages = {617--644},
  note = {[reprinted in: Proceedings of the IEEE, vol. 90, no. 2, pp. 280-305, February 2002]},
  journal = {Transactions of the AIEE},
  author = {Nyquist, H.}
}
@article{Thurnhofer1996,
  number = {6},
  month = {June},
  year = {1996},
  title = {A General Framework for Quadratic {V}olterra Filter for Edge Enhancement},
  pages = {950--963},
  journal = {IEEE Transactions on Image Processing},
  volume = {5},
  author = {Thurnhofer, S. and Mitra, S.K.}
}
@article{Kybic2002,
  number = {8},
  year = {2002},
  title = {Generalized sampling: A variational approach - Part I: Theory},
  pages = {1965--1976},
  journal = {IEEE Transactions on Signal Processing},
  volume = {50},
  author = {Kybic, J. and Blu, T. and Unser, M.}
}
@article{Maybank1986,
  year = {1986},
  title = {Optical Flow and the Taylor Expansion},
  pages = {243-246},
  journal = {Pattern Recognition Letters},
  volume = {4},
  author = {Maybank, S.J.}
}
@inproceedings{Breen1996,
  year = {1996},
  title = {An Attribute-Based Approach to Mathematical Morphology},
  booktitle = {Mathematical Morphology and its Applications to Image and Signal Processing},
  pages = {41-48},
  editor = {Maragos, P. and Schafer, R. W. and Akmal Butt, M.},
  address = {Boston},
  publisher = {Kluwer Academic Publishers},
  author = {Breen, E. J. and Jones, R.}
}
@inproceedings{Ronse1986,
  year = {1986},
  title = {Erosion of Narrow Image Features by Combination of Local Low Rank and Max Filters},
  booktitle = {Proceedings of the Second IEE International Conference on Image Processing and its Applications},
  pages = {77-81},
  address = {London},
  author = {Ronse, C.}
}
@article{Khaneja1998,
  number = {11},
  year = {1998},
  title = {Dynamic Programming Generation of Curves on Brain Surfaces},
  pages = {1260--1265},
  journal = {IEEE Transaction on Pattern Analysis and Machine Intelligence},
  volume = {20},
  author = {Khaneja, N. and Miller, M. I. and Grenander, U.}
}
@article{Nogales2001,
  year = {2--1},
  title = {Molecular Machines: Putting the Pieces Together},
  pages = {F1-F10},
  journal = {Journal of Cell Biology},
  volume = {152},
  author = {Nogales, E. and Grigorieff, N.}
}
@article{Campbell2001,
  number = {6},
  year = {2001},
  title = {Spontaneous Assembly of Magnetic {LEGO} Bricks},
  pages = {321--323},
  journal = {The Chemical Educator},
  volume = {6},
  author = {Campbell, D.J. and Freidinger, E.R. and Querns, M.K.}
}
@article{Pike1995,
  number = {3},
  year = {1995},
  title = {Plan 9 from {Bell} Labs},
  pages = {221--254},
  journal = {Computing Systems},
  volume = {8},
  author = {Pike, R. and Presotto, D. and Dorward, S. and Flandrena, B. and Thompson, K. and Trickey, H. and Winterbottom, P.}
}
@article{Jiang2003,
  year = {2003},
  title = {Applications of a bilateral denoising filter in biological electron microscopy},
  pages = {114-122},
  journal = {Journal of Structural Biology},
  volume = {144},
  author = {Jiang, W. and Baker, M.L. and Wu, Q. and Bajaj, C. and Chiu, W.}
}
@misc{Koenderink1988,
  year = {1988},
  title = {Image Structure},
  howpublished = {NATO ASI Series, vol. F39, Mathematics and Computer Science in Medical Imaging, Springer-Verlag},
  author = {Koenderink, J.J.}
}
@article{Back1997,
  number = {4},
  month = {Aug},
  year = {1997},
  title = {A first application of independent component analysis to extracting structure from stock returns},
  pages = {473-484},
  journal = {International Journal of Neural Systems},
  volume = {8},
  author = {Back, A. D. and Weigend, A. S.}
}
@article{Koenderink1984,
  year = {1984},
  title = {The Structure of Images},
  pages = {363--370},
  journal = {Biological Cybernetics},
  volume = {50},
  author = {Koenderink, J.J.}
}
@article{Koenderink1987,
  year = {1987},
  title = {Representation of Local Geometry in the Visual System},
  pages = {367--375},
  journal = {Biological Cybernetics},
  volume = {55},
  author = {Koenderink, J.J. and Doorn, A.J. van}
}
@article{Jarvis1976,
  month = {August},
  year = {1976},
  title = {A New Technique for Displaying Continuous Tone Images on a Bilevel Display},
  pages = {891--898},
  journal = {IEEE Transactions on Communications},
  author = {Jarvis, J.F. and Roberts, C.S.}
}
@article{Saito1994,
  number = {11},
  year = {1994},
  title = {New algorithms for euclidean distance transformation of an n-dimensional digitized picture with applications},
  pages = {1551-1565},
  journal = {Pattern Recognition},
  volume = {27},
  author = {Saito,T. and Toriwaki, J.}
}
@article{Bonneau2005,
  number = {9},
  year = {2005},
  title = {Single Quantum Dot Tracking Based on Perceptual Grouping Using Minimal Paths in a Spatiotemporal Volume},
  pages = {1384-1395},
  journal = {IEEE Transactions on Image Processing},
  volume = {14},
  author = {Bonneau, S. and Dahan, M. and Cohnen, L.D.}
}
@inproceedings{Boomgaard2002a,
  month = {1 June},
  year = {2002},
  title = {Robust Estimation of Orientation for Texture Analysis},
  booktitle = {Texture 2002, The 2nd international workshop on texture analysis and synthesis},
  pages = {135-138},
  address = {Copenhagen, Denmark},
  author = {Boomgaard, R. van den and Weijer, J. van de}
}
@article{Koenderink1988a,
  number = {7},
  month = {July},
  year = {1988},
  title = {Two-dimensional Curvature Operators},
  pages = {1136--1141},
  journal = {Journal of the Optical Society of America A},
  volume = {5},
  author = {Koenderink, J.J. and Richards, W.}
}
@article{Neher2004,
  year = {2004},
  title = {Applying Spectral Fingerprinting to the Analysis of {FRET} Images},
  pages = {185-195},
  journal = {Microscopy Research and Technique},
  volume = {64},
  author = {Neher, R.A. and Neher, E.}
}
@article{Wouters2001,
  year = {2001},
  title = {Imaging biochemistry inside cells},
  pages = {203-211},
  journal = {Trends in Cell Biology},
  volume = {11},
  author = {Wouters, F.S. and Verveer, P.J. and Bastiaens, P.I.H.}
}
@article{Einstein1905,
  year = {1905},
  title = {{\"Uber} die von der molekularkinetischen {T}heorie der {W\"a}rme geforderte {B}ewegung von in ruhenden {Fl\"u}ssigkeiten suspendierten {T}eilchen},
  pages = {549--560},
  journal = {Annalen der Physik},
  volume = {17},
  author = {Einstein, A.}
}
@article{Wimberly2000,
  year = {2005},
  title = {Structure of the {30S} ribosomal subunit},
  pages = {327-339},
  journal = {Nature},
  volume = {407},
  author = {Wimberly, B.T. and Brodersen, D.E. and Clemons, W.M. Jr. and Morgan-Warren, R.J. and Carter, A.P. and Vonrhein, C. and Hartsch, T. and Ramakrishnan, V.}
}
@article{Weickert1998,
  number = {3},
  year = {1998},
  title = {Efficient and reliable schemes for nonlinear diffusion filtering},
  pages = {398--410},
  journal = {IEEE Transactions on Image Processing},
  volume = {7},
  author = {Weickert, J. and ter Haar Romeny, B.M. and Viergever, M.A. }
}
@article{Lindeberg1990,
  number = {3},
  year = {1990},
  title = {Scale-Space for Discrete Signals},
  pages = {234--254},
  journal = {IEEE Transactions on Pattern Analysis and Machine Intelligence},
  volume = {12},
  author = {Lindeberg, T.}
}
@article{Nason2000,
  year = {2000},
  title = {Wavelet Processes and Adaptive Estimation of the Evolutionary Wavelet Spectrum},
  pages = {271--292},
  journal = {Journal of the Royal Statistical Society B},
  volume = {62},
  author = {Nason, G.P. and Sachs, R. von and Kroisandt, G.}
}
@article{Gibbons1975,
  number = {11},
  year = {1975},
  title = {Inelastic electron scattering spectrometer},
  pages = {1546-1554},
  journal = {Review of Scientific Intstruments},
  volume = {46},
  author = {Gibbons, P.C. and Ritsko, J.J. and Schnatterly, S.E.}
}
@article{Bouma2005,
  number = {9},
  year = {2005},
  title = {Correction for the Dislocation of Curved Surfaces Caused by the {PSF} in {2D} and {3D} {CT} Images},
  pages = {1501-1507},
  journal = {Ultramicroscopy},
  volume = {27},
  author = {Bouma, H. and Vilanova, A. and Vliet, L.J. van and Gerritsen, F.A.}
}
@book{Lindeberg1994,
  year = {1994},
  title = {Scale-Space Theory in Computer Vision},
  publisher = {Kluwer},
  author = {Lindeberg, T.}
}
@article{Ober2003,
  number = {10},
  year = {2003},
  title = {Calculations of the Fisher information matrix for multidimensional data sets},
  pages = {2679-2691},
  journal = {IEEE Transactions on Signal Processing},
  volume = {51},
  author = {Ober, R.J. and Lin, Z. and Zou, Q.}
}
@article{Mattfeldt2000,
  month = {May},
  year = {2000},
  title = {Classification of Spatial Textures in Benign and Cancerous Glandular Tissues by Stereology and Stochastic Geometry using Artificial Neural Networks},
  pages = {143--158},
  journal = {Journal of Microscopy},
  volume = {198, Pt 2},
  author = {Mattfeldt, T. and Gottfried, H.-W. and Schmidt, V. and Kestler, H.A.}
}
@article{Ober2004,
  number = {2},
  year = {2004},
  title = {Localization Accuracy in Single-Molecule Microscopy},
  pages = {1185-1200},
  journal = {Biophysical Journal},
  volume = {86},
  author = {Ober, R.J. and Ram, S. and Ward, S.E.}
}
@article{Hummel1987,
  year = {1987},
  title = {Deblurring Gaussian Blur},
  pages = {66--80},
  journal = {Computer Vision, Graphics, and Image Processing},
  volume = {38},
  author = {Hummel, R.A. and Kimia, B. and Zucker, S.W.}
}
@article{Hummel1989,
  number = {12},
  month = {December},
  year = {1989},
  title = {Reconstructions from Zero Crossings in Scale Space},
  pages = {2111--2130},
  journal = {IEEE Transactions on Acoustics, Speech and Signal Processing},
  volume = {37},
  author = {Hummel, R. and Moniot, R.}
}
@article{Pons1999,
  year = {1999},
  title = {Particle morphology: from cisulatisation to measurement},
  pages = {44--57},
  journal = {Powder Technology},
  volume = {103},
  author = {Pons, M.N. and Vivier, H. and Belaroui, K. and Bernard-Michel, B. and Cordier, F. and Oulahana, D. and Dodds, J.A. }
}
@inproceedings{Holmes1999,
  year = {1999},
  title = {Developing a Measure of Similarity between Pixel Signatures},
  booktitle = {10th British Machine Vision Conference},
  pages = {614--623},
  editor = {Pridmore, T. and Elliman, D.},
  volume = {2},
  author = {Holmes, A. and Taylor, C.}
}
@article{Keys1981,
  number = {6},
  year = {1981},
  title = {Cubic Convolution Interpolation for Digital Image Processing},
  pages = {1153-1160},
  journal = {IEEE Transactions on Acoustics, Speech, and Signal Processing},
  volume = {29},
  author = {Keys, R. G.}
}
@inproceedings{Hummel1986,
  year = {1986},
  title = {Representation Based on Zero-crossings in Scale-Space},
  booktitle = {IEEE Proceedings of the International Conference on Computer Vision and Pattern Recognition},
  pages = {204--209},
  author = {Hummel, R.A.}
}
@article{Nielsen1997,
  number = {4},
  year = {1997},
  title = {Regularization, scale-space and edge-detection filters},
  pages = {291--307},
  journal = {Journal of Mathematical Imaging and Vision},
  volume = {7},
  author = {Nielsen, N. and Florack, L. and Deriche, R.}
}
@inbook{Adam1968,
  year = {1968},
  title = {Structural Chemistry and Molecular Biology},
  pages = {198-215},
  editor = {Rich, A. and Davidson, N. },
  address = {San Francisco, USA},
  chapter = {Reduction of Dimensionality in Biological Diffusion Processes},
  publisher = {Freeman},
  author = {Adam, G. and {Delbr\"uck}, M.}
}
@article{Frontali1979,
  number = {6},
  year = {1979},
  title = {An absolute method for the determination of the persistence length of native {DNA} from electron micrographs},
  pages = {1353-1373},
  journal = {Biopolymers},
  volume = {18},
  author = {Frontali, C. and Dore, E. and Ferrauto, A. and Gratton, E. and Bettini, A. and Pozzan, M.R. and Valdevit, E.}
}
@inbook{Thomas1963,
  year = {1963},
  title = {Applications of Digital Computers},
  chapter = {Using Computers to Solve Problems in Physics},
  publisher = {Ginn and Co., Boston},
  author = {Thomas, L.H.}
}
@article{Yang2005,
  year = {2005},
  title = {Unified {3-D} structure and projection orientation refinement using {quasi-Newton} algorithm},
  pages = {53-64},
  journal = {Journal of Structural Biology},
  volume = {149},
  author = {Yang, C. and Ng, E.G. and Penczek, P.A.}
}
@article{Almeida1997,
  year = {1997},
  title = {Anisotropic Textures with Arbitrary Orientation},
  pages = {241--251},
  journal = {Journal of Mathematical Imaging and Vision},
  volume = {7},
  author = {Almeida, M.P.}
}
@mastersthesis{Okker2003,
  month = {January},
  year = {2003},
  title = {Contour continuation using space variant mathematical morphology},
  school = {Delft University of Technology},
  author = {Okker, B.H.}
}
@article{Kempen2000a,
  number = {4},
  year = {2000},
  title = {Mean and Variance of Ratio Estimators Used in Fluorescence Ratio Imaging},
  pages = {300-305},
  journal = {Cytometry},
  volume = {39},
  author = {Kempen, G.M.P. van and Vliet, L.J. van}
}
@article{Almeida1994,
  number = {11},
  month = {November},
  year = {1994},
  title = {The Fractional {F}ourier Transform and Time-Frequency Representations},
  pages = {3084--3091},
  journal = {IEEE Transactions on Signal Processing},
  volume = {42},
  author = {Almeida, L.B.}
}
@article{Malandain1998,
  number = {5},
  year = {1998},
  title = {Euclidean Skeletons},
  pages = {317--327},
  journal = {Image and Vision Computing},
  volume = {16},
  author = {Malandain, G. and {Fern\'andez-Vidal}, S.}
}
@article{Hekrdla1986,
  number = {4},
  month = {August},
  year = {1986},
  title = {Index Transforms of Multidimensional Cyclic Convolutions and Discrete {Fourier} Transforms},
  pages = {996--996},
  journal = {IEEE Transactions on Acoustics, Speech, and Signal Processing},
  volume = {34},
  annote = {key_fft},
  author = {Hekrdla, J.}
}
@article{Kues2001,
  number = {6},
  year = {2001},
  title = {Visualization and Tracking of Single Protein Molecules in the Cell Nucleus},
  pages = {2954-2967},
  journal = {Biophysical Journal},
  volume = {80},
  author = {Kues, T. and Peters, R. and Kubitscheck, U.}
}
@article{Heilemann2002,
  number = {14},
  year = {2002},
  title = {High-resolution colocalization of single dye molecules by fluorescence lifetime imaging microscopy},
  pages = {3511-3517},
  journal = {Analytical Chemistry},
  volume = {74},
  author = {Heilemann, M. and Herten, D.P. and Heintzmann, R. and Cremer, C. and {M\"uller}, C. and Tinnefeld, P. and Weston, K.D. and Wolfrum, J. and Sauer, M.}
}
@article{Kehtarnavaz1988,
  number = {5},
  month = {September},
  year = {1988},
  title = {A 3-D contour segmentation scheme based on curvature and torsion},
  pages = {707--713},
  journal = {IEEE Transactions on Pattern Analysis and Machine Intelligence},
  volume = {10},
  author = {Kehtarnavaz, N. and Figueiredo, R.J.P. de}
}
@article{Gil1993,
  number = {5},
  month = {May},
  year = {1993},
  title = {Computing {2-D} Min, Median, and Max Filters},
  pages = {504--507},
  journal = {IEEE Transactions on Pattern Analysis and Machine Intelligence},
  volume = {15},
  author = {Gil, J. and Werman, M.}
}
@article{Engel1981,
  number = {1},
  year = {1981},
  title = {Shapes, domain organizations and flexibility of laminin and fibronectin, two multifunctional proteins of the extracellular matrix},
  pages = {97-120},
  journal = {Journal of Molecular Biology},
  volume = {150},
  author = {Engel, J. and Odermatt, E. and Engel, A. and Madri, J.A. and Furthmayr, H. and Timpl, H.R.}
}
@article{Ruiz2001,
  year = {2001},
  title = {The first three-dimensional structure of phosphofructokinase from Saccharomyces cerevisiae determined by electron microscopy of single particles},
  pages = {167-180},
  journal = {Journal of Structural Biology},
  volume = {136},
  author = {Ruiz, T. and {Koppenschl\"ager}, G. and Radermacher, M.}
}
@techreport{Nordberg1992a,
  year = {1992},
  title = {Signal Representation and Signal Processing using Operators},
  note = {LiTH-ISY-I-1387},
  address = {{Link\"oping}, Sweden},
  institution = {{Link\"oping} University},
  author = {Nordberg, K.}
}
@article{Faydi2001,
  year = {2001},
  title = {Experimental Study and Modeling of the Ice Crystal Morphology of Model Standard Ice Cream. Part {I}: Direct Characterization Method and Experimental Data},
  pages = {283--291},
  journal = {Journal of Food Engineering},
  volume = {48},
  author = {Faydi, E. and Andrieu, J. and Laurent, P.}
}
@article{Griffin1997,
  number = {5},
  year = {1997},
  title = {Scale-Imprecision Space},
  pages = {369--398},
  journal = {Image and Vision Computing},
  volume = {15},
  author = {Griffin, L.D.}
}
@phdthesis{Cavallo2002,
  month = {June},
  year = {2002},
  title = {Four Dimensional Particle Tracking in Biological Dynamic Processes},
  address = {Heidelberg, Germany},
  school = {Ruprechts-Karls-{Universit\"at}},
  author = {Cavallo, A.}
}
@phdthesis{Leeuw1997,
  year = {1997},
  title = {Presentation and Exploration of Flow Data},
  address = {The Netherlands},
  school = {Delft University of Technology},
  author = {Leeuw, W. de}
}
@article{Unser1993a,
  number = {2},
  month = {February},
  year = {1993},
  title = {{B}-Spline Signal Processing: Part {II} - Efficient Design and Applications},
  pages = {834--848},
  journal = {IEEE Transactions on Signal Processing},
  volume = {41},
  author = {Unser, Michael and Aldroubi, Akram and Eden, Murray}
}
@article{Deschamps2001,
  number = {4},
  year = {2001},
  title = {Fast extraction of minimal paths in 3D images and applications to virtual endoscopy},
  pages = {281-299},
  journal = {Medical Image Analysis},
  volume = {5},
  author = {Deschamps, T. and Cohen, L.D.}
}
@article{Torok1998,
  number = {4-6},
  year = {1998},
  title = {On the general properties of polarised light conventional and confocal microscopes},
  pages = {300-315},
  journal = {Optics Communications},
  volume = {148},
  author = {{T\"or\"ok}, P. and Higdon, P.D. and Wilson, T.}
}
@article{Rose2004,
  year = {2004},
  title = {Outline of an ultracorrector compensating for all primary chromatic and geometrical aberrations of charged-particle lenses},
  pages = {12-27},
  journal = {Nuclear Instruments and Methods in Physics Research A},
  volume = {519},
  author = {Rose, H.}
}
@article{Jain1979,
  number = {4},
  month = {October},
  year = {1979},
  title = {A Sinusoidal Family of Unitary Transforms},
  pages = {356--365},
  journal = {IEEE Transactions on Pattern Analysis and Machine Intelligence},
  volume = {1},
  annote = {key_fft},
  author = {Jain, A.K.}
}
@article{Weickert1999a,
  number = {3},
  year = {1999},
  title = {Linear scale-space has first been proposed in {Japan}},
  pages = {237--252},
  journal = {Journal of Mathematical Imaging and Vision},
  volume = {10},
  author = {Weickert, J. and Ishikawa, S. and Imiya, A.}
}
@article{Doel1998,
  number = {3},
  year = {1998},
  title = {Quantitative evaluation of light microscopes based on image processing techniques},
  pages = {138-149},
  journal = {Bioimaging},
  volume = {6},
  author = {Doel, L.R. van den and Vliet, L.J. van}
}
@article{Mallat1992,
  number = {7},
  month = {June},
  year = {1992},
  title = {Characterization of Signals from Multiscale Edges},
  pages = {710--732},
  journal = {IEEE Transactions on Pattern Analysis and Machine Intelligence},
  volume = {14},
  author = {Mallat, S.G. and Zhong, S.}
}
@inproceedings{Bulow1997,
  month = {June 9-11},
  year = {1997},
  title = {Algebraically Extended Representations of Multi-Dimensional Signals},
  booktitle = {Proceedings of the 10th Scandinavian Conference on Image Analysis (Lappeenranta, Finland)},
  pages = {559--566},
  volume = {I},
  author = {{B\"ulow}, T. and Sommer, G.}
}
@article{Bailey1990,
  year = {1990},
  title = {{FFT}s in External or Hierarchical Memory},
  pages = {23--35},
  journal = {The Journal of Supercomputing},
  volume = {4},
  annote = {key_fft},
  author = {Bailey, D.H.}
}
@article{Boddeke1997,
  number = {3},
  year = {1997},
  title = {Calibration of the automated z-axis of a microscope using focus functions},
  pages = {270-274},
  journal = {Journal of Microscopy},
  volume = {186},
  author = {Boddeke, F.R. and Vliet, L.J. van and Young, I.T.}
}
@inproceedings{Bulow1998,
  month = {August 17--20},
  title = {Quaternionic {G}abor Filters for Local Structure Classification},
  booktitle = {14th International Conference on Pattern Recognition (Brisbane, Australia)},
  pages = {808--810},
  author = {{B\"ulow}, T. and Sommer, G.}
}
@article{Boddeke1994,
  number = {4},
  year = {1994},
  title = {Autofocusing in microscopy based on the {OTF} and sampling},
  pages = {193-203},
  journal = {Bioimaging},
  volume = {2},
  author = {Boddeke, F.R. and Vliet, L.J. van and Netten, H. and Young, I.T.}
}
@inproceedings{Breton1996,
  year = {1996},
  title = {Shadows and Shading Flow Fields},
  booktitle = {Proc. IEEE Conference on Computer Vision and Pattern Recognition - CVPR'96},
  pages = {782--789},
  address = {San Francisco, USA},
  author = {Breton, P. and Zucker, S.W.}
}
@article{Nikolaidis1998,
  number = {12},
  month = {December},
  year = {1998},
  title = {Nonlinear Processing and Analysis of Angular Signals},
  pages = {3181--3194},
  journal = {IEEE Transactions on Signal Processing},
  volume = {46},
  author = {Nikolaidis, N. and Pitas, I.}
}
@article{Monga1992,
  number = {6},
  year = {1992},
  title = {From voxel to intrinsic surface features},
  pages = {403--417},
  journal = {Image and Vision Computing},
  volume = {10},
  author = {Monga, O. and Ayache,N. and Sander,P.T.}
}
@article{Monga1995,
  number = {2},
  year = {1995},
  title = {Using Partial Derivatives of 3D Images to Extract Typical Surface Features},
  pages = {171--189},
  journal = {Computer Vision and Image Understanding},
  volume = {61},
  author = {Monga, O. and Benayoun, S.}
}
@article{Efros1997,
  number = {6},
  year = {1997},
  title = {Random Telegraph Signal in the Photoluminescence Intensity of a Single Quantum Dot},
  pages = {1110-1113},
  journal = {Physical Review Letters},
  volume = {78},
  author = {Efros, A.L. and Rosen, M.}
}
@article{Illingworth1988,
  number = {1},
  year = {1988},
  title = {A Survey of the {H}ough Transform},
  pages = {87--116},
  journal = {Computer Vision, Graphics and Image Processing},
  volume = {44},
  annote = {key_radon},
  author = {Illingworth, J. and Kittler, J.}
}
@inproceedings{Dorst1993,
  year = {1993},
  title = {An Analytical Theory of Mathematical Morphology},
  booktitle = {Mathematical Morphology and its Applications to Signal Processing},
  pages = {245--250},
  editor = {Serra, J. and Salembier, P.},
  author = {Dorst, L. and Boomgaard, R. van den},
  organization = {Universitat Politecnica de Catalunya (Barcelona, Spain)}
}
@article{Zwier2004,
  number = {1},
  year = {2004},
  title = {Image calibration in fluorescence microscopy},
  pages = {15-24},
  journal = {Journal of Microscopy},
  volume = {216},
  author = {Zwier, J.M. and Rooij, G.J. van and Hofstraat, J.W. and Brakenhoff, G.J.}
}
@article{Heun2001,
  number = {5549},
  month = {December},
  year = {2001},
  title = {Chromoson Dynamics in the Yeast Interphase Nucleus},
  pages = {2181-2187},
  journal = {Science},
  volume = {294},
  author = {Heun, P. and Laroche, T. and Shimada, K. and Furrer, P. and Gasser, S.M.}
}
@inbook{Dorst1995,
  year = {1995},
  title = {World Scientific},
  pages = {13--22},
  editor = {Dori, D. and Bruckstein, A.},
  chapter = {Orientation-based Representations for Mathematical Morphology},
  author = {Dorst, L. and Boomgaard, R. van den}
}
@misc{Dorst1999,
  month = {December},
  year = {1999},
  title = {{GABLE}: A Matlab Tutorial for Geometric Algebra},
  author = {Dorst, L. and Mann, S. and Bouma, T.}
}
@article{Dorst1994,
  year = {1994},
  title = {Morphological Signal Processing and the Slope Transform},
  pages = {79--98},
  journal = {Signal Processing},
  volume = {38},
  author = {Dorst, L. and Boomgaard, R. van den}
}
@article{Lichte1996a,
  year = {1996},
  title = {Artefacts in electron holography},
  pages = {67-77},
  journal = {Ultramicroscopy},
  volume = {64},
  author = {Lichte, H. and Geiger, D. and Harscher, A. and Heindl, E. and Lehman, M. and Malamidis, D. and Orchowski, A. and Rau, W.-D.}
}
@article{Thust1996,
  year = {1996},
  title = {Numerical correction of lens aberrations in phase-retrieval {HRTEM}},
  pages = {249-264},
  journal = {Ultramicroscopy},
  volume = {64},
  author = {Thust, A. and Overwijk, M.H.F. and Coene, W.M.J. and Lentzen, M.}
}
@article{Katsevich1997,
  number = {4},
  month = {August},
  year = {1997},
  title = {Local Tomography for the Generalized Radon Transform},
  pages = {1128--1162},
  journal = {SIAM J. Appl. Math.},
  volume = {57},
  annote = {key_radon},
  author = {Katsevich, A.I.}
}
@article{Lopez1999,
  number = {4},
  month = {April},
  year = {1999},
  title = {Evaluation of Methods for Ridge and Valley Detection},
  pages = {327--335},
  journal = {IEEE Transactions on Pattern Analysis and Machine Intelligence},
  volume = {21},
  author = {{L\'opez}, A.M. and Lumbreras, F. and Serrat, J. and Villanueva, J.J.}
}
@article{Beil1994,
  year = {1994},
  title = {Steerable Filters and Invariance Theory},
  pages = {453--460},
  journal = {Pattern Recognition Letters},
  volume = {15},
  author = {Beil, W.}
}
@book{Stauffer1985,
  edition = {second},
  year = {1985, 1994},
  title = {Introduction to Percolation Theory},
  publisher = {Taylor \& Francis},
  author = {Stauffer, D. and Aharony, A.}
}
@inproceedings{Simoncelli1996a,
  year = {1996},
  title = {Noise Removal via Bayesian Wavelet Coring},
  booktitle = {3rd IEEE International Conference on Image Processing (Lausanne, Switzerland)},
  pages = {379--382},
  author = {Simoncelli, E.P. and Adelson, E.H.}
}
@article{Shafarenko1997,
  number = {11},
  month = {November},
  year = {1997},
  title = {Automatic Watershed Segmentation of Randomly Textured Color Images},
  pages = {1530--1544},
  journal = {IEEE Transactions on Image Processing},
  volume = {6},
  author = {Shafarenko, Leila and Petrou, Maria and Kittler, Josef}
}
@article{Duhamel1988,
  number = {2},
  month = {February},
  year = {1988},
  title = {On Computing the Inverse DFT},
  pages = {285--286},
  journal = {IEEE Transactions on Acoustics, Speech and Signal Processing},
  volume = {36},
  annote = {key_fft},
  author = {Duhamel, P. and Piron, B. and Etcheto, J.M.}
}
@article{Moser2006,
  year = {2006},
  title = {Filter cubes with built-in ultrabright light-emitting diodes as exchangeable excitation light sources in fluorescence microscopy},
  pages = {135-140},
  journal = {Journal of Microscopy},
  volume = {222},
  author = {Moser, C. and Mayr, T. and Klimant, I.}
}
@article{Morrone1988,
  year = {1988},
  title = {Feature Detection in Human Vision: a Phase-Dependent Energy Model},
  pages = {221--245},
  journal = {Proc. Roc. Soc. Lond. B},
  volume = {235},
  author = {Morrone, M.C. and Burr, D.C.}
}
@article{Giordano2002,
  year = {2002},
  title = {Diheteroarylethenes as Thermally Stable Photoswitchable Acceptors in Photochromic Fluorescence Resonance Energy Transfer ({pcFRET})},
  pages = {7481-7489},
  journal = {Journal of the American Chemical Society},
  volume = {124},
  author = {Giordano, L. and Jovin, T.M. and Irie, M. and Jare-Erijman, E.A.}
}
@article{Iddir2005,
  year = {2005},
  title = {Atomic scale characterization of the Pt/TiO$_2$ interface},
  pages = {233-241},
  journal = {Micron},
  volume = {36},
  author = {Iddir, H. and Disko, M.M. and Ogut, S. and Browning, N.D.}
}
@article{Bleau1992a,
  number = {2},
  month = {September},
  year = {1992},
  title = {A New Set of Fast Algorithms for Mathematical Morphology, {II}. Identification of Topographic Features on Grayscale Images},
  pages = {210--229},
  journal = {CVGIP: Image Understanding},
  volume = {56},
  author = {Bleau, A. and Guise, J. de and LeBlanc, A.-R.}
}
@article{Starink1996,
  year = {1996},
  title = {Background correction in scanning probe microscope recordings of macromolecules},
  pages = {291-305},
  journal = {Surface Science},
  volume = {359},
  author = {Starink, J.P.P. and Jovin, T.M.}
}
@inproceedings{Barth2000,
  year = {2000},
  title = {The minors of the structure tensor},
  booktitle = {Mustererkennung 2000},
  pages = {221--228},
  editor = {Sommer, G. and Krger, N. and Perwass, C.},
  address = {Berlin},
  publisher = {Springer},
  author = {Barth, E.}
}
@article{Sander2003,
  year = {2003},
  title = {Automatic CTF correction for single particles based upon multivariate statistical analysis of individual power spectra},
  pages = {392-401},
  journal = {Journal of Structural Biology},
  volume = {142},
  author = {Sander, B. and Golas, M.M. and Stark, H.}
}
@misc{Waagepetersen1997,
  year = {1997},
  title = {Contributions to the Statistical Modeling of Image Data and Spatial Point Processes},
  note = {University of Aarhus},
  howpublished = {www},
  author = {Waagepetersen, R.}
}
@article{Hentschell1983,
  number = {3},
  year = {1983},
  title = {The Infinite Number of Generalized Dimensions of Fractals and Strange Attractors},
  pages = {435--444},
  journal = {Physica D},
  volume = {8},
  author = {Hentschell, H.G.E. and Procaccia, I.}
}
@inproceedings{Croisier1976,
  month = {August},
  year = {1976},
  title = {Perfect Channel Splitting by Use of Interpolation/Decimation/Tree Decomposition Techniques},
  booktitle = {International Conference on Information Sciences and Systems},
  pages = {443--446},
  address = {Patras, Greece},
  author = {Croisier, A. and Esteban, D. and Galand, C.}
}
@article{Barnard1980,
  number = {4},
  month = {July},
  year = {1980},
  title = {Disparity Analysis of Images},
  pages = {527--534},
  journal = {IEEE Transactions on Pattern Analysis and Machine Intelligence},
  volume = {2},
  author = {Barnard, S.T. and Thompson, W.B.}
}
@article{Desolneux2001,
  year = {2001},
  title = {Edge Detection by {Helmholtz} Principle},
  pages = {271--284},
  journal = {Journal of Mathematical Imaging and Vision},
  volume = {14},
  author = {Desolneux, A. and Moisan, L. and Morel, J.-M.}
}
@phdthesis{Picka1996,
  month = {December},
  year = {1996},
  title = {Variance-Reducing Modifications for Estimators of Dependence in Random Sets},
  address = {Chicago, USA},
  school = {University of Chicago},
  author = {Picka, J.D.}
}
@inproceedings{Dijk2003,
  series = {Lecture Notes in Computer Science},
  month = {Aug 25-27},
  year = {2003},
  title = {A new sharpness measure based on Gaussian lines and edges},
  booktitle = {CAIP'03, 10th International Conference on Computer Analysis of Images and Patterns (Groningen, The Netherlands)},
  pages = {149-156},
  editor = {Petkov, N. and Westenberg, M.A.},
  volume = {2756},
  address = {Berlin},
  publisher = {Springer},
  author = {Dijk, J. and Ginkel, M. van and Asselt, R.J. van and Vliet, L.J. van and Verbeek, P.W.}
}
@inproceedings{Dijk2002,
  month = {June 19-21},
  year = {2002},
  title = {A new sharpness measure based on Gaussian lines and edges},
  booktitle = {Proc. ASCI 2002, 8th Annual Conf. of the Advanced School for Computing and Imaging},
  pages = {39--44},
  editor = {Deprettere, E.F. and Belloum, A. and Heijnsdijk, J.W.J. and Stappen, F. van der},
  address = {Delft},
  publisher = {ASCI},
  author = {Dijk, J. and Ginkel, M. van and Asselt, R.J. van and Vliet, L.J. van and Verbeek, P.W.}
}
@article{Bruijne2003,
  year = {2003},
  title = {Localization and segmentation of aortic endografts using marker detection},
  pages = {473-482},
  journal = {IEEE Transactions on Medical Imaging},
  volume = {22},
  author = {Bruijne, M. de and Niessen, W.J. and Maintz, J.B.A. and Viergever, M.A.}
}
@article{Rader1968,
  number = {6},
  month = {June},
  year = {1968},
  title = {Discrete {Fourier} Transforms When the Number of Data Samples is Prime},
  pages = {1107--1108},
  journal = {Proceedings of the IEEE},
  volume = {56},
  annote = {key_fft},
  author = {Rader, C.M.}
}
@phdthesis{Robbins1996,
  month = {August},
  year = {1996},
  title = {The Detection of {2D} Image Features using Local Energy},
  address = {Australia},
  school = {University of Western Australia},
  author = {Robbins, B.J.}
}
@article{Ando2004,
  year = {2004},
  title = {Regulated fast nucleocytoplasmic shuttling observed by reversible protein highlighting},
  pages = {1370-1373},
  journal = {Science},
  volume = {306},
  author = {Ando, R. and Muzuno, H. and Miyawaki, A.}
}
@article{Robbins1997,
  number = {5},
  year = {1997},
  title = {{2D} Feature Detection via Local Energy},
  pages = {353--368},
  journal = {Image and Vision Computing},
  volume = {15},
  author = {Robbins, B. and Owens, R.}
}
@article{Stokke1990,
  number = {13},
  year = {1990},
  title = {The reliability of wormlike polysaccharides chain dimensions estimated from electron micrographs},
  pages = {1161-1181},
  journal = {Biopolymers},
  volume = {30},
  author = {Stokke, B.T. and Brant, D.A.}
}
@article{Ando2000,
  number = {3},
  month = {March},
  year = {2000},
  title = {Consistent Gradient Operators},
  pages = {252--265},
  journal = {IEEE Transactions on Pattern Analysis and Machine Intelligence},
  volume = {22},
  author = {Ando, S.}
}
@techreport{Cullip1990,
  year = {1990},
  title = {Algorithms for 2D and 3D Image Description Based on the IAS},
  note = {TR90-034},
  institution = {University of North Carolina, U.S.A.},
  author = {Cullip, T.J. and Fredericksen, R.E. and Gauch, J.M. and Pizer, S.M.}
}
@article{Dempster1977,
  year = {1977},
  title = {Maximum Likelihood from Incomplete Data via the {EM} algorithm},
  pages = {1--37},
  journal = {Journal of the Royal Statistical Society B},
  volume = {39},
  author = {Demster, A.P. and Laird, N.M. and Rubin, D.B.}
}
@article{Marshall1997,
  number = {12},
  year = {1998},
  title = {Interphase chromosomes undergo constrained diffusional motion in living cells},
  pages = {930-939},
  journal = {Current Biology},
  volume = {7},
  author = {Marshall, W.F. and Straight, A. and Marko, J.F. and Swedlow, J. and Dernburg, A. and Murray, A.W. and Agard, D.A. and Sedat, J.W.}
}
@inproceedings{Borga1997,
  month = {June 9-11},
  year = {1997},
  title = {Learning Canonical Correlations},
  booktitle = {Proceedings of the 10th Scandinavian Conference on Image Analysis (Lappeenranta, Finland)},
  pages = {1--8},
  volume = {I},
  author = {Borga, M. and Knutsson, H. and Landelius, T.}
}
@article{Perona1998,
  number = {3},
  month = {March},
  year = {1998},
  title = {Orientation Diffusions},
  pages = {457--467},
  journal = {IEEE Transactions on Image Processing},
  volume = {7},
  author = {Perona, P.}
}
@phdthesis{Borga1998,
  year = {1998},
  title = {Learning Multidimensional Signal Processing},
  address = {{Link\"oping, Sweden}},
  school = {{Link\"oping University}},
  author = {Borga, M.}
}
@article{Perona1990,
  number = {7},
  month = {July},
  year = {1990},
  title = {Scale-Space and Edge Detection Using Anisotropic Diffusion},
  pages = {629--639},
  journal = {IEEE Transactions on Pattern Analysis and Machine Intelligence},
  volume = {12},
  author = {Perona, P. and Malik, J.}
}
@inproceedings{Wink2001,
  year = {2001},
  title = {Vessel Axis Determination Using Wave Front Propagation Analysis},
  booktitle = {MICCAI'01},
  pages = {845-853},
  editor = {Niessen, W. and Viergever, M.A.},
  author = {Wink, O. and Niessen, W.J. and Verdonck, B. and Viergever, M.A.}
}
@article{Perona1995,
  number = {5},
  month = {May},
  year = {1995},
  title = {Deformable Models for Early Vision},
  pages = {488--499},
  journal = {IEEE Transactions on Pattern Analysis and Machine Intelligence},
  volume = {17},
  author = {Perona, P.}
}
@book{Gauss1801,
  year = {1801},
  title = {Disquisitiones Arithmeticae},
  address = {{G\"ottingen} },
  publisher = {{K\"oniglichen Gesellschaft der Wissenschaft}},
  author = {Gauss, C.F.}
}
@article{Dirks2003,
  number = {1},
  year = {2003},
  title = {Visualizing {RNA} molecules inside the nucleus of living cells},
  pages = {51-57},
  journal = {Methods},
  volume = {29},
  author = {Dirks, R.W. and Molenaar, C. and Tanke, H.J.}
}
@article{Dirks2001,
  number = {1},
  year = {2001},
  title = {Methods for visualizing RNA processing and transport pathways in living cells},
  pages = {3-11},
  journal = {Histochemistry and Cell Biology},
  volume = {115},
  author = {Dirks, R.W. and Molenaar, R.W. and Tanke, H.J.}
}
@article{Bangham1994,
  number = {3},
  year = {1994},
  title = {Multiscale Median and Morphological Filters for 2D Pattern Recognition},
  pages = {387--415},
  journal = {Signal Processing},
  volume = {38},
  author = {Bangham, J.A. and Campbell, T.G. and Aldridge, R.V.}
}
@book{HandbookCP1992,
  edition = {82th},
  year = {1992},
  title = {Handbook of Chemistry and Physics },
  editor = {Lide, D.R. },
  publisher = {CRC Press }
}
@article{Bangham1996,
  number = {5},
  month = {May},
  year = {1996},
  title = {Multiscale Nonlinear Decomposition: The Sieve Decomposition Theorem},
  pages = {529--539},
  journal = {IEEE Transactions on Pattern Analysis and Machine Intelligence},
  volume = {18},
  author = {Bangham, J.A. and Chardaire, P. and Pye, C.J. and Ling, P.D.}
}
@article{Clerc2002,
  number = {4},
  month = {April},
  year = {2002},
  title = {The Texture Gradient Equation for Recovering Shape from Texture},
  pages = {536--549},
  journal = {IEEE Transactions on Pattern Analysis and Machine Intelligence},
  volume = {24},
  author = {Clerc, M. and Mallat, S.}
}
@article{Dijkstra1959,
  year = {1959},
  title = {A note on two problems in connexion with graphs.},
  pages = {269--271},
  journal = {Numerische Mathematik },
  volume = {1},
  author = {Dijkstra, E.W.}
}
@article{Andrey1998,
  number = {3},
  month = {March},
  year = {1998},
  title = {Unsupervised Segmentation of {M}arkov Random Field Modeled Textured Images Using Selectionist Relaxation},
  pages = {252--262},
  journal = {IEEE Transactions on Pattern Analysis and Machine Intelligence},
  volume = {20},
  author = {Andrey, P. and Tarroux, P.}
}
@article{Hestenes1994,
  number = {1},
  year = {1994},
  title = {Invariant Body Kinematics: {I}. Saccadic and Compensatory Eye Movements},
  pages = {65--77},
  journal = {Neural Networks},
  volume = {7},
  author = {Hestenes, D.}
}
@article{Osher1988,
  year = {1988},
  title = {Fronts Propagating with Curvature-Dependent Speed: Algorithms Based on {H}amilton-{J}acobi Formulations},
  pages = {12--49},
  journal = {Journal of Computational Physics},
  volume = {79},
  author = {Osher, S. and Sethian, J.A.}
}
@article{Ram2006,
  number = {12},
  year = {2006},
  title = {Beyond {Rayleighs} criterion: {A} resolution measure with application to single-molecule microscopy},
  pages = {4457-4462},
  journal = {Proceedings of the National Academy of Sciences USA},
  volume = {103},
  author = {Ram, S. and Ward, E.S. and Ober, R.J.}
}
@article{Schwertner2004a,
  number = {1},
  year = {2004},
  title = {Measurement of specimen induced aberrations of biological samples using phase stepping interferometry},
  pages = {11-19},
  journal = {Journal of Microscopy},
  volume = {213},
  author = {Schwertner, M. and Booth, M.J. and Neil, M.A.A. and Wilson, T.}
}
@article{Schwertner2004b,
  number = {3},
  year = {2004},
  title = {Simulation of specimen-induced aberrations for objects with spherical and cylindrical symmetry},
  pages = {271-280},
  journal = {Journal of Microscopy},
  volume = {215},
  author = {Schwertner, M. and Booth, M.J. and Wilson, T.}
}
@article{Simoncelli1992,
  number = {2},
  month = {March},
  year = {1992},
  title = {Shiftable Multi-scale Transforms},
  pages = {587--607},
  journal = {IEEE Transactions on Information Theory},
  volume = {38},
  author = {Simoncelli, E.P. and Freeman, W.T. and Adelson, E.H. and Heeger, D.J.}
}
@article{Simoncelli1996,
  number = {9},
  year = {1996},
  title = {Steerable wedge filters for local orientation analysis},
  pages = {1377--1382},
  journal = {IEEE Transactions on Image Processing},
  volume = {5},
  author = {Simoncelli, E.P. and Farid, H.}
}
@article{Viero1995,
  number = {4},
  month = {December},
  year = {1995},
  title = {Morphological Extraction of Line Networks from Noisy Low-Contrast Images},
  pages = {335--347},
  journal = {Journal of Visual Communication and Image Representation},
  volume = {6},
  author = {Viero, T. and Jeulin, D.}
}
@article{Simoncelli1990,
  number = {4},
  month = {April},
  year = {1990},
  title = {Non-Separable Extensions of Quadrature Mirror Filters to Multiple Dimensions},
  pages = {652--664},
  journal = {Proceedings of the IEEE},
  volume = {78},
  author = {Simoncelli, E.P. and Adelson, E.H.}
}
@inproceedings{Luengo2001b,
  series = {Lecture Notes on Computer Science},
  year = {2001},
  title = {A Rotation-Invariant Morphology for Shape Analysis of Anisotropic Objects and Structures},
  booktitle = {Proc. 4th International Workshop on Visual Form},
  pages = {378--387},
  editor = {Arcelli, C. and Cordella, L.P. and Sanniti, G. di Baja},
  volume = {2059},
  address = {Capri, Italy},
  publisher = {Springer-Verlag},
  author = {Luengo Hendriks, C.L. and Vliet, L.J. van}
}
@inproceedings{Luengo2001a,
  year = {2001},
  title = {Segmentation-Free Estimation of Length Distributions Using Sieves and RIA Morphology},
  booktitle = {Proc. 7th Annual Conference of the Advanced School for Computing and Imaging},
  pages = {129--136},
  address = {Heijen, the Netherlands},
  publisher = {ASCI, Delft},
  author = {Luengo Hendriks, C.L. and Vliet, L.J. van}
}
@article{Khotanzad1990,
  number = {5},
  month = {May},
  year = {1990},
  title = {Invariant Image Recognition by {Z}ernike Moments},
  pages = {489--497},
  journal = {IEEE Transactions on Pattern Analysis and Machine Intelligence},
  volume = {12},
  author = {Khotanzad, A. and Hong, Y.H.}
}
@article{Lindenbaum1993,
  number = {1},
  year = {1993},
  title = {On {G}abor's contribution to image enhancement},
  pages = {1--8},
  journal = {Pattern Recognition},
  volume = {27},
  author = {Lindenbaum, M. and Fischer, M. and Bruckstein, A.}
}
@article{Rose2002,
  year = {2002},
  title = {Theory of electron-optical achromats and apochromats},
  pages = {293-303},
  journal = {Ultramicroscopy},
  volume = {93},
  author = {Rose, H.}
}
@inproceedings{Hertzmann2001,
  year = {2001},
  title = {Image Analogies},
  booktitle = {{SIGGRAPH}, Computer Graphics Proceedings},
  pages = {327--340},
  publisher = {ACM Press},
  author = {Hertzmann, A. and Jacobs, C.E. and Oliver, N. and Curless, B. and Salesin, D.H.}
}
@article{Rose2005,
  year = {2005},
  title = {Prospects for aberration-free electron microscopy},
  pages = {1-6},
  journal = {Ultramicroscopy},
  volume = {103},
  author = {Rose, H.}
}
@article{Rioul1991,
  month = {October},
  year = {1991},
  title = {Wavelets and Signal Processing},
  pages = {14--38},
  journal = {IEEE Signal Processing Magazine},
  author = {Rioul, O. and Vetterli, M.}
}
@article{Torok1995,
  number = {2},
  year = {1995},
  title = {Electromagnetic diffraction of light focused through a planar interface between materials of mismatched refractive indices: an integral representation},
  pages = {325-332},
  journal = {Journal of the Optical Society of America A},
  volume = {12},
  author = {{T\"or\"ok}, P. and Varga, P. and Laczik, Z. and Booker, G.R. }
}
@article{Acton2001,
  year = {2001},
  title = {Fast Algorithms for Area Morphology},
  pages = {187--203},
  journal = {Digital Signal Processing},
  volume = {11},
  author = {Acton, S.T.}
}
@article{Acton2000,
  number = {4},
  month = {April},
  year = {2000},
  title = {Scale Space Classification Using Area Morphology},
  pages = {623--635},
  journal = {IEEE Transactions on Image Processing},
  volume = {9},
  author = {Acton, Scott T. and Mukherjee, Dipti Prasad}
}
@article{Vonck2000,
  year = {2000},
  title = {Parameters a?ecting specimen flatness of two-dimensional crystals for electron crystallography},
  pages = {123-129},
  journal = {Ultramicroscopy},
  volume = {85},
  author = {Vonck, J.}
}
@book{Bishop1998,
  year = {1998},
  title = {Neural Networks for Pattern Recognition},
  address = {New York},
  publisher = {Oxford University Press},
  author = {Bishop, C.M.}
}
@book{Bishop1995,
  year = {1995},
  title = {Neural Networks for Pattern Recognition},
  publisher = {Oxford University Press},
  author = {Bishop, C.M.}
}
@misc{Hough1962,
  year = {1962},
  title = {Method and Means for Recognizing Complex Patterns},
  howpublished = {US misc nr. 3069654},
  author = {Hough, P.V.C.}
}
@article{Clayton2004,
  year = {2004},
  title = {Graphical representation and multicomponent analysis of single-frequency fluorescence lifetime imaging microscopy data},
  pages = {1-5},
  journal = {Journal of Microscopy},
  volume = {213},
  author = {Clayton, A.H.A. and Hanley, Q.S. and Verveer, P.J.}
}
@article{Maintz1996kort,
  number = {4},
  year = {1996},
  title = {Evaluation of ridge seeking operators for multimodality medical image matching },
  pages = {353--365},
  journal = {PAMI},
  volume = {18},
  author = {Maintz, J.B.A. and Elsen, P.A. van den and Viergever, M.A. }
}
@phdthesis{SMALLSMALLGinkel2002,
  year = {2002},
  title = {Image Analysis using Orientation Space based on Steerable Filters},
  address = {Delft, The Netherlands},
  school = {Delft University of Technology},
  author = {Ginkel, M. van}
}
@misc{Stereology2000,
  month = {20-25 May},
  year = {2000},
  title = {Summer School on Stereology and Geometric Tomography},
  note = {Sandberg Manor, Denmark },
  howpublished = {www}
}
@article{Clayton2002,
  number = {3},
  year = {2002},
  title = {Dynamic Fluorescence Anisotropy Imaging Microscopy in the Frequency Domain {(rFLIM)}},
  pages = {1631-1649},
  journal = {Biophysical Journal},
  volume = {83},
  author = {Clayton, A.H.A. and Hanley, Q.S. and Arndt-Jovin, D.J. and Subramaniam, V. and Jovin, T.M.}
}
@article{Desolneux2002,
  number = {10},
  year = {2002},
  title = {Dequantizing image orientation},
  pages = {1129--1140},
  journal = {IEEE Transactions on Image Processing},
  volume = {11},
  author = {Desolneux, A. and Ladjal, S. and Moisan, L. and Morel, J.-M.}
}
@inproceedings{Bigun1987,
  month = {June 8-11},
  year = {1987},
  title = {Optimal orientation detection of linear symmetry},
  booktitle = {Proceedings of the first IEEE International Conference on Computer Vision},
  pages = {433-438},
  address = {London},
  publisher = {IEEE Computer Society Press},
  author = {{Big\"un}, J. and Granlund, G.H.}
}
@techreport{Bigun1986,
  number = {LIU-TEK-LIC-1986:25},
  title = {Circular Symmetry Models in Image Processing.},
  note = {Thesis No. 85},
  type = {Lic. Thesis},
  address = {{Link\"oping University}, Sweden},
  institution = {Computer Vision Laboratory},
  author = {{Big\"un}, J.}
}
@article{Bowie1977a,
  number = {6},
  year = {1977},
  title = {An Analysis Technique for Biological Shape -- {III}},
  pages = {739--746},
  journal = {Acta Cytologica},
  volume = {21},
  author = {Bowie, J.E. and Young, I.T.}
}
@article{Glossop1999,
  number = {1},
  month = {April},
  year = {1999},
  title = {An implementation of the Hough Transformation for the Identification and Labeling of Fixed Period Sinusoidal Curves},
  pages = {96--100},
  journal = {Computer Vision and Image Understanding},
  volume = {74},
  annote = {key_radon},
  author = {Glossop, K. and Lisboa, P.J.G. and Russell, P.C. and Siddans, A. and Jones, G.R.}
}
@article{Crowley1984,
  number = {2},
  month = {March},
  year = {1984},
  title = {A Representation for Shape Based on Peaks and Ridges in the Difference of Low-Pass Transform},
  pages = {156--170},
  journal = {IEEE Transactions on Pattern Analysis and Machine Intelligence},
  volume = {6},
  author = {Crowley, J.L. and Parker, A.C.}
}
@inproceedings{Kraaijveld2000,
  month = {June 4-7},
  year = {2000},
  title = {Harnessing Advanced Image Analysis Technology for Quantitative Core and Borehole Image Interpretation},
  booktitle = {proceedings of the 41st SPWLA annual symposium, Dallas},
  pages = {paper VV},
  author = {Kraaijveld, M.A. and Epping, W.J.M.}
}
@article{Joanicot1987,
  number = {2},
  year = {1987},
  title = {{DNA} conformational studies from electron microscopy. {I. Excluded} volume effect and structure dimensionality},
  pages = {315-326},
  journal = {Biopolymers},
  volume = {26},
  author = {Joanicot, M. and Revet, B.}
}
@article{Brown2003,
  number = {8},
  month = {August},
  year = {2003},
  title = {Advances in Computational Stereo},
  pages = {993--1007},
  journal = {IEEE Transactions on Pattern Analysis and Machine Intelligence},
  volume = {25},
  author = {Brown, M.Z. and Burschka, D. and Hager, G.D.}
}
@article{Typke2004,
  year = {2004},
  title = {Electron Microscopy of Biological Macromolecules: Bridging the GAp between What Physics Allows and What We Currently Can Get},
  pages = {21-27},
  journal = {Microscopy and Microanalysis},
  volume = {10},
  author = {Typke, D. and Duwning, K.H. and Glaeser, R.M.}
}
@book{Simmonds1982,
  year = {1982},
  title = {A Brief on Tensor Analysis},
  publisher = {Springer-Verlag},
  author = {Simmonds, J.G.}
}
@article{Li2004,
  number = {8},
  year = {2004},
  title = {A maximum likelihood approach for image registration using control point and intensity},
  pages = {1115-1127},
  journal = {IEEE Transactions on Image Processing},
  volume = {13},
  author = {Li, W. and Leung, W.}
}
@book{Cressie1993,
  edition = {Revised},
  year = {1993},
  title = {Statistics for Spatial Data},
  publisher = {John Wiley \& Sons, inc},
  author = {Cressie, N.A.C.}
}
@article{McLaughlin1998,
  number = {4},
  month = {April},
  year = {1998},
  title = {The Hough Transform Versus the Upwrite},
  pages = {396--400},
  journal = {IEEE Transactions on Pattern Analysis and Machine Intelligence},
  volume = {20},
  annote = {key_radon},
  author = {McLaughlin, R.A. and Alder, M.D.}
}
@inproceedings{Rieger2003b,
  series = {LNCS 2756},
  month = {August 25-27 },
  year = {2003},
  title = {Representing Orientation in n-Dimensional Spaces},
  booktitle = {CAIP'03, 10th International Conference on Computer Analysis of Images and Patterns (Groningen, The Netherlands) },
  pages = {17-24},
  editor = {Petkov, N. and Westenberg, M.A.},
  address = {Berlin},
  publisher = {Springer Verlag},
  author = {Rieger, B. and Vliet, L.J. van}
}
@article{Rieger2003c,
  number = {3},
  year = {2003},
  title = {Ring Formation in Nanoliter Cups: Quantitative Measurements of Flow in Micromachined Wells},
  pages = {036312},
  journal = {Physical Review E},
  volume = {68},
  author = {Rieger, B. and Doel, L.R. van den and Vliet, L.J. van }
}
@inproceedings{Rieger2003a,
  month = {June 4-6},
  year = {2003},
  title = {Affine correction without correspondence applied to 4D cellular motion in confocal microscopy},
  booktitle = {ASCI'03, Proceedings of the 9th Annual Conference of the Advanced School for Computing and Imaging (Lommel, Belgium) },
  editor = {Vassiliadis, S. and Florak, L.M.J. and Heijnsdijk, J.W.J and Steen, A. van den},
  author = {Rieger, B. and Molenaar, C. and Dirks, R.W. and Vliet, L.J. van}
}
@article{Grayson1987,
  year = {1987},
  title = {The heat equation shrinks embedded plane curves to round points},
  pages = {285--314},
  journal = {Journal of Differential Geometry},
  volume = {26},
  author = {Grayson, M.}
}
@article{Danielsson1990,
  number = {2},
  year = {1990},
  title = {Rotation Invariance in Gradient and Higher Order Derivative Detectors},
  pages = {198--221},
  journal = {Computer Vision, Graphics, and Image Processing},
  volume = {49},
  author = {Danielsson, P.-E. and Seger, O.}
}
@article{Hanley2001,
  year = {2001},
  title = {Fluorescence Lifetime Imaging: Multi-point Calibration, Minimum Resolvable Differences, and Artifact Suppression},
  pages = {248-260},
  journal = {Cytometry},
  volume = {43},
  author = {Hanley, Q.S. and Subramaniam, V. and Arndt-Jovin, D.J. and Jovin, T.M.}
}
@article{Hanley2002,
  number = {56},
  year = {2002},
  title = {Spectrally resolved fluorescence lifetime imaging microscopy},
  pages = {155-166},
  journal = {Applied Spectroscopy},
  author = {Hanley, Q.S. and Ardent-Jovin, D.J. and Jovin, T.M.}
}
@article{Saffman1975,
  number = {8},
  year = {1975},
  title = {Brownian motion in biolocial membranes},
  pages = {3111-3113},
  journal = {Proc. Nat. Acad. Sci. USA},
  volume = {72},
  author = {Saffman, P.G. and {Delbr\"uck}, M.}
}
@article{Casadio1999,
  month = {February},
  year = {1999},
  title = {Characterization of the Range of the {Radon} Transform on Homogeneous Trees},
  pages = {11--17},
  journal = {Electronic Research Announcements of the American Mathematical Society},
  volume = {5},
  author = {Casadio Tarabusi, E. and Cohen, J.M. and Colonna, F.}
}
@article{Goldberg1991a,
  number = {1},
  year = {1991},
  title = {What Every Computer Scientist Should Know about Floating-Point Arithmetic},
  pages = {5--48},
  note = {A reprint. Extended?},
  journal = {ACM Computing Surveys},
  volume = {23},
  author = {Goldberg, D.}
}
@article{Willert1991,
  year = {1991},
  title = {Digital particle image velocimetry},
  pages = {181-193},
  journal = {Experiments in Fluids},
  volume = {10},
  author = {Willert, C.E. and Gharib, M.}
}
@article{Soille2001,
  number = {11},
  month = {November},
  year = {2001},
  title = {Directional Morphological Filtering},
  pages = {1313--1329},
  journal = {IEEE Transactions on Pattern Analysis and Machine Intelligence},
  volume = {23},
  author = {Soille, Pierre and Talbot, Hugues}
}
@article{Soille2002,
  year = {2002},
  title = {Short Survey on Morphological Operators Based on Rank Filters},
  pages = {527-535},
  journal = {Pattern Recognition},
  volume = {35},
  author = {Soille, P.}
}
@book{Landau1999,
  edition = {third},
  year = {1999},
  title = {Statistical Physics, Part 1},
  publisher = {Butterworth-Heinemann},
  author = {Landau, L.D. and Lifshitz, E.M.}
}
@article{Rintoul1997,
  year = {1997},
  title = {Precise determination of the critical threshold and exponents in a three-dimensional continuum percolation model},
  pages = {585--592},
  journal = {J. Phys. A: Math Gen},
  volume = {30},
  author = {Rintoul, M.D. and Torquato, S.}
}
@article{Belongie2002,
  number = {4},
  month = {April},
  year = {2002},
  title = {Shape Matching and Object Recognition Using Shape Contexts},
  pages = {509--522},
  journal = {IEEE Transactions on Pattern Analysis and Machine Intelligence},
  volume = {24},
  author = {Belongie, S. and Malik, J. and Puzicha, J.}
}
@phdthesis{Reinders2001,
  year = {2001},
  title = {Feature-Based Visualization of Time-Dependent Data},
  address = {The Netherlands},
  school = {Delft University of Technology},
  author = {Reinders, F.}
}
@article{Deans1981,
  number = {2},
  month = {March},
  year = {1981},
  title = {{H}ough Transform from the {R}adon Transform},
  pages = {185--188},
  journal = {IEEE Transactions on Pattern Analysis and Machine Intelligence},
  volume = {3},
  annote = {key_radon},
  author = {Deans, S.R.}
}
@article{Meijering2003,
  number = {4},
  month = {April},
  year = {2003},
  title = {A Note on Cubic Convolution Interpolation},
  pages = {477--479},
  journal = {IEEE Transactions on Image Processing},
  volume = {12},
  author = {Meijering, E. and Unser, M.}
}
@article{Meijering2002,
  number = {3},
  month = {March},
  year = {2002},
  title = {A Chronology of Interpolation: From Ancient Astronomy to Modern Signal and Image Processing},
  pages = {319--342},
  journal = {Proceedings of the IEEE},
  volume = {90},
  author = {Meijering, E.}
}
@incollection{Jovin1989,
  year = {1989},
  title = {{FRET} Microscopy: Digital Imaging of Fluorescence Resonance Energy Transfer. Application in Cell Biology},
  booktitle = {Cell Structure and Function by Microspectrofluorometry},
  pages = {99-117},
  editor = {Kohen, E.},
  address = {New York},
  publisher = {Academic Press},
  author = {Jovin, T.M. and Arndt-Jovin, D.J.}
}
@article{Egner2004,
  number = {1},
  year = {2004},
  title = {{4Pi}-microscopy of the {Golgi} apparatus in live mammalian cells},
  pages = {70-76},
  journal = {Journal of Structural Biology},
  volume = {147},
  author = {Egner, A. and Verrier, S. and Goroshkov, A. and Shing, H-D. and Hell, S.W.}
}
@article{Dorst1987,
  year = {1987},
  title = {Length Estimators for Digitized Contours},
  pages = {311--333},
  journal = {Computer Vision, Graphics and Image Processing},
  volume = {40},
  author = {Dorst, L. and Smeulders, A.W.M.}
}
@article{Dorst1986,
  number = {2},
  month = {March},
  year = {1986},
  title = {Best Linear Unbiased Estimators for Properties of Digitized Straight Lines},
  pages = {276--282},
  journal = {IEEE Transactions on Pattern Analysis and Machine Intelligence},
  volume = {8},
  author = {Dorst, L. and Smeulders, A.W.M.}
}
@incollection{Olver1994,
  year = {1994},
  title = {Differential invariant signatures and flows in computer vision: a symmetry group approach},
  booktitle = {Geometry-driven diffusion in computer vision},
  pages = {255--306},
  editor = {Ter Haar Romeny B.M.},
  chapter = {11},
  publisher = {Kluwer Academic Publishers},
  author = {Olver, P. and Sapiro, G. and Tannenbaum, A.}
}
@techreport{Dorst1980,
  year = {1980},
  title = {A Coordinate System for the Crystal Ball},
  institution = {CERN},
  author = {Dorst, L.}
}
@article{Hoyer2002,
  number = {2},
  year = {2002},
  title = {Dependence of $\alpha$-synuclein aggregate morphology on solution conditions},
  pages = {383-393},
  journal = {Journal of Molecular Biology},
  volume = {322},
  author = {Hoyer, W. and Antony, T. and Cherny, D.I. and Heim, G. and Jovin, T.M. and Subramaniam, V.}
}
@inproceedings{Ginneken1999,
  series = {Lecture Notes on Computer Science},
  title = {Applications of Locally Orderless Images},
  booktitle = {Scale-Space Theories in Computer Vision (Second International Conference, Scale-Space'99, Corfu, Greece)},
  pages = {10--21},
  editor = {Nielsen, Mads and Johansen, Peter and Olsen, Ole F. and Weickert, Joachim},
  volume = {1682},
  publisher = {Springer-Verlag},
  author = {Ginneken, B. van and Haar Romeny, B. M. ter}
}
@article{Mitiche1988,
  number = {6},
  year = {1988},
  title = {On smoothness of a vector field-application to optical flow},
  pages = {943--949},
  journal = {IEEE Transactions on Pattern Analysis and Machine Intelligence},
  volume = {10},
  author = {Mitiche, A. and Grisell, R. and Aggarwal, J.K.}
}
@article{Cognet1999,
  number = {3},
  year = {1999},
  title = {Static curvature and flexibility measurements of {DNA} with microscopy. {A} simple renormalization method, its assessment by experiment and simulation},
  pages = {997-1009},
  journal = {Journal of Molecular Biology},
  volume = {285},
  author = {Cognet, J.A.H. and Pakleza, C. and Cherny, D.I. and Delain, E. and Cam, E. le}
}
@article{Segall2006,
  year = {2006},
  title = {Volume-Exclusion Effects in Tethered-Particle Experiments: Bead Size Matters},
  pages = {088306},
  journal = {Physical Review Letters},
  volume = {96},
  author = {Segall, D.E. and Nelson, P.C. and Phillips, R.}
}
@article{Krieger1996,
  number = {6},
  month = {June},
  year = {1996},
  title = {Nonlinear Image Operators for the Evaluation of Local Intrinsic Dimensionality},
  pages = {1026--1042},
  journal = {IEEE Transactions on Image Processing},
  volume = {5},
  author = {Krieger, G. and Zetzsche, C.}
}
@book{Rudin1991,
  edition = {second},
  year = {1991, 1973},
  title = {Functional Analysis},
  publisher = {McGraw-Hill},
  author = {Rudin, W.}
}
@article{Mattfeldt2000a,
  month = {November},
  year = {2000},
  title = {Improved Estimation of the Pair Correlation Function of Random Sets},
  pages = {158--173},
  journal = {Journal of Microscopy},
  volume = {200, Pt 2},
  author = {Mattfeldt, T. and Stoyan, D.}
}
@article{Toprak2007,
  number = {7},
  year = {2007},
  title = {Three-Dimensional Particle Tracking via Bifocal Imaging},
  pages = {2043-2045},
  journal = {Nano Letters},
  volume = {7},
  author = {Toprak, E. and Balci, H. and Blehm, B.H. and  Selvin, P.R.}
}
@article{Xu2010,
  year = {2010},
  title = {From thickness dependent exit waves to projected potential: Thickness derivative approach},
  pages = {535-542},
  journal = {Ultramicroscopy},
  volume = {110},
  author = {Xu, Q. and Dyck, D. van and Zandbergen, H.W.}
}
@article{Zewail2010,
  year = {2010},
  title = {Four-Dimensional Electron Microscopy},
  pages = {187-193},
  journal = {Science},
  volume = {328},
  author = {Zewail, A. H. and }
}
@article{Pertsinidis2010,
  year = {2010},
  title = {Subnanometre single-molecule localization, registration and distance measurements},
  pages = {647-651},
  journal = {Nature},
  volume = {466},
  author = {Pertsinidis, A. and Zhang, Y. and Chu, S.}
}
@article{Okamoto2010,
  year = {2010},
  title = {Subnanometre single-molecule localization,
registration and distance measurements},
  pages = {043807},
  journal = {Physical Review A},
  volume = {38},
  author = {Okamoto, H.}
}
@article{Muller2010,
  year = {2010},
  title = {Image Scanning Microscopy},
  pages = {198101},
  journal = {Physical Review Letters},
  volume = {104},
  author = {{M\"uller}, C.B. and Enderlein, J.}
}
@article{Jonge2010,
  year = {2010},
  title = {Nanometer-resolution electron microscopy through micrometers-thick water layers},
  pages = {1114-1119},
  journal = {Ultramicroscopy},
  volume = {110},
  author = {Jonge, N. de and Poirier-Demes, N. and Dermes, H. and Peckys, D.B. and Drouin, D.}
}
@article{Kouskousis2010,
  number = {7},
  year = {2010},
  title = {Super-resolution imaging and statistical analysis
of {CdSe/CdS} Core/Shell semiconductor nanocrystals},
  pages = {437-445},
  journal = {Journal of Biophotonics},
  volume = {3},
  author = {Kouskousis, B.P. and Embden J. van and Morrish, D. and Russell, S.M. and Gu, M.}
}
@article{Stark2001,
  year = {2001},
  title = {Arrangement of RNA and proteins in the spliceosomal U1 small nuclear ribonucleoprotein particle},
  pages = {539-541},
  journal = {Nature},
  volume = {409},
  author = {Stark, H. and Dube, P. and {L\"uhrmann}, R. and Kastner, B.}
}
@article{Milazzo2010,
  year = {2010},
  title = {Characterization of a direct detection device imaging camera for transmission electron microscopy},
  pages = {744-747},
  journal = {Ultramicroscopy},
  volume = {110},
  author = {Milazzo, A-C. and Moldovan, G. and Lanman, J. and Jin, L. and Bouwer, J.C. and Klienfelder, S. and Peltier, S.T. and Ellisman, M.H. and Kirkland, A.I. and Xoung, N.-H.}
}
@article{Lupini2010,
  year = {2010},
  title = {Aberration measurement using the Ronchigram contrast transfer function},
  pages = {891-898},
  journal = {Ultramicroscopy},
  volume = {110},
  author = {Lupini, A.R. and Wang, P. and Nellist, P.D. and Kirkland, A.I. and Pennycook, S.J.}
}
@article{Saxton1982,
  number = {2},
  year = {1982},
  title = {The correlation averaging of a regularly arranged bacterial cell envelope protein},
  pages = {127-138},
  journal = {Journal of Microscopy},
  volume = {127},
  author = {Saxton, W.O. and Baumeister, W.}
}
@article{Rudnaya2010,
  year = {2010},
  title = {Evaluating sharpness functions for automated scanning
electron microscopy},
  journal = {Journal of Microscopy},
  author = {Rudnaya, M.E. and Mattheij, R.M.M. and Maubach, J.M.L.}
}
@inproceedings{Brinkers2010,
  month = {April 14-17},
  year = {2010},
  title = {Single Molecule Detection Of Tuberculosis Nucleic Acid Using Dark Field Tethered Particle Motion},
  booktitle = {IEEE International Symposium on Biomedical Imaging},
  pages = {1269},
  address = {Rotterdam, The Netherlands},
  author = {Brinkers, Sanneke and Dietrich, Heidelinde R. C. and Stallinga, Sjoerd and Mes, Jurriaan J. and Young, Ian T. and Rieger, Bernd}
}
@article{Cordes2010,
  number = {7},
  year = {2010},
  title = {Single-Molecule Redox Blinking of Perylene Diimide Derivatives in Water},
  pages = {2404-2409},
  journal = {Journal of the American Chemical Society},
  volume = {132},
  author = {Cordes, T. and Vogelsang, J. and Anaya, M. and Spaguolo, C. and Gietl, A. and Summerer, W. and Herrmann, A. and {M\"ullen}, K. and Tinnefeld, P.}
}
@article{Jiang2010,
  year = {2010},
  title = {A novel approximation method of CTF amplitude correction of 3D single particle reconstruction},
  journal = {Ultramicroscopy},
  author = {Jiang, L. and Liu, Z. and Georgieva, D. and Kuil, M.E. and Abrahams, J.P.}
}
@article{Dwyer2010,
  year = {2010},
  title = {Simulation of scanning transmission electron microscope images on desktop computers},
  pages = {195-198},
  journal = {Ultramicroscopy},
  volume = {110},
  author = {Dwyer, C.}
}
@article{Tamura2010,
  year = {2010},
  title = {Third-order spherical aberration correction using multistage self-aligned quadrupole correction-lens systems},
  journal = {Journal of Electron Microscopy},
  author = {Tamrua, K. and Okayama, S. and Shimizu, R.}
}
@article{Paik2009,
  number = {8},
  year = {2009},
  title = {Integrating a High-Force Optical Trap with Gold Nanoposts and a Robust Gold-DNA Bond},
  pages = {2978-2983},
  journal = {Nano Letters},
  volume = {9},
  author = {Paik, D.H. and Seol, Y. and Halsey, W.A. and Perkins, T.T.}
}
@article{Oijen1998,
  year = {1998},
  title = {3-Dimensional super-resolution by spectrally selective imaging},
  pages = {183-187},
  journal = {Chemical Physics Letters},
  volume = {292},
  author = {Oijen, A.M. van and {K\"ohler}, J. and Schmidt, J. and {M\"uller}, M. and Brakenhoff, G.J.}
}
@article{Marzetta1993,
  number = {6},
  year = {1993},
  title = {A Simple derivation of the constrained multiple parameter Cramer-Rao Bound},
  pages = {2247-2249},
  journal = {IEEE Transactions on Signal Processing},
  volume = {41},
  author = {Marzetta, T.L.}
}
@article{Mortensen2010,
  number = {5},
  year = {2010},
  title = {Optimized localization analysis for single-molecule tracking and super-resolution microscopy},
  pages = {377-384},
  journal = {Nature Methods},
  volume = {7},
  author = {Mortensen, K.I. and Churchman, L.S. and Spudich, J.A. and Flyvbjerg, H.}
}
@article{Chang2010,
  year = {2010},
  title = {Zernike Phase Plate Cryoelectron Microscopy
Facilitates Single Particle Analysis of Unstained
Asymmetric Protein Complexes},
  pages = {17-27},
  journal = {Structure},
  volume = {18},
  author = {Chang, W-H. and Chiu, M.T.K. and CHen, C.-Y. and Yen, C.F. and Lin,Y.-C. and Weng, Y.-P. and Chang, J.-C. and Wu, Y.-M. and Cheng, H. and Fu, J. and Tu, I-P.}
}
@article{Smith2010,
  number = {5},
  year = {2010},
  title = {Fast, single-molecule localization that achieves theoretically minimum uncertainty},
  pages = {373-375},
  journal = {Nature Methods},
  volume = {7},
  author = {Smith, C.S. and Joseph, N. and Rieger, B. and Lidke, K.A.}
}
@article{Serge2008,
  number = {8},
  year = {2008},
  title = {Dynamic multiple-target tracing to probe
spatiotemporal cartography of cell membranes},
  pages = {687-694},
  journal = {Nature Methods},
  volume = {5},
  author = {Serge, A. and Bertaux, N. and Rigneault, H. and Marguet, D.}
}
@article{Aguet2005,
  number = {26},
  year = {2005},
  title = {Dynamic multiple-target tracing to probe spatiotemporal cartography of cell membranes},
  pages = {10503-10522},
  journal = {Optics Express},
  volume = {13},
  author = {Aguet, F. and Ville, D. van de and Unser, M.}
}
@article{Harauz1997,
  number = {4},
  year = {1997},
  title = {Exact filters for general geometry three dimensional reconstruction},
  pages = {146-156},
  journal = {Optik},
  volume = {78},
  author = {Harauz, G. and Heel, M. van}
}
@article{Lingwood2009,
  year = {2009},
  title = {Lipid rafts as a membrane organizing principle},
  pages = {46-53},
  journal = {Science},
  volume = {327},
  author = {Lingwood, D. and Simons, K.}
}
@article{Baddeley2010,
  year = {2010},
  title = {Visualization of localization microscopy data},
  pages = {64-72},
  journal = {Microscopy and Microanalysis},
  volume = {16},
  author = {Baddeley, D. and Cannell, M.B. and Soeller, C.}
}
@inbook{Krivanek2010,
  year = {2010},
  title = {Advances in Imaging and Electron Physics},
  pages = {121-160},
  volume = {153},
  chapter = {Advances in Aberration-Corrected Scanning Transmission Electron Microscopy and Electron Energy-Loss Spectroscopy},
  publisher = {Elsevier},
  author = {Krivanek, O.L. and Delby, N. and Keyse, R.J. and Murfitt, M.F. and Own, C.S. and Szilagyi, Z.S.}
}
@article{Jaqaman2008,
  number = {8},
  year = {2008},
  title = {Robust single-particle tracking in live-cell time-lapse sequences},
  pages = {695-702},
  journal = {Nature Methods},
  volume = {5},
  author = {Jaqaman, K. and Loerke, D. and Mettlen, M. and Kuwara, H. and Grinstein, S. and Schmid, S.L. and Danuser, G.}
}
@article{Li2010,
  year = {2010},
  title = {Measurement of the Instantaneous Velocity of a Brownian Particle},
  pages = {1673-1676},
  journal = {Science},
  volume = {328},
  author = {Li, T. and Kheifets, S. and Medellin, D. and Raizen, M.G.}
}
@article{Kwon2010,
  number = {328},
  year = {2010},
  title = {4D Electron Tomography},
  pages = {1668-1673},
  journal = {Science},
  author = {Kwon, O.-H. and Zewail, A.H.}
}
@article{Brinkers2009,
  number = {21},
  year = {2009},
  title = {The Persistence Length of Double Stranded {DNA} Determined Using Dark Field Tethered Particle Motion},
  pages = {215105},
  journal = {Journal of Chemical Physics},
  volume = {130},
  author = {Brinkers, S. and Dietrich, H.R.C. and Groote, F.H. de and Young, I.T. and Rieger, B.}
}
@article{Snijdervanderas2009,
  number = {1},
  year = {2009},
  title = {A hybrid total internal reflection fluorescence and optical tweezers microscope to study cell adhesion and membrane protein dynamics of single living cells },
  pages = {84-92},
  journal = {Journal of Microscopy},
  volume = {223},
  author = {Snijder-van As, M.I. and Rieger, B. and Joosten, B. and Figdor, C. and Subramaniam, V. and Kanger, J.S.}
}
@article{Faas2009,
  number = {4},
  year = {2009},
  title = {{DNA} deformations near charged surfaces: electron and atomic force microscopy views},
  pages = {1148-1157},
  journal = {Biophysical Journal},
  volume = {97},
  author = {Faas, F.G.A. and Rieger, B. and Vliet, L.J. van and Cherny, D.I.}
}
@article{Castaldo2008,
  number = {6},
  year = {2008},
  title = {Sputtering limits versus signal-to-noise limits in the observation of {Sn} balls in a {Ga+} microscope},
  pages = {2107-2115},
  journal = {Journal of Vacuum Science and Technology B},
  volume = {26},
  author = {Castaldo, V. and  Hagen, C.W. Rieger, B. and Kruit, P.}
}
@article{Lidke2010,
  year = {2010},
  title = {{ERK} nuclear translocation is dimerization-independent but controlled by the rate of phosphorylation},
  pages = {3092-3102},
  journal = {Journal of Biological Chemistry},
  volume = {285},
  author = {Lidke, D.S. and Huang, F. and Post, J.N. and Rieger, B. and Thomas, J.L.and Pouyssegur, J. and Jovin, T.M. and Lenormand, P. }
}
@inbook{Hagen2008,
  year = {2008},
  title = {Single Molecule Dynamics in Life Sciences},
  pages = {117-130},
  editor = {Yanagida, T. and Ishii, Y.},
  chapter = {Dynamics of membrane receptors: single molecule tracking of quantm dot liganded epidermal growth factor},
  publisher = {Wiley},
  author = {Hagen, G.M. and Lidke, K.A. and Rieger, B. and Lidke,  D.S. and Caarls, W. and  Arndt-Jovin, D.J. and Jovin, T.M.}
}
@article{Haider2010,
  year = {2010},
  title = {Information Transfer in a TEM Corrected for Spherical
and Chromatic Aberration},
  pages = {393-408},
  journal = {Microscopy and Microanalysis},
  volume = {16},
  author = {Haider, M .and Hartel, P. and {M\"uller}, H. and Uhlemann, S. and Zach, J.}
}
@article{Borgnia2004,
  year = {2004},
  title = {Visualization of $\alpha$-helical features in a density map constructed using 9 molecular images of the {1.8MDa} icosahedral core of pyruvate dehydrogenase},
  pages = {136-145},
  journal = {Journal of Structural Biology},
  volume = {147},
  author = {Borgnia, M.J. and Shi, D. and Zhang, P. and Milne, J.L.S.}
}
@article{Dubochet1988,
  year = {1988},
  title = {Cryo-electron microscopy of vitrified specimens},
  pages = {129-228},
  journal = {Quarterly Review of Biophysics},
  volume = {21},
  author = {Dubochet, J. and Adrian, M. and Chang, J.-J. and Homo, J.-C. and Lepault, J. and McDowall, A.W.and Schultz, P.}
}
@article{Khursheed2007,
  year = {2007},
  title = {Redesign of the scanning electron microscope for parallel energy spectral acquisition},
  pages = {151-157},
  journal = {Ultramicroscopy},
  volume = {108},
  author = {Khursheed, A. and Hoang, H.Q.}
}
@article{Arslan2006,
  year = {2006},
  title = {Reducing the missing wedge: High-resolution dual axis tomography of inorganic materials},
  pages = {944-1000},
  journal = {Ultramicroscopy},
  volume = {106},
  author = {Arslan, I. and Tong, J.R. and Midgley, P.A.}
}
@article{Dierksen1992,
  year = {1992},
  title = {Towards automatic electron tomography},
  pages = {71-87},
  journal = {Ultramicroscopy},
  volume = {40},
  author = {Dierksen, K. and Typke, D. and Hegerl, R. and Koster, A.J. and Baumeister, W.}
}
@book{Born1999,
  edition = {7th},
  year = {1999},
  title = {Principles of Optics},
  publisher = {Cambridge University Press},
  author = {Born, M. and Wolf, E.}
}
@article{Dyck1996,
  year = {1996},
  title = {Sub-{\aa}ngstr{\"o}m structure characterisation: the {Brite-Euram} route towarde one {\AA}ngstr{\"o}m},
  pages = {1-15},
  journal = {Ultramicroscopy},
  volume = {64},
  author = {Dyck, D. van and Lichte, H. and Mast, K.D. van der}
}
@article{Billinge2007,
  year = {2007},
  title = {The Problem with Determining Atomic Structure at the Nanoscale},
  pages = {561-565},
  journal = {Science},
  volume = {316},
  author = {Billinge, S.J.L. and Levin, I.}
}
@article{Stoeger2008,
  year = {2008},
  title = {Optical properties and bandgaps from low loss EELS: Pitfalls and solutions},
  pages = {1092-1110},
  journal = {Micron},
  volume = {39},
  author = {Stoeger-Pollach, M.}
}
@article{Kim1997a,
  year = {1997},
  title = {Performance of Zr/O/W Schottky emitters at reduced temperatures},
  pages = {2284-2288},
  journal = {Journal of Vaccum Science and Technology B},
  volume = {15},
  author = {Kim, H.S. and Yu, M.L. and Thomson, M.G.R. and Kratchmer, E. and Chang, T.H.P.}
}
@inproceedings{Mitterbauer2003a,
  year = {2003},
  title = {High energy resolution {EELS} using a monochromoized {200kV TEM}: Comparative investigation of titanum oxides},
  booktitle = {Microscoc. Microanal.},
  pages = {1-2},
  volume = {9S3},
  author = {Mitterbauer, C. and Kothleitner, G. and Hofer, F. and Tiemeijer, P.C. and Freitag, B.H. and Zandbergen, H.W.}
}
@article{Gyobu2004,
  year = {2004},
  title = {Improved specimen preparation for cryo-electron microscopy using a symmetric carbon sandwich technique},
  pages = {325-333},
  journal = {Journal of Structural Biology},
  volume = {146},
  author = {Gyobu, N. and Tani, K. and Hiroaki, Y. and Kamegawa, A. and Mitsuoka, K. and Fujiyoshi, Y.}
}
@article{Hebert2003,
  year = {2003},
  title = {A proposal for dichroic experiments in the electron microscope},
  pages = {463-468},
  journal = {Ultramicroscopy},
  volume = {96},
  author = {Hebert, C. and Schattschneider, P.}
}
@article{Oshima2010,
  year = {2010},
  title = {Direct imaging of lithium atoms in {$LiV_2O_4$} by spherical aberration-corrected electron microscopy},
  pages = {1-5},
  journal = {Journal of Electron Microscopy},
  author = {Oshima, Y. and et al.}
}
@article{Ishitani2002,
  number = {6},
  year = {2002},
  title = {Contrast-to-gradient method for the evaluation of image resolution in scanning electron microscopy},
  pages = {369-382},
  journal = {Journal of Electron Mircoscopy},
  volume = {51},
  author = {Ishitani, T. and Sato, M.}
}
@article{Ishitani2005,
  number = {2},
  year = {2005},
  title = {Influence of random noise on the contrast-to-gradient image resolution in scanning electron microscopy},
  pages = {85-97},
  journal = {Journal of Electron Mircoscopy},
  volume = {54},
  author = {Ishitani, T. and Kamiya, C. and Sato, M.}
}
@article{Ishitani2004,
  number = {3},
  year = {2004},
  title = {Contrast-to-gradient method for the evaluation of image resolution taking account of random noise in scanning electron microscopy},
  pages = {245-255},
  journal = {Journal of Electron Mircoscopy},
  volume = {53},
  author = {Ishitani, T. and Sato, M.}
}
@article{Loane1991,
  year = {1991},
  title = {Thermal vibrations in convergent-beam electron diffraction},
  pages = {267-278},
  journal = {Acta Crystallography},
  volume = {A47},
  author = {Loane, R.F. and Xu, P. and Slicox, J.}
}
@article{Zaneti2009,
  year = {2009},
  title = {Contrast transfer function correction applied to cryo-electron tomography and sub-tomogram averaging},
  pages = {305-312},
  journal = {Journal of Structural Biology},
  volume = {168},
  author = {Zaneti, G. and Riches, J.D. and Fuller, S.D. and Briggs, J.A.G.}
}
@article{Diez2006,
  number = {2},
  year = {2006},
  title = {Tilt-series and electron microscope alignment for the correction of the non-perpendicularity of beam and tilt-axis},
  pages = {195-205},
  journal = {Journal of Strcutural Biology},
  volume = {154},
  author = {Diez, D.C. and Seybert, A. and Frangakis, A.S.}
}
@article{Diez2007,
  year = {2007},
  title = {Implementation and performance evaluation of reconstruction algorithms on graphics processors},
  pages = {288-295},
  journal = {Journal of Strcutural Biology},
  volume = {157},
  author = {Diez, C.D. and Mueller, H. and Frangakis, A.S.}
}
@article{Barth1996,
  year = {1996},
  title = {Addition of different contributions to the charged particle probe size},
  pages = {101-109},
  journal = {Optik},
  volume = {101},
  author = {Barth, J.E. and Kruit, P.}
}
@article{Uchida2010,
  year = {2010},
  title = {Generation of electron beams carrying orbital angular momentum},
  journal = {Nature},
  volume = {464},
  author = {Uchida, M. and Tonomura, A.}
}
@article{Jacobsen2001,
  number = {2},
  year = {2001},
  title = {Soft X-ray spectroscopy from image sequences with sub-100nm spatial resolution},
  pages = {173-184},
  journal = {Journal of Microscopy},
  volume = {197},
  author = {Jacobsen, C. and Wirick, S. and Flynn, G. and Zimba, C.}
}
@article{Hammel1995,
  year = {1995},
  title = {Optimum rotationally symmetric detector configurations for phase-contrast imaging in scanning transmission electron microscopy},
  pages = {403-415},
  journal = {Ultramicroscopy},
  volume = {58},
  author = {Hammel, M. and Rose, H.}
}
@article{Braat2005,
  number = {12},
  year = {2005},
  title = {Extended {Nijboer-Zernike} approach to aberration and birefringence retrieval in a high-numerical-aperture optical system},
  pages = {2635-26550},
  journal = {Journal of the Optical Society of America A},
  volume = {22},
  author = {Braat, J.J.M. and Dirksen, P. and Janssen, A.J.E.M. and Haver, S. van and Nes, S. van de}
}
@article{Swanson2009,
  year = {2009},
  title = {A review of the cold-field electron cathode},
  pages = {63-100},
  journal = {Advances in Imaging and Electron Physics},
  volume = {159},
  author = {Swanson, L.W. and Schwind, G.A.}
}
@article{Nakanishi2005,
  year = {2005},
  title = {An expanded approach to noise reduction from high-resolution STEM images based on the maximum entropy method},
  note = {accepted},
  journal = {Ultramicroscopy},
  author = {Nakanishi, N. and Kotaka, Y. and Yamazaki, T.}
}
@article{Carragher2000,
  year = {2000},
  title = {Leginon: an automated system for acquisition of images from vitrecus ice specimens},
  pages = {33-45},
  journal = {Journal of Structural Biology},
  volume = {132},
  author = {Carragher, B. and Kisseberth, N. and Kriegman, D. and Milligan, R.A. and Potter, C.S. and Pulokas, J. and Reilein, A.}
}
@article{Finn2000,
  number = {24},
  year = {2000},
  title = {Escherichia coli {RNA} polymerase core and holoenzyme structures},
  pages = {6833-6844},
  journal = {EMBO Journal},
  volume = {19},
  author = {Finn, R.D. and Orlova, E.V. and Gowen, B. and Buck, M. and Heel, M. van}
}
@article{Rubenstein2007,
  year = {2007},
  title = {Structural analysis of membrane protein complexes by single particle electron microscopy},
  pages = {409-416},
  journal = {Methods},
  volume = {41},
  author = {Rubenstein, J.L.}
}
@article{Wang2007,
  year = {2007},
  title = {Probing the electronic structure of ZnO nanowires by valence electron energy loss spectroscopy},
  pages = {346-353},
  journal = {Micron},
  volume = {38},
  author = {Wang, J. and Li, Q. and Egerton, R.F.}
}
@article{Wang2004,
  year = {2004},
  title = {Off-axis electron holography with a dual-lens imaging system andits usefulness in 2-D potential mapping of semiconductor devices},
  pages = {63-72},
  journal = {Ultramicroscopy},
  volume = {101},
  author = {Wang, Y.Y. and Kawasaki, M. and Bruley, J. and Gribelyuk, M. and Domenicucci, A. and Gaudiello, J.}
}
@article{Wang2008,
  year = {2008},
  title = {Nanomaterial electronic structure investigation by valence electron energy loss spectroscopy - An example of doped ZnO nanowires},
  pages = {703-708},
  journal = {Micron},
  volume = {39},
  author = {Wang, J. and Li, Q. and Ronning, C. and Stichtenoth, D. and Muller, S. and Tang, D.}
}
@article{Okayama2005,
  number = {4},
  year = {2005},
  title = {Reference sample for the evaluation of {SEM} image resolution at a high magnification - nanometer-scale {Au} particles on an {HOPG} substrate},
  pages = {345-350},
  journal = {Journal of Electron Mircoscopy},
  volume = {54},
  author = {Okayama, S. and Haraichi, S. and Matsuhata, H.}
}
@book{Slayter1992,
  year = {1992},
  title = {Ligth and Electron Microscopy},
  address = {Cambridge, United Kingdom},
  publisher = {Cambridge University Press},
  author = {Slayter,E.M. and Slayter, H.S.}
}
@article{Ortalan2009,
  year = {2009},
  title = {Application of image processing to STEM tomography of low-contrast materials},
  pages = {67-81},
  journal = {Ultramicroscopy},
  volume = {110},
  author = {Ortalan, V. and Herra, M. and Morgan, D.G. and Browning, N.D.}
}
@article{Lazar2010,
  year = {2010},
  title = {Imaging, Core-Loss, and Low-Loss Electron-Energy-Loss Spectroscopy Mapping in Aberration-Corrected STEM},
  pages = {1-9},
  journal = {Microscopy and Microanalysis},
  volume = {16},
  author = {Lazar, S. and Shao, Y. and Gunawan, L. and Nechache, R. and Pignolet, A. and Botton, G.A.}
}
@article{Takaoka2006,
  year = {2006},
  title = {Observations of unstained biological specimens using a low-energy, high-resolution STEM},
  pages = {157-163},
  journal = {Journal of Electron Microscopy},
  volume = {55},
  author = {Takaoka, A. and Hasegawa, T.}
}
@article{Batson2002,
  year = {2002},
  title = {Sub-{\AA}ngstrom resolution using aberration corrected electron optics},
  pages = {617-622},
  journal = {Nature},
  volume = {418},
  author = {Batson, P.E. and Dellby, N. and Krivanek, O.L.}
}
@article{Batson2006,
  year = {2006},
  title = {Characterizing probe performance in the aberration corrected {STEM}},
  pages = {1104-1114},
  journal = {Ultramicroscopy},
  volume = {106},
  author = {Batson, P.E.}
}
@article{Wang2007a,
  year = {2007},
  title = {Local electronic structure and luminescence properties of Er doped ZnO nanowires},
  pages = {221917},
  journal = {Applied Physics Letters},
  volume = {89},
  author = {Wang, J. and Zhou, M.J. and Hark, S.K. and Li, Q.}
}
@article{Eisebit2004,
  year = {2004},
  title = {Lensless imaging of magnetic nanostructures by {X-ray} spectro-holography},
  pages = {885-888},
  journal = {Nature},
  volume = {432},
  author = {Eisebit, S. and {J\"uning}, J. and Schlotter, W.F. and {L\"orgen}, M. and Hellwig, O. and Eberhardt, W. and {St\"ohr}, J.}
}
@phdthesis{Tuggle1984,
  year = {1984},
  title = {Emission Characteristics and Electron optical properties of the ZrO/W point cathode},
  address = {Oregon State University},
  school = {Oregon, USA},
  author = {Tuggle, D.W.}
}
@article{Cowley1959a,
  year = {1959},
  title = {The Scattering of Electrons by Atoms and Crystals. {III.} {The} Single-Crytal Diffraction Patterns},
  pages = {360-368},
  journal = {Acta Crystallography},
  volume = {12},
  author = {Cowley, J.M. and Moodie, A.F.}
}
@article{Harrach2009,
  year = {2009},
  title = {Development of the 300-kV Vacuum Generator STEM (1985-1996)},
  pages = {287-322},
  journal = {Advances in Imaging and Electron Physics},
  volume = {159},
  author = {Harrach, H.S. von}
}
@article{Plaisier2007,
  year = {2007},
  title = {Cyclops: New modular software suite for cryo-EM},
  pages = {19-27},
  journal = {Journal of Strcutural Biology},
  volume = {157},
  author = {Plaisier, J.R. and Jiang, L. and Abrahams, J.P.}
}
@article{Benthem2006,
  year = {2006},
  title = {Three-dimensional {ADF} imaging of individual atoms by through-focal series scanning transmission electron microscopy},
  pages = {1062-1068},
  journal = {Ultramicroscopy},
  volume = {106},
  author = {Benthem, K. van and Lupini, A.R. and Oxley, M.P. and Findlay, S.D. and Alleen, L.J. and Pennycook, S.J.}
}
@misc{Rieger2009,
  year = {2009},
  title = {Method for determining the aberration coefficients of the aberration function of a particle-opticle lens},
  howpublished = {EP1804272},
  author = {Zande, M. van der and Kok, C. and Rieger, B.},
  organization = {FEI Company}
}
@article{Fujita2005,
  number = {5},
  year = {2005},
  title = {A new evaluation method of electron optical performance of high beam current probe forming systems},
  pages = {413-427},
  journal = {Journal of Electron Mircoscopy},
  volume = {54},
  author = {Fujita, S. and Shimoyama, H.}
}
@article{Heel1997,
  year = {1997},
  title = {Angular reconstitution in three-dimensional electron microscopy: historical and theoretical aspects},
  pages = {195-210},
  journal = {Scanning Microscopy},
  volume = {11},
  author = {Heel, M. van and Orlova, E.V. and Harauz, G. and Stark, H. and Dube, P. and Zemlin, F. and Schatz, M.}
}
@article{Sawada2010,
  year = {2010},
  title = {Higher-order aberration corrector for an image-forming system in a transmission electron microscope},
  pages = {1-4},
  journal = {Ultramicroscopy},
  author = {Sawada, H. and Sasaki, T. and Hosokawa, F. and Yuasa, S. and Terao, M. and Kawazoe, M. and Nakamichi, T. and Kaneyama, T. and Kondo. Y. and Kimoto, K. and Suenaga, K.}
}
@article{Rau1999,
  number = {12},
  year = {1999},
  title = {Two-Dimensional Mapping of the Electrostatic Potential in Transistors by Electron Holography},
  pages = {2614-2617},
  journal = {Physical Review Letters},
  volume = {82},
  author = {Rau, W.D. and Schwander, P. and Baumann, F.H. and Hoeppner, W. and Ourmazd, A.}
}
@article{Kishita2009,
  year = {2009},
  title = {Development of an analytical environmental TEM system and its application},
  pages = {331-339},
  journal = {Journal of Electron Microscopy},
  volume = {58},
  author = {Kishita, K. and Sakai, H. and Tanaka, H. and Saka, H. and Kuroda, K. and Sakamoto, M. and Watabe, A. and Kamnio, T.}
}
@article{Bartle2008,
  year = {2008},
  title = {Energy width reduction using an electrostatic Omega-monochromator},
  pages = {479},
  journal = {Physics Procedia},
  volume = {1},
  author = {Bartle, J. and Plies, E.}
}
@article{Armstrong2007,
  year = {2007},
  title = {Practical considerations for high spatial and temporal resolution dynamic transmission electron microscopy},
  pages = {356-367},
  journal = {Ultramicroscopy},
  volume = {107},
  author = {Armstrong, M. R. and Boyden, K. and Browning, N.D. and Campbell, G.H. and Colvin, J.D. and DeHope, W.J. and Frank, A.M. and hartemann, F. and Kim, J.S. and King, W.E. and LaGrange, T.B. and Pyke, B.J. and Reed, B.W. and Shuttleswoth, M. and Stuart, B.C. and Torralava, B.R.}
}
@article{Lichte1993,
  year = {1993},
  title = {Parameters for gih-resolution electron holography},
  pages = {15-20},
  journal = {Ultramicroscopy},
  volume = {51},
  author = {Lichte, H.}
}
@article{Blom2006,
  year = {2006},
  title = {Early Results from an Aberration-Corrected {JEOL 2200FS} {STEM/TEM} at {Oak} {Ridge} {National} {Laboratory}},
  pages = {483-491},
  journal = {Microscopy and Microanalysis},
  volume = {12},
  author = {Blom, D.A. and Allard, L.F. and Mishina, S. and O'Keefe, M.A.}
}
@article{Zach2009,
  year = {2009},
  title = {Chromatic correction: a revolution in electron microscopy?},
  pages = {3699-3707},
  journal = {Philosophical Transactions of the Royal Society},
  volume = {367},
  author = {Zach2009}
}
@article{Arslan2005,
  year = {2005},
  title = {Embedded nanostructures revealed in three dimensions},
  pages = {2195-2198},
  journal = {Sciences},
  volume = {309},
  author = {Arslan, I. and Yates, T.J.V. and Browning, N.D. and Midgley, P.A.}
}
@article{Urban2008,
  year = {2008},
  title = {Studying Atomic Structures by Aberration-Corrected Transmission Electron Microscopy},
  pages = {506-510},
  journal = {Science},
  volume = {321},
  author = {Urban, K.}
}
@article{Christenson1988,
  year = {1988},
  title = {Skew thoughts on parallelism},
  pages = {113-132},
  journal = {Ultramicroscopy},
  volume = {26},
  author = {Christenson, K.K. and Eades, J.A.}
}
@article{Lupini2003,
  year = {2003},
  title = {Localization in Elastic and Inelastic Scattering},
  pages = {313-322},
  journal = {Ultramicroscopy},
  volume = {96},
  author = {Lupini, A.R. and Pennycook, S.J.}
}
@article{Loane1992,
  year = {1992},
  title = {Incoherent imaging of zone axis crystals with {ADF STEM}},
  pages = {121-138},
  journal = {Ultramicroscopy},
  volume = {40},
  author = {Loane, R.F. and Xu, P. and Slicox, J.}
}
@phdthesis{Lupini2001,
  year = {2001},
  title = {Aberration correction in {STEM}},
  note = {Copy Bernd Rieger},
  address = {Cambridge, United Kingdom},
  school = {University of Cambridge},
  author = {Lupini, A.R.}
}
@article{Deptuch2007,
  year = {2007},
  title = {Direct electron imaging in electron microscopy with monolithic active pixel sensors},
  pages = {674-684},
  journal = {Ultramicroscopy},
  volume = {107},
  author = {Deptuch, G. and Besson, A. and Rehak, P. and Szelezniak, M. and Wall, J. and Winter, M. and Zhu, Y.}
}
@article{Yamasaki2005,
  number = {2},
  year = {2005},
  title = {First experiments of selected area nano-diffraction from semiconductor interfaces using a spherical aberration corrected {TEM}},
  pages = {123-126},
  journal = {Journal of Electron Microscopy},
  volume = {54},
  author = {Yamasaki, J. and Sawada, H. and Tanaka, N.}
}
@article{Rodenburg2006,
  year = {2006},
  title = {Transmission microscopy without lenses for objects of unlimited size},
  pages = {227-231},
  journal = {Ultramicroscopy},
  volume = {107},
  author = {Rodenburg, J.M. and Hurst, A.C. and Cullis, A.G.}
}
@article{Stewart2004,
  year = {2004},
  title = {Noise bias in the refinement of structures deried from single particles},
  pages = {67-84},
  journal = {Ultramicroscopy},
  volume = {102},
  author = {Stewart, A. and Grigorieff, N.}
}
@inproceedings{CheynetXXXX,
  title = {{VEELS} experiments using a monochromated {FEG-TEM}},
  pages = {1-2},
  author = {Cheynet, M.C. and Tichelaar, F.R. and Lazar, S. and Jullian, S. and Pantel, R.}
}
@article{Fan1996,
  number = {3},
  year = {1996},
  title = {A new electron-optical mode for high contrast imaging and online stereo observation in {TEM}},
  pages = {137-146},
  journal = {Journal of Microscopy},
  volume = {2},
  author = {Fan, G.Y. and Young, S.J. and Deerinck, T. and Ellisman, M.H.}
}
@inproceedings{SaorzanoXXXX,
  title = {Transfer function restoration in {3D} electron microscopy via iterative data refinement},
  pages = {1-4},
  author = {Sorzano, C.O.S. and {Fern\'andez}, J.J. and Marabini, R. and Herman, G.T. and Censor, Y. and Carazo, J.M.}
}
@article{Miao2002,
  year = {2002},
  title = {Atomic Resolution Three-Dimensional Electron Diffraction Microscopy},
  journal = {Physical Review Letters},
  volume = {89},
  author = {Miao, J. and Ohsuna, T. and Terasaki, O. and Hodgson, K.O. and O'Keefe, M.A.}
}
@article{Lentzen2004,
  year = {2004},
  title = {The tuning of a {Zernike} phase plate with defocus and variable spherical aberration and its use in {HRTEM} imaging},
  pages = {211-220},
  journal = {Ultramicroscopy},
  volume = {99},
  author = {Lentzen, M.}
}
@article{Lentzen2002,
  year = {2002},
  title = {High-resolution imaging with an aberration-corrected transmission electron microscope},
  pages = {233-242},
  journal = {Ultramicroscopy},
  volume = {92},
  author = {Lentzen, M. and Jahnen, B. and Jia, C.L. and Thust, A. and Tillmann, K. and Urban, K.}
}
@article{Cowley1957,
  year = {1957},
  title = {The Scattering of Electrons by Atoms and Crystals. {I.} {A} New Theorectial Approach},
  pages = {609-620},
  journal = {Acta Crystallography},
  volume = {10},
  author = {Cowley, J.M. and Moodie, A.F.}
}
@article{Sander2005,
  year = {2005},
  title = {Advantages of CCD detectors for de novo three-dimensional structure determination in single-particle electron microscopy},
  pages = {92-105},
  journal = {Journal of Structural Biology},
  volume = {151},
  author = {Sander, B. and Golas, M.M. and Stark, H.}
}
@article{Alloyeau2009,
  year = {2009},
  title = {Atomic-resolution three-dimensional imaging of germanium self-interstitials near a surface: Aberration-corrected transmission electron microscopy},
  pages = {014114},
  journal = {Physical Review B},
  volume = {80},
  author = {Alloyeau, D. and Freitag, B. and Dag, S. and Wang, L.W. and Kisielowski, C.}
}
@article{Fujiyoshi1998,
  year = {1998},
  title = {The structural study of membranse proteins by electron crystallography},
  pages = {25-80},
  journal = {Adv. Biophysics},
  volume = {35},
  author = {Fujiyoshi, Y.}
}
@article{Cowley1959,
  year = {1959},
  title = {The Scattering of Electrons by Atoms and Crystals. {II.} {The} Effect of Finite Source Size},
  pages = {353-360},
  journal = {Acta Crystallography},
  volume = {12},
  author = {Cowley, J.M. and Moodie, A.F.}
}
@article{Baba2001,
  year = {2001},
  title = {An auto-tunning method for focusing and astigmatism correction in HAADF-STEM, based on the image contrast transfer function},
  pages = {163-176},
  journal = {Journal of Electron Micrsocopy},
  volume = {50},
  author = {Baba, N. Teryama, K. and Yoshimizu, T. and Ichise, N. and Tanaka, N.}
}
@article{Miyashita2004,
  number = {6},
  year = {2004},
  title = {Direct observation of electrostatic microfields by four-electron-wave interference using two electron biprisms},
  pages = {577-582},
  journal = {Journal of Electron Microscopy},
  volume = {53},
  author = {Miyashita, K. and Yamamoto, K. and Hirayama, T. and Tanji, T.}
}
@article{Barthel2008,
  year = {2008},
  title = {Quantification of the Information Limit of Transmission Electron Microscopes},
  pages = {200801},
  journal = {Physical Review Letters},
  volume = {101},
  author = {Barthel, J. and Thust, A.}
}
@inproceedings{Barthel2005,
  year = {2005},
  title = {Ultra-Precise Measurement of Optical Aberrations for Sub-\AA ngstrom {HRTEM}},
  booktitle = {{Dreil\"andertagung}, 28 August - 2 September, Davos, Zwitserland},
  author = {Barthel, J. and Thust, A.}
}
@article{Winkler2007,
  year = {2007},
  title = {3D reconstruction and processing of volumetric data in cryo-electron tomography},
  pages = {126-137},
  journal = {Journal of Strcutural Biology},
  volume = {157},
  author = {Winkler, H.}
}
@article{Kohl1985,
  year = {1985},
  title = {Theory of image formation by inelastically scattered electrons in the electron microscope},
  pages = {173-224},
  journal = {Advances in Electronics and Electron Physics},
  volume = {65},
  author = {Kohl, H. and Rose, H.}
}
@article{Henderson1992,
  year = {1992},
  title = {Image contrast in high-resolution electron microscopy of biological macromlecules: {TMV} in ice},
  pages = {1-18},
  journal = {Ultramicroscopy},
  volume = {46},
  author = {Henderson, R.}
}
@article{Einspahr2006,
  year = {2006},
  title = {Prospects for {3D}, nanometer-resolution imaging by confocal {STEM}},
  pages = {1041-1052},
  journal = {Ultramicroscopy},
  volume = {106},
  author = {Einspahr, J.J. and Voyles, P.M.}
}
@article{Bohm2000,
  year = {2000},
  title = {Toward detecting and identifying macromolecules in a cellular context: Template matching applied to electron tomograms},
  pages = {14245-14250},
  journal = {Biophysical Journal},
  volume = {97},
  author = {{B\"ohm}, J. and Frangakis, A.S. and Hegerl, R. and Nickell, S. and Typke, D. and Baumeister, W.}
}
@article{Zhou1996,
  number = {1},
  year = {1996},
  title = {{CTF} Determination of Images of Ice-Embedded Single Particles Using from Cryoelectron Micrographs to Subnanometer Resolution},
  pages = {216-22},
  journal = {Journal of Strcutural Biology},
  volume = {116},
  author = {Zhou, Z.H. and Hardt, S. and Wang, B. and Sherman, M.B. and Jakana, J. and Chiu, W.}
}
@article{Mitome2009,
  year = {2009},
  title = {Quantitativeness of phase measurement by transport of intensity equation},
  pages = {1-9},
  journal = {Journal of electron microscopy},
  author = {Mitome, M. and Ishizuka, K. and Bando, Y.}
}
@article{Schiske1956,
  year = {1956},
  title = {Die untere Grenze des Farbfehlers magnetischer Linsen bei vorgeschriebener Maximalfeldstaerke},
  pages = {502-503},
  journal = {Optik},
  volume = {13},
  author = {Schiske, P.}
}
@article{Edgcombe1999,
  year = {1999},
  title = {Robust optimization for magnetic lens design},
  pages = {306-309},
  journal = {Nuclear Instruments and Methods in Physics Research A},
  volume = {427},
  author = {Edgcombe, C.J. and Lupini, A.R. and Taylor, J.H.}
}
@article{Abajo2010,
  year = {2010},
  title = {Optical excitations in electron microscopy},
  pages = {209-275},
  journal = {REVIEWS OF MODERN PHYSICS},
  volume = {82},
  author = {Abajo, F.J. Garcia de}
}
@article{Chang2006,
  year = {2006},
  title = {On the importance of fifth-order spherical aberration for a fully corrected electron microscope},
  pages = {in press},
  journal = {Ultramicroscopy},
  author = {Chang, L.Y. and Kirkland, A.I. and Tichmarsh, J.M.}
}
@article{Treacy2007,
  year = {2007},
  title = {When structural noise is the signal: Speckle statistics in fluctuation electron microscopy},
  pages = {166-171},
  journal = {Ultramicroscopy},
  volume = {107},
  author = {Treacy, M.M.J.}
}
@article{Yi2010,
  year = {2010},
  title = {Flexible formation of coherent probes on an aberrationcorrected STEM with three condensers},
  pages = {1-7},
  journal = {Journal of Electron Microscopy},
  author = {Yi, F. and Tiemeijer, P. and Voyles, P.M.}
}
@article{Erni2005,
  year = {2005},
  title = {Analysis of extraterrestrial particles using monochromated electron energy-loss spectroscopy},
  pages = {369-379},
  journal = {Micron},
  volume = {36},
  author = {Erni, R. and Browning, N.D. and Dia, Z.R. and Bradley, J.P.}
}
@article{Erni2006,
  year = {2006},
  title = {Atomic Scale Analysis of Planar Defects in Polycrystalline Diamond},
  pages = {492-497},
  journal = {Microscopy and Microanalysis},
  volume = {12},
  author = {Erni, R. and Freitag, B. and Hartel, P. and {M\"uller}, H. and Tiemeijer, P. and Stam, M. van der and Stekelenburg, M. and Hubert, D. and Specht, P. and Garibay-Febles, V.}
}
@article{Erni2007,
  year = {2007},
  title = {Quantification of the size-dependent energy gap of individual {CdSe} quantum dots by valence electron energy-loss spectroscopy},
  pages = {267-273},
  journal = {Ultramicroscopy},
  volume = {107},
  author = {Erni, R. and Browning, N.D.}
}
@article{Peng2004,
  year = {2004},
  title = {{HAADF-STEM} Imaging With Sub-{\AA}ngstrom Probes, a full Bloch wave analysis},
  pages = {257},
  journal = {Journal of Electron Microscopy},
  volume = {53},
  author = {Peng, Y. and Nellist, P.D. and Pennycook, S.J.}
}
@article{Erni2008,
  year = {2008},
  title = {Prospects for analyzing the electronic properties in nanoscale systems by {VEELS}},
  pages = {270-276},
  journal = {Ultramicroscopy},
  volume = {108},
  author = {Erni, R. and Lazar, S. and Browning, N.D.}
}
@article{Erni2009,
  year = {2009},
  title = {Atomic-resolution Imaging with sub-50-pm Electron Probe},
  pages = {096101},
  journal = {Physical Review Letters},
  volume = {102},
  author = {Erni, R. and Rossell, M.D. and Kisielowski, C. and Dahmen, U.}
}
@article{Malac2007,
  year = {2007},
  title = {Imaging of radiation-sensitive samples in transmission electron microscopes equipped with Zernike phase plates},
  pages = {126-140},
  journal = {Ultramicroscopy},
  volume = {108},
  author = {Malac, M. and Beleggia, M. and Egerton, R. and Zhu, Y.}
}
@article{Bron1999,
  year = {1999},
  title = {The 9 {\AA} projection structure of cytochrome $b_6f$ complex determined by electron crystallography},
  pages = {117-126},
  journal = {Journal of Molecular Biology},
  volume = {287},
  author = {Bron, P. and {Lacap\'ere}, J.-J. and Breyton, C. and Mosser, G.}
}
@inproceedings{Kothleitner2003a,
  year = {2003},
  title = {First Applications of Electron Energy-Loss Spectroscopy with High Energy Resolution},
  booktitle = {Mat. Res. Soc. Symp. Proc.},
  pages = {27-32},
  volume = {738},
  author = {Kothleitner, G. and Mitterbauer, C. and Grogger, W. and Zandbergen, H. and Tiemeijer, P.C. and Freitag, B. and Barfels, M. and Hofer, F.}
}
@article{Saxton1998,
  year = {1998},
  title = {Quantitative comparision of images and transforms},
  pages = {52-60},
  journal = {Journal of Microscopy},
  volume = {1-2},
  author = {Saxton, W.O.}
}
@article{Kothleitner1998,
  number = {5},
  year = {1998},
  title = {Optimization of the Signal to Noise Ratio in {EFTEM} Elemental Maps with Regard to Different Eonization Edge Types},
  pages = {349-357},
  journal = {Micron},
  volume = {29},
  author = {Kothleitner, G. and Hofer, F.}
}
@article{Dwyer2007,
  year = {2007},
  title = {Electron nanodiffraction using sharply focused parallel probes},
  pages = {151104},
  journal = {Applied Physics Letters},
  volume = {90},
  author = {Dwyer, C. and Kirkland, A.I. and Hartel, P. and {M\"uller}, H. and Haider, M.}
}
@article{Dwyer2008,
  year = {2008},
  title = {Method to measure spatial coherence of subangstrom electron beams},
  pages = {021115},
  journal = {Applied Physics Letters},
  volume = {93},
  author = {Dwyer, C. and Erni, R. and Etheridge, J.}
}
@book{Reisner,
  edition = {73},
  year = {1989},
  title = {An early history of the electron microsope in the united states},
  note = {sold out, reprint 2006},
  publisher = {Adavances in electronics and electron physics},
  author = {Reisner, J.H.}
}
@article{Bottcher1995,
  year = {1995},
  title = {Electron cryo-micrsocopy of graphite in amorphous ice},
  pages = {417-424},
  journal = {Ultramicroscopy},
  volume = {58},
  author = {{B\"ottcher}, B.}
}
@article{Coene1992,
  number = {26},
  year = {1992},
  title = {Phase retrieval through focus variation for ultra-resolution in field-emission transmission electron microscopy},
  pages = {3743-3749},
  journal = {Physical Review Letters},
  volume = {69},
  author = {Coene, W.M.J. and Jansen, G. and Beeck, M. op de and Dyck, D. van}
}
@article{Atsuzawa2009,
  year = {2009},
  title = {High-contrast imaging of plastic-embedded tissues by phase contrast electron microscopy},
  pages = {35-45},
  journal = {Journal of Electron Microscopy},
  volume = {58},
  author = {Atusuzawa, K. and et al.}
}
@article{Bailey2004,
  year = {2004},
  title = {Performance Evaluation of a Transmission Scintillator-Based Lens-Coupled 4K CCD Camera for Use in Low-Dose Electron Cryo-Microscopy},
  pages = {S2},
  journal = {Mircoscopy Mircoanal},
  volume = {10},
  author = {Bailey, B. and Agard, D.A. and Sedat, J.W. and Barfels, M. and Chao, H. and Mooney, P.E.}
}
@article{Muto2006,
  number = {4},
  year = {2006},
  title = {Spectral restoration and energy resolution improvement of electron energy-loss spectra by Pixon reconstruction: {I. Principle} and test examples},
  pages = {215-223},
  journal = {Journal of Electron Microscopy},
  volume = {55},
  author = {Muto, S. and Pueter, R.C. and Tatsumi, K.}
}
@article{Alem2009,
  year = {2009},
  title = {Atomically thin hexagonal boron nitride probed by ultrahigh-resolution transmission electron microscopy},
  pages = {155425},
  journal = {Physics Review B},
  volume = {80},
  author = {Alem, N. and Erni, R. and Kisielowski, C. and Rosell, M.D. and Gannett, W. and Zettl, A.}
}
@article{Meyer2008a,
  year = {2008},
  title = {Direct Imaging of Lattice Atoms and Topological Defects in Graphene Membranes},
  pages = {3582-3586},
  journal = {Nano Letters},
  volume = {8},
  author = {Meyer, J.C. and Kisielowski, C. and Erni, R. and Rossell, M.D. and Crommie, M.F. and Zettl, A.}
}
@article{Ishizuka1980,
  year = {1980},
  title = {Contrast transfer of crystal images in {TEM}},
  pages = {55-65},
  journal = {Ultramicroscopy},
  volume = {5},
  author = {Ishizuka, K.}
}
@article{Jia2008,
  year = {2008},
  title = {Atomic-scale study of electric dipoles near charged and uncharged domain walls in ferroelectric films},
  pages = {57-61},
  journal = {Nature},
  volume = {7},
  author = {Jia, C.-L. and Mi, S.-B. and Urban, K. and Verjoiu, I. and Alexe, M. and Hesse, D.}
}
@article{Gonen2004,
  year = {2004},
  title = {Aquaporin-O membrane junctions reveal the structure of a closed water pore},
  pages = {193-196},
  journal = {Nature},
  volume = {429},
  author = {Gonen, T. and Sliz, P. and Kistler, J. and Cheng, Y. and Walz, T.}
}
@article{Jia2004,
  year = {2004},
  title = {High-Resolution Transmission Electron Microscopy Using Negative Spherical Aberration},
  pages = {174-184},
  journal = {Microscopy and Mircoanalysis},
  volume = {10},
  author = {Jia, C.-L. and Lentzen, M. and Urban, K.}
}
@article{Ishitani2002a,
  number = {4},
  year = {2003},
  title = {A Method for Personal Expertise-Independent Evaluation of Image Resolution in Scanning Electron Microscopy},
  pages = {191-203},
  journal = {Scanning},
  volume = {24},
  author = {Ishitani, T. and Sato, M.}
}
@article{Oho2001,
  number = {5},
  year = {2001},
  title = {Strategies for Optimum Use of Superposition Diffractogram in Scanning Electron Microscopy},
  pages = {351-356},
  journal = {Scanning},
  volume = {23},
  author = {Oho, E. and Toyomura, K.}
}
@article{Kazemian2006,
  year = {2006},
  title = {Quantitative secondary electron energy filtering in a scanning electron microscope and its applications},
  pages = {140-150},
  journal = {Ultramicroscopy},
  volume = {107},
  author = {Kazemian, P. and Mentink, S.A.M. and Rodenburg, C. and Humphreys, C.J.}
}
@article{Rau1996,
  year = {1996},
  title = {An Annular Toroidal Backscattered Electron Energy Analyser for Use in Scanning Electron Microscopy},
  pages = {556-561},
  journal = {Scanning},
  volume = {18},
  author = {Rau, E.I. and Robinson, V.N.E.}
}
@article{Bronsgeest2007,
  number = {6},
  year = {2007},
  title = {Extracting the Boersch effect contribution from experimental energy spread measurements for Schottky electron emitters},
  pages = {2049-254},
  journal = {Journal of Vaccuum Science Technology B},
  volume = {25},
  author = {Bronsgeest, M.S. and Barth, J.E. and Schwind, G.A. and Swanson, L.W. and Kruit, P.}
}
@article{Nellist1999,
  year = {1999},
  title = {Incoherent imaging using dynamically scattered coherent electrons},
  pages = {111-124},
  journal = {Ultramicroscopy},
  volume = {78},
  author = {Nellist, P.D. and Pennycook, S.J.}
}
@article{Nellist1998,
  number = {19},
  year = {1998},
  title = {Subangstrom Resolution by Underfocused Incoherent Transmission Electron Microscopy},
  pages = {4156-4159},
  journal = {Physical Review Letters},
  volume = {81},
  author = {Nellist, P.D. and Pennycook, S.J.}
}
@article{Yonekura2006,
  year = {2006},
  title = {Electron energy filtering significantly improves amplitude contrast of frozen-hydrated protein at 300 kV},
  pages = {524-536},
  journal = {Journal of Structural Biology},
  volume = {156},
  author = {Yonekura, K. and Braunfeld, M.B. and Mari-Yonekura, S. and Agard, D.A.}
}
@article{Park2009,
  year = {2009},
  title = {4D ultra fast electron microscopy: Imaging of atomic motions, acoustic resonances, and moire fringe dynamics},
  pages = {7-19},
  journal = {Ultramicroscopy},
  volume = {110},
  author = {Park, H.S. and Baskin, J.S. and Barwick, B. and Kwon, O.H. and Zewail, A.H.}
}
@article{Bahn2008,
  number = {6},
  year = {2008},
  title = {Range of validity of field emission equations},
  pages = {2080-2084},
  journal = {Journal of Vaccuum Science Technology B},
  volume = {26},
  author = {Bahn, A.S. and J.E. and Schwind, G.A. and Swanson}
}
@article{Beck2004,
  year = {2004},
  title = {Nuclear Pore Complex Structure and Dynamics Revealed by Cryoelectron Tomography},
  pages = {1387-1390},
  journal = {Science},
  volume = {306},
  author = {Beck, M. and {F\"orster}, F. and Ecke, M. and Plitzko, J.M. and Melchior, F. and Gerisch, G. and Baumeister, W. and Medalia, O.}
}
@article{Ban2000,
  year = {2000},
  title = {The Complete Atomic Structure of the Large Ribosomal Subunit at 2.4 {\AA} Resolution},
  pages = {905-920},
  journal = {Science},
  volume = {289},
  author = {Ban, N. and Nissen, P. and Hansen, J. and Moore, P.B. and Steitz, T.A.}
}
@article{Havelka1993,
  year = {1993},
  title = {Projection structure of Halorhodopsin from Halobacterium halobium at 6 {\AA} resolution obtrained by electron cryo-microscopy},
  pages = {837-846},
  journal = {Journal of Molecular Biology},
  volume = {234},
  author = {Havelka, W. A. and Henderson, R. and Heymann, J.A.W. and Oesterhelt, D.}
}
@article{Havelka1995,
  year = {1995},
  title = {Three-dimensional structure of halorhodopsin at 7 {\AA} resolution},
  pages = {726-738},
  journal = {Journal of Molecular Biology},
  volume = {247},
  author = {Havelka, W.A. and Henderson, R. and Oesterhelt, D.}
}
@article{Ruprecht2001,
  year = {2001},
  title = {Determining the structure of biological macromolecules by transmission electron microscopy, single particle analysis and 3D reconstruction},
  pages = {121-164},
  journal = {Biophysics and Molecular Biology},
  volume = {75},
  author = {Ruprecht, J. and Nield, J.}
}
@article{Pennycook2000,
  year = {2000},
  title = {Z-Contrast Imaging in an Aberration-Corrected Scanning Transmission Electron Microscope},
  pages = {343},
  journal = {Microscopy and Microanalysis},
  volume = {6},
  author = {Pennycook, S.J. and Rafferty, B. and Nellist, P.D.}
}
@inproceedings{Pennycook2003,
  year = {2003},
  title = {Quantum Mechanical Resolution Limits to Imaging and Spectroscopy in the Transmission Electron Microscope},
  booktitle = {From the Atomic to the Nano Scale},
  pages = {126},
  editor = {McGuire, J.},
  publisher = {Old Dominion Universtity},
  author = {Pennycook, S.J. and Lupini, A.R. and Varela, M. and Borisevich, A. and Peng, Y. and Nellist, P.D.}
}
@article{Pennycook2009,
  year = {2009},
  title = {Aberration corrected scanning transmission electron microscopy: from atomic imaging and analysis to solving energy problems},
  pages = {3709-3733},
  journal = {Philosophical Transactions of the Royal Society},
  volume = {367},
  author = {Zach2009}
}
@article{Pennycook1990,
  year = {1990},
  title = {High-Resolution Incoherent Imaging of Crystals},
  pages = {938},
  journal = {Physical Review Letters},
  volume = {64},
  author = {Pennycook, S.J. and Jesson, D.E.}
}
@article{Muto2006a,
  number = {4},
  year = {2006},
  title = {Spectral restoration and energy resolution improvement of electron energy-loss spectra by Pixon reconstruction: {II. Application} to practical {ELNES} analysis of low {SNR}},
  pages = {225-230},
  journal = {Journal of Electron Microscopy},
  volume = {55},
  author = {Muto, S. and Tatsumi, K. and Puetter, R.C. and Yosida, T. and Yamamoto, Y. and Sasano, Y.}
}
@article{Kujawa1990,
  year = {1990},
  title = {Second-rank aberrations of a magnetic imaging energy filter: measurement and correction},
  pages = {39-46},
  journal = {Optik},
  volume = {86},
  author = {Kujawa, S. and Krahl, D. and Niedrig, H. and Zeitler, E.}
}
@article{Kujawa1992,
  year = {1992},
  title = {Performance of a low-noise CCD camera adapted to a transmission electron microscope},
  pages = {395-403},
  journal = {Ultramicrosopy},
  volume = {46},
  author = {Kujawa, S. and Krahl, D.}
}
@article{Lugg2010,
  year = {2010},
  title = {Energy-filtered transmission electron microscopy based on inner-shell ionization},
  journal = {Ultramicroscopy},
  author = {Lugg, N.R. and Freitag, B. and Findlay, S.D. and Allen, L.J..}
}
@article{Avoort2005,
  number = {12},
  year = {2005},
  title = {Aberration retrieval from the intensity point-spread function in the focal region using the extended {Nijboer-Zernike} approach},
  pages = {1695-1728},
  journal = {Journal of Modern Optics},
  volume = {52},
  author = {Avoort, C. van der and Braat, J.J.M. and Dirksen, P. and Janssen, A.J.E.M.}
}
@article{Eastham2009,
  year = {2009},
  title = {A design for a subminiature, low energy scanning electron microscope with atomic resolution},
  pages = {014702},
  journal = {Journal of Appplied Physics},
  volume = {105},
  author = {Eastham, D.A. and Edmondson, P. and Greene, S. and Donnelly, S. and Olsson, E. and Svensson, K. and Bleloch, A.}
}
@article{Schonhense2002,
  number = {6},
  year = {2002},
  title = {Correction of chromatic and spherical aberration in electron microscopy utilizing the time structure of pulsed excitation sources},
  pages = {2526-2534},
  journal = {Journal of Vacuum Science Technology B},
  volume = {20},
  author = {{Sch\"onhense}, G. and Spiecker, H.}
}
@article{Sawada2005,
  number = {2},
  year = {2005},
  title = {Experimental evaluation of a spherical aberration-corrected {TEM} and {STEM}},
  pages = {119-121},
  journal = {Journal of Electron Microscopy},
  volume = {54},
  author = {Sawada, H. and Tomita, T. and Naruse, M. and Honda, T. and Hambridge, P. and Hartel, P. and Haider, M. and Hetherington, C. and Doole, R. and Kirkland, A. and Hutchison, J. and Titchmarsh, J. and Cockayne, D.}
}
@article{Hartel1996,
  year = {1996},
  title = {Conditions and reasons for incoherent imaging in {STEM}},
  pages = {93-114},
  journal = {Ultramicroscopy},
  volume = {63},
  author = {Hartel, P. and Rose, H. and Dinges, C.}
}
@article{Egelman2007,
  year = {2007},
  title = {The iterative helical real space reconstruction method: Surmounting the problems posed by real polymers},
  pages = {83-94},
  journal = {Journal of Strcutural Biology},
  volume = {157},
  author = {Egelman, E.H.}
}
@article{Sawada2009,
  year = {2009},
  title = {Correction of higher order geometrical aberration by triple 3-fold astigmatism field},
  pages = {1-7},
  journal = {Journal of electron microscopy},
  author = {Sawada, H. and Sasaki, T. and Hosokawa, F. and Yuasa, S. and Terao, M. and Kawazoe, M .and Nakamichi, T. and Kaneyama, T. and Kondo, Y. and Kimoto, K. and Suenada, K.}
}
@article{Sawada2008,
  year = {2008},
  title = {Measurement method of aberration from Ronchigram by autocorrelation function},
  pages = {1467-1475},
  journal = {Ultramicroscopy},
  volume = {108},
  author = {Sawada, H. and Sannomiya, T. and Hosokawa, F. and Nakamichi, T. and Kaneyama, T. and Tomita, T. and Kondo, Y. and Tanaka, T. and Oshima, Y. and Tanishiro, Y. and Takayanagi, K.}
}
@article{Erni2005a,
  year = {2005},
  title = {Valence electron energy-loss spectroscopy in monochromated scanning transmission electron microscopy},
  pages = {176-192},
  journal = {Ultramicroscopy},
  volume = {104},
  author = {Erni, R. and Browning, N.D.}
}
@article{Gilbert1972,
  number = {1},
  year = {1972},
  title = {Iterative Methods for the three-dimensional reconstruction of a object from projections},
  pages = {105-117},
  journal = {Journal of Theoretical Biology},
  volume = {36},
  author = {Gilbert, P.}
}
@article{Shiue2009,
  year = {2009},
  title = {Phase TEM for biological imaging utilizing a Boersch electrostatic phase plate: theory and practice},
  pages = {135-145},
  journal = {Journal of Electron Microscopy},
  volume = {58},
  author = {Shiue, J. and et al.}
}
@techreport{Zande2005,
  number = {PR-TN-2005/00002},
  year = {2005},
  title = {Local magnification in Ronchigrams (Aberration retrieval in {STEM})},
  type = {Technical Note},
  address = { Eindhoven, The Netherlands},
  institution = {Philips Research},
  author = {Zande, M.J. van der and Kok, C.}
}
@article{Rafferty1998,
  number = {16},
  year = {1998},
  title = {Direct and indirect transitions in the region of the band gap using electron-energy-loss spectroscopy},
  pages = {10326-10337},
  journal = {Physical Review B},
  volume = {58},
  author = {Rafferty, B. and Brown, L.M.}
}
@article{Lichte1986,
  year = {1986},
  title = {Electron Holography approaching atomic resolution},
  pages = {293-304},
  journal = {Ultramicroscopy},
  volume = {20},
  author = {Lichte, H.}
}
@article{Bosman2009,
  year = {2009},
  title = {Nanoscale band gap spectroscopy on ZnO and GaN-based compounds with a monochromated electron microscope},
  pages = {101110},
  journal = {Applied Physics Letters},
  volume = {95},
  author = {Bosman, M. and Tang, L.J. and Ye, J.D. and Zhang, Y. and Keast, V.J.}
}
@article{Conway1999,
  year = {1999},
  title = {Methods for Reconstructing Density Maps of Single Particles from Cryoelectron Micrographs to Subnanometer Resolution},
  pages = {106-118},
  journal = {Journal of Strcutural Biology},
  volume = {128},
  author = {Conway, J.F. and Steven, A.C.}
}
@article{Muller2008a,
  year = {2008},
  title = {Aberration-corrected optics: from an idea to a device},
  pages = {167-178},
  journal = {Physcis Procedia},
  volume = {1},
  author = {Muller, H. and Uhlemann, S. and Hartel, P. and Haider, M.}
}
@article{Chiu1977,
  year = {1977},
  title = {Factors affecting high resolution fixed-beam transmission electron microscopy},
  pages = {207-217},
  journal = {Ultramicroscopy},
  volume = {2},
  author = {Chiu, W. and Glaeser, R.M.}
}
@article{HitatchiSEM2007,
  number = {3},
  year = {2007},
  title = {{STEM} Imaging of Lattic Fringes and beyond in a {UHR} In-Lens Field-Emission {SEM}},
  pages = {12-16},
  journal = {Microscopy Today},
  author = {Ngo, V. van and Hernandez, M. and Roth, B. and Joy, D.C.}
}
@article{Schatz1997,
  year = {1997},
  title = {Angular reconstitution in three-dimensional electron microscopy: practical and technical aspects},
  pages = {179-193},
  journal = {Scanning Microscopy},
  volume = {11},
  author = {Schatz, M. and Orlova, E.V. and Harauz, G. and Stark, H. and Dube, P. and Zemlin, F. and Heel, M. van}
}
@article{Isabell2009,
  year = {2009},
  title = {Development of a 200kV Atomic resolution Analytical Electron Microscope},
  pages = {8-10},
  journal = {Microscopy Today},
  author = {Isabell, T. and Brink, J. and Kawasaki, M. and Armbruster, B. and Ishikawa, I. and Okunishi, E. and Sawada, H. and Okura, Y. and Yamazaki, K. and Ishikawa, T. and Kawazu, M. and Hori, M. and Terao, M. and Kanno, M. and Tanba, S. and Kondo, Y.}
}
@article{Penczek2002a,
  year = {2002},
  title = {Resolution Measures in Single Particle Analysis},
  author = {Penczek, P.A.}
}
@article{Majorovits2007,
  year = {2007},
  title = {Optimizing phase contrast in transmission electron microscopy with an electrostatic (Boersch) phase plate},
  pages = {213-226},
  journal = {Ultramicroscopy},
  volume = {107},
  author = {Majorovits, E. and Barton, B. and {Schulthei\ss}, K. and Perez-Willard, F. and Gerthsen, D. and {Schr\"oder}, R.R.}
}
@article{Baumeister2004,
  year = {2004},
  title = {Mapping molecular landscapes inside cells},
  pages = {865-872},
  journal = {Biological Chemistry},
  volume = {385},
  author = {Baumeister, W.}
}
@article{Harrach1995,
  year = {1995},
  title = {Instrumental factors in high-resolution {FEG STEM}},
  pages = {1-5},
  journal = {Ultramicroscopy},
  volume = {58},
  author = {Harrach, H.S. von}
}
@article{Baxter2007,
  year = {2007},
  title = {SPIRE: The SPIDER Reconstruction Engine},
  pages = {56-63},
  journal = {Journal of Strcutural Biology},
  volume = {157},
  author = {Baxter, W.T. and Leith, A. and Frank, J.}
}
@article{Rafferty2001,
  number = {3},
  year = {2001},
  title = {On the origin of transverse incoherence in {Z-}constrast {STEM}},
  pages = {227-233},
  journal = {Journal of Electron Microscopy},
  volume = {50},
  author = {Rafferty, B. and Nellist, P.D. and Pennycook, S.J.}
}
@article{Drummy2004,
  year = {2004},
  title = {Low-voltage electron microscopy of polymer and organic molecular thin films},
  pages = {247-256},
  journal = {Ultramicroscopy},
  volume = {99},
  author = {Drummy, L.F. and Yang, J. and Martin, D.C.}
}
@article{Jiang2006,
  year = {2006},
  title = {Experimental and theoretical improvements on understanding of the {O K-edge} of {TeO}$_2$},
  pages = {123-129},
  journal = {Ultramicroscopy},
  volume = {106},
  author = {Jiang, N. and Jiang, B. and Erni, R. and Browning, N.D. and Spence, J.C.H.}
}
@article{Jiang2005,
  year = {2003},
  title = {Applications of a bilateral denoising filter in biological electron microscopy},
  pages = {114-122},
  journal = {Journal of Structural Biology},
  volume = {144},
  author = {Jiang, W. and Baker, M.L. and Wu, Q. and Bajaj, C. and Chiu, W.}
}
@article{Jiang2008,
  year = {2008},
  title = {Spatial control over atomic layer deposition using microcontact-printed resists},
  pages = {8799-8807},
  journal = {Surface & Coatings Technology},
  volume = {201},
  author = {Jiang, X. and chen, R. and Bent, S.F.}
}
@article{Chen2007,
  year = {2007},
  title = {A dose-rate effect in single-particle electron microscopy},
  pages = {92-100},
  journal = {Journal of Structural Biology},
  volume = {161},
  author = {Chen, J.Z. and Sachse, C. and Xu, C. and Mielke, T. and Spahn, C.M.T. and Grigorieff, N.}
}
@article{Alloyeau2010,
  year = {2010},
  title = {Imaging of soft and hard materials using a Boersch phase plate in a transmission electron microscope},
  pages = {563-570},
  journal = {Ultramicroscopy},
  volume = {110},
  author = {Alloyeau, D. and Hsieh, W.K. and Anderson, E.H. and Hilken, L. and Benner, G. and Meng, X. and Chen, F.R. and Kisielowski, C.}
}
@article{Heel2005,
  year = {2005},
  title = {Fourier shell correlation threshold criteria},
  pages = {250-262},
  journal = {Journal of Structural Biology},
  volume = {151},
  author = {Heel, M. van and Schatz, M.}
}
@article{Heel2000,
  number = {4},
  year = {2000},
  title = {Single-particle electron cryo-microscopy: towards atomic resolution},
  pages = {307-369},
  journal = {Quarterly Review of Biophysics},
  volume = {33},
  author = {Heel, M. van and Gowen, B. and Matadeen, R. and Orlova, E.V. and Finn, R. and Pape, T. and Cohen, D. and Stark, H. and Schmidt, R. and Schatz, M. and Patwardhan, A.}
}
@article{Walther2006a,
  year = {2006},
  title = {Preliminary Results from the First Monochromated and Aberration Corrected 200-kV Field-Emission Scanning Transmission Electron Microscope},
  pages = {498-505},
  journal = {Microscopy and Microanalysis},
  volume = {12},
  author = {Walther, T. and Stegmann, H.}
}
@article{Yamaguchi2009,
  year = {2009},
  title = {Smart specimen preparation for freeze substitution and serial ultrathin sectioning of yeast cells},
  pages = {261-266},
  journal = {Journal of Electron Microscopy},
  volume = {58},
  author = {Yamaguchi, M. and Okada, H. and Namiki, Y.}
}
@article{Sparrow1916,
  year = {1916},
  title = {On spectroscopic resolving power},
  pages = {76-86},
  journal = {Astrophysical Journal},
  volume = {44},
  author = {Sparrow, C.M.}
}
@article{Rose1984,
  year = {1984},
  title = {Information transfer in transmission electron microscopy},
  pages = {173-192},
  journal = {Ultramicroscopy},
  volume = {15},
  author = {Rose, H.}
}
@article{Martinez2008,
  year = {2008},
  title = {The use of multipole fields for aberration correctionin pi/2 Wien filters},
  pages = {193-198},
  journal = {Physics Procedia},
  volume = {1},
  author = {Martinez, G. and Tsuno, K.}
}
@article{Driel2009,
  year = {2009},
  title = {Tools for correlative cryo-fluorescence microscopy and cryo-electron tomography applied to whole mitochondria in human endothelial cells},
  pages = {669-684},
  journal = {European Journal of Cell Biology},
  volume = {88},
  author = {Driel, L.F. van and Valentijn, J.A. and Valentijn, K.M. and Koning, R.I. and Koster, A.J.}
}
@article{Pomfret2007,
  year = {2007},
  title = {Application of the iterative helical real-space reconstruction method to large membranous tubular crystals of P-type ATPases},
  pages = {106-116},
  journal = {Journal of Strcutural Biology},
  volume = {157},
  author = {Pomfret, A.J. and Rice, W.J. and Stokes, D.L.}
}
@article{Beek1996,
  year = {1996},
  title = {Wave function reconstruction in {HRTEM}: the parabola method},
  pages = {167-183},
  journal = {Ultramicroscopy},
  volume = {64},
  author = {Beek, M. op de and Dyck, D. van and Coene, W.}
}
@article{Lichte2008,
  year = {2007},
  title = {Performance limits of electron holography},
  pages = {256-262},
  journal = {Ultramicroscopy},
  volume = {108},
  author = {Lichte, H.}
}
@article{Hue2005,
  year = {2005},
  title = {Calibration of Projector Lens Distortions for Quantitative High-Resolution TEM},
  pages = {552-553},
  journal = {Microsc Microanal},
  volume = {11 (Suppl 2)},
  author = {Hue, F. and Johnson, C.L. and Lartigue-Korinek, S. and Wang, G. and Buseck, P.R. and Hytch, M.J.}
}
@article{Kaiser2002,
  year = {2002},
  title = {Direct observation of defect-mediated cluster nucleation},
  pages = {102-106},
  journal = {Nature materials},
  volume = {1},
  author = {Kaise, U. and Muller, D.A. and Grazul, J.L. and Chuvilin, A. and Kawasaki, M.}
}
@article{Turchanin2009,
  year = {2009},
  title = {One Nanometer Thin Carbon Nanosheets with Tunable Conductivity and Stiffness},
  pages = {1233-1237},
  journal = {Advanced Materials},
  volume = {21},
  author = {Turchanin, A. and Beyer, A. and Nottbohm, T. and Zhang, X. and Stosch, R. and and Sologubenko, A.S. and Mayer, J. and Hinze, P. and Weimann, T. and {G\"olzh\"auser}}
}
@article{Mkhoyan2006,
  year = {2006},
  title = {Direct Determination of Local Lattice Polarity in Crystals},
  pages = {1354},
  journal = {Science},
  volume = {312},
  author = {Mkhoyan, K.A. and Batson, P.E. and Cha, J. and Schaff, W.J. and Silcox, J.}
}
@inproceedings{Sawada2006,
  title = {Method to Measure Aberrations from Ronchigram by Auto-Correlation Function},
  journal = {Journal of Electron Microscopy},
  volume = {IMC 16},
  address = {Sapporo, Japan},
  author = {Sawada, H. and Sannomiya, T. and Hosokawa, F. and Kaneyama, T. and Kondo, Y. and Tanishiro, Y. and Takayanagi, K.}
}
@article{Allen2003,
  year = {2003},
  title = {Atomic Resolution Electron Energy Loss Spectroscopy Imaging in Aberration Corrected Scanning Transmission Electron Microscopy},
  pages = {105503},
  journal = {Physical Review Letters},
  volume = {91},
  author = {Allen, L.J. and Findlay, S.D. and Lupini, A.R. and Oxley, M.P. and Pennycook, S.J.}
}
@article{Erni2010,
  year = {2010},
  title = {Optimization of exit-plane waves restored from {HRTEM} through-focal series},
  pages = {151-161},
  journal = {Ultramicroscopy},
  volume = {110},
  author = {Erni, R. and Rossell, M.D. and Nakashima, P.N.H.}
}
@article{Meyer1998,
  year = {1998},
  title = {The effects of electron and photon scattering on signal and noise transfer properties of scintillators in CCD cameras used for electron detection},
  pages = {23-33},
  journal = {Ultramicroscopy},
  volume = {75},
  author = {Meyer, R.R. and Krikland, A.I.}
}
@article{Lencova2008,
  year = {2008},
  title = {A pitfall in the calculation of higher order aberrations},
  pages = {737-740},
  journal = {Ultramicroscopy},
  volume = {108},
  author = {Lencova, B. and Lenc, M. and Hawkes, P.W.}
}
@article{Browning1996,
  year = {1996},
  title = {Direct Experimental Determination of the Atomic Structure at Internal Interfaces},
  pages = {1779},
  journal = {Journal of Physics D},
  volume = {29},
  author = {Browning, N.D. and Pennycook, S.J.}
}
@article{Fellmann2002,
  year = {2002},
  title = {A relational database for {cryoEM}: experience at one year and 50000 images},
  pages = {273-282},
  journal = {Journal of Structural Biology},
  volume = {137},
  author = {Fellmann, D. and Pulokas, J. and MIlligan, R.A. and Carragher, B. and Potter, C.S.}
}
@article{Mueller2007,
  number = {11},
  year = {2006},
  title = {Biological Scanning Transmission Electron Microscopy: Imaging and Single Molecule Mass Determination},
  pages = {749-752},
  journal = {Chimia},
  volume = {60},
  author = {{M\"uller}, S.A. and Engel, A.}
}
@article{Rhinow2008,
  year = {2008},
  title = {Electron cryo-microscopy of biological specimens on conductive titanium-silicon metal glass films},
  pages = {698-705},
  journal = {Ultramicroscopy},
  volume = {108},
  author = {Rhinow, D. and Kuhlbrandt, W.}
}
@article{Nomaguchi2004,
  year = {2004},
  title = {Separation of linear and non-linear imaging components in high-resolution transmission electron microscope images},
  pages = {403-406},
  journal = {Journal of Electron Microscopy},
  volume = {53},
  author = {Nomaguchi, T. and Kawasaki, T. and Kimura, Y. and Takai, Y.}
}
@article{Browning1997,
  year = {1997},
  title = {{EELS} in the {STEM}: Determination of Materials Properties on the Atomic Scale},
  pages = {333},
  journal = {Micron},
  volume = {28},
  author = {Browning, N.D. and Wallis, D.J. and Nllist, P.D. and Pennycook, S.J.}
}
@article{Gipson2007,
  year = {2007},
  title = {2dx - User-friendly image processing for 2D crystals},
  pages = {64-72},
  journal = {Journal of Strcutural Biology},
  volume = {157},
  author = {Gipson, B. and Zeng, X. and Zhang, Z.Y. and Stahlberg, H.}
}
@article{Oho1997,
  number = {7},
  year = {1997},
  title = {New Generation Scanning Electron Microscopy Technology Based on the Concept of Active Image Processing},
  pages = {483-488},
  journal = {Scanning},
  volume = {19},
  author = {Oho, E. and Hoshino, Y. and Ogashiwa, T.}
}
@article{Penczek2002,
  year = {2002},
  title = {Three-dimensional spectral signal-to-noise ratio for a class of reconstruction algorithms},
  pages = {34-46},
  journal = {Journal of Structural Biology},
  volume = {138},
  author = {Penczek, P.A.}
}
@article{Gu2003,
  number = {23},
  year = {2003},
  title = {3D electron microscopy reveals the variables deposition and protein dynamics of the peripheral pyruvate dehydrogenase component about the core},
  pages = {7015-7020},
  journal = {Proceedings of the National Academy of Sciences of the United States of America},
  volume = {100},
  author = {Gu, Y. and Zhou, Z.H. and McCarthy, D.B. and Reed, L.J. and Stoops, J.K.}
}
@article{Bouwer2004,
  year = {2004},
  title = {Automated most-probable loss tomography of thick selectively stained biological specimens with quantitative measurement of resolution improvement},
  pages = {297-306},
  journal = {Journal of Structural Biology},
  volume = {148},
  author = {Bouwer, J.C. and Mackey, M.R.and Lawrence, A. and Deerinck, T.J. and Jones, Y.Z. and Terada, M. and Martone, M.E. and Peltier, S. and Ellisman, M.H.}
}
@article{Hell2007,
  year = {2007},
  title = {Far-Field Optical Nanoscopy},
  pages = {1153-1158},
  journal = {Science},
  volume = {316},
  author = {Hell, S.W.}
}
@techreport{Bosch2004,
  number = {PR-TN-2004/00364},
  year = {2004},
  title = {The use of mutual information in image registration},
  type = {Technical Note},
  address = { Eindhoven, The Netherlands},
  institution = {Philips Research},
  author = {Bosch, E.G.T.}
}
@article{Kunji2001,
  year = {2001},
  title = {Electron Crystallographic Analysis of Two-Twodimensional Crystals of Sensory Rhodopsin II:A 6.9 {\AA} Projection Structure},
  pages = {279-293},
  journal = {Journal of Molecular Biology},
  volume = {308},
  author = {Kunji, E.R.S. and Spudich, E.N. and Grisshammer, R. and Henderson, R. and Spudich, J.L.}
}
@article{Reichenbach1991,
  year = {1991},
  title = {Characterizing digital image acquisition devices},
  pages = {170-177},
  journal = {Optical Engineering},
  volume = {30},
  author = {Reichenbach, S.E. and Park, S.K. and Narayanswamy, R.}
}
@article{Bos1993,
  year = {1993},
  title = {Resolvability of the parameters of multiexponentials and other sum models},
  pages = {313-322},
  journal = {IEEE Transactions of Signal Processing},
  volume = {41},
  author = {Bos, A. van den and Swarte, J.H.}
}
@article{Gu2007,
  year = {2007},
  title = {Band-gap measurements of direct and indirect semiconductors using monochromated electrons},
  pages = {195214},
  journal = {Physical Review B},
  volume = {75},
  author = {Gu, L. and Srot, V. and Sigle, W. and Koch, C. and Aken, P. van and Scholz, F. and Thapa, S.B. and Kirchner, C. and Jetter, M. and Ruehle, M.}
}
@article{Kisielowski2008,
  year = {2008},
  title = {Detection of Single Atoms and Buried Defects in Three Dimensions by Aberration-Corrected Electron Microscope with 0.5-AA Information Limit},
  pages = {469-477},
  journal = {Microscopy and Microanalysis},
  volume = {14},
  author = {Kisielowski, C.}
}
@article{Nellist2006,
  year = {2006},
  title = {Confocal operation of a transmission electron microscope with two aberration correctors},
  pages = {124105},
  journal = {Applied Physics Letters},
  volume = {89},
  author = {Nellist, P.D. and behan, G. and Kirkland, A.I. and Hetherington, C.J.D.}
}
@article{Scheres2005,
  year = {2005},
  title = {Fast maximum-likelihood refinement of electron microscopy images},
  pages = {ii243-ii244},
  journal = {Bioinfomatics},
  volume = {21 S2},
  author = {Scheres, S.H.W. and Valle, M. and Carazo, J.-M.}
}
@article{Girit2009,
  year = {2009},
  title = {Graphene at the Edge: Stability and Dynamics},
  pages = {1705-1707},
  journal = {Science},
  volume = {323},
  author = {Girit, C.O. and Meyer, J.C. and Erni, R.and Rossel, M.D. and Kisielowski, C. and Yang, Li. and Park, C.-H. and Crommie, M.F. and Cohen, M.L. and Louie, S.G. and Zettl, A.}
}
@article{Yamazaki2005,
  year = {2005},
  title = {Precise measurement of third-order spherical aberration using low-order zone-axis {Ronchigrams}},
  note = {in press},
  journal = {Ultramicroscopy},
  author = {Yamazaki, T. and Kotaka, Y. and Kikuchi, Y. and Watanabe, K.}
}
@article{Ronchi1964,
  number = {4},
  year = {1964},
  title = {Forty years of history of a grating interferometer},
  pages = {437-452},
  journal = {Applied Optics},
  volume = {3},
  author = {Ronchi, V.}
}
@article{Lorusso2003,
  number = {4},
  year = {2003},
  title = {Experimental Resolution Measurement in Critical Dimension Scanning Electron Microscope Metrology},
  pages = {175-180},
  journal = {Scanning},
  volume = {25},
  author = {Lorusso, G.F. and Joy, D.C.}
}
@article{Yin2003,
  year = {2003},
  title = {A statistical approach to computer processing of cryo-electron microscope images: virion classification and {3-D} reconstruction},
  pages = {24-50},
  journal = {Journal of Structural Biology},
  volume = {144},
  author = {Yin, Z. and Zheng, Y. and Doerschuk, P.C. and Nararajan, P. and Johnson, J.E.}
}
@article{Bammes2009,
  year = {2009},
  title = {Radiation damage effects at four specimen temperatures from 4 K to 100 K},
  journal = {Journal of Structural Biology},
  author = {Bammes, B.E. and Jakana, J. and Schmid, M.F. and Chiu, W.}
}
@article{Shao1988,
  number = {11},
  year = {1988},
  title = {On the fifth order aberration in a sextupole corrected probe forming system},
  pages = {2428-2437},
  journal = {Rev. Sci. Instrum.},
  volume = {59},
  author = {Shao, Z.}
}
@article{Haas1999,
  year = {1999},
  title = {A Symmetry Mismatch at the Site of {RNA} Packaging in the Polymerase Complex of {dsRNA} Bacteriophage $\phi$6},
  pages = {357-372},
  journal = {Journal of Molecular Biology},
  volume = {294},
  author = {Haas, F. de and Paatero, A.O. and Mindich, L. and Bamford, D.H. and Fuller, S.D.}
}
@article{Glaeser2004,
  year = {2004},
  title = {Specimen charging on thin films with one conducting layer: discussion of physical principles},
  pages = {790-796},
  journal = {Microscopy and Microanalysis},
  volume = {10},
  author = {Glaeser, R.M. and Downing, K.H.}
}
@article{Takai2006,
  year = {2006},
  title = {Molecular-scale imaging of unstained deoxyribonucleic acid fibers by phase transmission electron microscopy},
  pages = {133903},
  journal = {Applied Physics Letters},
  volume = {89},
  author = {Takai, Y. and Nomaguchi, T. and Matsushita, S. and Kimura, Y.}
}
@article{Gabashvili2000,
  year = {2000},
  title = {Solution Structure of the {E. coli} {70S} Ribosome at 11.5{\AA} Resolution},
  pages = {537-549},
  journal = {Cell},
  volume = {100},
  author = {Gabashvili, I.S. and Agrawal, R.K. and Spahn, C.M.T. and Gracssucci, R.A. and Svergun, D.I. and Frank, J. and Penczek, P.}
}
@article{Kabius2009,
  year = {2009},
  title = {First application of Cc-corrected imaging for high-resolution and energy-filtered TEM},
  pages = {1-9},
  journal = {Journal Of Electron Microscopy},
  volume = {1},
  author = {Kabius, B. and Hartel, P. and Haider, M. and {M\"uller}, H. and Uhlemann, S. and Loebau, U. and Zach, J. and Rose, H.}
}
@article{Rose1977,
  year = {1977},
  title = {Nonstandard imaging methods in electron microscopy},
  pages = {251-267},
  journal = {Ultramicroscopy},
  volume = {2},
  author = {Rose, H.}
}
@article{HohmannMarriott2009_SI,
  number = {10},
  year = {2009},
  title = {Nanoscale 3D cellular imaging by axial scanning transmission electron tomography},
  pages = {729-732},
  note = {Supplementary Information},
  journal = {Nature Methods},
  volume = {6},
  author = {Hohmann-Marriott, M.F. and Sousa, A.A. and Azari, A.A. and Glushakova, S. and Zhang, G. and Zimmerberg, J. and Leapmann, R.D.}
}
@article{Zhu2009,
  year = {2009},
  title = {Imaging single atoms using secondary electrons with an aberration-corrected electron microscope},
  pages = {808-811},
  journal = {Nature Methods},
  volume = {8},
  author = {Zhu, Y. and Inada, H. and Nakamura, K. and Wall, J.}
}
@article{Pennycook1988,
  year = {1988},
  title = {Chemically Sensitive Structure Imaging with a Scanning Transmission Electron Microscope},
  pages = {565},
  journal = {Nature},
  volume = {336},
  author = {Pennycook, S.J. and Boatner, L.A.}
}
@article{Lehmann1999,
  year = {1999},
  title = {Electron Holography at atomic dimensions - present state},
  pages = {249-263},
  journal = {Materials Characterization},
  volume = {42},
  author = {Lehmann, M. and Lichte, H. and Geiger, D. and Lang, G. and Schweda, E.}
}
@article{Zuo2003,
  year = {2003},
  title = {Atomic Resolution Imaging of a Carbon Nanotube from Diffraction Intensities},
  pages = {1419-1421},
  journal = {Science},
  volume = {300},
  author = {Zuo, J.M. and Vartanyants, I. and Gao, M. and Zhang, R. and Nagahara, L.A.}
}
@article{Sousa2009,
  year = {2009},
  title = {Monte Carlo electron-trajectory simulations in bright-field and dark-field STEM:Implications for tomography of thick biological sections},
  pages = {213-221},
  journal = {Ultramicroscopy},
  volume = {109},
  author = {Sousa, A.A. and Hohmann-Marriott, M.F. and Zhang, G. and Leapman, R.D.}
}
@article{Downing1975,
  year = {1975},
  title = {Discrimination of Heavy and Ligth Components in Electron Microscopy Using Single-Sideband Holographic Techniques},
  pages = {155-175},
  journal = {Optik},
  volume = {42},
  author = {Downing, K.H. and Siegel, B.M.}
}
@article{Takeguchi2008,
  year = {2008},
  title = {Development of a stage-scanning system for high-resolution confocal STEM},
  pages = {123-127},
  journal = {Journal of Electron Microscopy},
  volume = {57},
  author = {Takeguchi, M. and Hasimoto, A. and Shimojo, M. and Mitsuishi, K. and Furuya, K.}
}
@article{Nottbohm2008,
  year = {2008},
  title = {Novel carbon nanosheets as support for ultrahigh-resolution structural analysis of nanoparticles},
  pages = {885-892},
  journal = {Ultramicroscopy},
  volume = {108},
  author = {Nottbohm, C.T. and Beyer, A. and Sologubenko, A.S. and Ennen, I. and {H\"utten}, A. and {R\"osner}, H. and Eck, W. and Mayer, J. and {G\"olzh\"auser}}
}
@article{Mitterbauer2003,
  year = {2003},
  title = { Electron energy-loss near-edge structures of 3d transition metal oxides recorded at high-energy resolution},
  pages = {469-480},
  journal = {Ultramicroscopy},
  volume = {96},
  author = {Mitterbauer, C. and Kothleitner, G. and Grogger, W. and Zandbergen, H. and Freitag, B. and Tiemeijer, P.C. and Hofer, F.}
}
@article{Morniroli1992,
  year = {1992},
  title = {Microdiffratction as a tool for crystal structure identification and determination},
  pages = {219-239},
  journal = {Ultramicroscopy},
  volume = {45},
  author = {Morniroli, J.P. and Steeds, J.W.}
}
@article{Hetherington2008,
  year = {2008},
  title = {High-Resolution TEM and the Application of Direct and Indirect Aberration Correction},
  pages = {60-67},
  journal = {Microscopy and Microanalysis},
  volume = {14},
  author = {Hetherington, C.J.D. and Chang, L.Y.S. and Haigh, S. and Nellist, P.D. and Gontard, L.C. and Dunin-Borkowski, R.E. and Kirkland, A.I.}
}
@article{Hartwell1999,
  year = {1999},
  title = {From molecular to modular cell biology},
  pages = {C47-C50},
  journal = {Nature},
  volume = {402},
  author = {Hartwell, L.H. and Hopfield, J.J. and Leibler, S. and Murray, A.M.}
}
@article{Uno2005,
  year = {2005},
  title = {Aberration correction and its automatic control in scanning electron microscopes},
  pages = {438-448},
  journal = {Optik},
  volume = {116},
  author = {Uno, S. and Honda, K. and Nakamura, N. and Matsuya, M. and Zach, J.}
}
@article{Joy2002,
  number = {1},
  year = {2002},
  title = {{SMART}- a programm to measure {SEM} resolution and imaging performance},
  pages = {24-34},
  journal = {Journal of Microscopy},
  volume = {208},
  author = {Joy, D.C.}
}
@article{Danev2006,
  year = {2006},
  title = {Applicability of thin film phase plates in biological electron microscopy},
  pages = {35-43},
  journal = {Biophysics},
  volume = {2},
  author = {Danev, R. and Nagayama, K.}
}
@article{Malac2006,
  year = {2006},
  title = {Bright-field {TEM} imaging of single molecules: Dream or near future?},
  pages = {40-49},
  journal = {Ultramicroscopy},
  volume = {107},
  author = {Malac, M. and Beleggia, M. and Egerton, R. and Zhu, Y.}
}
@article{Harutyunyan2009,
  year = {2009},
  title = {Preferential Growth of Single-Walled Carbon Nanotubes with Metallic Conductivity},
  pages = {116-120},
  journal = {Science},
  volume = {326},
  author = {Harutyunyan, A.R. and Chen, G. and Paronyan, T.M. and Pigos, E.M. and Kuznetsov, O.A. and Hewaparakrama, K. and Kim, S.M. and Zakharov, D. and Stach, E.A. and Sumanasekera, G.U.}
}
@article{Yan2007,
  year = {2007},
  title = {AUTO3DEM - an automated and high throughput program for image reconstruction of icosahedral particles},
  pages = {73-82},
  journal = {Journal of Strcutural Biology},
  volume = {157},
  author = {Yan, X. and Sinkovits, R.S. and Baker, T.S.}
}
@article{Buban2009,
  year = {2009},
  title = {High-resolution low-dose scanning transmission electron microscopy},
  pages = {1-10},
  journal = {Journal of Electron Microscopy},
  author = {Buban, J.P. and Ramasse, Q. and Gipson, B. and Browning, N.D. and Stahlberg, H.}
}
@article{Bleloch2004,
  year = {2004},
  title = {Imaging at the picometer scale},
  pages = {42-48},
  journal = {Materials Today},
  author = {Bleloch, A. and Lupini, A. }
}
@article{Nelayah2009,
  number = {7},
  year = {2009},
  title = {Direct imaging of surface plasmon resonances on single triangular silver nanoprisms at optical wavelength using low-loss EFTEM imaging},
  pages = {1003-1005},
  journal = {Optics Letters},
  volume = {34},
  author = {Nelayah, J. and Gu, L. and Sigle, W. and Koch, C.T. and Pastoriza-Santos, I. and Liz-Marzan, L.M. and Aken, P.A. van}
}
@article{Penrose1956,
  year = {1956},
  title = {On best approximate solution of linear matrix equations},
  pages = {17-19},
  journal = {Proceedings of the Cambridge Philosophical Society},
  volume = {52},
  author = {Penrose, R.}
}
@article{Buczko2000,
  year = {2000},
  title = {Excitonic Effects in Core-Excitation Spectra of Semiconductors},
  pages = {2168},
  journal = {Physical Review Letters},
  volume = {85},
  author = {Buczko, R. and Duscher, G. and Pennycook, S>J. and Pantelides, S.T.}
}
@article{Penrose1955,
  year = {1955},
  title = {A generalized inverse for matrices},
  pages = {406-413},
  journal = {Proceedings of the Cambridge Philosophical Society},
  volume = {51},
  author = {Penrose, R.}
}
@article{Cooper2007,
  year = {2007},
  title = {Medium resolution off-axis electron holography with mV sensitivity},
  journal = {Applied Physics Letters},
  author = {Cooper, D. and Truche, R. and Rivallin, P. and Hartmann, J.-M. and Laugier, F. and Bertin, F. and Chabli, A. and Rouviere, J.-L.}
}
@article{Frank2009,
  number = {3},
  year = {2009},
  title = {Single-particle reconstructionof biological macromolecules in electron microscopy - 30 years},
  pages = {139-158},
  journal = {Quaterly Reviews of Biophysics},
  volume = {42},
  author = {Frank, J.}
}
@book{Bronstein1991,
  edition = {25th},
  year = {1991},
  title = {Taschenbuch der Mathematik},
  address = {Thun, Frankfurt (Main)},
  publisher = {Teubner},
  author = {Bronstein, I.N. and Semendjajew, K.A.}
}
@article{Krivanek2008a,
  year = {2008},
  title = {Advances in Aberration-Corrected Scanning Transmission Electron Microscopy and Electron Energy-Loss Spectroscopy},
  pages = {121-160},
  journal = {Advances in Imaging and Electron Physics},
  volume = {153},
  author = {Krivanek, O.L. and Delby, N. and keyse, R.J. and Murfitt, M.F. and Own, C.S. and Szilagyi, Z.S.}
}
@article{Nellist2000,
  year = {2000},
  title = {The principles and interpretation of annular dark-field z-contrast imaging},
  pages = {147-203},
  note = {Copy Bernd,Rolf},
  journal = {Advances in Imaging and Electron Physics},
  volume = {113},
  author = {Nellist, P.D. and Pennycook, S.J.}
}
@article{Chu2009a,
  year = {2009},
  title = {Probing surface plasmons in individual Ag nanoparticles in the ultra-violet spectral regime},
  pages = {235705},
  journal = {Nanotechnology},
  volume = {20},
  author = {Chu, M.-W. et al.}
}
@article{Boisset1997,
  year = {1997},
  title = {Effects of angular oversampling in three-dimensional reconstruction},
  pages = {131-145},
  journal = {Scanning Microscopy},
  volume = {11},
  author = {Boisset, N. and Penczek, P.A. and Taveau, J-C. and You, V. and Haas, F. de and Lamy, J.}
}
@article{Vincent1994,
  year = {1994},
  title = {Double concial beam-rocking system for measurement of integrated electron diffreation intensities},
  pages = {271-282},
  journal = {Ultramicroscopy},
  volume = {53},
  author = {Vincent, R. and Midgley, P.A.}
}
@article{Scheres2005a,
  year = {2005},
  title = {Maximum-likelihood Multi-reference Refinement for Electron Microscopy Images},
  pages = {139-149},
  journal = {Journal of Molecular Biology},
  volume = {348},
  author = {Scheres, S.H.W. and Valle, M. and {Nu\~nez}, R. and Sorzano, C.O.S. and Marabini, R. and Herman, G.T. and Carazo, J.-M.}
}
@article{Cowley2001,
  number = {3},
  year = {2001},
  title = {{STEM} imaging with a thin annular detector},
  pages = {147-155},
  journal = {Journal of Electron Microscopy},
  volume = {50},
  author = {Cowley, J.M.}
}
@article{Uhlemann1996,
  year = {1996},
  title = {Acceptance of imaging energy filters},
  pages = {161-167},
  journal = {Ultramicroscopy},
  volume = {63},
  author = {Uhlemann, S. and Rose, H.}
}
@article{Frank1981,
  year = {1981},
  title = {Computer Averaging of Electron Micrographs of 40S Ribosomal Subunits},
  journal = {Science},
  volume = {214},
  author = {Frank, J. and Verschoor, A. and Boublik, M.}
}
@article{Maccagnano-Zacher2008,
  year = {2008},
  title = {Effects of tilt on high-resolution ADF-STEM imaging},
  pages = {718-726},
  journal = {Ultramicroscopy},
  volume = {187},
  author = {Maccagnano-Zacher, S.E. and Mkhoyan, K.A. and Kirkland, E.J. and Silcox, J.}
}
@article{Gubbens2010,
  year = {2010},
  title = {The GIF quantum, a next generation post-column imaging energy filter},
  journal = {Ultramicroscopy},
  author = {Gubbens, A. and Barfels, M. and Trevor, C. and Twesten, R. and Mooney, P. and Thomas, P. and Menon, N. and Kraus, B. and Mao, C. and Mcginn, B.}
}
@article{James1999,
  year = {1999},
  title = {Practical aspects of atomic resolution imaging and analysis in {STEM}},
  pages = {125-139},
  journal = {Ultramicroscopy},
  volume = {78},
  author = {James, E.M. and Browning, N.D.}
}
@article{Du2007,
  year = {2007},
  title = {Quantitative comparison of image contrast and pattern between experimental and simulated high-resolution transmission electron micrographs},
  pages = {281-292},
  journal = {Ultramicroscopy},
  volume = {107},
  author = {Du, K. and Hochmeister, K. von and Philipp, F.}
}
@article{Krivanek1991,
  year = {1999},
  title = {Developments in EELS instrumentation for spectroscopy and imaging},
  pages = {315-332},
  journal = {Mirosc. Mircoanal. Microstruct},
  volume = {2},
  author = {Krivanek, O.L. and Gubbens, A.J. and Dellby, N.}
}
@article{Moore1920,
  year = {1920},
  title = {On the reciprocal of the general algebraic matrix},
  pages = {394-395},
  journal = {Bulletin of the American Mathematical Society},
  volume = {26},
  author = {Moore, E.H.}
}
@article{James1997,
  year = {1997},
  title = {A method for measuring the effective source coherence in a field emission transmission electron microscope},
  pages = {174-179},
  journal = {Applied Surface Science},
  volume = {111},
  author = {James, E.M. and Rodenburg, J.M}
}
@article{Davey2002,
  year = {2002},
  title = {{DNA}-dependent divalent cation binding in the nucleosome core particle},
  pages = {11169-11174},
  journal = {Proceedings of the National Academy of Sciences of the United States of America},
  volume = {99},
  author = {Davey, C.A. and Richmond, T.J.}
}
@article{Kisielowski2001,
  year = {2001},
  title = {Imaging columns of the light elements carbon,nitrogen and oxygen with sub {\AA}ngstrom resolution},
  pages = {243-263},
  journal = {Ultramicroscopy},
  volume = {89},
  author = {Kisielowski, C. and Hetherington, C.J.D. and Wang, Y.C. and Kilaas, R. and O'keefe, M.A. and Thust, A.}
}
@article{Chu2009,
  year = {2009},
  title = {Crystal Structure of the {30S} Ribosomal Subunit from Thermus thermophilus: Purification, Crystallization and Structure Determination},
  journal = {Journal of Molecualar Biology},
  author = {Chu, M.-W. and Myroshnchenko, V. and Chen, C.H. and Deng, J.-P. and Mou, C.-Y. and Garcia de Abajo, F.J.G.}
}
@article{Chu2008,
  year = {2008},
  title = {Surface exciton polaritons in individual Au nanoparticles in the far-ultraviolet spectral regime},
  pages = {245402},
  journal = {Physical Review B},
  volume = {77},
  author = {Chu, M.-W. and Chen, C.-H. and Garcia de Abajo, F.J.G. and Deng, J.-P. and Mou, C.-Y.}
}
@article{Duscher2001,
  year = {2001},
  title = {Core-Hole Effects on Energy-Loss Near-Edge Structure},
  pages = {355},
  journal = {Ultramicroscopy},
  volume = {86},
  author = {Duscher, G. and Buczko, R. and Pennycook, S.J. and Pantelides, S.T.}
}
@article{Hytch1998,
  year = {1998},
  title = {Quantitative measurement of displacement and strain fields from HREM micrographs},
  pages = {131-146},
  journal = {Ultramicroscopy},
  volume = {74},
  author = {Hytch, M.J. and Snoeck, E. and Kilaas, R.}
}
@article{Lazar2006,
  year = {2006},
  title = {Enhancement of resolution in core-loss and low-loss spectroscopy in a monochromated microscope},
  pages = {1091-1103},
  journal = {Ultramicroscopy},
  volume = {106},
  author = {Lazar, S. and Botton, G.A. and Zandbergen, H.W.}
}
@article{Bullogh1999,
  year = {1999},
  title = {The Projection Structure of the Low Temperature K Intermediate of the Bacteriorhodopsin Photocycle D etermined by Electron Diffraction},
  pages = {1663-1671},
  journal = {Journal of Molecular Biology},
  volume = {286},
  author = {Bullough, P.A. and Henderson, R.}
}
@article{Rohde2005,
  year = {2005},
  title = {Estimating intensity variance due to noise in registered images: Applications to diffusion tensor {MRI}},
  pages = {673-684},
  journal = {NeuroImage},
  volume = {26},
  author = {Rohde, G.K. and Barnett, A.S. and Basser, P.J. and Pierpaoli, C.}
}
@article{Lichte2008a,
  year = {2008},
  title = {Electron holography - basics and applications},
  pages = {1-43},
  journal = {Reports on Progress in Physics},
  author = {Lichte, H. and Lehmann, M.}
}
@article{HohmannMarriott2009,
  number = {10},
  year = {2009},
  title = {Nanoscale 3D cellular imaging by axial scanning transmission electron tomography},
  pages = {729-732},
  journal = {Nature Methods},
  volume = {6},
  author = {Hohmann-Marriott, M.F. and Sousa, A.A. and Azari, A.A. and Glushakova, S. and Zhang, G. and Zimmerberg, J. and Leapmann, R.D.}
}
@article{Sawada2009a,
  year = {2009},
  title = {STEM imaging of 47-pm-separated atomic columns by a spherical aberration-corrected electron microscope with a 300-kV cold field emission gun},
  pages = {357-361},
  journal = {Journal of electron microscopy},
  volume = {58},
  author = {Sawada, H. and Tanishiro, Y. and Ohashi, N. and Tomita, T. and Hosokawa, F. and Kaneyama, T. and Kondo, Y. and Takayanagi, K.}
}
@article{Kim1997,
  year = {1997},
  title = {Energy distributions of Zr/O/W Schottky electron emission},
  pages = {461-465},
  journal = {Journal of Applied Physics},
  volume = {81},
  author = {Kim, H.S. and Yu, M.L. and Thomson, M.G.R. and Kratchmer, E. and Chang, T.H.P.}
}
@article{Baldock2002,
  year = {2002},
  title = {Three-dimensional reconstructions of extracellular matrix polymers using automated electron tomography},
  pages = {130-136},
  journal = {Journal of Structural Biology},
  volume = {138},
  author = {Baldock, C. and Gilpin, C.J. and Koster, A.J. and Ziese, U. and Kadler, K.E. and Kielty, C.M. and Holmes, D.F.}
}
@article{Grigorieff1996,
  year = {1996},
  title = {Electron-crystallographic Refinement of the Structure of Bacteriorhopdopsin},
  pages = {393-421},
  journal = {Journal of Molecular Biology},
  volume = {259},
  author = {Grigorieff, N. and Ceska, T.A. and Downing, K.H. and Baldwin, J.M. and Henderson, R.}
}
@article{Heel1987,
  year = {1987},
  title = {Similarity measures between images},
  pages = {95-100},
  journal = {Ultramicroscopy},
  volume = {21},
  author = {Heel, M. van}
}
@article{Akase2010,
  year = {2010},
  title = {In situ Lorentz microscopy in an alternating magnetic field},
  pages = {1-75},
  journal = {Journal of Electron Microscopy},
  author = {Akase, Z. and Shindo, D.}
}
@article{Xiong2009,
  year = {2009},
  title = {CTF determination and correction for low dose tomographic tilt series},
  pages = {378-387},
  journal = {Journal of Structural Biology},
  volume = {168},
  author = {Xiong, Q. and Morphew, M.K. and Schwartz, C.L. and Hoenger, A.H. and Mastronarde, D.N.}
}
@article{Unser1987,
  year = {1987},
  title = {A new resolution criterion based on spectral signal-to-noise ratio},
  pages = {39-52},
  journal = {Ultramicroscopy},
  volume = {23},
  author = {Unser, M. and Trus, B.L. and Steven, A.C.}
}
@article{Morniroli2007,
  year = {2007},
  title = {LACDIF, a new electron diffraction technique obtained with the LACBED configuration and a Cs corrector: Comparison with electron precession},
  pages = {100-115},
  journal = {Ultramicroscopy},
  volume = {108},
  author = {Morniroli, J.P. and Houdellier, F. and Roucau, C. and Puiggali, J. and Gesti, S. and Redjaimia, A.}
}
@article{Fu1999,
  year = {1999},
  title = {Yeast {RNA} Polymerase {II} at 5{\AA} Resolution},
  pages = {799-810},
  journal = {Cell},
  volume = {98},
  author = {Fu, J. and Gnatt, A.L. and Bushnell, D.A. and Jensen, G.J. and Thompson, N.E. and Burgess, R.R. and David, P.R. and Kornberg, R.D.}
}
@article{Stadelmann1987,
  year = {1987},
  title = {{EMS} - {A} software package for electron diffration analysis and {HREM} image simulation in material science},
  pages = {131-146},
  journal = {Ultramicroscopy},
  volume = {21},
  author = {Stadelmann, P.A.}
}
@inproceedings{Pennycook2003a,
  series = {AIP Conference},
  year = {2003},
  title = {Transmission Electron Microscopy: Overview and Challenges},
  booktitle = {Characterization and Metrology for ULSI Technology},
  pages = {627},
  volume = {683},
  publisher = {American Institute of Physics},
  author = {Pennycook, S.J. and Lupini, A.R. and Borisevich, A. and Varela, M. and Peng, Y. and Nellist, P.D. and Duscher, G. and Buczko, R. and Pantelides, S.T.}
}
@article{Ronchi1961,
  year = {1961},
  title = {Resolving power of calculates and detected images},
  pages = {458-460},
  journal = {Journal of the Optical Society of America},
  volume = {51},
  author = {Ronchi, V.}
}
@article{Philippsen2007,
  year = {2007},
  title = {The contrast-imaging function for tilted specimens},
  pages = {202-212},
  journal = {Ultramicroscopy},
  volume = {107},
  author = {Philippsen, A. and Engel, H.-A. and Engel, A.}
}
@article{Haurauz1986,
  year = {1986},
  title = {Exact filters for general geometry three dimensional reconstruction},
  pages = {146-156},
  journal = {Optik},
  volume = {78},
  author = {Haurauz, G. and Heel, M. van}
}
@article{Walther2006,
  year = {2006},
  title = {First experimental test of a new monochromated and aberration-corrected 200 {kV} field-emission scanning transmission electron microscope},
  pages = {963-969},
  journal = {Ultramicroscopy},
  volume = {106},
  author = {Walther, T. and Quandt, E. and Stegmann, H. and Thesen, A. and Benner, G.}
}
@article{Muller2006a,
  year = {2006},
  title = {Advancing the Hexapole Cs-Corrector for the Scanning Transmission Electron Microscope},
  pages = {442-455},
  journal = {Microscopy and Microanalysis},
  volume = {12},
  author = {{M\"uller}, H. and Uhlemann, S. and Hartel, P. and Haider, M.}
}
@article{Aoyama2008,
  year = {2008},
  title = {STEM tomography for thick biological specimens},
  pages = {70-80},
  journal = {Ultramicroscopy},
  volume = {109},
  author = {Aoyama, K. and takagi, T. and Hirase, A. and Miyazawa, A.}
}
@techreport{Zande2004,
  number = {PR-TN-2004/00608},
  year = {2004},
  title = {Aberration analysis in electron microscopy ({T}heory)},
  type = {Technical Note},
  address = { Eindhoven, The Netherlands},
  institution = {Philips Research},
  author = {Zande, M.J. van der and Kok, C.}
}
@article{Shibata2004,
  year = {2004},
  title = {Observation of rare-earth segregation in silicon nitride ceramics at subnanometre dimensions},
  pages = {730-734},
  journal = {Nature},
  volume = {428},
  author = {Shibata, N. and Pennycook, S.J. and Gosnell, T.R. and Painter, G.S. and Shelton, W.A. and Becher, P.F.}
}
@article{DeRosier1999,
  year = {1999},
  title = {Averaging Data Derived from Images of Helical Structures with Different Symmetries},
  pages = {159-165},
  journal = {Journal of Molecular Biology},
  volume = {289},
  author = {DeRosier, D. and Stokes, D.L. and Darst, S.A.}
}
@article{Crozier2006,
  year = {2006},
  title = {Book review: Transmission Electron Energy Loss Spectrometry in Materials Science and the EELS Atlas},
  pages = {332},
  journal = {Micron},
  volume = {38},
  author = {Crozier, P.A.}
}
@article{Carlo2002,
  year = {2002},
  title = {Cryo-negative staining reduces electron-beam sensitivity of vitrified biological particles},
  pages = {216-222},
  journal = {Journal of Structural Biology},
  volume = {138},
  author = {Carlo, S. de and El-Bez, C. and Alvarez-Rua, C. and Borge, J. and Dubochet, J.}
}
@inproceedings{Tiemeijer1999a,
  series = {Electron Microscopy and Analysis Group Conference EMAG99},
  year = {1999},
  title = {Operation modes of a {TEM} monochromator},
  pages = {191-196},
  volume = {161},
  address = {Sheffiled, UK},
  publisher = {IOP Publishing Ltd},
  author = {Tiemeijer, P.C.}
}
@article{Thust2009,
  year = {2009},
  title = {High-Resolution Transmission Electron Microscopy on an Absolute Contrast Scale},
  pages = {220801},
  journal = {Physical Review Letters},
  volume = {102},
  author = {Thust, A.}
}
@article{Suenaga2009,
  year = {2009},
  title = {Visualizing and identifying single atoms using electron energy-loss spectroscopy with low accelerating voltage},
  pages = {1-4},
  journal = {Nature Chemistry},
  author = {Suenaaga, K. and Sato, Y. and Liu, Z. and kataura, H. and Okazaki, T. and Kimoto, K. and Sawada, H. and Sasaki, T. and Omoto, K. and Kaneyama, T. and Kondo, Y.}
}
@article{Hill2008,
  year = {2008},
  title = {The ALIS He ion source and its application to high resolution microscopy},
  pages = {135-141},
  journal = {Physics Procedia},
  volume = {1},
  author = {Hill, R.and Notte, J. and Ward, B.}
}
@article{Hohn2007,
  year = {2007},
  title = {SPARX, a new environment for Cryo-EM image processing},
  pages = {47-55},
  journal = {Journal of Strcutural Biology},
  volume = {157},
  author = {Hohn, M. and Tang, G. and Goodyear, G. and Baldwin, P.R. and Huang, Z. and Penczek, P.A. and Yang, C. and Glaeser, R.M. and Adama, P.D. and Ludtke, S.J.}
}
@article{Tang2007,
  year = {2007},
  title = {EMAN2: An extensible image processing suite for electron microscopy},
  pages = {38-46},
  journal = {Journal of Strcutural Biology},
  volume = {157},
  author = {Tang, G. and Peng, L. and Baldwin, P.R. and Mann, D.S. and Jiang, W. and Rees, I. and Ludtke, S.J.}
}
@article{Krivanek2009,
  year = {2009},
  title = {High-energy resolution monochromator for aberration-corrected scanning transmission electron microscopy/electron energy-loss spectroscopy},
  pages = {3683-3697},
  journal = {Philosophical Transactions of the Royal Society},
  volume = {367},
  author = {Krivanek, O.L. and Ursin, J.P. and Bacon, N.J. and Corbin, G.J. and Delby, N. and Hrncirik, P. and Murfitt, M.F. and Own, C.S. and Szilagyi, Z.S.}
}
@article{Krivanek2008,
  year = {2008},
  title = {An electron microscope for the aberration-corrected era},
  pages = {179-195},
  journal = {Ultramicroscopy},
  volume = {108},
  author = {Krivanek, O.L. and Corbin, G.K. and Dellby, N. and Elston, B.F. and Keyse, R.J. and Murfitt, M.F. and Own, C.S. and Szilagyi, Z.S. and Woodruff,J.W.}
}
@article{Gunawan2009,
  year = {2009},
  title = {Locating La atoms in epitaxial $Bi_{3.25}La_{0.75}Ti_3O_{12}$ films through atomic resolution electron energy loss spectroscopy mapping},
  pages = {192902},
  journal = {Applied Physics Letters},
  volume = {95},
  author = {Gunawan, L. and Lazar, S. and Gautreau, O. and Narnagea, C. and Pignolet, A. and Botton, G.A.}
}
@misc{Krivanek2001,
  year = {2001},
  title = {Autoadjusting charged-particle probe-forming apparatus},
  note = {pending},
  howpublished = {EP application number: 01308443.9},
  author = {Krivanek, O.L. and Dellby, N. and Lupini, A.R.},
  organization = {NION}
}
@article{Cox1986,
  year = {1986},
  title = {Information capacity and resolution in an optical system},
  pages = {1152-1158},
  journal = {Journal of the Optical Society of America A},
  volume = {3},
  author = {Cox, I.J. and Sheppard, C.J.R.}
}
@article{Downing2004,
  year = {2004},
  title = {Experimental characterization and mitigation of specimen charging on thin films with one conducting layer},
  pages = {783-789},
  journal = {Microscopy and Microanalysis},
  volume = {10},
  author = {Downing, K.H. and McCartney, M.R. and Glaeder, R.M.}
}
@article{Hohenstein1992,
  year = {1992},
  title = {Single Sideband Imagin in High-Resolution Electron Microscopy},
  pages = {485-492},
  journal = {Applied Physics A},
  volume = {54},
  author = {Hohenstein, M.}
}
@article{Mitsuishi2006,
  year = {2006},
  title = {Ultrahigh-Vacuum Third-Order Spherical Aberration (Cs) Corrector for a Scanning Transmission Electron Microscope},
  pages = {1-5},
  journal = {Microscopy and Microanalysis},
  volume = {12},
  author = {Mitsuishi, K. and Takeguchi, M. and Kondo, Y. and Hosokawa, F. and Okamoto, K. and Sannomiva, T. and Hori, M. and Iwama, T.}
}
@article{Koster1987,
  year = {1987},
  title = {An autofocus method for a {TEM}},
  pages = {209-222},
  journal = {Ultramicroscopy},
  volume = {21},
  author = {Koster, A.J. and Bos, A. van den and Mast, K.D. van der}
}
@article{Egerton2003,
  year = {2003},
  title = {New techniques in electron energy-loss spectroscopy and energy-filtered imaging},
  pages = {127-139},
  journal = {Micron},
  volume = {34},
  author = {Egerton, R.F.}
}
@article{Egerton2004,
  year = {2004},
  title = {Radiation damage in the TEM and SEM},
  pages = {399-409},
  journal = {Micron},
  volume = {35},
  author = {Egerton, R.F. and Li, P. and Malac, M.}
}
@article{Egerton2007,
  year = {2007},
  title = {Limits to the spatial, energy and momentum resolution of electron energy-loss spectroscopy},
  pages = {575-586},
  journal = {Ultramicroscopy},
  volume = {107},
  author = {Egerton, R.F.}
}
@article{Egerton2009,
  year = {2009},
  title = {Electron energy-loss spectroscopy in the TEM},
  pages = {016502},
  journal = {Reports on Progress in Physics},
  volume = {72},
  author = {Egerton, R.F.}
}
@article{Baldwin1988,
  year = {1988},
  title = {Images of purple membrane at 2.8{\AA} resolution obtained by cryo-electron microscopy},
  pages = {585-591},
  journal = {Journal of Molecular Biology},
  volume = {202},
  author = {Baldwin, J.M. and Henderson, R. and Backman, E. and Zemlin, F.}
}
@article{Zhang2008,
  number = {6},
  year = {2008},
  title = {Near-atomic resolution using electron cryomicroscopy and single-particle reconstruction},
  pages = {1867-1872},
  journal = {Proceedings of the National Academy of Science of America},
  volume = {105},
  author = {Zhang, X. and Settembre, E. and Xu. Chen, Dormitzer, P.R. and Bellamy, R. and Harrison, S.C. and Grigorieff, N.}
}
@article{Downing1979,
  year = {1979},
  title = {Possibilities of heavy atom discrimination using single-sideband techniques},
  pages = {13-31},
  journal = {Ultramicroscopy},
  volume = {4},
  author = {Downing, K.H.}
}
@article{Zheng2007,
  year = {2007},
  title = {Automated acquisition of electron microscopic random conical tilt sets},
  pages = {148-155},
  journal = {Journal of Strcutural Biology},
  volume = {157},
  author = {Zheng, S.Q. and Kollman, J.M. and Braunfeld, M.B. and Sedat, J.W. and Agard, D.A.}
}
@article{Eyidi2006,
  year = {2006},
  title = {Short note on parallel illumination in the {TEM}},
  pages = {1144-1149},
  journal = {Ultramicroscopy},
  volume = {106},
  author = {Eyidi, D. and Hebert, C. and Schattschneider, P.}
}
@article{Mallick2005,
  year = {2005},
  title = {ACE: Automated CTF Estimation},
  pages = {8-29},
  journal = {Ultramicroscopy},
  volume = {104},
  author = {Mallick, S.P. and Carragher, B. and Potter, C.S. and Kriegman, D.J.}
}
@article{Liu2009,
  year = {2009},
  title = {Off-axis emission properties for the extended Schottky electron source},
  pages = {2547-2552},
  journal = {J. Vac. Sci. Technol. B},
  volume = {27},
  author = {Liu, K. and Schwind, G.A. and Swanson, L.W.}
}
@article{Kirkland1987,
  year = {1987},
  title = {Simulation of annular dark field {STEM} images using a modified mutlislice method},
  pages = {77-96},
  journal = {Ultramicroscopy},
  volume = {23},
  author = {Kirkland, E.J. and Loane, R.F. and Silcox, J.}
}
@article{Sigworth1998,
  year = {1998},
  title = {A Maximum-Likelihood Approach to Single-Particle Image Refinement},
  pages = {328-339},
  journal = {Journal of Structural Biology},
  volume = {122},
  author = {Sigworth, F.J.}
}
@article{Harada2004,
  number = {17},
  year = {2004},
  title = {Double-biprism electron interferometry},
  pages = {3219-3231},
  journal = {Applied Physics Letters},
  volume = {84},
  author = {Harada, K. and Akashi, T. and Togawa, Y. and Matsuda, T.}
}
@article{Mooney2007,
  year = {2007},
  title = {Optimization of Image Collection for Cellular Electron Microscopy},
  pages = {661-719},
  journal = {Methods in cell biology},
  volume = {79},
  author = {Mooney, P..}
}
@article{Brarnova1999,
  year = {2004},
  title = {The optics of round and multipole electrostatic lenses},
  pages = {1-207},
  journal = {Advances in electronics and electron physics},
  volume = {76},
  author = {Baranova, L.A. and Yavor, S.Y.}
}
@article{Kuramochi2008,
  year = {2008},
  title = {Measurement of twofold astigmatism of probe-forming lens using low-order zone-axis ronchigram},
  pages = {339-345},
  journal = {Ultramicroscopy},
  volume = {108},
  author = {Kurmochi, K. and Yamazaki, T. and Kotaka, Y. and Kikuchi, Y. and Hashimoto, I. and Watanabe, K.}
}
@article{Kuramochi2009,
  year = {2009},
  title = {Effect of chromatic aberration on atomic-resolved spherical aberration corrected STEM images},
  pages = {36-42},
  journal = {Ultramicroscopy},
  volume = {110},
  author = {Kurmochi, K. and Yamazaki, T. and Kotaka, Y. and Ohtsuka, M. and Hashimoto, I. and Watanabe, K.}
}
@article{Crewe1980,
  year = {1980},
  title = {The physics of the high-resolution scanning microscope},
  pages = {621-642},
  journal = {Rep. Prog. Phys.},
  volume = {43},
  author = {Crewe, A.V.}
}
@article{Haider2008,
  year = {2008},
  title = {Present and Future Hexapole Aberration Correctors for High-Resolution Electron Microscopy},
  pages = {43-119},
  journal = {Advances in Imaging and Electron Physics},
  volume = {153},
  author = {Haider, M. and Mueller, H. and Uhlemann, S.}
}
@article{Pogany1968,
  year = {1968},
  title = {Reciprocity in Electron Diffraction and Microscopy},
  pages = {103-109},
  journal = {Acta Crystallography A},
  volume = {24},
  author = {Pogany, A.P. and Turner, P.S.}
}
@article{Sasaki2010,
  year = {2010},
  title = {Performance of low-voltage STEM/TEM with delta corrector and cold field emission gun},
  journal = {Journal of Electron Microscopy},
  author = {Sasaki, T. and Sawada, H. and Hosokawa, F. and Kohno, Y. and Tomita, T. and Kaneyama, T. and Kondo, Y. and Kimoto, K. and Sato, Y. and Suenaga, K.}
}
@article{Muller2008,
  year = {2008},
  title = {Atomic-Scale Chemical Imaging of Composition and Bonding by Aberration-Corrected Microscopy},
  pages = {1073-1076},
  journal = {Science},
  volume = {319},
  author = {Muller, D.A. and Fitting Kourkoutis, L. and Murfitt, M. and Song, J.H. and Hwang, H.Y. and Silcox, J. and Dellby, N. and Krivanek, O.L.}
}
@article{Meyer2008,
  year = {2008},
  title = {Imaging and dynamics of light atoms and molecules on graphene},
  pages = {319-323},
  journal = {Nature},
  volume = {454},
  author = {Meyer, J.C. and Girit, C.O. and Crommie, M.F. and Zettl, A.}
}
@article{Muller2006,
  year = {2006},
  title = {Room design for high-performance electron microscopy},
  pages = {1033-1040},
  journal = {Ultramicroscopy},
  volume = {106},
  author = {Muller, D.A. and Kirkland, E.J. and Thomas, M.G. and Grazul, J.L. and Fitting, L. and Weyland, M.}
}
@article{Xing2009,
  year = {2009},
  title = {A rapid method to correct objective lens astigmatism in a TEM},
  pages = {287-290},
  journal = {Ultramicroscopy},
  volume = {109},
  author = {Xing, Q. and Lograsso, T.A.}
}
@article{Nellist1998a,
  year = {1998},
  title = {Accurate structure determination from image reconstruction in {ADF} {STEM}},
  pages = {159-170},
  journal = {Journal of Microscopy},
  volume = {1-2},
  author = {Nellist, P.D. and Pennycook, S.J.}
}
@article{Schaffer2009,
  year = {2009},
  title = {High-resolution surface plasmon imaging of gold nanoparticles by energy-filtered transmission electron microscopy},
  pages = {041401},
  journal = {Physical Review B},
  volume = {79},
  author = {Schaffer, B. and Hohenester, U. and Truegler, A. and Hofer, F.}
}
@inproceedings{Rieger2008,
  month = {September 1-5},
  year = {2008},
  title = {Method to determine image sharpness and resolution
in Scanning Electron Microscopy images},
  booktitle = {EMC 2008, Vol.1: Instrumentation and Methods},
  pages = {613-614},
  editor = {Luysberg, M. and Tillmann, K. and Weirich, T.},
  address = {Berline},
  publisher = {Springer Verlag},
  author = {Rieger, B. and Veen, G.N.A. van}
}
@mastersthesis{Smith2009,
  year = {2009},
  title = {Improving single molecule 
fluorescence superresolution techniques},
  school = {Delft University of Technology},
  author = {Smith, S.C.}
}
@mastersthesis{Vroonland2010,
  month = {June},
  year = {2010},
  title = {Superresolution Using Blinking Emitters},
  address = {Delft, The Netherlands},
  school = {Delft University of Technology},
  author = {Vroonland, S.}
}
@article{Hell2009,
  year = {2009},
  title = {Microscopy and its focal switch},
  pages = {24-32},
  journal = {Nature Methods},
  volume = {6},
  author = {Hell, S.W.}
}
@article{Small2009,
  number = {2},
  year = {2009},
  title = {Theoretical Limits on Errors and Acquisition Rates in Localizing Switchable Fluorophores},
  pages = {L16-L18},
  journal = {Biophysical Journal - Biophysical Letters},
  volume = {92},
  author = {Small, A.R.}
}
@article{Podczeck1997,
  year = {1997},
  title = {A shape factor to assess the shape of particles using image analysis},
  pages = {47-53},
  journal = {Powder Technology},
  volume = {93},
  author = {Podczeck, F.}
}
@article{Shaner2004,
  number = {12},
  year = {2004},
  title = {Improved monomeric red, orange and yellow fluorescent proteins derived from Discosoma sp. red fluorescent protein},
  pages = {1567-1672},
  journal = {Nature Biotechnology},
  volume = {22},
  author = {Shaner, N.C. and Campbell, R.E. and Steinbach, P.A. and Giepmans, B.N.G. and Palmer, A.E. and Tsien, R.Y.}
}
@article{Sader2010,
  year = {2010},
  title = {Quantitative analysis of image contrast in phase contrast {STEM} for low dose imaging},
  pages = {1324-1331},
  journal = {Ultramicroscopy},
  volume = {110},
  author = {Sader, K. and Brown, A. and Brydon, R. and Bleloch, A.}
}
@article{Aert2010,
  year = {2010},
  title = {Linear versus non-linear structural information limit in high-resolution transmission electron microscopy},
  pages = {1404-1410},
  journal = {Ultramicroscopy},
  volume = {110},
  author = {Aert, s. van and Chen, J.H. and Dyck, D. van}
}
@article{Donzel2001,
  number = {{15}},
  year = {2001},
  title = {{Hydrophilic Poly(dimethylsiloxane) Stamps for Microcontact Printing}},
  journal = {{Advanced Materials}},
  volume = {{13}},
  author = {Donzel, Christian and Geissler, Matthias and Bernard, Andr\\\'e and Wolf, Heiko and Michel, Bruno and Hilborn, J\\\"ons and Delamarche, Emmanuel}
}
@article{Wang1997,
  number = {{3}},
  year = {1997},
  title = {{Stretching DNA with Optical Tweezers}},
  pages = {{1335-1346}},
  journal = {{Biophysical Journal}},
  volume = {{72}},
  author = {Wang, Michelle D. and Yin, Hong and Landick, Robert and Gelles, Jeff and Block, Steven M.}
}
@article{Blanchard1999,
  number = {{32}},
  year = {1999},
  title = {{Simultaneous multiplane imaging with a distorted diffraction grating}},
  pages = {{6692-6699}},
  journal = {{Applied Optics}},
  volume = {{38}},
  author = {Blanchard, Paul M.
 Greenaway, Alan H.}
}
@article{Eversole2007,
  year = {2007},
  title = {{Plasmonic laser nanoablation of silicon by the scattering of femtosecond pulses near gold nanospheres}},
  pages = {{283-291}},
  journal = {{Applied Physics A}},
  volume = {{89}},
  author = {Eversole, D. and Luk'Yanchuk, B. and Ben-Yakar, A.}
}
@article{Dessinges2002,
  number = {{24}},
  year = {2002},
  title = {{Stretching Single Stranded DNA, a Model Polyelectrolyte}},
  pages = {{248102-248106}},
  journal = {{Physical Review Letters}},
  volume = {{89}},
  author = {Dessinges, M. N. and Maier, B. and Zhang, Y. and Peliti, M. and Bensimon, D. and Croquette, V.}
}
@article{Taylor1990,
  number = {{2}},
  year = {1990},
  title = {{Application of the Method of Phage T4 DNA Ligase-catalyzed Ring-closure to the Study of DNA Structure}},
  pages = {{363-376}},
  journal = {{Journal of Molecular Biology}},
  volume = {{212}},
  author = {Taylor, William H. and Hagerman, Paul J.}
}
@article{Uhlenbeck1930,
  year = {1930},
  title = {{On the Theory of the Brownian Motion}},
  journal = {{Physical Review}},
  volume = {{36}},
  author = {Uhlenbeck, G.E. and Ornstein, L.S.}
}
@article{Yguerabide2001,
  number = {{S37}},
  year = {2001},
  title = {{Resonance Light Scattering Particles as Ultrasensitive Labels for Detection of Analytes in a Wide Range of Applications}},
  pages = {{71-81}},
  journal = {{Journal of Cellular Biochemistry Supplement}},
  volume = {{84}},
  author = {Yguerabide, Juan and Yguerabide, Evangelina E.}
}
@article{Samuel2002,
  year = {2002},
  title = {{Elasticity of semiflexible polymers}},
  pages = {{050801}},
  journal = {{Physical Review E}},
  volume = {{66}},
  author = {Samuel, Joseph and Sinha, Supurna}
}
@article{Porschke1991,
  year = {1991},
  title = {{Persistence length and bending dynamics of DNA from electrooptical measurements at high salt concentrations}},
  pages = {{169-179}},
  journal = {{Biophysical Chemistry}},
  volume = {{40}},
  author = {Porschke, Dietmar}
}
@article{Schutz2000,
  number = {{1}},
  year = {2000},
  title = {{3D Imaging of Individual Ion Channels in Live Cells at 40 nm Resolution}},
  pages = {{25-31}},
  journal = {{Single Molecules}},
  volume = {{1}},
  author = {Sch\\\"utz, Gerhard J. and Pastushenko, Vassili, Ph. and Gruber, Hermann J. and Knaus, Hans-G\\\"unter and Pragl, Bernt and Schindler, Hansgeorg}
}
@incollection{Vilfan2009,
  year = {2009},
  title = {{Magnetic Tweezers for Single-Molecule Experiments}},
  booktitle = {{Springer Handbook of Single-Molecule Biophysics}},
  editor = {Hinterdorfer, P. and A., van Oijen},
  publisher = {{Springer Science+Business Media}},
  author = {Vilfan, I.D. and Lipfert, J. and Koster, D.A. and Lemay, S.G. and Dekker, N.H.}
}
@article{Dvorak2003,
  number = {{2}},
  year = {2003},
  title = {{Approaches to Messenger RNA Detection - Comparison of Methods}},
  pages = {{131-135}},
  journal = {{Biomedical Papers}},
  volume = {{147}},
  author = {Dvor\\\'ak, Zdenek and Pascussi, Jean-Marc and Modriansk\\\'y, Martin}
}
@article{Medalion2010,
  number = {{4}},
  year = {2010},
  title = {{Coupling of twist and writhe in short DNA loops
 }},
  pages = {{045101}},
  journal = {{The Journal of Chemical Physics}},
  volume = {{132}},
  author = {Medalion, Shlomi and Rappaport, Shay M. and Rabin, Yitzhak}
}
@article{Cherif2006,
  number = {{2}},
  year = {2006},
  title = {{Clinically Related Protein-Peptide Interactions Monitored in Real Time on Novel Peptide Chips by Surface Plasmon Resonance Imaging}},
  pages = {{255-262}},
  journal = {{Clinical Chemistry}},
  volume = {{52}},
  author = {Cherif, Boutheina and Roget, Andr\\\'e and Villiers, Christian L. and Calemczuk, Roberto and Leroy, Vincent and Marche, Patrice N. and Livache, Thierry and Villiers, Marie-Bernadette}
}
@article{Gibson1991,
  number = {{10}},
  year = {1991},
  title = {{Experimental test of an analytical model of aberration in an oil-immersion objective lens used in three-dimensional light microscopy}},
  pages = {{1601-1613}},
  journal = {{Journal of the Optical Society of America A}},
  volume = {{8}},
  author = {Gibson, Sarah Frisken and Lanni, Frederick}
}
@misc{Bouchiat2007,
  year = {2007},
  title = {{Spatial Constraint Corrections to the Elasticity of dsDNA Measured with Magnetic Tweezers}},
  author = {Bouchiat, C.}
}
@article{Bouchiat2006,
  number = {{03}},
  year = {2006},
  title = {{Entropic elasticity of double-strand DNA subject to simple spatial constraints}},
  pages = {{P03019}},
  journal = {{Journal of Statistical Mechanics: Theory and Experiment}},
  author = {Bouchiat, C.}
}
@article{Yoshinaga2002,
  number = {{22}},
  year = {2002},
  title = {{Multiscaling in a long semiflexible polymer chain in two dimensions}},
  journal = {{Journal of Chemical Physics}},
  volume = {{116}},
  author = {Yoshinaga, Natsuhiko and Yoshikawa, Kenichi and Kidoaki, Satoru}
}
@article{Sottas1999,
  year = {1999},
  title = {{Brownian Dynamics Simulation of DNA Condensation}},
  pages = {{1858-1870}},
  journal = {{Biophysical Journal}},
  volume = {{77}},
  author = {Sottas, Pierre-Edouard and Larquet, Eric and Stasiak, Andrzej and Dubochet, Jacques}
}
@article{Yamakawa1976a,
  number = {{12}},
  year = {1976},
  title = {{Statistical mechanics of helical wormlike chains. I. Differential equations and moments}},
  pages = {{5222-5228}},
  journal = {{The Journal of Chemical Physics}},
  volume = {{64}},
  author = {Yamakawa, Hiromi and Fujii, Motoharu}
}
@article{Odijk1979,
  year = {1979},
  title = {{On the Ionic-Strength Dependence of the Intrinsic Viscosity of DNA}},
  pages = {{3111-3113}},
  journal = {{Biopolymers}},
  volume = {{18}},
  author = {Odijk, Theo}
}
@article{Sheppard1997,
  number = {{3}},
  year = {1997},
  title = {{Effects of specimen refractive index on confocal imaging}},
  pages = {{366-374}},
  journal = {{Journal of Microscopy}},
  volume = {{185}},
  author = {Sheppard, C. J. R. and T\\\"or\\\"ok, P.}
}
@article{Vologodskii1994,
  number = {{20}},
  year = {1994},
  title = {{DNA Extension under the Action of an External Force}},
  pages = {{5623-5625}},
  journal = {{Macromolecules}},
  volume = {{27}},
  author = {Vologodskii, Alexander}
}
@article{Rayleigh1919,
  year = {1919},
  title = {{On the problem of random vibrations, and of random flights in one, two, or three dimensions}},
  pages = {{321-347}},
  journal = {{Philosophical Magazine}},
  volume = {{37}},
  author = {Rayleigh, Lord}
}
@article{Lukic2007,
  year = {2007},
  title = {{Motion of a colloidal particle in an optical trap}},
  pages = {{011112}},
  journal = {{Physical Review E}},
  volume = {{76}},
  author = {{Luki\c{c}}, B. and Jeney, S. and Sviben, Z. and Kulik, A. and Florin, E.-L. and {Forr\'o}, L.}
}
@article{Storm2003a,
  number = {{5}},
  year = {2003},
  title = {{The bend stiffness of S-DNA}},
  pages = {{760-766}},
  journal = {{Europhysics Letters (EPL)}},
  volume = {{62}},
  author = {Storm, C. and Nelson, P. C.}
}
@article{Odijk1977,
  year = {1977},
  title = {{Polyelectrolytes near the Rod Limit}},
  pages = {{477-483}},
  journal = {{Journal of Polymer Science: Polymer Physics Edition}},
  volume = {{15}},
  author = {Odijk, Theo}
}
@article{Beausang2007b,
  year = {2007},
  title = {{Diffusive hidden Markov model characterization of DNA looping dynamics in tethered particle experiments}},
  journal = {{Physical Biology}},
  author = {Beausang, John F. and Nelson, Philip C.}
}
@article{Fixman1973,
  number = {{4}},
  year = {1973},
  title = {{Polymer conformational statistics. I. Probability distribution}},
  pages = {{1553-1558}},
  journal = {{The Journal of Chemical Physics}},
  volume = {{58}},
  author = {Fixman, Marshall and Alben, Richard}
}
@article{Gupta1993,
  number = {{2}},
  year = {1993},
  title = {{Mean-field theory of phase transitions in liquid-crystalline polymers}},
  pages = {{1588-1596}},
  journal = {{Journal of Chemical Physics}},
  volume = {{98}},
  author = {Gupta, Anshu M. and Edwards, Sam F.}
}
@article{Butler2005,
  year = {2005},
  title = {{Brownian dynamics simulations of a flexible polymer chain which includes continuous resistance and multibody hydrodynamic interactions}},
  journal = {{The Journal of Chemical Physics}},
  volume = {{122}},
  author = {Butler, Jason E. and Shaqfeh, Eric S.G.}
}
@article{Csiszar1991,
  number = {{4}},
  year = {1991},
  title = {{Why Least Squares and Maximum Entropy? An Axiomatic Approach to Inference for Linear Inverse Problems}},
  pages = {{2032-2066}},
  journal = {{The Annals of Statistics}},
  volume = {{19}},
  author = {Csiszar, Imre}
}
@inproceedings{Dietrich2006,
  year = {2006},
  title = {{Advances in the Development of a Novel Method to be used in Proteomics using Gold Nanobeads}},
  booktitle = {{Ultrasensitive and Single-Molecule Detection Technologies}},
  editor = {Enderlein, J\\\"org and Gryczynski, Zygmunt K.},
  volume = {{6092}},
  publisher = {{Proceedings of SPIE}},
  author = {Dietrich, Heidelinde R.C. and Young, Ian T. and Garini, Yuval}
}
@inproceedings{Dietrich2007,
  year = {2007},
  title = {A New Optical Method for Characterizing Single Molecule Interactions based on Dark Field Microscopy},
  booktitle = {{Ultrasensitive and Single-Molecule Detection Technologies II}},
  pages = {644403-1 - 64403-8},
  editor = {Enderlein, J. and Gryczynski, Z.K.},
  volume = {{6444}},
  publisher = {{Proceedings of SPIE}},
  author = {Dietrich, Heidelinde R.C. and Vermolen, Bart J. and Rieger, Bernd and Young, Ian T. and Garini, Yuval}
}
@article{Torok1996,
  number = {{3}},
  year = {1996},
  title = {{Dark-field and differential phase contrast imaging modes in confocal microscopy using a half-aperture stop}},
  pages = {{101-106}},
  journal = {{Optik}},
  volume = {{103}},
  author = {T\\\"or\\\"ok, P. and Sheppard, C. J. R. and Laxzik, Z.}
}
@article{Dietrich2002,
  number = {{1}},
  year = {2002},
  title = {{Relationship of Lipid Rafts to Transient Confinement Zones Detected by Single Particle Tracking}},
  pages = {{274-284}},
  journal = {{Biophysical Journal}},
  volume = {{82}},
  author = {Dietrich, Chrisian and Yang, Bing and Fujiwara, Takahiro and Kusumi, Akihiro and Jacobson, Ken}
}
@article{Schafer1991,
  number = {{6334}},
  year = {1991},
  title = {{Transcription by single molecules of RNA polymerase observed by light microscopy}},
  pages = {{444-448}},
  journal = {{Nature}},
  volume = {{352}},
  author = {Schafer, Dorothy A. and Gelles, Jeff and Sheetz, Michael P. and Landick, Robert}
}
@book{Mazo2002,
  series = {{International series of monographs on physics}},
  year = {2002},
  title = {{Brownian Motion: fluctuations, dynamics, and applications}},
  address = {{Oxford}},
  publisher = {{Clarendon Press}},
  author = {Mazo, Robert M.}
}
@article{Deng2009,
  number = {{10}},
  year = {2009},
  title = {{Effect of aberration on height calibration in three-dimensional localization-base microscoyp and particle tracking}},
  pages = {{1886-1890}},
  journal = {{Applied Optics}},
  volume = {{48}},
  author = {Deng, Yi. and Shaevitz, Joshua W.}
}
@article{Han2006,
  year = {2006},
  title = {{Brownian Motion of an Ellipsoid}},
  journal = {{Science}},
  volume = {{314}},
  author = {Han, Y. and Alsayed, A.M. and Nobili, M. and Zhang, J. and Lubensky, T.C. and Yodh, A.G.}
}
@article{Dietrich2009,
  year = {2009},
  title = {Tethered Particle Motion Mediated by Scattering from Gold Nanoparticles and Darkfield Microscopy},
  pages = {{031795}},
  journal = {{Journal of Nanophotonics}},
  volume = {{3}},
  author = {Dietrich, Heidelinde R. C. and Rieger, Bernd and Wiertz, Frank G.M. and de Groote, Frederik H. and Heering, Hendrik A. and Young, Ian T. and Garini, Yuval}
}
@article{Shaevitz2007,
  number = {{9}},
  year = {2007},
  title = {{Enhanced three-dimensional deconvolution microscopy using a measured depth-varying point-spread function}},
  pages = {{2622-2627}},
  journal = {{Journal of the Optical Society of America A}},
  volume = {{24}},
  author = {Shaevitz, Joshua W. and Fletcher, Daniel A.}
}
@book{Doi1986,
  year = {1986},
  title = {{The Theory of Polymer Dynamics}},
  address = {{New York}},
  publisher = {{Oxford University Press}},
  author = {Doi, M. and Edwards, S.F. }
}
@article{Dhar2002,
  number = {{6}},
  year = {2002},
  title = {{Triple Minima in the Free Energy of Semiflexible Polymers}},
  pages = {{065502}},
  journal = {{Physical Review Letters}},
  volume = {{89}},
  author = {Dhar, Abhishek and Chaudhuri, Debasish}
}
@article{Watkins2004,
  number = {{6}},
  year = {2004},
  title = {{Information Bounsd and Optimal Analysis of Dynamic Single Molecule Measurements}},
  pages = {{4015-4029}},
  journal = {{Biophysical Journal}},
  volume = {{86}},
  author = {Watkins, Lucas P. and Yang, Haw}
}
@article{Elburg2007,
  number = {{1}},
  year = {2007},
  title = {{Improved correction of axial geometrical distortion in index-mismatched fluorescent confocal microscopic images using high-aperture objective lenses}},
  pages = {{45-54}},
  journal = {{Journal of Microscopy}},
  volume = {{228}},
  author = {Elburg, H.J. van and Kuypers, L.C. and Decraemer, W.F. and Dirckx, J.J.J.}
}
@phdthesis{Li2006,
  year = {2006},
  title = {{DNA entropic elasticity for short molecules attached to beads}},
  author = {Li, Jinyu and Nelson, Philip C. and Betterton, M.D.}
}
@book{Cohen1988,
  series = {{Statistics: Textbooks and monographs}},
  year = {1988},
  title = {{Parameter estimation in reliability and life span models}},
  volume = {{96}},
  address = {{New York}},
  publisher = {{Marcel Dekker, Inc}},
  author = {Cohen, A. Clifford and Whitten, Betty Jones}
}
@article{Cocco2002,
  year = {2002},
  title = {{Theoretical models for single-molecule DNA and RNA experiments: from elasticity to unzipping}},
  pages = {{569-584}},
  journal = {{Comptes rendus de l'Academie des Sciences Physique}},
  volume = {{3}},
  author = {Cocco, S. and Marko, J.F. and Monasson, R.}
}
@article{Cocco2003,
  year = {2003},
  title = {{Force-extension behavior of folding polymers}},
  pages = {{249-263}},
  journal = {{The European Physical Journal E}},
  volume = {{10}},
  author = {Cocco, S. and Marko, J.F. and Monasson, R. and Sarkar, A. and Yan, J.}
}
@article{Hughes2001,
  year = {2001},
  title = {{DNA microarrays for expression profiling}},
  pages = {{21-25}},
  journal = {{Current Opinion in Chemical Biology}},
  volume = {{5}},
  author = {Hughes, Timothy R. and Shoemaker, Daniel D.}
}
@article{Tinland1997,
  number = {{19}},
  year = {1997},
  title = {{Persistence Length of Single-Stranded DNA}},
  pages = {{5763-5765}},
  journal = {{Macromolecules}},
  volume = {{30}},
  author = {Tinland, Bernard and Pluen, Alain and Sturm, Jean and Weill, Gilbert}
}
@article{Massey1951,
  year = {1951},
  title = {{The Kolmogorov-Smirnov test for goodness of fit}},
  pages = {{68-78}},
  journal = {{Journal of the American Statistical Association}},
  volume = {{46}},
  author = {Massey, Frank J., Jr.}
}
@article{Burkhardt1993,
  year = {1993},
  title = {{Semiflexible polymer in the half plane and statistics of the integral of a Brownian curve}},
  pages = {{L1157-L1162}},
  journal = {{Journal of Physics A: Mathematical and General}},
  volume = {{26}},
  author = {Burkhardt, Theodore W.}
}
@article{Stepanow2002,
  number = {{4}},
  year = {2002},
  title = {{The distribution function of a semiflexible polymer and random walks with constraints}},
  pages = {{546-551}},
  journal = {{Europhysics Letters (EPL)}},
  volume = {{60}},
  author = {Stepanow, S. and Sch\\\"utz, G. M.}
}
@article{Smith1992,
  number = {{5085}},
  year = {1992},
  title = {{Direct Mechanical Measurement of the Elasticity of Single DNA Molecules by Using Magnetic Beads}},
  pages = {{1122-1126}},
  journal = {{Science}},
  volume = {{258}},
  author = {Smith, Steven B. and Finzi, Laura and Bustamante, Carlos}
}
@article{Bao2002,
  number = {{8}},
  year = {2002},
  title = {{High-Sensitivity Detection of DNA Hybridization on Microarrays Using Resonance Light Scattering}},
  pages = {{1792-1979}},
  journal = {{Analytical Chemistry}},
  volume = {{74}},
  author = {Bao, Paul and Frutor, Anthony G. and Greef, Charles and Lahiri, Joydeep and Muller, Uwe and Peterson, Todd C. and Warden, Laurence and Xie, Xinying}
}
@article{Baumann1997,
  year = {1997},
  title = {{Ionic effects on the elasticity of single DNA molecules}},
  pages = {{6185-6190}},
  journal = {{Proceedings of the National Academy of Sciences of the USA}},
  volume = {{94}},
  author = {Baumann, Christoph G. and Smith, Steven B. and Bloomfield, Victor A. and Bustamante, Carlos}
}
@article{Vandenberg1991,
  number = {{1}},
  year = {1991},
  title = {{Structure of 3-aminopropyl triethoxy silane on silicon oxide}},
  pages = {{103-118}},
  journal = {{Journal of Colloid and Interface Science}},
  volume = {{147}},
  author = {Vandenberg, Elaine T. and Bertilsson, Lars and Liedberg, Bo and Uvdal, Kajsa and Erlandsson, Ragnar and Elwing, Hans and Lundstrom, Ingemar}
}
@article{Blumberg2005,
  year = {2005},
  title = {{Three-Dimensional Characterization of Tethered Microspheres by Total Internal Reflection Fluorescence Microscopy}},
  pages = {{1272-1281}},
  journal = {{Biophysical Journal}},
  volume = {{89}},
  author = {Blumberg, Seth and Gajraj, Arivalagan and Pennington, Matthew W.}
}
@misc{Neumann2001,
  month = {January 22, 2001},
  year = {2001},
  title = {{Entropic Elasticity of Weakly Perturbed Polymers}},
  pages = {11},
  publisher = {{The Energy Institute, The Pennsylvania State University}},
  author = {Neumann, Richard M.}
}
@article{Ommering2010,
  number = {{15}},
  year = {2010},
  title = {{Mobility and height detection of particle labels in an optical evanescent wave biosensor with single-label resolution}},
  pages = {{155501}},
  journal = {{Journal of Physics D: Applied Physics}},
  volume = {{43}},
  author = {van Ommering, Kim and Somers, Philip A. and Koets, Marjo and Schleipen, Jean J.H.B. and van Ijzendoorn, Leo J. and Prins, Menno W.J.}
}
@article{Heaton2001,
  number = {{7}},
  year = {2001},
  title = {{Electrostatic surface plasmon resonance: Direct electric field-induced hybridization and denaturation in monolayer nucleic acid films and label-free discrimination of base mismatches}},
  pages = {{3701-3704}},
  journal = {{Proceedings of the National Academy of Sciences of the USA}},
  volume = {{98}},
  author = {Heaton, Richard J. and Peterson, Alexander W. and Georgiadis, Rosina M.}
}
@article{Gobush1972,
  number = {{7}},
  year = {1972},
  title = {{Statistical Mechanics of Wormlike Chains. I. Asymptotic Behavior}},
  pages = {{2839-2843}},
  journal = {{The Journal of Chemical Physics}},
  volume = {{57}},
  author = {Gobush, William and Yamakawa, Hiromi and Stockmayer, W. H. and Magee, W. S.}
}
@article{Henderson2001,
  number = {{4}},
  year = {2001},
  title = {{Exploring the Confidence Interval for a Binomial Parameter in a First Course in Statistical Computing}},
  pages = {{337-344}},
  journal = {{The American Statistician}},
  volume = {{55}},
  author = {Henderson, Michael and Meyer, Mary C.}
}
@article{Winkler1994,
  number = {{9}},
  year = {1994},
  title = {{Models and equilibrium properties of stiff molecular chains}},
  pages = {{8119-8129}},
  journal = {{journal of Chemical Physics}},
  volume = {{101}},
  author = {Winkler, Roland G. and Reineker, Peter and Harnau, Ludger}
}
@article{William1972,
  number = {{7}},
  year = {1972},
  title = {{Statistical Mechanics of Wormlike Chains. I. Asymptotic Behavior}},
  pages = {{2839-2843}},
  journal = {{The Journal of Chemical Physics}},
  volume = {{57}},
  author = {William, Gobush and Hiromi, Yamakawa and Stockmayer, W. H. and Magee, W. S.}
}
@article{Peterlinz1997,
  year = {1997},
  title = {{Observation of Hybridization and Dehybridization of Thiol-Tethered DNA Using Two-Color Surface Plasmon Resonance Spectroscopy}},
  pages = {{3401-3402}},
  journal = {{Journal of the American Chemical Society}},
  volume = {{119}},
  author = {Peterlinz, Kevin A. and Georgiadis, Rosina M. and Herne, Tonya M. and Tarlov, Michael J.}
}
@article{Morriss2010,
  number = {{3}},
  year = {2010},
  title = {{A systematically coarse-grained model for DNA and its predictions for persistence length, stacking, twist, and chirality}},
  pages = {{035105}},
  journal = {{The Journal of Chemical Physics}},
  volume = {{132}},
  author = {Morriss-Andrews, Alex and Rottler, Joerg and Plotkin, Steven S.}
}
@article{Chandrasekhar1943,
  number = {{1}},
  year = {1943},
  title = {{Stochastic Problems in Physics and Astronomy}},
  pages = {{2-87}},
  journal = {{Revieuws of Modern Physics}},
  volume = {{15}},
  author = {Chandrasekhar, S.}
}
@inproceedings{Ram2005,
  series = {{Proceedings of SPIE}},
  year = {2005},
  title = {{How accurately can a single molecule be localized in three dimensions using a fluorescence microscope?}},
  booktitle = {{Imaging, Manipulation and Analysis of Biomolecule and Cells: Fundamentals and Applications III}},
  pages = {426-435},
  volume = {{5699}},
  author = {Ram, Sripad and Ward, E. Sally and Ober, Raimond J.}
}
@book{Papoulis1991,
  series = {{McGraw-Hill series in electrical engineering, Communications and signal processing}},
  edition = {{Third edition}},
  year = {1991},
  title = {{Probability, random variables, and stochastic processes}},
  address = {{Singapore}},
  publisher = {{McGraw-Hill}},
  author = {Papoulis, Athanasios}
}
@inproceedings{Ram2007,
  year = {2007},
  title = {{A novel approach to determining the three-dimensional location of microscopic objects with applications to 3D particle tracking}},
  booktitle = {{Three-Dimensional and Multidimensional Microscopy: Image Acquisition and Processing XIV}},
  pages = {64430D},
  editor = {Conchello, Jose-Angel and Cogswell, Carol J. and Wilson, Tony},
  volume = {{6443}},
  publisher = {{Proceedings of SPIE}},
  author = {Ram, Sripad and Chao, Jerry and Prabhat, Prashant and Ward, E. Sally and Ober, Raimond J.}
}
@article{Wu2005,
  year = {2005},
  title = {{Three-dimensional fluorescent particle tracking at micron-scale using a single camera}},
  pages = {{461-465}},
  journal = {{Experiments in Fluids}},
  volume = {{38}},
  author = {Wu, Mingming and Roberts, John W. and Buckley, Mark}
}
@article{Maier2000,
  number = {{22}},
  year = {2000},
  title = {{Replication by a single DNA polymerase of a stretched single-stranded DNA}},
  pages = {{12002-12007}},
  journal = {{Proceedings of the National Academy of Sciences of the USA}},
  volume = {{97}},
  author = {Maier, Berenike and Bensimon, David and Croquette, Vincent}
}
@misc{Odijk2005,
  month = {August 4, 2005},
  year = {2005},
  title = {{Note on DNA grafted to a surface (experiments Heidi Dietrich, TU Delft)}},
  author = {Odijk, Theo}
}
@article{Zimm1956,
  number = {{2}},
  year = {1956},
  title = {{Dynamics of Polymer Molecules in Dilute Solution: Viscoelasticity, Flow Birefringence and Dielectric Loss}},
  pages = {{269-278}},
  journal = {{The Journal of Chemical Physics}},
  volume = {{24}},
  author = {Zimm, Bruno H.}
}
@article{Sadr2007,
  year = {2007},
  title = {{Diffusion-induced bias in near-wall velocimetry}},
  pages = {{443-456}},
  journal = {{Journal of Fluid Mechanics}},
  volume = {{577}},
  author = {Sadr, Reza and Hohenegger, Christel and Li, Haifeng and Mucha, Peter J. and Yoda, Minami}
}
@article{Qian2000b,
  number = {{1}},
  year = {2000},
  title = {{Single-Particle Tracking: Brownian Dynamics of Viscoelastic Materials}},
  pages = {{137-143}},
  journal = {{Biophysical Journal}},
  volume = {{79}},
  author = {Qian, Hong}
}
@article{Pirrung2002,
  number = {{8}},
  year = {2002},
  title = {{How to Make a DNA Chip}},
  pages = {{1276-1289}},
  journal = {{Angewandte Chemie International Edition}},
  volume = {{41}},
  author = {Pirrung, Michael C.}
}
@article{Marko2003,
  number = {{3}},
  year = {2003},
  title = {{The micromechanics of DNA}},
  journal = {{Physics World}},
  volume = {{16}},
  author = {Marko, John F. and Cocco, Simona}
}
@article{Qian2000a,
  number = {{4}},
  year = {2000},
  title = {{A mathematical analysis for the Brownian dynamics of a DNA tether}},
  pages = {{331-340}},
  journal = {{Journal of Mathematical Biology}},
  volume = {{41}},
  author = {Qian, Hong}
}
@misc{Marko2005,
  month = {June 2, 2005},
  year = {2005},
  title = {{Introduction to Single-DNA Micromechanics}},
  pages = {63},
  publisher = {{Department of Physics, University of Illinois at Chicago}},
  author = {Marko, J.F.}
}
@article{Schaefer1980,
  number = {{5}},
  year = {1980},
  title = {{Dynamics of Semiflexible Polymers in Solution}},
  pages = {{1280-1289}},
  journal = {{Macromolecules}},
  volume = {{13}},
  author = {Schaefer, D.W. and Joanny, J.F. and Pincus, P.}
}
@article{Zurla2006,
  year = {2006},
  title = {{Novel tethered particle motion analysis of CI protein-mediated DNA looping in the regulation of bacteriophage lambda}},
  pages = {{S225-S234}},
  journal = {{Journal of Physics: Condensed Matter}},
  volume = {{18}},
  author = {Zurla, C. and Franzini, A. and Galli, G. and Dunlap, D. D. and Lewis, D. E. A. and Adhya, S. and Finzi, L.}
}
@article{Prabhat2007,
  number = {{14}},
  year = {2007},
  title = {{Elucidation of intracellular recycling pathways leading to exocytosis of the Fc receptor, FcRn, by using multifocal plane microscopy}},
  pages = {{5889-5894}},
  journal = {{Proceedings of the National Academy of Sciences of the USA}},
  volume = {{104}},
  author = {Prabhat, Prashant and Gan, Zhuo and Chao, Jerry and Ram, Sripad and Vaccaro, Carlos and Gibbons, Steven and Ober, Raimond J. and Ward, E. Sally}
}
@inproceedings{Prabhat2006,
  year = {2006},
  title = {{Simultaneous imaging of several focal planes in fluorescence microscopy for the study of cellular dynamics in 3D}},
  booktitle = {{Three-Dimensional and Multidimensional Microscopy: Image Acquisition and Processing XIII}},
  pages = {60900L},
  editor = {Conchello, Jose-Angel and Cogswell, Carol J. and Wilson, Tony},
  volume = {{6090}},
  publisher = {{Proceedings of SPIE}},
  author = {Prabhat, Prashant and Ram, Sripad and Ward, E. Sally and Ober, Raimond J.}
}
@article{Marko1994,
  number = {{5171}},
  year = {1994},
  title = {{Fluctuations and Supercoiling of DNA}},
  pages = {{506-508}},
  journal = {{Science}},
  volume = {{265}},
  author = {Marko, John F. and Siggia, Eric D.}
}
@article{Marko1995,
  number = {{26}},
  year = {1995},
  title = {{Stretching DNA}},
  pages = {{8759-8770}},
  journal = {{Macromolecules}},
  volume = {{28}},
  author = {Marko, John F. and Siggia, Eric D.}
}
@article{Winkler1992,
  number = {{24}},
  year = {1992},
  title = {{Finitie Size Distribution and Partition Functions of Gaussian Chains: Maximum Entropy Approach}},
  pages = {{6891-6896}},
  journal = {{Macromolecules}},
  volume = {{25}},
  author = {Winkler, R.G. and Reineker, P.}
}
@article{Berciaud2005,
  number = {{3}},
  year = {2005},
  title = {{Observation of Intrinsic Size Effects in the Optical Response of Individual Gold Nanoparticles}},
  pages = {{515-518}},
  journal = {{Nano Letters}},
  volume = {{5}},
  author = {Berciaud, St\\\'ephane and Cognet, Laurent and Tamarat, Philippe and Lounis, Brahim}
}
@article{Lahtinen2001,
  year = {2001},
  title = {{Diffusion of hard disks and rodlike molecules on surfaces}},
  journal = {{Physical Review E}},
  volume = {{64}},
  author = {Lahtinen, J.M. and Hjelt, T. and Ala-Nissila, T. and Chvoj, Z.}
}
@article{Wong2006,
  number = {{25}},
  year = {2006},
  title = {{The effect of integration time on fluctuation measurements: calibrating an optical trap in the presence of motion blur}},
  pages = {{12517-12531}},
  journal = {{Optics Express}},
  volume = {{14}},
  author = {Wong, Wesley P. and Halvorsen, Ken}
}
@article{Perkins1994,
  year = {1994},
  title = {{Relaxation of a Single DNA Molecule Observed by Optical Microscopy}},
  pages = {{822-826}},
  journal = {{Science}},
  volume = {{264}},
  author = {Perkins, Thomas T. and Quake, Stephern R. and Smith, Douglas E. and Chu, Steven}
}
@article{Lu2002,
  year = {2002},
  title = {{DNA Persistencde Length Revisited}},
  pages = {{261-275}},
  journal = {{Biopolymers}},
  volume = {{61}},
  author = {Lu, Yongjun and Weers, Brock and Stellwagen, Nancy C.}
}
@article{Laurens2009,
  year = {2009},
  title = {{Dissecting protein-induced DNA looping dynamics in real time}},
  journal = {{Nucleic Acids Research}},
  author = {Laurens, Niels and Bellamy, Stuart R. W. and Harms, August F. and Kovacheva, Yana S. and Halford, Stephen F. and Wuite, Gijs J. L.}
}
@article{Yguerabide1998b,
  year = {1998},
  title = {{Light-Scattering Submicroscopic Particles as Highly Fluorescent Analogs and Their Use as Tracer Labels in Clinical and Biological Applications. II. Experimental Characterization}},
  pages = {{157-176}},
  journal = {{Analytical Biochemistry}},
  volume = {{262}},
  author = {Yguerabide, Juan and Yguerabide, Evangelina E.}
}
@article{Capitanio2004,
  year = {2004},
  title = {{Exploring Molecular Motors and Switches at the Single-Molecule Level}},
  pages = {{194-204}},
  journal = {{Microscopy Research and Technique}},
  volume = {{65}},
  author = {Capitanio, M. and Vanzi, F. and Broggio, C. and Cicchi, R. and Normanno, D. and Romano, G. and Sacconi, L. and Pavone, F.S.}
}
@article{Sheppard2004,
  number = {{22}},
  year = {2004},
  title = {{Annular pupils, radial polarization, and superresolution}},
  pages = {{4322-4327}},
  journal = {{Applied Optics}},
  volume = {{43}},
  author = {Sheppard, Colin J.R.}
}
@article{Zhu2006,
  number = {{5}},
  year = {2006},
  title = {{Direct Numerical Simulation of Single-Molecule DNA by Cable Dynamics}},
  pages = {{1078-1087}},
  journal = {{Journal of Microelectromechanical Systems}},
  volume = {{15}},
  author = {Zhu, Qiang and Zeng, Jun and Triantafyllou, Michael S. and Yue, Dick K.P.}
}
@article{Strick1998,
  year = {1998},
  title = {{Behavior of Supercoiled DNA}},
  pages = {{2016-2028}},
  journal = {{Biophysical Journal}},
  volume = {{74}},
  author = {Strick, T.R. and Allemand, J.-F. and Bensimon, D. and Croquette, V.}
}
@article{Pouget2004,
  number = {{9}},
  year = {2004},
  title = {{Single-particle tracking for DNA tether length monitoring}},
  journal = {{Nucleic Acids Research}},
  volume = {{32}},
  author = {Pouget, Noelle and Dennis, Cynthia and Turlan, Catherine and Grigoriev, Mikhail and Chandler, Michael and Salome, Laurence}
}
@article{Saito1967,
  number = {{1}},
  year = {1967},
  title = {{The Statistical Mechanical Theory of Stiff Chains}},
  pages = {{219-226}},
  journal = {{Journal of the Physical Society of Japan}},
  volume = {{22}},
  author = {Saito, Nobuhiko and Takahashi, Kunihiko and Yunoki, Yasuo}
}
@article{Smith1996,
  number = {{5250}},
  year = {1996},
  title = {{Overstretching B-DNA: The Elastic Response of Individual Double-Stranded and Single-Stranded DNA Molecules}},
  pages = {{795-799}},
  journal = {{Science}},
  volume = {{271}},
  author = {Smith, Steven B. and Cui, Yujia and Bustamante, Carlos}
}
@article{Roeffaers2007,
  number = {{31}},
  year = {2007},
  title = {{Single-molecule fluorescence spectroscopy in (bio)catalysis}},
  pages = {{12603-12609}},
  journal = {{Proceedings of the National Academy of Sciences of the USA}},
  volume = {{104}},
  author = {Roeffaers, Maarten B.J. and De Cremer, Gert and Uji-i, Hiroshi and Muls, Beniot and Sels, Bert F. and Jacobs, Pierre A. and De Schryver, Frans C. and De Vos, Dirk E. and Hofkens, Johan}
}
@book{Pluta1989,
  year = {1989},
  title = {{Advanced Light Microscopy}},
  volume = {{2: Specialized Methods}},
  address = {{Amsterdam}},
  publisher = {{Elsevier}},
  author = {Pluta, Maksymilian}
}
@book{Pluta1988,
  year = {1988},
  title = {{Advanced Light Microscopy}},
  volume = {{1: Principles and Basic Properties}},
  address = {{Amsterdam}},
  publisher = {{Elsevier}},
  author = {Pluta, Maksymilian}
}
@article{Broek2006,
  number = {{1}},
  year = {2006},
  title = {{Real-time observation of DNA looping dynamics of Type IIE restriction enzymes NaeI and NarI}},
  pages = {{167-174}},
  journal = {{Nucleic Acids Research}},
  volume = {{34}},
  author = {Broek, Bram van den and Vanzi, Francesco and Normanno, Davide and Pavone, Francesco S. and Wuite, Gijs J. L.}
}
@article{Braslavsky2003,
  number = {{7}},
  year = {2003},
  title = {{Sequence Information can be Obtained from Single DNA Molecules}},
  pages = {{3960-3964}},
  journal = {{Proceedings of the National Academy of Sciences of the USA}},
  volume = {{100}},
  author = {Braslavsky, Ido and Hebert, Benedict and Kartalov, Emil and Quake, Stephern R.}
}
@article{Ariel2003,
  number = {{1}},
  year = {2003},
  title = {{Persistence length of a strongly charged rodlike polyelectrolyte in the presence of salt}},
  pages = {{011805-1-011805-11}},
  journal = {{Physical Review E}},
  volume = {{67}},
  author = {Ariel, Gil and Andelman, David}
}
@article{Yamakawa1972,
  number = {{7}},
  year = {1972},
  title = {{Statistical Mechanics of Wormlike Chains. II. Excluded Volume Effects}},
  pages = {{2843-2854}},
  journal = {{The Journal of Chemical Physics}},
  volume = {{57}},
  author = {Yamakawa, Hiromi and Stockmayer, W. H.}
}
@article{Davidson1995,
  year = {1995},
  title = {{Arrays of Uniform Latex Spheres as Test Objects in Optical Microscopy}},
  pages = {{173-178}},
  journal = {{Particle and Particle Systems Characterization}},
  volume = {{12}},
  author = {Davidson, John A.}
}
@article{Huisken2004,
  number = {{5686}},
  year = {2004},
  title = {{Optical Sectioning Deep Inside Live Embryos by Selective Plane Illumination Microscopy}},
  pages = {{1007-1009}},
  journal = {{Science}},
  volume = {{305}},
  author = {Huisken, Jan and Swoger, Jim and Del Bene, Filippo and Wittbrodt, Joachim and Stelzer, Ernst H. K.}
}
@article{Goldman1967,
  number = {{4}},
  year = {1967},
  title = {{Slow viscous motion of a sphere parallel to a plane wall - I Motion through a quiescent fluid}},
  pages = {{637-651}},
  journal = {{Chemical Engineering Science}},
  volume = {{22}},
  author = {Goldman, A.J. and Cox, R.G. and Brenner, H.}
}
@article{Maher2007,
  year = {2007},
  title = {{Spring theory}},
  pages = {{984-986}},
  journal = {{Nature}},
  volume = {{448}},
  author = {Maher, Brendan}
}
@article{Cui2008,
  number = {{31}},
  year = {2008},
  title = {{Lensless high-resolution on-chip optrofluidic microscopes for Caenorhabditis elegans and cell imaging}},
  pages = {{10670-10675}},
  journal = {{Proceedings of the National Academy of Sciences of the USA}},
  volume = {{105}},
  author = {Cui, Xiquan and Lee, Lap Man and Heng, Xin and Zhong, Weiwei and Sternberg, Paul W. and Psaltis, Demetri and Yang, Changhuei}
}
@article{Hagerman1988,
  year = {1988},
  title = {{Flexibility of DNA}},
  pages = {{265-286}},
  journal = {{Annual Review of Biophysics and BioEngineering}},
  volume = {{17}},
  author = {Hagerman, P.J.}
}
@article{Vanzi2006,
  number = {{12}},
  year = {2006},
  title = {{Lac repressor hinge flexibility and DNA looping: single molecule kinetics by tethered particle motion}},
  pages = {{3409-3420}},
  journal = {{Nucleic Acids Research}},
  volume = {{34}},
  author = {Vanzi, Francesco and Broggio, Chiara and Sacconi, Leonardo and Pavone, Francesco Saverio}
}
@article{Bronstein2009,
  number = {{1}},
  year = {2009},
  title = {{Transient Anomalous Diffusion of Telomeres in the Nucleus of Mammalian Cells}},
  pages = {{018102}},
  journal = {{Physical Review Letters}},
  volume = {{103}},
  author = {Bronstein, I. and Israel, Y. and Kepten, E. and Mai, S. and Shav-Tal, Y. and Barkai, E. and Garini, Y.}
}
@article{Bawendi1985,
  number = {{5}},
  year = {1985},
  title = {{A Wiener integral model for stiff polymer chains}},
  pages = {{2491}},
  journal = {{Journal of Chemical Physics}},
  volume = {{83}},
  author = {Bawendi, M.G. and Freed, Karl F.}
}
@article{Martin2002,
  number = {{4}},
  year = {2002},
  title = {{Apparent Subdiffusion Inherent to Single Particle Tracking}},
  pages = {{2109-2117}},
  journal = {{Biophysical Journal}},
  volume = {{83}},
  author = {Martin, Douglas S. and Forstner, Martin B. and K\\\"as, Josef A.}
}
@article{Savelkoul2006,
  number = {{1}},
  year = {2006},
  title = {{Detection of Mycobacterium tuberculosis complex with Real Time PCR: Comparison of different primer-probe sets based on the IS6110 element}},
  pages = {{177-180}},
  journal = {{Journal of Microbiological Methods}},
  volume = {{66}},
  author = {Savelkoul, Paul H.M. and Catsburg, Arnold and Mulder, Sije and Oostendorp, Ludo and Schirm, Jurjen and Wilke, Hans and van der Zanden, Adri G.M. and Noordhoek, Gerda T.}
}
@article{Bustamante2000,
  number = {{3}},
  year = {2000},
  title = {{Single-molecule studies of DNA mechanics}},
  pages = {{279-285}},
  journal = {{Current Opinion in Structural Biology}},
  volume = {{10}},
  author = {Bustamante, Carlos and Smith, Steven B. and Liphardt, Jan and Smith, Doug}
}
@article{Bustamante2003,
  year = {2003},
  title = {{Ten years of tension: single-molecule DNA mechanics}},
  pages = {{423-427}},
  journal = {{Nature}},
  volume = {{421}},
  author = {Bustamante, Carlos and Bryant, Zev and Smith, Steven B.}
}
@article{Holtzer2007,
  year = {2007},
  title = {Nanometric three-dimensional tracking of individual quantom dots in cells},
  pages = {053902},
  journal = { Applied Physics Letters},
  volume = {90},
  author = {Holtzer, L. and Meckel, T. and Schmidt, T.}
}
@article{Huang2008,
  year = {2008},
  title = {Three-Dimensional Super-Resolution Imaging by Stochastic Optical Reconstruction Microscopy},
  pages = {810-813},
  journal = {Science},
  volume = {319},
  author = {Huang, B. and Wang, W. and Bates, M. and Zhuang, X.}
}
@article{Lindner2009,
  year = {2009},
  title = {{Studies of Single Molecules in their Natural Form}},
  pages = {{283-291}},
  journal = {{Israel Journal of Chemistry}},
  volume = {{49}},
  author = {Lindner, Moshe and Nir, Guy and Dietrich, Heidelinde R. C. and Young, Ian T. and Tauber, Elad and Bronshtein, I. and Altman, Liat and Garini, Yuval}
}
@article{Wilhelm1996,
  number = {{12}},
  year = {1996},
  title = {{Radial Distribution Function of Semiflexible Polymers}},
  pages = {{2581}},
  journal = {{Physical Review Letters}},
  volume = {{77}},
  author = {Wilhelm, Jan and Frey, Erwin}
}
@article{Clercx1992,
  number = {{4}},
  year = {1992},
  title = {{Brownian particles in shear flow and harmonic potentials: A study of long-time tails}},
  pages = {{1942-1950}},
  journal = {{Physical Review A}},
  volume = {{46}},
  author = {Clercx, H.J.H. and Schram, P.P.J.M.}
}
@inproceedings{Subotic2004,
  year = {2004},
  title = {{On the Feasability of Axial Tracking of a Fluorescent Nano-Particle Using a Defocusing Model}},
  booktitle = {{Proceedings IEEE International Symposium on Biomedical Imaging: From Macro to Nano}},
  pages = {1231-1234},
  volume = {{2}},
  author = {Subotic, Nadja and van de Ville, Dimitri and Unser, Michael}
}
@article{Ebenstein2009,
  number = {{4}},
  year = {2009},
  title = {Lighting Up Individual {DNA} Binding Proteins with Quantum Dots},
  pages = {{1598-1603}},
  journal = {{Nano Letters}},
  volume = {{9}},
  author = {Ebenstein, Y. and Gassman, N. and Kim, S. and Antelman, J. and Kim, Y. and Ho, S. and Samuel, R. and Michalet, X. and Weiss, S.}
}
@article{Harlepp2004,
  number = {{17}},
  year = {2004},
  title = {{Subnanometric measurements of evanescent wave penetration depth using total internal reflection microscopy combined with fluorescent correlation spectroscopy}},
  journal = {{Applied Physics Letters}},
  volume = {{85}},
  author = {Harlepp, S. and Robert, J. and Darnton, N.C. and Chateney, D.}
}
@inproceedings{Nguyen2000,
  year = {2000},
  title = {{Magnification Corrected Optical Image Splitting for Simultaneous Multiplanar Acquisition}},
  booktitle = {{Optical Diagnostics of Living Cells III}},
  pages = {31-40},
  editor = {Farkas, Daniel L. and Leif, Robert C.},
  volume = {{3921}},
  publisher = {{Proceedings of SPIE}},
  author = {Nguyen, Lam K. and Bravo-Zanoguera, Miguel and Kellner, Albert L. and Price, Jeffrey H.}
}
@article{Braslavsky2001,
  number = {{31}},
  year = {2001},
  title = {{Objective-type dark-field illumination for scattering from microbeads}},
  pages = {{5650-5667}},
  journal = {{Applied Optics}},
  volume = {{40}},
  author = {Braslavsky, Ido and Amit, Roee and Jaffar Ali, B.M. and Gileadi, Opher and Oppenheim, Amos and Stavans, Joel}
}
@article{Stepanow2004,
  number = {{4}},
  year = {2004},
  title = {{Statistical mechanics of semiflexible polymers}},
  pages = {{499-512}},
  journal = {{The European Physical Journal B}},
  volume = {{39}},
  author = {Stepanow, S.}
}
@article{Gelles1988,
  number = {{6155}},
  year = {1988},
  title = {{Tracking kinesin-driven movements with nanometric-scale precision}},
  pages = {{450-453}},
  journal = {{Nature}},
  volume = {{331}},
  author = {Gelles, Jeff and Schnapp, Bruce J. and Sheetz, Michael P.}
}
@book{Rubinstein2006,
  year = {2006},
  title = {{Polymer Physics}},
  address = {{New York}},
  publisher = {{Oxford University Press Inc.}},
  author = {Rubinstein, Michael and Colby, Ralph H.}
}
@article{Seol2007,
  number = {{12}},
  year = {2007},
  title = {{Elasticity of Short DNA Molecules: Theory and Experiment for Contour Lengths of 0.6-7 um}},
  pages = {{4360-4373}},
  journal = {{Biophysical Journal}},
  volume = {{93}},
  author = {Seol, Yeonee and Li, Jinyu and Nelson, Philip C. and Perkins, Thomas T. and Betterton, M.D.}
}
@article{Cohen2007,
  number = {{31}},
  year = {2007},
  title = {{Principle-component analysis of shape fluctuations of single DNA molecules}},
  pages = {{12622-12627}},
  journal = {{Proceedings of the National Academy of Sciences of the USA}},
  volume = {{104}},
  author = {Cohen, Adam E. and Moerner, W.E.}
}
@article{Saxton2007,
  number = {{4}},
  year = {2007},
  title = {{A Biological Interpretation of Transient Anomalous Subdiffusion. I. Qualitative Model}},
  pages = {{1178-1191}},
  journal = {{Biophysical Journal}},
  volume = {{92}},
  author = {Saxton, M.J.}
}
@article{Otto1994,
  number = {{3}},
  year = {1994},
  title = {{Persistence lengths of semiflexible chains - Methods and approximations}},
  pages = {{543-555}},
  journal = {{Macromolecular Theory and Simulations}},
  volume = {{3}},
  author = {Otto, Matthias and Eckert, Jochen and Vilgis, Thomas A.}
}
@article{Vennemann2007,
  number = {{3}},
  year = {2007},
  title = {{In vivo whole-field blood velocity measurement techniques}},
  pages = {{495-511}},
  journal = {{Experiments in Fluids}},
  volume = {{42}},
  author = {Vennemann, Peter and Lindken, Ralph and Westerweel, Jerry}
}
@article{Vosch2007,
  number = {{31}},
  year = {2007},
  title = {{Strongly emissive individual DNA-encapsulated Ag nanoclusters as single-molecule fluorophores}},
  pages = {{12616-12621}},
  journal = {{Proceedings of the National Academy of Sciences of the USA}},
  volume = {{104}},
  author = {Vosch, Tom and Antoku, Yasuko and Hsiang, Jung-Cheng and Richards, Chris I. and Gonzalez, Jose I. and Dickson, Robert M.}
}
@article{Galletto2006,
  number = {{7113}},
  year = {2006},
  title = {{Direct observation of individual RecA filaments assembling on single DNA molecules}},
  pages = {{875-878}},
  journal = {{Nature}},
  volume = {{443}},
  author = {Galletto, Roberto and Amitani, Ichiro and Baskin, Ronald J. and Kowalczykowski, Stephen C.}
}
@article{Singh-Zocchi2003,
  number = {{13}},
  year = {2003},
  title = {{Single-molecule detection of DNA hybridization}},
  pages = {{7605-7610}},
  journal = {{Proceedings of the National Academy of Sciences of the USA}},
  volume = {{100}},
  author = {Singh-Zocchi, Mukta and Dixit, Sanhita and Ivanov, Vassili and Zocchi, Giovanni}
}
@article{Frej1993,
  number = {{9}},
  year = {1993},
  title = {{Hindered diffusion of a single sphere very near a wall in a nonuniform force field}},
  pages = {{7552-7564}},
  journal = {{Journal of Chemical Physics}},
  volume = {{98}},
  author = {Frej, Nasser A. and Prieve, Dennis C.}
}
@article{Lagowski1991,
  number = {{2}},
  year = {1991},
  title = {{Stiff chain model-functional integral approach}},
  pages = {{1266-1296}},
  journal = {{Journal of Chemical Physics}},
  volume = {{95}},
  author = {Lagowski, Jolanta B. and Noolandi, Jaan and Nickel, Bernie}
}
@article{Bednar1995,
  number = {{4}},
  year = {1995},
  title = {Determination of {DNA} Persistence Length by Cryo-electron Microscopy. Separation of the Static and Dynamic Contributions to the Apparent Persistence Length of {DNA}},
  pages = {{579-594}},
  journal = {{Journal of Molecular Biology}},
  volume = {{254}},
  author = {Bednar, J. and Furrer, P. and Katritch, V. and Stasiak, A.Z. and Dubochet, J. and Stasiak, A.}
}
@article{McIntosh2009,
  number = {{4}},
  year = {2009},
  title = {{Detailed scaling analysis of low-force polyelectrolyte elasticity}},
  pages = {{041803}},
  journal = {{Physical Review E}},
  volume = {{80}},
  author = {McIntosh, D.B. and Ribeck, N. and Saleh, O.A.}
}
@article{Hyeon2006b,
  number = {{3}},
  year = {2006},
  title = {{Size, shape, and flexibility of RNA structures}},
  pages = {{194905}},
  journal = {{The Journal of Chemical Physics}},
  volume = {{125}},
  author = {Hyeon, Changbong and Dima, Ruxandra I. and Thirumalai, D.}
}
@article{Caarls2011,
  number = {1},
  year = {2011},
  title = {Minimizing light exposure with the programmable array microscope},
  pages = {101-110},
  journal = {Journal of Microscopy},
  volume = {241},
  author = {Caarls, W. and Rieger, B and Vries, A.H.B. de and Arndt-Jovin, D.J. and Jovin, T.M.}
}
@article{Jacobsen2006,
  number = {{1}},
  year = {2006},
  title = {{Interferometric optical detection and tracking of very small gold nanoparticles at a water-glass interface}},
  pages = {{405}},
  journal = {{Optics Express}},
  volume = {{14}},
  author = {Jacobsen, Volker and Stoller, Patrick and Brunner, Christian and Vogel, Viola and Sandoghdar, Vahid}
}
@article{Crut2007,
  number = {{29}},
  year = {2007},
  title = {{Fast dynamics of supercoiled DNA revealed by single-molecule experiments}},
  pages = {{11957-11962}},
  journal = {{Proceedings of the National Academy of Sciences of the USA}},
  volume = {{104}},
  author = {Cut, Aur\\\'elien and Koster, Daniel A. and Seidel, Ralf and Wiggins, Chris H. and Dekker, Nynke H.}
}
@article{Yguerabide1998a,
  year = {1998},
  title = {{Light-Scattering Submicroscopic Particles as Highly Fluorescent Analogs and Their Use as Tracer Labels in Clinical and Biological Applications. I. Theory}},
  pages = {{137-156
 }},
  journal = {{Analytical Biochemistry}},
  volume = {{262}},
  author = {Yguerabide, Juan and Yguerabide, Evangelina E.}
}
@article{Strick1998b,
  number = {{3-4}},
  year = {1998},
  title = {{Physical Approaches to the Study of DNA}},
  pages = {{647-672}},
  journal = {{Journal of Statistical Physics}},
  volume = {{93}},
  author = {Strick, T.R. and Allemand, J.-F. and Croquette, V. and Bensimon, D.}
}
@article{Rechendorff2009,
  number = {{9}},
  year = {2009},
  title = {{Persistence length and scaling properties of single-stranded DNA adsorbed on modified graphite}},
  pages = {{095103}},
  journal = {{Journal of Chemical Physics}},
  volume = {{131}},
  author = {Rechendorff, Kristian and Witz, Guillaume and Adamcik, Jozef and Dietler, Giovanni}
}
@article{Graff2006,
  number = {{1}},
  year = {2006},
  title = {{Resonance Light Scattering (RLS) Detection of Nanoparticle Separations in a Microelectrical Field-Flow Fractionation System}},
  pages = {{8-13}},
  journal = {{IEEE Transactions on Nanotechnology}},
  volume = {{5}},
  author = {Graff, Mason and Frazier, A. Bruno}
}
@article{Kao1994,
  number = {{3}},
  year = {1994},
  title = {{Tracking of single fluorescent particles in three dimensions: use of cylindrical optics to encode particle position}},
  pages = {{1291-1300}},
  journal = {{Biophysical Journal}},
  volume = {{67}},
  author = {Kao, H.P. and Verkman, A.S.}
}
@article{Jo2007,
  number = {{8}},
  year = {2007},
  title = {{A single-molecule barcoding system using nanoslits for DNA analysis}},
  pages = {{2673-2678}},
  journal = {{Proceedings of the National Academy of Sciences of the USA}},
  volume = {{104}},
  author = {Jo, Kyubong and Dhingra, Dalia M. and Odijk, Theo and de Pablo, Juan J. and Graham, Michael D. and Runnheim, Rod and Forrest, Dan and Schwartz, David C.}
}
@article{Speidel2003,
  number = {{2}},
  year = {2003},
  title = {{Three-dimensional tracking of fluorescent nanoparticles with subnanometer precision by use of off-focus imaging}},
  pages = {{69-71}},
  journal = {{Optics Letters}},
  volume = {{28}},
  author = {Speidel, Michael and Jonas, Alexandr and Florin, Ernst-Ludwig}
}
@article{Pounder2006,
  number = {{3}},
  year = {2006},
  title = {{Comparison of real-time polymerase chain reaction using the Smart Cycler and the Gen-Probe amplified Mycobacterium tuberculosis direct test for detection of M. tuberculosis complex in clinical specimens }},
  pages = {{217-222}},
  journal = {{Diagnostic Microbiology and Infectious Disease}},
  volume = {{54}},
  author = {Pounder, June I. and Aldous, Wade K. and Woods, Gail L.}
}
@article{Harris1966,
  number = {{7}},
  year = {1966},
  title = {{On Polymer Dynamics}},
  pages = {{2595}},
  journal = {{The Journal of Chemical Physics}},
  volume = {{44}},
  author = {Harris, R.A. and Hearst, J.E.}
}
@article{Willert1992,
  year = {1992},
  title = {{Three-dimensional particle imaging with a single camera}},
  pages = {{353-358}},
  journal = {{Experiments in Fluids}},
  volume = {{12}},
  author = {Willert, C. E. and Gharib, M.}
}
@article{Oberholzer1997,
  number = {21},
  year = {1997},
  title = {Grand canonical Brownian dynamics simulation of colloidal adsorption},
  pages = {9157-9167},
  journal = {Journal of Chemical Physics},
  volume = {107},
  author = {Oberholzer, M.R. and Wagner, N.J. and Lenhoff, Abraham M.}
}
@article{Wiggins2006,
  year = {2006},
  title = {Generalized theory of semiflexible polymers},
  pages = {031906},
  journal = {Physical Review E},
  volume = {73},
  author = {Wiggins, P.A. and Nelson, P.C.}
}
@article{Brenner1961,
  number = {{3-4}},
  year = {1961},
  title = {{The slow motion of a sphere through a viscous fluid towards a plane surface}},
  pages = {{242-251}},
  journal = {{Chemical Engineering Science}},
  volume = {{16}},
  author = {Brenner, Howard}
}
@article{Bhattacharjee1987,
  number = {{1}},
  year = {1987},
  title = {{Statistical mechanics of solutions of semiflexible chains: A path integral formulation}},
  pages = {{411-418}},
  journal = {{the Journal of Chemical Physics}},
  volume = {{86}},
  author = {Bhattacharjee, Somendra M. and Muthukumar, M.}
}
@article{Armani2007,
  year = {2007},
  title = {{Label-Free, Single-Molecule Detection with Optical Microcavities}},
  journal = {{Sciencexpress}},
  author = {Armani, Andrea M. and Kulkarni, Rajan P. and Fraser, Scott E. and Flagan, Richard C. and Vahala, Kerry J.}
}
@article{Hegner1999,
  number = {{18}},
  year = {1999},
  title = {{Polymerization and mechanical properties of single RecA-DNA filaments}},
  pages = {{10109-10114}},
  journal = {{Proceedings of the National Academy of Sciences of the USA}},
  volume = {{96}},
  author = {Hegner, Martin and Smith, Steven B. and Bustamante, Carlos}
}
@article{Zhu2001,
  number = {{1}},
  year = {2001},
  title = {{Protein arrays and microarrays}},
  pages = {{40-45}},
  journal = {{Current Opinion in Chemical Biology}},
  volume = {{5}},
  author = {Zhu, Heng and Snyder, Michael}
}
@article{Wiggins2006b,
  year = {2006},
  title = {{High flexibility of DNA on short length scales probed by atomic force microscopy}},
  pages = {{137-141}},
  journal = {{Nature Nanotechnology}},
  volume = {{1}},
  author = {Wiggins, P. A. and van der Heijden, T. and Moreno-Herrero, F. and Spakowitz, A. and Philips, R. and Windom, J. and Dekker, C. and Nelson, P. C.}
}
@article{Zhang2007,
  number = {{10}},
  year = {2007},
  title = {{Gaussian approximations of fluorescence microscope point-spread function models}},
  pages = {{1819-1829}},
  journal = {Applied Optics},
  volume = {{46}},
  author = {Zhang, B. and Zerubia, J. and Olivio-Marin, J.-C.}
}
@article{Scott1979,
  number = {{3}},
  year = {1979},
  title = {{On optimal and data-based histograms}},
  pages = {{605-610}},
  journal = {{Biometrika}},
  volume = {{66}},
  author = {Scott, David W.}
}
@article{Mlodzianoski2009,
  number = {{10}},
  year = {2009},
  title = {Experimental characterization of 3D localization techniques for particle-tracking and super-resolution microscopy},
  pages = {{8264-8277}},
  journal = {{Optics Express}},
  volume = {{17}},
  author = {Mlodzianoski, M.J. and Juette, M.F. and Beane, G.L. and Bewersdorf, J.}
}
@article{Carre2003,
  year = {2003},
  title = {{Molecular interactions between DNA and an aminated glass substrate}},
  pages = {{49-55}},
  journal = {{Journal of Colloid and Interface Science}},
  volume = {{260}},
  author = {Carr\\\'e, Alain and Lacarri\\\`ere, Val\\\'erie and Birch, William}
}
@article{Sage2005,
  number = {9},
  year = {2005},
  title = {Automatic Tracking of Individual Fluorescence Particles: Application to the Study of Chromosome Dynamics},
  pages = {1372-1383},
  journal = {IEEE Transactions on Image Processing},
  volume = {14},
  author = {Sage, D. and Neumann, F.R. and Hediger, F. and Gasser, S.M. and Unser, M.}
}
@article{Dohoney2001,
  year = {2001},
  title = {{Chi-Sequence recognition and DNA translocation by single RecBCD helicase/nuclease molecules}},
  pages = {{370-374}},
  journal = {{Nature}},
  volume = {{409}},
  author = {Dohoney, Kathleen M. and Gelles, Jeff}
}
@article{Saleh2009,
  number = {{6}},
  year = {2009},
  title = {{Nonlinear Low-Force Elasticity of Single-Stranded DNA Molecules}},
  pages = {{068301}},
  journal = {{Physical Review Letters}},
  volume = {{102}},
  author = {Saleh, O.A. and McIntosh, D.B. and Pincus, P. and Ribeck, N.}
}
@article{Moerner2007,
  number = {{31}},
  year = {2007},
  title = {{New directions in single-molecule imaging and analysis}},
  pages = {{12596-12602}},
  journal = {{Proceedings of the National Academy of Sciences of the USA}},
  volume = {{104}},
  author = {Moerner, W.E.}
}
@article{Spakowitz2005,
  year = {2005},
  title = {{End-to-end distance vector distribution with fixed end orientations for the wormlike chain model}},
  journal = {{Physical Review E}},
  volume = {{72}},
  author = {Spakowitz, Andrew J. and Wang, Zhen-Gang}
}
@article{Spakowitz2004,
  year = {2004},
  title = {{Exact Results for a Semiflexible Polymer Chain in an Aligning Field}},
  pages = {{5814-5823}},
  journal = {{Macromolecules}},
  volume = {{37}},
  author = {Spakowitz, Andrew J. and Wang, Zhen-Gang}
}
@article{Spakowitz2006,
  number = {{5}},
  year = {2006},
  title = {{Wormlike chain statistics with twist and fixed ends}},
  pages = {{684-690}},
  journal = {{Europhysics Letters (EPL)}},
  volume = {{73}},
  author = {Spakowitz, A. J.}
}
@article{Wieser2008,
  number = {12},
  year = {2008},
  title = {Versatile Analysis of Single-Molecule Tracking Data by Comprehensive Testing against {Monte Carlo} Simulations},
  pages = {5988-6001},
  journal = {Biophysical Journal},
  volume = {95},
  author = {Wieser, S. and Axmann, M. and {Sch\"utz}, G.J.}
}
@phdthesis{Sarkar2002,
  year = {2002},
  title = {{Theoretical micromechanics of DNA and DNA-protein complexes}},
  school = {{University of Illinois at Chicago}},
  author = {Sarkar, Abhijit}
}
@article{Ha1995,
  number = {{21}},
  year = {1995},
  title = {{A mean-field model for semiflexible chains}},
  pages = {{9408-9412}},
  journal = {{Journal of Chemical Physics}},
  volume = {{103}},
  author = {Ha, B.-Y. and Thirumalai, D.}
}
@misc{Beausang2006,
  month = {October 1, 2006},
  year = {2006},
  title = {{Elementary simulation of tethered Brownian motion}},
  author = {Beausang, John F. and Zurla, Chiara and Sullivan, Luke and Finzi, Laura and Nelson, Philip C.}
}
@article{Beausang2007,
  number = {{6}},
  year = {2007},
  title = {{Elementary simulation of tethered Brownian motion}},
  pages = {{520-523}},
  journal = {{American Journal of Physics}},
  volume = {{75}},
  author = {Beausang, John F. and Zurla, Chiara and Finzi, Laura and Sullivan, Luke and Nelson, Philip C.}
}
@phdthesis{Guasto2008,
  year = {2008},
  title = {{Micro- and Nano-scale Colloidal Dynamics Near Surfaces}},
  school = {{Brown University}},
  author = {Guasto, Jeffrey S.}
}
@misc{Nelson2001,
  year = {2001},
  title = {{Dynamical Theories of Brownian Motion}},
  volume = {Second edition},
  publisher = {{Princeton University Press}},
  author = {Nelson, Edward}
}
@article{Shivashankar1998,
  number = {{3}},
  year = {1998},
  title = {{Backscattering from a tethered bead as a probe of DNA flexibility}},
  pages = {{291-293}},
  journal = {{Applied Physics Letters}},
  volume = {{73}},
  author = {Shivashankar, G.V. and Stolovitzky, G. and Libchaber, A.}
}
@phdthesis{Niu2004,
  year = {2004},
  title = {{A Label-free, Fluorescence Based Assay for Microarray}},
  school = {{Virginia Polytechnic Institute and State University}},
  author = {Niu, Sanjun}
}
@article{Hiraoka1987,
  year = {1987},
  title = {The Use of a Charge-Coupled Device for Quantitative Optical Microscopy of Biological Structures},
  pages = {{36-41}},
  journal = {Science},
  volume = {{238}},
  author = {Hiraoka, Y. and Sedat, J.W. and Agard, D.A.}
}
@article{Yamakawa1976,
  number = {{6}},
  year = {1976},
  title = {{Statistical mechanics of helical wormlike chains. II. Operational method and moments}},
  pages = {{2371-2376}},
  journal = {{The Journal of Chemical Physics}},
  volume = {{65}},
  author = {Yamakawa, Hiromi and Fujii, Motoharu and Shimada, Jiro}
}
@article{Nelson2007,
  year = {2007},
  title = {{Colloidal particle motion as a diagnostic of DNA conformational transitions}},
  journal = {{Current Opinion in Colloid & Interface Science}},
  author = {Nelson, Philip C.}
}
@article{Allemand2003,
  year = {2003},
  title = {{Stretching DNA and RNA to probe their interactions with proteins}},
  pages = {{266-274}},
  journal = {{Current Opinion in Structural Biology}},
  volume = {{13}},
  author = {Allemand, Jean-Francois and Bensimon, David and Croquette, Vincent}
}
@article{Liu2007,
  number = {{12}},
  year = {2007},
  title = {{Quantized plasmon quenching dips nanospectroscopy via plasmon resonance energy transfer}},
  pages = {{1015-1017}},
  journal = {{Nature Methods}},
  volume = {{4}},
  author = {Liu, Gang Logan and Long, Yi-Tao and Choi, Yeonho and Kang, Taewook and Lee, Luke P.}
}
@article{Prieve1990,
  number = {{2}},
  year = {1990},
  title = {{Total Internal Reflection Microscopy: a Tool for Measuring Colloidal Forces}},
  pages = {{396-403}},
  journal = {{Langmuir}},
  volume = {{6}},
  author = {Prieve, Dennis C. and Frej, Nasser A.}
}
@article{Strick1996,
  number = {{5257}},
  year = {1996},
  title = {{The Elasticity of a Single Supercoiled DNA Molecule}},
  pages = {{1835-1837}},
  journal = {{Science}},
  volume = {{271}},
  author = {Strick, T.R. and Allemand, J.-F. and Bensimon, D. and Bensimon, A. and Croquette, V.}
}
@article{Prieve1993,
  number = {{9}},
  year = {1993},
  title = {{Scattering of an evanescent surface wave by a microscopic dielectric sphere}},
  journal = {{Applied Optics}},
  volume = {{32}},
  author = {Prieve, Dennis C. and Walz, John Y.}
}
@article{Montanari2001,
  number = {{10}},
  year = {2001},
  title = {{Hairpin Formation and Elongation of Biomolecules}},
  pages = {{2178-2181}},
  journal = {{Physical Review Letters}},
  volume = {{86}},
  author = {Montanari, Andrea and M\\\'ezard, Marc}
}
@article{Storm2003b,
  number = {{5}},
  year = {2003},
  title = {{Theory of high-force DNA stretching and overstretching}},
  pages = {{051906}},
  journal = {{Physical Review E}},
  volume = {{67}},
  author = {Storm, C. and Nelson, P. C.}
}
@article{Bouchiat1999,
  year = {1999},
  title = {{Estimating the Persistence Length of a Worm-Like Chain Molecule from Force-Extension Measurements}},
  pages = {{409-413}},
  journal = {{Biophysical Journal}},
  volume = {{76}},
  author = {Bouchiat, C. and Wang, M. D. and Allemand, J.-F. and Strick, T. and Block, S. M. and Croquette, V.}
}
@article{Cady2007,
  year = {2007},
  title = {{Optimized linkage and quenching strategies for quantum dot molecular beacons}},
  pages = {{116-124}},
  journal = {{Molecular and Cellular Probes}},
  volume = {{21}},
  author = {Cady, Nathaniel C. and Strickland, Aaron D. and Batt, Carl A.}
}
@article{Fraden1993,
  number = {{4}},
  year = {1993},
  title = {{Angular correlations and the isotropic-nematic phase transition in suspensions of tobacco mosaic virus}},
  pages = {{2816-2838}},
  journal = {{Physical Review E}},
  volume = {{48}},
  author = {Fraden, Seth and Maret, Georg}
}
@article{Bustamante1994,
  number = {{5178}},
  year = {1994},
  title = {{Entropic Elasticity of lambda-Phage DNA}},
  pages = {{1599-1601}},
  journal = {{Science}},
  volume = {{265}},
  author = {Bustamante, C. and Marko, J.F. and Siggia, E.D. and Smith, S.}
}
@article{Rouse1953,
  number = {{7}},
  year = {1953},
  title = {{A Theory of the Linear Viscoelastic Properties of Dilute Solutions of Coiling Polymers}},
  pages = {{1272-1280}},
  journal = {{The Journal of Chemical Physics}},
  volume = {{21}},
  author = {Rouse, Prince E.}
}
@article{Vanzi2003,
  number = {{10}},
  year = {2003},
  title = {{Protein synthesis by single ribosomes}},
  pages = {{1174-1179}},
  journal = {{RNA}},
  volume = {{9}},
  author = {Vanzi, Francesco and Vladimirov, Serguei and Knudsen, Charlotte R. and Goldman, Yale E. and Cooperman, Barry S.}
}
@article{Lambert2006,
  year = {2006},
  title = {{Mg2+-Induced Compaction of Single RNA Molecules Monitored by Tethered Particle Microscopy}},
  pages = {{3672-3685}},
  journal = {{Biophysical Journal}},
  volume = {{90}},
  author = {Lambert, Meredith Newby and {V\"ocker}, Eva and Blumberg, Seth and Redemann, Stefanie and Gajraj, Arivalagan and Meiners, Jens-Christian and Walter, Nils. G.}
}
@article{Kessler2004,
  number = {{2}},
  year = {2004},
  title = {{Distribution functions for filaments under tension}},
  pages = {{1155-1164}},
  journal = {{Journal of Chemical Physics}},
  volume = {{121}},
  author = {Kessler, David A. and Rabin, Yitzhak}
}
@article{Edwards1970,
  year = {1970},
  title = {{Theory of the Single Chain}},
  pages = {{43}},
  journal = {{Discussions of the Faraday Society}},
  volume = {{49}},
  author = {Edwards, S.F.}
}
@article{Bouzigues2008,
  number = {{11}},
  year = {2008},
  title = {{Nanofluidics in the Debye Layer at Hydrophilic and Hydrophobic Surfaces}},
  pages = {{114503}},
  journal = {{Physical Review Letters}},
  volume = {{101}},
  author = {Bouzigues, C. I. and Tabeling, P. and Bocquet, L.}
}
@misc{Odijk2008,
  month = {05 September 2008},
  year = {2008},
  title = {{Private communication}},
  author = {Odijk, Theo}
}
@article{Kirkpatrick2008,
  number = {{1}},
  year = {2008},
  title = {{Performance of a gradient-based shift estimator in a spatially sparse data environment: tracking the sub-pixel motion of fluorescent particles}},
  pages = {{64-72}},
  journal = {{Journal of Microscopy}},
  volume = {{212}},
  author = {Kirkpatrick, S.J. and Duncan, D.D.}
}
@article{Visnapuu2009,
  number = {{10}},
  year = {2009},
  title = {{Single-molecule imaging of DNA curtains reveals intrinsic energy landscapes for nucleosome deposition}},
  pages = {{1056-1062}},
  journal = {{Nature Structural & Molecular Biology}},
  volume = {{16}},
  author = {Visnapuu, Mari-Liis and Greene, Eric C.}
}
@book{Conover1980,
  series = {{Wiley series in probability and mathematical statistics}},
  edition = {{Second edition}},
  year = {1980},
  title = {{Practical Nonparametric Statistics}},
  address = {{New York}},
  publisher = {{Wiley}},
  author = {Conover, W.J.}
}
@article{Snyder1992,
  number = {{5}},
  year = {1992},
  title = {{Deblurring Subject to Nonnegativity Constraints}},
  pages = {{1143-1150}},
  journal = {{IEEE Transactions on Signal Processing}},
  volume = {{40}},
  author = {Snyder, Donald L. and Schulz, Timothy H. and O'Sullivan, Joseph A.}
}
@article{DiMarzio1965b,
  number = {{2}},
  year = {1965},
  title = {{One-Dimensional Model of Polymer Adsorption}},
  journal = {{The Journal of Chemical Physics}},
  volume = {{43}},
  author = {DiMarzio, Edmund A. and McCrackin, Frank L.}
}
@article{DiMarzio1965a,
  number = {{6}},
  year = {1965},
  title = {{Proper Accounting of Conformations of a Polymer Near a Surface}},
  pages = {{2101-2106}},
  journal = {{The Journal of Chemical Physics}},
  volume = {{42}},
  author = {DiMarzio, Edmund A.}
}
@article{Netopilik1990,
  year = {1990},
  title = {{Orientation-dependent rotational diffusion coefficient of rod-like macromolecules in semi-dilute solution}},
  pages = {{172-173}},
  journal = {{Rheologica Acta}},
  volume = {{29}},
  author = {Netopil\\\'{\\\i}k, M.}
}
@article{Hamaker1937,
  number = {{10}},
  year = {1937},
  title = {{The London-Van Der Waals Attraction Between Spherical Particles}},
  pages = {{1058-1072}},
  journal = {{Physica }},
  volume = {{4}},
  author = {Hamaker, H.C.}
}
@article{Cheezum2001,
  number = {{4}},
  year = {2001},
  title = {{Quantitative Comparison of Algorithms for Tracking Single Fluorescent Particles}},
  pages = {{2378-2388}},
  journal = {{Biophysical Journal}},
  volume = {{81}},
  author = {Cheezum, Michael K. and Walker, William F. and Guilford, William H.}
}
@article{Ritchie2005,
  number = {{3}},
  year = {2005},
  title = {{Detection of Non-Brownian Diffusion in the Cell Membrane in Single Molecule Tracking}},
  pages = {{2266-2277}},
  journal = {{Biophysical Journal}},
  volume = {{88}},
  author = {Ritchie, Ken and Sha, Xiao-Yuan and Kondo, Junko and Iwasawa, Kokoro and Fujiwara, Takahiro and Kusumi, Akihiro}
}
@incollection{Han2009,
  series = {{The IMA Volumes in Mathematics and its Applications}},
  year = {2009},
  title = {{Calibration of Tethered Particle Motion Experiments}},
  booktitle = {{Mathematics of DNA Structure, Funcion and Interactions}},
  editor = {Benham, C.J. and Harvey, S. and Olson, W.K. and Sumners, D.W. and Swigon, D.},
  volume = {150},
  publisher = {{Springer}},
  author = {Han, Lin and Lui, Bertrand and Blumberg, Seth and Beausang, John F. and Nelson, Philip C. and Philips, Rob}
}
@article{Towles2009,
  year = {2009},
  title = {{First-principles calculation of DNA looping in tethered particle experiments}},
  pages = {{025001}},
  journal = {{Physical Biology}},
  volume = {{6}},
  author = {Towles, Kevin B. and Beausang, John F. and Garcia, H.G. and Philips, Rob and Nelson, Philip C.}
}
@article{Pralle1999,
  number = {{5}},
  year = {1999},
  title = {{Three-Dimensional High-resolution Particle Tracking for Optical Tweezers by Forward Scattered Light}},
  pages = {{378-386}},
  journal = {{Microscopy Research and Technique}},
  volume = {{44}},
  author = {Pralle, A. and Prummer, M. and Florin, E.-L and Stelzer, E.H.K. and H\\\"orber, J.K.H.}
}
@article{Wrobel2003,
  number = {{12}},
  year = {2003},
  title = {{Optimization of high-density cDNA-microarray protocols by 'design of experiments'}},
  journal = {{Nucleic Acids Research}},
  volume = {{131}},
  author = {Wrobel, Gunnar and Schlingemann, Joerg and Hummerich, Lars and Kramer, Heidi and Lichter, Peter and Hahn, Meinhard}
}
@article{Gibson1989,
  number = {{9}},
  year = {1989},
  title = {{Diffraction by a Circular Aperture as a Model for Three-Dimensional Microscopy}},
  pages = {{1357-1367}},
  journal = {{Journal of the Optical Society of America A}},
  volume = {{6}},
  author = {Gibson, Sarah Frisken and Lanni, Frederick}
}
@article{Destainville2006,
  number = {{2}},
  year = {2006},
  title = {{Quantification and Correction of Systematic Erros Due to Detector Time-Averaging in Single-Molecule Tracking Experiments}},
  pages = {{L17-L19}},
  journal = {{Biophysical Journal}},
  volume = {{90}},
  author = {Destainville, Nicolas and Salom\\\'e, Laurence}
}
@article{Sader1997,
  number = {{2}},
  year = {1997},
  title = {{Accurate Analytic Formulae for the Far Field Effective Potential and Surface Charge Density of a Uniformly Charged Sphere}},
  pages = {{508-510}},
  journal = {{Journal of Colloid and Interface Science}},
  volume = {{188}},
  author = {Sader, John Elie}
}
@article{Durnin1987,
  number = {{15}},
  year = {1987},
  title = {{Diffraction-Free Beams}},
  pages = {{1499-1501}},
  journal = {{Physical Review Letters}},
  volume = {{58}},
  author = {Durnin, J. and Miceli, J.J., Jr. and Eberly, J.H.}
}
@article{Moroz1998,
  year = {1998},
  title = {{Entropic Elasticity of Twist-Storing Polymers}},
  pages = {{6333-6347}},
  journal = {{Macromolecules}},
  volume = {{31}},
  author = {Moroz, J. David and Nelson, Philip}
}
@article{Peters1998,
  number = {{7}},
  year = {1998},
  title = {{Three dimensional single-particle tracking with nanometer resolution}},
  pages = {{2762-2766}},
  journal = {{Review of Scientific Instruments}},
  volume = {{69}},
  author = {Peters, Inge M. and de Grooth, Bart G. and Schins, Juleon M. and Figdor, Carl G. and Greve, Jan}
}
@article{Kessler1991,
  year = {1991},
  title = {{The digoxigenin:anti-digoxigening (DIG) technology - a survey on the concept and realization of a novel bioanalytical indicator system}},
  pages = {{161-205}},
  journal = {{Molecular and Cellular Probes}},
  volume = {{5}},
  author = {Kessler, Christoph}
}
@article{Hyeon2006a,
  number = {{10}},
  year = {2006},
  title = {{Kinetics of interior loop formation in semiflexible chains}},
  pages = {{104905}},
  journal = {{The Journal of Chemical Physics}},
  volume = {{124}},
  author = {Hyeon, Changbong and Thirumalai, D.}
}
@article{Moroz1997,
  number = {{26}},
  year = {1997},
  title = {{Torsional directed walks, entropic elasticity, and DNA twist stiffness}},
  pages = {{14418-14422}},
  journal = {{Proceedings of the National Academy of Sciences of the USA}},
  volume = {{94}},
  author = {Moroz, J. David and Nelson, Philip}
}
@article{Massart2005,
  number = {{4}},
  year = {2005},
  title = {{Visual Presentation of Data by Means of Box Plots}},
  pages = {{215-218}},
  journal = {{LC-GC Europe}},
  volume = {{18}},
  author = {Massart, D.L. and Smeyers-Verbeke, J. and Capron, X. and Schlesier, Karin}
}
@article{Hynes2001,
  number = {3},
  year = {2001},
  title = {The ErbB receptor tyrosine family as signal integrators},
  pages = {151-9},
  journal = {Endocr Relat Cancer},
  volume = {8},
  author = {Hynes, N. E. and Horsch, K. and Olayioye, M. A. and Badache, A.}
}
@article{Michalet2001,
  number = {4},
  year = {2001},
  title = {Properties of fluorescent semiconductor nanocrystals and their application to biological labeling},
  pages = {261-276},
  journal = {Single Molecules},
  volume = {2},
  author = {Michalet, X. and Pinaud, F. and Lacoste, T. D. and Dahan, M. and Bruchez, M. P. and Alivisatos, A. P. and Weiss, S.}
}
@article{Kuno2001,
  number = {2},
  year = {2001},
  title = {"On"/"off" fluorescence intermittency of single semiconductor quantum dots},
  pages = {1028-1040},
  journal = {Journal of Chemical Physics},
  volume = {115},
  author = {Kuno, M. and Fromm, D. P. and Hamann, H. F. and Gallagher, A. and Nesbitt, D. J.}
}
@article{Martinez2003,
  number = {4},
  year = {2003},
  title = {Identification and removal of contaminating fluorescence from commercial and in-house printed DNA microarrays},
  pages = {e18},
  journal = {Nucleic Acids Research},
  volume = {31},
  author = {Martinez, M. J. and Aragon, A. D. and Rodriguez, A. L. and Weber, J. M. and Timlin, J. A. and Sinclair, M. B. and Haaland, D. M. and Werner-Washburne, M.}
}
@article{Stauffer1997,
  number = {6},
  year = {1997},
  title = {Compartmentalized IgE receptor-mediated signal transduction in living cells},
  pages = {1447-54},
  journal = {J Cell Biol},
  volume = {139},
  author = {Stauffer, T. P. and Meyer, T.}
}
@article{Hebert2005,
  number = {5},
  year = {2005},
  title = {Spatiotemporal image correlation Spectroscopy (STICS) theory, verification, and application to protein velocity mapping in living CHO cells},
  pages = {3601-3614},
  journal = {Biophysical Journal},
  volume = {88},
  author = {Hebert, B. and Costantino, S. and Wiseman, P. W.}
}
@article{Pyenta2003,
  year = {2003},
  title = {Lateral diffusion of membrane lipid-anchored probes before and after aggregation of cell surface IgE-receptors},
  pages = {8310-8318},
  journal = {J. Phys. Chem. A},
  volume = {107},
  author = {Pyenta, P. and Schwille, P. and Webb, W. and Holowka, D. and Baird, B.}
}
@misc{CUDA,
  year = {2007},
  title = {Compute Unified Device Architecture (CUDA)},
  note = {{http://www.nvidia.com}},
  author = {NVIDIA}
}
@article{Petersen1993,
  year = {1993},
  title = {Quantitation of membrane receptor distributions by image correlation spectroscopy: concept and application},
  pages = {1135-1146},
  journal = {Biophys. J.},
  volume = {65},
  author = {Petersen, N. and Hoddelius, P.L. and Wiseman, P. and Seger, O. and Magnusson, K.}
}
@article{Hess2006,
  number = {11},
  year = {2006},
  title = {Ultra-high resolution imaging by fluorescence photoactivation localization microscopy},
  pages = {4258-4272},
  journal = {Biophysical Journal},
  volume = {91},
  author = {Hess, S.T. and Girirajan, T.P.K. and Mason, M.D.}
}
@article{Kotula2004,
  year = {2004},
  title = {Automated analysis of SEM X-Ray spectral images: a powerful new microanalysis tool},
  pages = {1-17},
  journal = {Microscopy and Microanalysis },
  volume = {9},
  author = {Kotula, P. G. and Keenan, M. R. and Michael, J. R. }
}
@article{Yarden2001,
  number = {2},
  year = {2001},
  title = {Untangling the ErbB signalling network},
  pages = {127-37},
  journal = {Nat Rev Mol Cell Biol},
  volume = {2},
  author = {Yarden, Y. and Sliwkowski, M. X.}
}
@article{MinGW,
  year = {2008},
  title = {Minimalist GNU for Windows},
  url = {http://www.mingw.org/},
  author = {MinGW}
}
@article{Shroff2008,
  number = {5},
  year = {2008},
  title = {Live-cell photoactivated localization microscopy of nanoscale adhesion dynamics},
  pages = {417-423},
  journal = {Nature Methods},
  volume = {5},
  author = {Shroff, H. and Galbraith, C. G. and Galbraith, J. A. and Betzig, E.}
}
@book{Jain1988,
  year = {1988},
  title = {Algorithms for Clustering Data},
  publisher = {Prentice Hall},
  author = {Jain, A. and Dubes, R.}
}
@article{Grecco2004,
  number = {4-5},
  year = {2004},
  title = {Ensemble and single particle photophysical proper-ties (Two-Photon excitation, anisotropy, FRET, lifetime, spectral conversion) of commercial quantum dots in solution and in live cells},
  pages = {169-179},
  journal = {Microscopy Research and Technique},
  volume = {65},
  author = {Grecco, H. E. and Lidke, K. A. and Heintzmann, R. and Lidke, D. S. and Spagnuolo, C. and Martinez, O. E. and Jares-Erijman, E. A. and Jovin, T. M.}
}
@article{VanBenthem2002,
  year = {2002},
  title = {Application of equality constraints on variables during alternating least squares procedures},
  pages = {613-622},
  journal = {Journal of Chemometrics},
  volume = {16},
  author = {Van Benthem, M. H. and Keenan, M. R. and Haaland, D. M. }
}
@article{Manley2008,
  number = {2},
  year = {2008},
  title = {High-density mapping of single-molecule trajectories with photoactivated localization microscopy},
  pages = {155-157},
  journal = {Nature Methods},
  volume = {5},
  author = {Manley, S. and Gillette, J. M. and Patterson, G. H. and Shroff, H. and Hess, H. F. and Betzig, E. and Lippincott-Schwartz, J.}
}
@article{Wilson2000,
  number = {5},
  year = {2000},
  title = {Observing FcepsilonRI signaling from the inside of the mast cell membrane},
  pages = {1131-1142},
  journal = {Journal of Cell Biology},
  volume = {149},
  author = {Wilson, B. S. and Pfeiffer, J. R. and Oliver, J. M.}
}
@article{Wilson2004,
  number = {6},
  year = {2004},
  title = {Markers for detergent-resistant lipid rafts occupy distinct and dynamic domains in native membranes},
  pages = {2580-2592},
  journal = {Molecular Biology of the Cell},
  volume = {15},
  author = {Wilson, B. S. and Steinberg, S. L. and Liederman, K. and Pfeiffer, J. R. and Surviladze, Z. and Zhang, J. and Samelson, L. E. and Yang, L. H. and Kotula, P. G. and Oliver, J. M.}
}
@article{Timlin2005,
  number = {1},
  year = {2005},
  title = {Hyperspectral microarray scanning: impact on the accuracy and reliability of gene expression data},
  pages = {72},
  journal = {BMC Genomics},
  volume = {6},
  author = {Timlin, J. A. and Haaland, D. M. and Sinclair, M. B. and Aragon, A. D. and Martinez, M. J. and Werner-Washburne, M.}
}
@article{Forney1973,
  number = {3},
  year = {1973},
  title = {Viterbi Algorithm},
  pages = {268-278},
  journal = {Proceedings of the Ieee},
  volume = {61},
  author = {Forney, G. D.}
}
@article{Szent-Gyorgyi2008,
  number = {4},
  year = {2008},
  title = {Fluorogen-activating single-chain antibodies for imaging cell surface proteins (vol 26, pg 235, 2008)},
  pages = {470-470},
  journal = {Nature Biotechnology},
  volume = {26},
  author = {Szent-Gyorgyi, C. and Schmidt, B. F. and Creeger, Y. and Fisher, G. W. and Zakel, K. L. and Adler, S. and Fitzpatrick, J. A. J. and Woolford, C. A. and Yan, Q. and Vasilev, K. V. and Berget, P. B. and Bruchez, M. P. and Jarvik, J. W. and Waggoner, A.}
}
@article{Andrews2008,
  number = {8},
  year = {2008},
  title = {Actin restricts {Fc}$\epsilon${RI} diffusion and facilitates antigen-induced receptor immobilization},
  pages = {955-963},
  journal = {Nature Cell Biology},
  volume = {10},
  author = {Andrews, N. L. and Lidke, K. A. and Pfeiffer, J. R. and Burns, A. R. and Wilson, B. S. and Oliver, J. M. and Lidke, D. S.}
}
@inproceedings{Lidke2007ieee,
  year = {2007},
  title = {Localization fluorescence microscopy using quantum dot blinking},
  booktitle = {4th IEEE International Symposium on Biomedical Imaging},
  pages = {936-939},
  address = {Metro Washington DC, USA. },
  author = {Lidke, K. A. and Heintzmann, R.}
}
@article{Jinschek2010,
  year = {2010},
  title = {Quantitative atomic 3-D imaging of single/double sheet graphene structure},
  journal = {Carbon},
  author = {Jinschek, J.R. and Yucelen, E. and Calderon, H.A. and Freitag, B.}
}
@article{Bates2007,
  number = {5845},
  year = {2007},
  title = {Multicolor super-resolution imaging with photo-switchable fluorescent probes},
  pages = {1749-53},
  journal = {Science},
  volume = {317},
  author = {Bates, M. and Huang, B. and Dempsey, G. T. and Zhuang, X.}
}
@book{Bos2007,
  year = {2007},
  title = {Parameter Estimation for Scientists and Engineers},
  address = {New Jersey},
  publisher = {Wiley \& Sons},
  author = {A. van den Bos}
}
@article{Wolter2009,
  number = {1},
  year = {2010},
  title = {Real-time computation of subdiffraction-resolution fluorescence images},
  pages = {12-22},
  journal = {Journal of Microscopy},
  volume = {237},
  author = {Wolter, S. and Schuttpelz, M. and Tescherepanow, M. and Linde, van de S. and Heilemann, M. and Sauer, M.}
}
@article{Bock2007,
  number = {2},
  year = {2007},
  title = {Two-color far-field fluorescence nanoscopy based on photoswitchable emitters},
  pages = {161-165},
  journal = {Applied Physics B - Lasers and Optics},
  volume = {88},
  author = {Bock, H. and Geisler, C. and Wurm, C. A. and  Middendorff, C. von and Jakobs, S. and {Sch\"onle}, A. and Egner, A. and Hell, S. W. and Eggeling, C.}
}
@article{Rust2006,
  number = {10},
  year = {2006},
  title = {Sub-diffraction-limit imaging by stochastic optical reconstruction microscopy {(STORM)}},
  pages = {793-795},
  journal = {Nature Methods},
  volume = {3},
  author = {Rust, M.J. and Bates, M. and Zhuang, X.W.}
}
@article{Enderlein2006,
  number = {18},
  year = {2006},
  title = {Polarization effect on position accuracy of fluorophore localization},
  pages = {8112-8120},
  journal = {Optics Express},
  volume = {14},
  author = {Enderlein, J. and Toprak, E. and Selvin, P.R.}
}
@article{Enderlein2000,
  number = {9},
  year = {2000},
  title = {Theoretical Study of detection of a dipole emitter through an objective with high numerical aperture},
  pages = {634-636},
  journal = {Optics Letters},
  volume = {25},
  author = {Enderlein, J.}
}
@article{Dahan2003,
  number = {5644},
  year = {2003},
  title = {Diffusion dynamics of glycine receptors revealed by single-quantum dot tracking},
  pages = {442-445},
  journal = {Science},
  volume = {302},
  author = {Dahan, M. and Levi, S. and Luccardini, C. and Rostaing, P. and Riveau, B. and Triller, A.}
}
@misc{OberEstimationtool,
  year = {2009},
  title = {Estimation tool},
  note = {University of Texas, Southwestern {http://www4.utsouthwestern.edu/wardlab}},
  author = {Ober, R.J. and Ward, E.S.}
}
@article{Jin2007,
  number = {3},
  year = {2007},
  title = {Single-particle tracking of membrane protein diffusion in a potential: Simulation, detection, and application to confined diffusion of CFTR Cl- channels},
  pages = {1079-1088},
  journal = {Biophysical Journal},
  volume = {93},
  author = {Jin, S. and Haggie, P. M. and Verkman, A. S.}
}
@article{Jin2007b,
  number = {14},
  year = {2007},
  title = {Single particle tracking of complex diffusion in membranes: Simulation and detection of barrier, raft, and interaction phenomena},
  pages = {3625-3632},
  journal = {Journal of Physical Chemistry B},
  volume = {111},
  author = {Jin, S. and Verkman, A. S.}
}
@article{Rasnik2006,
  number = {11},
  year = {2006},
  title = {Nonblinking and longlasting single-molecule fluorescence imaging},
  pages = {891-893},
  journal = {Nature Methods},
  volume = {3},
  author = {Rasnik, I. and McKinney, S. A. and Ha, T.}
}
@article{Hell1992,
  number = {5-6},
  year = {1992},
  title = {Fundamental Improvement of Resolution with a 4Pi-Confocal Fluorescence Microscope Using 2-Photon Excitation},
  pages = {277-282},
  journal = {Optics Communications},
  volume = {93},
  author = {Hell, S. and Stelzer, E. H. K.}
}
@article{LidkeDS2007,
  year = {2007},
  title = {Exploring membrane protein dynamics by multicolor single quantum dot imaging using wide field, TIRF, and hyperspectral microscopy},
  pages = {6448Y1-8},
  journal = {Proc. of SPIE},
  volume = {6448},
  author = {Lidke, D. S. and Andrews, N. L. and Pfeiffer, J. R. and Jones, H. D. T. and Sinclair, M. B. and Haaland, D. M and Burns, A. R. and Wilson, B. S. and M., Oliver. J. and Lidke, K. A.}
}
@article{Warren1997,
  number = {4},
  year = {1997},
  title = {Compact prism spectrographs based on aplanatic principles},
  pages = {1174-1182},
  journal = {Optical Engineering},
  volume = {36},
  author = {Warren, D. W. and Hackwell, J. A. and Gutierrez, D. J.}
}
@article{Schlessinger2002,
  number = {6},
  year = {2002},
  title = {Ligand-induced, receptor-mediated dimerization and activation of EGF receptor},
  pages = {669-72},
  journal = {Cell},
  volume = {110},
  author = {Schlessinger, J.}
}
@article{Arndt-Jovin2006,
  year = {2006},
  title = {In vivo cell imaging with semiconductor quantum dots and noble-metal nanodots},
  journal = {Proc. of SPIE},
  volume = {6096, 60960P},
  author = {Arndt-Jovin, D. J. and Lopez-Quintela, M. A and Lidke, D. S. and Rodr\'{i}guez, M. J. and Santos, F. M. and Lidke, K. A. and Hagen, G. M. and Jovin, T. M.}
}
@article{Ehrensperger2007,
  number = {10},
  year = {2007},
  title = {Multiple association states between glycine receptors and gephyrin identified by SPT analysis},
  pages = {3706-3718},
  journal = {Biophysical Journal},
  volume = {92},
  author = {Ehrensperger, M. V. and Hanus, C. and Vannier, C. and Triller, A. and Dahan, M.}
}
@article{Gilfillan2006,
  number = {3},
  year = {2006},
  title = {Integrated signalling pathways for mast-cell activation},
  pages = {218-30},
  journal = {Nat Rev Immunol},
  volume = {6},
  author = {Gilfillan, A. M. and Tkaczyk, C.}
}
@article{Eggeling2009,
  year = {2009},
  title = {Direct observation of the nanoscale dynamics of membrane lipids in a living cell},
  pages = {1159-1163},
  journal = {Nature},
  volume = {457},
  author = {Eggeling, C. and Ringemann, C. and Medda, R. and 
Schwarzmann, G. and Sandhoff, K. and Polyakova, S. and Belov, V.N. and Hein, B. and Middendorff, C. von and {Sch\"onle}, A. and  Hell, S. W.}
}
@article{Huang2008a,
  number = {12},
  year = {2008},
  title = {Whole-cell {3D STORM} reveals interactions between cellular structures with nanometer-scale resolution},
  pages = {1047-1053},
  journal = {Nature Methods},
  volume = {5},
  author = {Huang, B. and Jones, S.A. and Brandenburg, B. and Zhuang, X.}
}
@article{Hess2007,
  number = {44},
  year = {2007},
  title = {Dynamic clustered distribution of hemagglutinin resolved at 40 nm in living cell membranes discriminates between raft theories},
  pages = {17370-17375},
  journal = {Proceedings of the National Academy of Sciences},
  volume = {104},
  author = {Hess, S.T. and Gould, T.J. and Gudhetl, M.V. and Maas, S.A. and Mills, K.D. and Zimmerberg, J.}
}
@article{Gustafsson2005,
  number = {37},
  year = {2005},
  title = {Nonlinear structured-illumination microscopy: Wide-field fluorescence imaging with theoretically unlimited resolution},
  pages = {13081-13086},
  journal = {Proceedings of the National Academy of Sciences of the United States of America},
  volume = {102},
  author = {Gustafsson, M. G. L.}
}
@article{Egner2007,
  number = {9},
  year = {2007},
  title = {Fluorescence nanoscopy in whole cells by asynchronous localization of photoswitching emitters},
  pages = {3285-3290},
  journal = {Biophysical Journal},
  volume = {93},
  author = {Egner, A. and Geisler, C. and Middendorff, C. von and Bock, H. and Wenzel, D. and Medda, R. and Andresen, M. and Stiel, A.C. and Jakobs, S. and Eggeling, C. and {Sch\"onle}, A. and Hell, S.W.}
}
@article{Bates2005,
  number = {10},
  year = {2005},
  title = {Short-range spectroscopic ruler based on a single-molecule optical switch},
  pages = {-},
  journal = {Physical Review Letters},
  volume = {94},
  author = {Bates, M. and Blosser, T. R. and Zhuang, X. W.}
}
@article{Sinclair2006,
  number = {24},
  year = {2006},
  title = {Hyperspectral confocal microscope},
  pages = {6283-91},
  journal = {Appl Opt},
  volume = {45},
  author = {Sinclair, M. B. and Haaland, D. M. and Timlin, J. A. and Jones, H. D.}
}
@article{Sinclair2004,
  number = {10},
  year = {2004},
  title = {Design, construction, characterization, and application of a hyperspectral microarray scanner},
  pages = {2079-2088},
  journal = {Applied Optics},
  volume = {43},
  author = {Sinclair, M. B. and Timlin, J. A. and Haaland, D. M. and Werner-Washburne, M.}
}
@article{Sark2002,
  number = {10},
  year = {2002},
  title = {Blueing, bleaching, and blinking of single CdSe/ZnS quantum dots},
  pages = {871-879},
  journal = {Chemphyschem},
  volume = {3},
  author = {Sark, W. G. J. H. M. van and Frederix, P. L. T. M. and Bol, A. A. and Gerritsen, H. C. and Meijerink, A.}
}
@book{Haaland2003,
  series = {In Spectral Imaging: Instrumentation, Applications, and Analysis},
  year = {2003},
  title = {Multivariate curve resolution for hyperspectral image analysis: applications to microarray technology},
  volume = {4959},
  address = {San Jose, CA.},
  publisher = {International Society for Optical Engineering},
  author = {Haaland, D. M. and Timlin, J. A. and Sinclair, M. B. and Van Benthem, M. H. and Martinez, M. J. and Aragon, A. D. and Werner-Washburne, M.}
}
@article{Geisler2007,
  number = {2},
  year = {2007},
  title = {Resolution of lambda/10 in fluorescence microscopy using fast single molecule photo-switching},
  pages = {223-226},
  journal = {Applied Physics A - Materials Science and Processing},
  volume = {88},
  author = {Geisler, C. and Schonle, A. and Middendorff, C. von and Bock, H. and Eggeling, C. and Egner, A. and Hell, S. W.}
}
@article{Metzger1992,
  year = {1992},
  title = {Transmembrane signalling: the joy of aggregation},
  pages = {1477-1487},
  journal = {Journal of Immunology },
  volume = {149},
  author = {Metzger, H.}
}
@article{Hanser2004,
  year = {2004},
  title = {Phase-retrieved pupil functions in wide-field fluorescence microscopy},
  pages = {32-48},
  journal = {Journal of Microscopy},
  volume = {216},
  author = {Hanser, B.M. and Gustafsson, M.G.L. and Agard, D.A. and Sedat, J.W.}
}
@book{Bharucha-Reid1960,
  year = {1960},
  title = {Elements of the Theory of Markov Processes and Their Applications},
  publisher = {New York: McGraw-Hill},
  author = {Bharucha-Reid, A. T}
}
@article{Herring2010,
  year = {2010},
  title = {Coherent electron interference from amorphous
TEM specimens},
  journal = {Journal of Electron Microscopy},
  author = {Herring, R.A. and Saitoh, K. and Tanaka, N. and Tanji, T.}
}
@article{Schmidt2008,
  number = {6},
  year = {2008},
  title = {Spherical nanosized focal spots unravels the interior of cells},
  pages = {539-544},
  journal = {Nature Methods},
  volume = {5},
  author = {Schmidt, R. and Wurm, C.A. and Jakobs, S. and Engelhardt, J. and Egner, A. and Hell, S.W.}
}
@article{Kner2009,
  number = {5},
  year = {2009},
  title = {Super-resolution video microscopy of live cells by structured illumination},
  pages = {339-344},
  journal = {Nature Methods},
  volume = {6},
  author = {Kner, P. and Chhun, B.B. and Griffs, E.R. and Winoto, L. and Gustafsson, M.G.L.}
}
@article{Heintzmann2009,
  year = {2009},
  title = {Subdiffraction resolution in continuous samples},
  pages = {362-364},
  journal = {Nature Photonics},
  volume = {3},
  author = {Heintzmann, R. and Gustafsson, M.G.L.}
}
@article{Boulanger2010,
  number = {2},
  year = {2010},
  title = {Patch-Based Nonlocal Functional for Denoising
Fluorescence Microscopy Image Sequences},
  pages = {442-454},
  journal = {IEEE Transactions on Medical Image Processing},
  volume = {29},
  author = {Boulanger, J. and Kervrann, C. and Bouthemy, P. and Elbau, P. and Sibarita, J.-B. and Salamero, J.}
}
@article{Carlton2010,
  year = {2010},
  title = {Fast live simultaneous multiwavelength four-dimensional optical microscopy},
  journal = {Proceedings of the National Academy of Sciences},
  author = {Carlton, P.M. and Boulanger, J. and Kervrann, C. and Sibarita, J.-B. and Salamero, J. and Gordon-Messer, S. and Bressan, D. and Haber, J.E. and Haase, S. and Shao, L. and Winoto, L. and Matsuda, A. and Kner, P. and Uzawa, S. and Gustafsson, M.G.F. and Kam, Z. and Agard, D.A. and Sedat, J.W.}
}
@article{Grabenbauer2005,
  year = {2005},
  title = {Correlative microscopy and electron tomography of GFP through photooxidation},
  pages = {857-862},
  journal = {Nature Methods},
  volume = {2},
  author = {Grabenbauer, M. and Geerts, W.J. and Fernadez-Rodriguez, J. and Hoenger, A. and Koster, A.J. and Nilsson, T.}
}
@article{Folling2008,
  year = {2008},
  title = {Fluorescence nanoscopy by ground-state depletion and single-molecule return},
  pages = {943-945},
  journal = {Nature Methods},
  volume = {5},
  author = {{F\"olling}, J. and Bossi, M. and Bock, H. and Medda, R. and Wurm, C.A. and Hein, B. and Jacobs, S. and Eggeling, C. and Hell, S.W.}
}
@article{Agronskaia2008,
  number = {2},
  year = {2008},
  title = {Integrated fluorescence and transmission electron microscopy},
  pages = {183-189},
  journal = {Journal of Structural Biology},
  volume = {164},
  author = {Agronskaia, A.V. and Valtentijn, J.A. and Driel, L.F. van and Schneidenberg, C. and Humbel, B.M. and Henegouwen, P. and Verkleij, A.J. and Koster, A.J. and Gerritsen, H.C.}
}
@article{Aguet2009,
  number = {8},
  year = {2009},
  title = {Super-resolution orientation estimation and localization of fluorescent dipoles using 3-D steerable filters},
  pages = {6829},
  journal = {Optics Express},
  volume = {17},
  author = {Aguet, F. and Geissbuhler, S. and Marki, I. and Lasser, T. and Unser, M.}
}
@article{Giepmans2005,
  year = {2005},
  title = {Correlated light and electron microscopic imaging of multiple endogenous proteins using quantum dots},
  pages = {743-749},
  journal = {Nature Methods},
  volume = {10},
  author = {Giepmans, B.N.G. and Deerinck, T.J. and Smarr, B.L. and Jones, Y.Z. and Ellisman, M.H.}
}
@article{Stallinga2004,
  number = {9},
  year = {2004},
  title = {Light distribution close to focus in biaxially       birefringent media
},
  pages = {1785-1788},
  journal = {Journal of the Optical Society of America A},
  volume = {21},
  author = {Stallinga, S.}
}
@article{Wang2010,
  number = {4},
  year = {2010},
  title = {In vitro and in vivo imaging with quantum dots },
  pages = {1397-1415},
  journal = {Analytical and Bioanalytical Chemistry },
  volume = {397},
  author = {Wang, C. and Gao, X. and Su, X.}
}
@article{Jamieson2007,
  number = {31},
  year = {2007},
  title = {Biological applications of quantum dots },
  pages = {4717-4732},
  journal = {Biomaterials},
  volume = {28},
  author = {Jamieson, T. and Bakhshi, R. and Petrova, D. and Pocock, R. and Imani, M. and Seifalian, A.M.}
}
@article{Abraham2009,
  number = {26},
  year = {2009},
  title = {Quantitative study of single molecule location estimation techniques },
  pages = {23352-23373},
  journal = {Optics Express},
  volume = {17},
  author = {Abraham, A.V. and Ram, S. and Chao, J. and Ward, E.S. and Ober, R.J.}
}
@article{Chao2009,
  number = {26},
  year = {2009},
  title = {A comparative study of high resolution microscopy imaging modalities using a three-dimensional resolution measure},
  pages = {24377-24401},
  journal = {Optics Express},
  volume = {17},
  author = {Chao, J. and Ram, S. and Ward, E.S. and Ober, R.J.}
}
@article{Ram2008,
  number = {12},
  year = {2008},
  title = {High accuracy 3D quantum dot tracking with multifocal plane microscopy for the study of fast intracellular dynamics in live cells },
  pages = {6025-6043},
  journal = {Biophysical Journal},
  volume = {95},
  author = {Ram, S. and Prabhar, P. and Chao, J. and Ward, E.S. and Ober, R.J.}
}
@article{Wilson1997,
  year = {1997},
  title = {The imaging of dielectric point scatterers in conventional and confocal polarisation microscopes},
  pages = {298-313},
  journal = {Optics Communications},
  volume = {141},
  author = {Wilson, T. and Juskaitis, R. and Higdon, P.D.}
}
@article{Stallinga2010,
  number = {24},
  year = {2010},
  title = {Accuracy of the {Gaussian} Point Spread Function model in {2D} localization microscopy
},
  pages = {24461-24476},
  journal = {Optics Express},
  volume = {18},
  author = {Stallinga, S. and Rieger, B.}
}
@article{Barrett1995,
  number = {5},
  year = {1995},
  title = {Objective assessment of image quality. II. Fisher information, Fourier crosstalk, and
figures of merit for task performance},
  pages = {834-853},
  journal = {Journal of the Optical Society of America A},
  volume = {12},
  author = {Barrett, H. H. and Denny, J.L. and Wagner, R.F. and Myers, K.J.}
}
@article{Foreman2007,
  number = {21},
  year = {2007},
  title = {Photon statistics in single molecule
orientational imaging},
  pages = {13597-13606},
  journal = {Optics Express},
  volume = {15},
  author = {Foreman, M.R. and Sherif, S.S. and {T\"or\"ok}, P.}
}
@article{Haeberle2003,
  number = {22},
  year = {2003},
  title = {Point spread function of optical microscopes
imaging through stratified media},
  pages = {2964-2969},
  journal = {Optics Express},
  volume = {11},
  author = {{Haeberl\'e}, O. and Ammar, M. and Furukawa, H. and Tenjimbayashi, K. and {T\"or\"ok}, P.}
}
@article{McGuire1994,
  number = {22},
  year = {1994},
  title = {Polarization aberrations.
1. Rotationally symmetric optical systems},
  pages = {5080-5100},
  journal = {Applied Optics},
  volume = {33},
  author = {McGuire, J.P. Jr. and Chipman, R.A.}
}
@article{McGuire1994a,
  number = {22},
  year = {1994},
  title = {Polarization aberrations.
2. Tilted and decentered optical systems},
  pages = {5101-5107},
  journal = {Applied Optics},
  volume = {33},
  author = {McGuire, J.P. Jr. and Chipman, R.A.}
}
@article{Muller2005,
  year = {2005},
  title = {Measures of performance in nonlinear estimation
tasks: prediction of estimation performance at low signal-to-noise ratio},
  pages = {3697-3715},
  journal = {Physics in Medicine and Biology},
  volume = {50},
  author = {{M\"uller}, S.P. and Abbey, C.K. and Rybicki, F.J. and Moore, S.C. and Kijewski, M.F.}
}
@article{Ji2010,
  number = {2},
  year = {2010},
  title = {Adaptive optics via pupil segmentation for
high-resolution imaging in biological tissues},
  pages = {141-150},
  journal = {Nature Methods},
  volume = {7},
  author = {Ji, N. and Milkie, D.E. and Betzig, E.}
}
@article{Wombacher2010,
  number = {9},
  year = {2010},
  title = {Live-cell super-resolution imaging with trimethoprim conjugates},
  pages = {717-722},
  journal = {Nature Methods},
  volume = {7},
  author = {Wormbacher, R. and Heidbreder, M. and Linde, S. van de and Sheetz, M.P. and Heilemann, M. and Cornish, V.W. and Sauer, M.}
}
@article{Henriques2010,
  number = {5},
  year = {2010},
  title = {Quick{PALM}: 3D real-time photoactivation nanoscopy image processing in {ImageJ}},
  pages = {339-340},
  journal = {Nature Methods},
  volume = {7},
  author = {Henriques, R. and Lelek, M. and Fornasiero, E.F. and Valtorta, F. and Zimmer, C. and Mhlanga, M.M.}
}
@article{Dertinger2009,
  number = {52},
  year = {2009},
  title = {Fast, background-free, {3D} super-resolution optical fluctuation imaging {(SOFI)}},
  pages = {22287-22292},
  journal = {Proceedings of the National Academy of Sciences USA},
  volume = {106},
  author = {Dertinger, T. and Colyer, R. and Iyer, G. and Weiss, S. and Enderlein, J.}
}
@article{Dertinger2010,
  number = {18},
  year = {2010},
  title = {Achieving increased resolution and more pixels
with Superresolution Optical Fluctuation
Imaging {(SOFI)}},
  pages = {18875-11885},
  journal = {Optics Express},
  volume = {18},
  author = {Dertinger, T. and Colyer, R. and Vogel, R. and  Enderlein, J. and Weiss, S.}
}
@article{Landau1967,
  number = {1},
  year = {1967},
  title = {Necessary  density conditions for sampling and interpolation of certain entire function},
  pages = {37-52},
  journal = {Acta Mathematica},
  volume = {117},
  author = {Landau, H.}
}
@article{Heilemann2008,
  number = {33},
  year = {2008},
  title = {Subdiffraction-Resolution Fluorescence Imaging with Conventional Fluorescent Probes},
  pages = {6172-6176},
  journal = {Angewannte Chemie},
  volume = {47},
  author = {Heilemann, M. and Linde, S. van de and {Sch\"uttpelz}, M. and Kasper, R. and Seefeldt, B. and Mukherjee, A. and Tinnefeld, P. and Sauer, M.}
}
@article{Gustafsson2000,
  number = {2},
  year = {2000},
  title = {Surpassing the lateral resolution limit by a factor of two using structured illumination microscopy},
  pages = {82-87},
  journal = {Journal of Microscopy},
  volume = {198},
  author = {Gustafsson, M.G.L.}
}
@article{Dedecker2007,
  year = {2007},
  title = {Orientational effects in the excitation
and de-excitation of single molecules interacting with donut-mode laser beams},
  pages = {3372-3383},
  journal = {Optics Express},
  volume = {15},
  author = {Dedecker, P. and Muls, B. and Hofkens, J. and  Enderlein, J. and Hotta, J. }
}
@article{Smal2010,
  year = {2010},
  title = {Quantitative Comparison of Spot Detection Methods in Fluorescence Microscopy},
  pages = {282-301},
  journal = {IEEE Transactions on Medical Imaging},
  volume = {29},
  author = {Smal, I. and Loog, M. and Niessen, W.J.  and  Meijering, E.}
}
@article{Akhmanova2008,
  year = {2008},
  title = {Tracking the ends: a dynamic protein network controls the fate of microtubule tips},
  pages = {309-322},
  journal = {Nature Reviews Molecular Cell Biology},
  volume = {9},
  author = {Akhmanova, A. and  Steinmetz, M.O.}
}
@article{Heuvel2008,
  year = {2008},
  title = {Single-Molecule Observation of Anomalous Electrohydrodynamic Orientation of Microtubules
},
  pages = {118301},
  journal = {Physical Review Letters},
  volume = {101},
  author = {Heuvel, M.G.L. van den and Bondesan, R. and Cosentino Langomarsino, M. and Dekker, C.}
}
@article{Lupini2008,
  number = {6},
  year = {2008},
  title = {Rapid autotuning for crystalline specimens from an inline hologram},
  pages = {195-201},
  journal = {Journal of Electron Microscopy},
  volume = {57},
  author = {Lupini, A.R. and Pennycook, S.J.}
}
@article{Hell2009a,
  year = {2009},
  title = {Diffraction-unlimited three-dimensional optical
nanoscopy with opposing lenses},
  pages = {381-387},
  journal = {Nature Photonics},
  volume = {3},
  author = {Hell, S.W. and Schmidt, R. and Egner, A.}
}
@article{Manghi2010,
  year = {2010},
  title = {Probing {DNA} conformational changes
with high temporal resolution by tethered
particle motion},
  pages = {046003},
  journal = {Physical Biology},
  volume = {7},
  author = {Manghi, M. and Tardin, C. and Baglio, J. and Rousseau, P. and Salome, L. and Destainville, N.}
}
@article{Destainville2009,
  number = {11},
  year = {2009},
  title = {Microscopic Mechanism for Experimentally Observed Anomalous Elasticity of DNA in Two Dimensions},
  pages = {4464-4469},
  journal = {Biophysical Journal},
  volume = {96},
  author = {Destainville, Nicolas and Manghi, Manoel and Palmeri, John}
}
@article{Barthel2010,
  year = {2010},
  title = {Aberration measurement in {HRTEM}: {Implementation} and diagnostic use of numerical procedures for the highly precise recognition of diffractogram patterns},
  pages = {27-46},
  journal = {Ultramicroscopy},
  volume = {111},
  author = {Barthel, J. and Thust, A.}
}
@article{Perfetti2010,
  year = {2010},
  title = {X-ray micro tomography and image analysis as complementary methods for morphological characterization and coating thickness measurement
of coated particles},
  pages = {663-675},
  journal = {Advanced Powder Technology},
  volume = {21},
  author = {Perfetti, G. and Casteele, E. van de and Rieger, B. and Wildeboer, W.J. and Meesters, G.M.H.}
}
@article{Stallinga2005,
  year = {2005},
  title = {Compact description of substrate-related aberrations in high numerical aperture optical disk readout},
  pages = {949-958},
  journal = {Applied Optics},
  volume = {44},
  author = {Stallinga, S.}
}
@article{Muhlich2009,
  number = {7},
  year = {2009},
  title = {Analysis of Multiple Orientations},
  pages = {1424-1437},
  journal = {IEEE Transactions on Image Processing},
  volume = {18},
  author = {M{\"u}hlich, M. and Aach, T.}
}
@inproceedings{Franken2007,
  series = {4485},
  year = {2007},
  title = {Nonlinear diffusion on the 2D Euclidean Motion group},
  booktitle = {LNCS},
  pages = {461-472},
  author = {Franken, E.M. and Duits, R. and Haar Romenij, B.M. ter}
}
@inproceedings{Franken2006,
  series = {3954},
  year = {2006},
  title = {An Efficient Method for Tensor Voting using Steerable Filters},
  booktitle = {LNCS},
  pages = {228-240},
  author = {Franken, E.M.  and  Almsick, M.A. van and  Rongen, P.M.J. and Florack, L.M.J. and  Haar Romenij, B.M. ter}
}
@inproceedings{Faas2007,
  series = {4678},
  year = {2007},
  title = {A crossing detector based on the structure tensor},
  booktitle = {LNCS},
  pages = {212-220},
  editor = {Blanc-Talon, J.},
  author = {Faas, F.G.A. and Vliet, L.J. van}
}
@inproceedings{Herberthsson2006,
  series = {SSBA},
  month = {March},
  year = {2006},
  title = {Pairs of Orientation in the Plane},
  booktitle = {Proceedings of the {SSBA} Symposium on Image Analysis},
  author = {Herberthsson, M. and Brun, A. and Knutsson, H.}
}
@book{Stein1971,
  year = {1971},
  title = {Introduction to Fourier Analysis on Euclidean Spaces},
  publisher = {Princeton University Press},
  author = {Stein, E. and Stein, E.M. and Weiss, G.}
}
@article{Cordes2010a,
  year = {2010},
  title = {Resolving Single-Molecule Assembled Patterns with Superresolution Blink-Microscopy},
  pages = {645-651},
  journal = {Nano Letters},
  volume = {10},
  author = {Cordes, T. and Strackharn, M. and Stahl, S.W.  and Summerer, W. and Steinhauer, C. and  Forthmann, C. and Puchner, E.M. and Vogelsang, J. and Gaub H.E. and  Tinnefeld, P.}
}
@article{Luengo2010,
  number = {6},
  year = {2010},
  title = {Constrained and Dimensionality-Independent Path Openings},
  pages = {1587-1595},
  journal = {IEEE Transactions on Image Processing},
  volume = {19},
  author = {Luengo Hendriks, C.L.}
}
@article{Luengo2007a,
  year = {2007},
  title = {Improving the accuracy of isotropic granulometries},
  pages = {865-872},
  journal = {Pattern Recognition Letters},
  volume = {28},
  author = {Luengo Hendriks, C.L. and Kempen, G.M.P. and Vliet, L.J. van}
}
@article{Luengo2007,
  number = {19},
  year = {2007},
  title = {Automatic channel unmixing for high-throughput quantitative analysis of fluorescence images},
  pages = {12306-123117},
  journal = {Optics Express},
  volume = {15},
  author = {Luengo Hendriks, C.L. and {Ker\"a}nen, S.V.E. and Biggin, M.D. and Knowles, D.W.}
}
@article{Caarls2010,
  year = {2010},
  title = {Characterization of Coupled Ground State and Excited State Equilibria by Fluorescence Spectral Deconvolution},
  pages = {181-190},
  journal = {Journal of Fluorescence},
  volume = {20},
  author = {Caarls, W. and Celej, M.S. and Demchenko, A.P. and Jovin, T.M.}
}
@article{Celej2009,
  year = {2009},
  title = {A Triple-Emission Fluorescent Probe Reveals Distinctive Amyloid Fibrillar Polymorphism of Wild-Type R-Synuclein and Its Familial Parkinson's Disease Mutants},
  pages = {7465-7472},
  journal = {Biochemistry},
  volume = {48},
  author = {Celej, M.S. and Caarls, W. and Demchenko, A.P. and Jovin, T.M.}
}
@article{Nagy2010,
  number = {38},
  year = {2010},
  title = {Distribution of resting and ligand-bound {ErbB1} and {ErbB2} receptor tyrosine kinases in living cells using number and brightness analysis},
  pages = {16524-16529},
  journal = {Proceedings of the National Academy of Sciences of the United States of America},
  volume = {107},
  author = {Nagy, P. and Claus, J. and Jovin, T.M. and Arndt-Jovin, D.J.}
}
@article{Finzi2010,
  number = {25},
  year = {2010},
  title = {Single-molecule Approaches to Probe the Structure, Kinetics, and Thermodynamics of Nucleoprotein Complexes That Regulate Transcription},
  pages = {18973-18978},
  journal = {JOURNAL OF BIOLOGICAL CHEMISTRY},
  volume = {285},
  author = {Finzi, L. and Dunlap, D.D.}
}
@article{Engelhardt2011,
  year = {2010},
  title = {Molecular Orientation Affects Localization Accuracy in Superresolution Far-Field Fluorescence Microscopy},
  pages = {209-213},
  journal = {Nano Letters},
  volume = {11},
  author = {Engelhardt, J. and Keller, J. and Hoyer, P. and Reuss, M. and Staudt, T. and Hell, S.W.}
}
@article{Lindner2011,
  year = {2011},
  title = {Force-free measurements of the conformations of {DNA} molecules tethered to a wall},
  pages = {011916},
  journal = {Physical Review E},
  volume = {83},
  author = {Lindner, M. and Nir, G. and Medalion, S. and Dietrich, H.R.C. and Rabin, Y. and Garini, Y.}
}
@article{Beleggia2004,
  year = {2004},
  title = {On the transport of intensity technique for phase retrieval},
  pages = {37-49},
  journal = {Ultramicroscopy},
  volume = {102},
  author = {Beleggia, M. and Schofield, M.A. and Volkov, V.V. and Zhu, Y.}
}
@article{Bronnikov2002,
  year = {2002},
  title = {Theory of quatitative phase-contrast computed tomography},
  pages = {472-480},
  journal = {Journal of the Optical Society of America A},
  volume = {19},
  author = {Bronnikov, A.V.}
}
@article{Donoho2006,
  number = {4},
  year = {2006},
  title = {Compressed Sensing},
  pages = {1289-1306},
  journal = {IEEE Transactions of Information Theory},
  volume = {52},
  author = {Donoho, D.L.}
}
@article{Jesacher2005,
  year = {2005},
  title = {Shadow Effects in Spiral Phase Contrast Microscopy},
  pages = {233902},
  journal = {Physics Review Letters},
  volume = {94},
  author = {Jesacher, A. and {F\"urhapter}, S. and Bernet, S. and Ritsch-Marte, M.}
}
@article{Furhapter2005,
  number = {15},
  year = {2005},
  title = {Spiral interferometry},
  pages = {1953-1955},
  journal = {Optics Letters},
  volume = {30},
  author = {{F\"urhapter}, S. and Jesacher, A. and Bernet, S. and Ritsch-Marte, M.}
}
@article{Aarts2011,
  year = {2011},
  title = {Three-dimensional atomic imaging of crystalline
nanoparticles},
  journal = {Nature},
  author = {Aaarts, S. van and Batenburg, K.J. and Rossell, M.D. and Erni, R. and Tendeloo, G. van}
}
@article{jensen_helium,
  year = {2006},
  title = {A comparison of liquid nitrogen and liquid helium as cryogens for electron cryotomography},
  pages = {231-240},
  journal = {Journal of Structural Biology},
  volume = {153},
  author = {Iancu, C.V. and Wright, E.R. and Heymann, J.B. and Jensen, G.J.}
}
@inproceedings{Noorden2010,
  series = {LNCS 6362},
  month = {September 20-24},
  year = {2010},
  title = {A Comparison of the Cingulum in Amyotrophic Lateral Sclerosis using Kernel Matchin},
  booktitle = {Medical Image Computing and Computer-Assisted Intervention - MICCAI 2010},
  pages = {249-256},
  editor = {T. Jiang, T. and Navab, N. and Pluim, J.P.W. and  Viergever, M.A.},
  address = {Beijing, China},
  publisher = {Springer},
  author = {Noorden, S. van and Caan, M.W.A. and Graaf, M. van der and Vliet, L.J. van and Vos, F.M.}
}
@article{McMorran2011,
  year = {2011},
  title = {Electron Vortex Beams with High Quanta of Orbital Angular Momentum},
  pages = {192-195},
  journal = {Science},
  volume = {331},
  author = {McMorran, B.J. and Agrawal, A. and Anderson, I.M. and Herzing, A.A. and Lezec, H.J. and McClelland, J.J. and unguris, J.}
}
@article{Voortman2011,
  year = {2011},
  title = {A fast algorithm for computing and correcting the
{CTF} for tilted, thick specimens in {TEM}},
  pages = {1029-1036},
  journal = {Ultramicroscopy},
  volume = {111},
  author = {Voortman, L.M. and Stallinga, S. and Schoenmakers, R.H.M. and Vliet, L.J. van and Rieger, B.}
}
@article{Karuppasamy2011,
  year = {2011},
  title = {Radiation damage in single-particle cryo-electron
microscopy: effects of dose and dose rate},
  pages = {398-412},
  journal = {Journal of Synchrotron Radiation},
  volume = {18},
  author = {Karuppasamy, M. and Karimi Nejadasl, F and Vulovic, M. and Koster, A.J. and Ravelli, R.B.G. }
}
@article{Krysting2011,
  year = {2011},
  title = {Heat Profiling of Three-Dimensionally Optically Trapped Gold Nanoparticles using Vesicle Cargo Release},
  pages = {888-892},
  journal = {Nano Letters},
  volume = {11},
  author = {Krysting, A. and Bendix, P.M. and Stamou, D.G. and Oddershede, L.B.}
}
@article{Schutz2001,
  number = {2},
  year = {2001},
  title = {Imaging Single Molecules in Three Dimensions},
  pages = {69-74},
  journal = {Single Molecules},
  volume = {2},
  author = {{Sch\"utz}, G.J. and Axman M. and Schindler, H.}
}
@article{vanElburg2007,
  number = {1},
  year = {2007},
  title = {Improved correction of axial geometrical distortion in index-mismatched fluorescent confocal            microscopic images using high-aperture objective lenses},
  pages = {45-54},
  journal = {Journal of Microscopy},
  volume = {228},
  author = {van Elburg, H.J. and Kuypers, L.C. and Decraemer, W.F. and Dirckx, J.J.J.}
}
@article{vandenBroek2006,
  number = {1},
  year = {2006},
  title = {Real-time observation of {DNA} looping dynamics of Type {IIE} restriction enzymes {NaeI} and {NarI}},
  pages = {167-174},
  journal = {Nucleic Acids Research},
  volume = {34},
  author = {van den Broek, B. and Vanzi, F. and Normanno, D. and Pavone, F.S. and Wuite, G.J.L.}
}
@article{Finzi1995,
  number = {5196},
  year = {1995},
  title = {Measurement of Lactose Repressor-Mediated Loop Formation and Breakdown in Single DNA Molecules},
  pages = {378-380},
  journal = {Science},
  volume = {267},
  author = {Finzi, L. and Gelles, J.}
}
@article{deGennes1976a,
  number = {4},
  year = {1976},
  title = {Dynamics of Entangled Polymer Solutions. {I.} The Rouse Model},
  pages = {587-593},
  journal = {Macromolecules},
  volume = {9},
  author = {De Gennes, P.G.}
}
@article{deGennes1976b,
  number = {4},
  year = {1976},
  title = {Dynamics of Entangled Polymer Solutions. {II.} Inclusion of Hydrodynamic Interactions},
  pages = {594-598},
  journal = {Macromolecules},
  volume = {9},
  author = {De Gennes, P.G.}
}
@article{Robertson2006,
  number = {19},
  year = {2006},
  title = {Diffusion of isolated DNA molecules: {Dependence} on length and topology},
  pages = {7310-7314},
  journal = {Proceedings of the National Academy of Sciences of the USA},
  volume = {103},
  author = {Robertson, R.M.}
}
@article{Derjaguin1941,
  year = {1941},
  title = {Theory of the stability of strongly charged lyophobic sols and of the adhesion of strongly charged      particles in solutions of electrolytes.},
  journal = {Acta Physico Chimica URSS},
  volume = {14},
  author = {Derjaguin, B. and Landau, L.}
}
@book{Verwey1948,
  year = {1948},
  title = {Theory of the stability of lyophobic colloids},
  publisher = {Elsevier},
  author = {Verwey, E.J.W. and Overbeek, J.Th.G.}
}
@article{Debye1923,
  year = {1923},
  title = {The theory of electrolytes. {I.} Lowering of freezing point and related phenomena},
  pages = {185-206},
  journal = {Physikalische Zeitschrift},
  volume = {24},
  author = {Debye, P. and {H\"uckel}, E.}
}
@book{Lyklema1991,
  year = {1991},
  title = {Fundamentals of Interface and Colloid Science},
  volume = {Volume I: Fundamentals},
  address = {London, UK},
  publisher = {Academic Press Limited},
  author = {Lyklema, J. and van Leeuwen, H.P. and van Vliet, T. and Cazabat, A.-M}
}
@book{Happel1973,
  edition = {2nd edition},
  year = {1973},
  title = {Low Reynolds number hydrodynamics},
  address = {Leyden, The Netherlands},
  publisher = {Noordhoff},
  author = {Happel, John}
}
@article{Bevan2000,
  number = {3},
  year = {2000},
  title = {Hindered diffusion of colloidal particles very near to a wall: Revisited},
  pages = {1128-1236},
  journal = {Journal of Chemical Physics},
  volume = {113},
  author = {Bevan, Michael A. and Prieve, Dennis C.}
}
@article{Stallinga2005a,
  year = {2005},
  title = {Finite conjugate spherical aberration compensation in high numerical-aperture optical disc read-out},
  pages = {7307-7312},
  journal = {Applied Optics},
  volume = {44},
  author = {Stallinga, S.}
}
@article{Fan2009,
  number = {5},
  year = {2009},
  title = {Studying {RecBCD} Helicase Translocation Along {chi-DNA} Using Tethered Particle Motion with a Stretching Force},
  pages = {1875-1883},
  journal = {Biophysical Journal},
  volume = {96},
  author = {Fan, Hsiu-Fang and Li, Hung-Wen}
}
@article{Geggier2010,
  number = {35},
  year = {2010},
  title = {Sequence dependence of {DNA} bending rigidity},
  pages = {15421-15426},
  journal = {Proceedings of the National Academy of Sciences of the USA},
  volume = {107},
  author = {Geggier, Stephanie and Vologodskii, Alexander}
}
@article{Smith1996b,
  number = {4},
  year = {1996},
  title = {Dynamical Scaling of {DNA} Diffusion Coefficients},
  pages = {1372-1373},
  journal = {Macromolecules},
  volume = {29},
  author = {Smith, Douglas E. and Perkins, Thomas T. and Chu, Steven}
}
@article{Hodgson1991,
  number = {10},
  year = {1991},
  title = {Dilute solution behavior of cyclic and linear polyelectrolytes},
  pages = {7653-7663},
  journal = {Journal of Chemical Physics},
  volume = {95},
  author = {Hodgson, Donald F. and Amis, Eric J.}
}
@inproceedings{Rieger2011,
  series = {LNCS 6688},
  month = {May 23-27},
  year = {2011},
  title = {Continuous orientation representation for arbitrary dimensions - a generalized Knutsson mapping},
  booktitle = {Proceedings of the 17th Scandinavian Conference on Image Analysis, SCIA 2011},
  pages = {774-783},
  editor = {Heyden, A. and Kahl, F.},
  address = {Heidelberg},
  publisher = {Springer},
  author = {Rieger, B. and Vliet, L.J. van and Verbeek, P.W.}
}
@book{FundFluidMech,
  edition = {3rd},
  year = {1998},
  title = {Fundamentals of Fluid Mechanics},
  address = {New York},
  publisher = {John Wiley \& Sons, Inc},
  author = {Munson, Bruce R. and Young, Donald F. and Okiishi, Theodore H.}
}
@article{Rosenthal2003,
  number = {4},
  year = {2003},
  title = {Optimal Determination of Particle Orientation,
Absolute Hand, and Contrast Loss in Single-particle Electron Cryomicroscopy},
  pages = {721-745},
  journal = {Journal of Molecular Biology},
  volume = {333},
  author = {Rosenthal, P.B. and Henderson, R.}
}
@article{Wicker2009,
  number = {18},
  year = {2009},
  title = {Characterisation of a resolution enhancing image inversion interferometer},
  pages = {15491-15501},
  journal = {Optics Express},
  volume = {17},
  author = {Wicker, K. and Sindbert, S. and Heintzmann, R.}
}
@article{Wicker2007,
  number = {19},
  year = {2007},
  title = {Interferometric resolution improvement for confocal microscopes},
  pages = {12206-12216},
  journal = {Optics Express},
  volume = {15},
  author = {Wicker, K. and Heintzmann, R.}
}
@article{Schermelleh2010,
  number = {2},
  year = {2010},
  title = {A guide to super-resolution fluorescence microscopy},
  pages = {165-175},
  journal = {The journal of cell biology},
  volume = {190},
  author = {Schermelleh, L. and Heintzmann, R. and Leonhardt, H.}
}
@article{Ruckstuhl2004,
  number = {18},
  year = {2004},
  title = {Supercritical angle fluorescence {(SAF)} microscopy},
  pages = {4246-4254},
  journal = {Optics Express},
  volume = {12},
  author = {Ruckstuhl, T. and Verdes, D.}
}
@article{Rohrbach2009,
  number = {19},
  year = {2009},
  title = {Artifacts resulting from imaging in scattering media: a theoretical prediction},
  pages = {3041-3043},
  journal = {Optics Letters},
  volume = {34},
  author = {Rohrbach, A.}
}
@article{Murdy2010,
  year = {2010},
  title = {Isotropic Diffraction-Limited Focusing Using a Single Objective Lens},
  pages = {203903},
  journal = {Physical Review Letters},
  volume = {105},
  author = {Murdy, E. and Moral, E. le and Ferrand, P. and Chaumet, P.C. and Sentenac, A. }
}
@article{Min2009,
  number = {22},
  year = {2009},
  title = {Imaging chromophores with undetectable fluorescence by stimulated emission microscopy},
  pages = {1105-1109},
  journal = {Nature},
  volume = {461},
  author = {Min, W. and Lu, S. and Chong, S. and Roy, R. and Holtom, G.R. and Xie, X.S.}
}
@inbook{Manley2010,
  series = {Methods in Enzymology},
  year = {2010},
  title = {Single-Particle Tracking Photoactivated Localization
Microscopy for Mapping Single-Molecule Dynamics},
  pages = {109-120},
  volume = {475},
  chapter = {5},
  publisher = {Elsevier},
  author = {Manely, S. and Gillette, J.M. and Lippincott-Schwartz, J.}
}
@article{Luisier2007,
  number = {3},
  year = {2007},
  title = {A New {SURE} Approach to Image Denoising:
Interscale Orthonormal Wavelet Thresholding},
  pages = {593-606},
  journal = {IEEE Transactions on Image Processing},
  volume = {16},
  author = {Luisier, F. and Blu, T. and Unser, M.}
}
@article{Krizek2011,
  number = {4},
  year = {2011},
  title = {Minimizing detection errors in single molecule localization microscopy},
  pages = {3226-3235},
  journal = {Optics Express},
  volume = {19},
  author = {Krizek, P. and Raska, I. and Hagen, G.M}
}
@article{Kaufmann2011a,
  year = {2011},
  title = {Imaging label-free intracellular structures by localisation microscopy},
  pages = {348-352},
  journal = {Micron},
  volume = {42},
  author = {Kaufmann, R. and {M\"uller}, P. and Hausmann, M. and Cremer, C.}
}
@article{Kaufmann2011,
  number = {1},
  year = {2011},
  title = {Analysis of {Her2/neu} membrane protein clusters in different types of breast cancer cells using localization microscopy},
  pages = {46-54},
  journal = {Journal of Microscopy},
  volume = {242},
  author = {Kaufmann, R. and {M\"uller}, P. and Hildenbrand, G. and Hausmann, M. and Cremer, C.}
}
@article{Fujita2007,
  year = {2007},
  title = {High-Resolution Confocal Microscopy by Saturated Excitation of Fluorescence},
  pages = {228105},
  journal = {Physical Review Letters},
  volume = {99},
  author = {Fujita, K. and Kobayashi, M. and Kawano, S. and YTamanaka, M. and Kawata, S.}
}
@article{Fahrbach2010,
  year = {2010},
  title = {Microscopy with self-reconstructing beams},
  note = {DOI: 10.1038/NPHOTON.2010.204},
  journal = {Nature photonics},
  author = {Fahrbach, F.O. and Simon, P. and Rohrbach, A.}
}
@article{Debarre2007,
  number = {13},
  year = {2007},
  title = {Image based adaptive optics through optimisation of low spatial frequencies},
  pages = {8176-8190},
  journal = {Optics Express},
  volume = {15},
  author = {Debarre, D. and Booth, M.J. and Wilson, T.}
}
@article{Cox2004,
  year = {2004},
  title = {Practical Limits of Resolution in Confocal and Non-Linear Microscopy},
  pages = {18-22},
  journal = {MICROSCOPY RESEARCH AND TECHNIQUE},
  volume = {63},
  author = {Cox, G. and Sheppard, C.J.R.}
}
@article{Cox1982,
  number = {5},
  year = {1982},
  title = {Improvement in resolution by nearly confocal microscopy},
  pages = {778-781},
  journal = {Applied Optics},
  volume = {21},
  author = {Cox, I.J. and Sheppard, C.J.R. and Wilson, T.}
}
@article{Dobrucki2007,
  year = {2007},
  title = {Scattering of Exciting Light by Live Cells in Fluorescence Confocal Imaging: Phototoxic Effects and Relevance for {FRAP} Studies},
  pages = {1778-1786},
  journal = {Biophysical Journal},
  volume = {93},
  author = {Dobrucki, J.W. and Feret, D. and Noatynska, A.}
}
@phdthesis{Wicker2010,
  month = {October},
  year = {2010},
  title = {Increasing resolution and light efficiency
in fluorescence microscopy},
  address = {United Kingdom},
  school = {King's College London},
  author = {Wicker, K.}
}
@article{PoissonNoise,
  number = {1},
  year = {1965},
  title = {Noise in Photoemission Current},
  pages = {79-80},
  journal = {Applied Optics},
  volume = {4},
  author = {Fried, D.L.}
}
@article{Kiel2007,
  year = {2007},
  title = {Direct Monitoring of Formation and Dissociation of Individual Metal Complexes by Single-Molecule Fluorescence Spectroscopy},
  pages = {3363-3366},
  journal = {Angewandte Chemie Interational Edition},
  volume = {46},
  author = {Kiel, A. and Kovacs, J. and Mokhir, A. and {Kr\"amer}, R. and Herten, D.-P.}
}
@article{Schwering2011,
  year = {2011},
  title = {Far-Field Nanoscopy with Reversible Chemical Reactions},
  pages = {2940-2945},
  journal = {Angewandte Chemie International Edition},
  volume = {50},
  author = {Schwering, M. and Kiel, A. and Kurz, A. and Lymperopoulos,K. and {Spr\"odefeld}, A. and {Kr\"amer}, R. and Herten, D.-P. }
}
@article{Rossow2010,
  number = {11},
  year = {2010},
  title = {Raster image correlation spectroscopy in live cells},
  pages = {1761-1773},
  journal = {Nature Protocols},
  volume = {5},
  author = {Rossow, M.J. and Sasaki, J.M. and Digmann, M.A. and Gratton, E.}
}
@inproceedings{Knutsson1987,
  month = {September},
  year = {1987},
  title = {A tensor representation of 3-D structure},
  booktitle = {5th IEEE-ASSP and EURASIP Workshop on Multidimensional Signal Processing},
  address = {Noorwijkerhoudt, Netherlands},
  author = {Knutsson, H.}
}
@inproceedings{Serino2011,
  series = {Lecture Notes in Computer Science 6688},
  year = {2011},
  title = {Using the Skeleton for 3D Object Decomposition},
  booktitle = {Image Analysis},
  pages = {447-456},
  editor = {Heyden, A. and Kahl, F.},
  address = {Heidelberg},
  publisher = {Springer},
  author = {Serino, L. and Sanniti di Baja, G. and Arcelli, C.}
}
@inproceedings{Schlager2011,
  series = {Lecture Notes in Computer Science 6688},
  year = {2011},
  title = {Coherence Probe Microscopy Imaging and
Analysis for Fiber-Reinforced Polymers},
  booktitle = {Image Analysis},
  pages = {424-434},
  editor = {Heyden, A. and Kahl, F.},
  address = {Heidelberg},
  publisher = {Springer},
  author = {Schlager1, V. and Schausberger, S.E. and Stifter, D. and Heise1, B.}
}
@inproceedings{Malmberg2011,
  series = {Lecture Notes in Computer Science 6688},
  year = {2011},
  title = {Generalized Hard Constraints for Graph
Segmentation},
  booktitle = {Image Analysis},
  pages = {36-47},
  editor = {Heyden, A. and Kahl, F.},
  address = {Heidelberg},
  publisher = {Springer},
  author = {Malmberg, F. and Strand, R. and {Nystr\"om}, I.}
}
@inproceedings{Larsson2011,
  series = {Lecture Notes in Computer Science 6688},
  year = {2011},
  title = {Using Fourier Descriptors and Spatial Models
for Traffic Sign Recognition},
  booktitle = {Image Analysis},
  pages = {238-249},
  editor = {Heyden, A. and Kahl, F.},
  address = {Heidelberg},
  publisher = {Springer},
  author = {Larsson, F. and Felsberg, M.}
}
@inproceedings{Landstrom2011,
  series = {Lecture Notes in Computer Science 6688},
  year = {2011},
  title = {Image Reconstruction by Prioritized
Incremental Normalized Convolution},
  booktitle = {Image Analysis},
  pages = {176-185},
  editor = {Heyden, A. and Kahl, F.},
  address = {Heidelberg},
  publisher = {Springer},
  author = {{Landstr\"om}, A. and Nellros, F. and Jonsson, H. and Thurley, M.}
}
@inproceedings{Knutsson2011,
  series = {Lecture Notes in Computer Science 6688},
  year = {2011},
  title = {Representing Local Structure Using Tensors {II}},
  booktitle = {Image Analysis},
  pages = {545-556},
  editor = {Heyden, A. and Kahl, F.},
  address = {Heidelberg},
  publisher = {Springer},
  author = {Knutsson, H. and Westin, C.-F. and Andersson, M.}
}
@inproceedings{Josth2011,
  series = {Lecture Notes in Computer Science 6688},
  year = {2011},
  title = {Real-Time Line Detection Using Accelerated
High-Resolution Hough Transform},
  booktitle = {Image Analysis},
  pages = {784-793},
  editor = {Heyden, A. and Kahl, F.},
  address = {Heidelberg},
  publisher = {Springer},
  author = {Josth, R. and Dubska, M. and Herout, A. and Havel, J.}
}
@inproceedings{Eklund2011,
  series = {Lecture Notes in Computer Science 6688},
  year = {2011},
  title = {Using the Local Phase of the Magnitude of the
Local Structure Tensor for Image Registration},
  booktitle = {Image Analysis},
  pages = {414-423},
  editor = {Heyden, A. and Kahl, F.},
  address = {Heidelberg},
  publisher = {Springer},
  author = {Eklund, A. and Forsberg, D. and Andersson, M. and Knutsson, H.}
}
@inproceedings{Astrom2011,
  series = {Lecture Notes in Computer Science 6688},
  year = {2011},
  title = {Color Persistent Anisotropic Diffusion of Images},
  booktitle = {Image Analysis},
  pages = {262-272},
  editor = {Heyden, A. and Kahl, F.},
  address = {Heidelberg},
  publisher = {Springer},
  author = {{\AAstr\"om}, F. and Felsberg, M. and Lenz, R.}
}
@article{Unser2011,
  number = {11},
  year = {2011},
  title = {Multiresolution Monogenic Signal Analysis Using
the {Riesz-Laplace} Wavelet Transform},
  pages = {2402-2418},
  journal = {IEEE TRANSACTIONS ON IMAGE PROCESSING},
  volume = {18},
  author = {Unser, M. and Sage, D. and Ville, D. van de}
}
@article{Frank1976,
  year = {1975},
  title = {Signal to noise ratio of electron micrographs obtained by cross correlation},
  pages = {376-379},
  journal = {Nature},
  volume = {256},
  author = {Frank, J. and Al-Ali, L.}
}
@article{Patra2005,
  year = {2005},
  title = {Defocused imaging of quantum-dot angular distribution of radiation},
  pages = {101103},
  journal = {Applied Physics Letters},
  volume = {87},
  author = {Patra, D. and Gergor, I. and Enderlein, J.}
}
@article{Toprak2006,
  number = {17},
  year = {2006},
  title = {Defocused orientation and position imaging
{(DOPI)} of myosin {V}},
  pages = {6495-6499},
  journal = {Proceedings of the National Academy of Sciences USA},
  volume = {103},
  author = {Toprak, E. and Enderlein, J. and Syed, S. and McKinney, S.A. and Petschek, R.G. and Ha, T. and Goldman, Y.E. and Selvin, P.R.}
}
@article{Geissbuehler2011,
  number = {3},
  year = {2011},
  title = {Comparison between {SOFI} and {STORM}},
  pages = {408-420},
  journal = {BIOMEDICAL OPTICS EXPRESS},
  volume = {2},
  author = {Geissbuehler, S. and Dellagiacoma, C. and Lasser, T.}
}
@article{Enderlein2005,
  year = {2005},
  title = {Performance of Fluorescence Correlation
Spectroscopy for Measuring Diffusion and
Concentration},
  pages = {2324-2336},
  journal = {ChemPhysChem},
  volume = {6},
  author = {Enderlein, J. and Gregor, I. and Patra, D. and Dertinger, T. and Kaupp, U.B.}
}
@article{Dertinger2007,
  year = {2007},
  title = {Two-Focus Fluorescence Correlation
Spectroscopy: A New Tool for Accurate and
Absolute Diffusion Measurements},
  pages = {433-443},
  journal = {ChemPhysChem},
  volume = {8},
  author = {Dertinger, T. and Pacheco, V. and Hocht, I. van der and Hartmann, R. and Gregor, I. and Enderlein, J.}
}
@article{Pusey2011,
  year = {2011},
  title = {Brownian Motion Goes Ballistic},
  pages = {802-803},
  journal = {Science},
  volume = {332},
  author = {Pusey, P.N.}
}
@article{Maye2010,
  year = {2010},
  title = {Switching binary states of nanoparticle
superlattices and dimer clusters by {DNA} strands},
  pages = {116},
  journal = {Nature Nanotechnology},
  volume = {5},
  author = {Maye, M.M. and Kumara, M.T. and Nykypanchuk, D. and Sherman, W.B. and Gang, O.}
}
@article{Leunissen2011,
  year = {2011},
  title = {Numerical study of {DNA}-functionalized microparticles and nanoparticles: Explicit pair potentials and their implications for phase behavior},
  pages = {084702},
  journal = {Journal of Chemical Physics},
  volume = {134},
  author = {Leunissen, M.E. and Frenkel, D.}
}
@article{Chan2001,
  number = {2},
  year = {2001},
  title = {Active Contours Without Edges},
  pages = {266-277},
  journal = {IEEE TRANSACTIONS ON IMAGE PROCESSING},
  volume = {10},
  author = {Chan, T.T. and Vese, L.A.}
}
@article{Yen1995,
  number = {3},
  year = {1995},
  title = {A new criterion for automatic multilevel thresholding},
  pages = {370-378},
  journal = {IEEE Transactions on Image Processing},
  volume = {4},
  author = {Yen, J.-C. and Chang, F.-J. and Chang, S.}
}
@article{Kapur1985,
  number = {3},
  year = {1985},
  title = {A new method for gray-level picture thresholding using the entropy of the histogram},
  pages = {273-285},
  journal = {Computer Vision, Graphics, and Image Processing},
  volume = {29},
  author = {Kapur, J.N. and Sahdoo, P.K. and Wong, A.K.C.}
}
@article{Sezgin2004,
  number = {1},
  year = {2004},
  title = {Survey over image thresholding techniques
and quantitative performance evaluation},
  pages = {146-165},
  journal = {Journal of Electronic Imaging},
  volume = {13},
  author = {Sezgin, M. and Sankur, B.}
}
@article{Kittler1986,
  number = {1},
  year = {1986},
  title = {Minimum error thresholding},
  pages = {41-47},
  journal = {Pattern Recognition},
  volume = {19},
  author = {Kittler, J. and Illingworth, J.}
}
@article{Otsu1979,
  year = {1979},
  title = {A threshold selection method from gray-level histograms},
  pages = {62-66},
  journal = {IEEE Transactions on Systems, Man and Cybernetics },
  volume = {9},
  author = {Otsu, N.}
}
@article{Zeskind2007,
  number = {7},
  year = {2007},
  title = {Nucleic acid and protein mass mapping by live-cell deep-ultraviolet microscopy},
  pages = {567-569},
  journal = {Nature Methos},
  volume = {4},
  author = {Zeskind, B.J. and Jordan, C.D. and Timp, W. and Trapani, L. and Waller, G. and Horodincu, V. and Ehrlich, D.J. and Matsudaira, P.}
}
@article{Dorenbos2008,
  year = {2008},
  title = {Low noise superconducting single photon detectors on silicon},
  pages = {131101},
  journal = {Applied Physics Letters},
  volume = {93},
  author = {Dorenbos, S.N. and Reiger, E.M. and Perinetti, U. and Zwiller, V. and Zijlstra, T. and Klapwijk, T.M.}
}
@article{Goltsman2001,
  number = {6},
  year = {2001},
  title = {Picosecond superconduction single-photon optical detector},
  pages = {705-707},
  journal = {Applied Physics Letters},
  volume = {79},
  author = {Gol'tsman, G.N. and Okunev, O. and Chulkova, G. and Lipatov, A. and Semenov, A. and Smirnov, K. and Voronov, B. and Dzardanov, A. and Williams, C. and Sobolewski, R.}
}
@article{Shore2011,
  number = {2},
  year = {2011},
  title = {Optimal acquisition scheme for subwavelength localization microscopy of bleachable fluorophores},
  pages = {289-291},
  journal = {Optics Letters},
  volume = {36},
  author = {Shore, E. and Small, A.}
}
@article{Stallinga2011,
  year = {2011},
  title = {Optical trapping at low numerical aperture},
  pages = {11027},
  journal = {Journal of the European Optical Society},
  volume = {6},
  author = {Stallinga, S.}
}
@article{Ulbrich2007,
  number = {4},
  year = {2007},
  title = {Subunit counting in membrane-bound proteins},
  pages = {319-321},
  journal = {Nature Methods},
  volume = {4},
  author = {Ulbrich, M.H. and Isacoff, E.Y.}
}
@article{Ulbrich2007-S3,
  number = {4},
  year = {2007},
  title = {Subunit counting in membrane-bound proteins},
  pages = {319-321},
  note = {Supplementary Methods},
  journal = {Nature Methods},
  volume = {4},
  author = {Ulbrich, M.H. and Isacoff, E.Y.}
}
@article{Grunwald2011,
  year = {2011},
  title = {Nuclear export dynamics of {RNA}-protein complexes},
  pages = {333-341},
  journal = {Nature},
  volume = {475},
  author = {{Gr\"unwald}, D. and Singer, R.H. and Rout, M.}
}
@inbook{Luengo2011,
  series = {Biological and Medical Physics, Biomedical Engineering Series},
  year = {2011},
  title = {Medical Image Processing: Techniques and Applications},
  note = {ISBN 978-1-4419-9769-2},
  editor = {Dougherty, G.},
  chapter = {Rapid prototyping of image analysis applications},
  publisher = {Springer},
  author = {Luengo Hendriks, C. L. and Malm, P. and  Bengtsson, E.}
}
@article{Knowles2011,
  number = {36},
  year = {2011},
  title = {Observation of spatial propagation of amyloid
assembly from single nuclei},
  pages = {14746-14751},
  journal = {Proceedings of the National Academy of Science USA},
  volume = {108},
  author = {Knowles, T.P.J. and White, D.A. and Abate, A.A. and Agresti, J.J. and Cohen, S.I.A. and Sperling, R.A. and Genst, E.J. de and Dobson, C.M. and Weitz, D.A.}
}
@article{Kampmannetal2011,
  number = {6},
  year = {2011},
  title = {Mapping the orientation of nuclear pore proteins in living cells with polarized fluorescence microscopy},
  pages = {643-650},
  journal = {Nature structural & molecular biology},
  volume = {18},
  author = {Kampmann, M. and Atkinson, C.E. and Mattheyses, A.L. and Simon, S.M.}
}
@article{Nature08-2011,
  year = {2011},
  title = {Suppression of the coffee-ring effect by
shape-dependent capillary interactions},
  pages = {308-311},
  journal = {Nature},
  volume = {476},
  author = {Yunker, P.J. and Still, T. and Lohr, M.A. Yodh, A.G.}
}
@article{Park2004,
  number = {3},
  year = {2004},
  title = {Nanometre localization of single {ReAsH} molecules},
  pages = {199-205},
  journal = {Journal of Microscopy},
  volume = {216},
  author = {Park, H. and Hanson, T. and Duff, S.R. and Selvin, P.R.}
}
@article{Martin2005,
  number = {10},
  year = {2005},
  title = {Mammalian cell-based optimization of the biarsenical binding tetracysteine motif for improved fluorescence and affinity},
  pages = {1308-1314},
  journal = {Nature biotechnology},
  volume = {23},
  author = {Martin, B.R. and Giepmanns, B.N.G. and Adams, S.R. and Tsien, R.Y.}
}
@article{Kampmann2009,
  number = {7},
  year = {2009},
  title = {Three-dimensional structure and flexibility of a membrane-coating module of the nuclear pore complex},
  pages = {782-789},
  journal = {Nature structural & molecular biology},
  volume = {16},
  author = {Kampmann, M. and Blobel, G.}
}
@phdthesis{Hein2009,
  year = {2009},
  title = {Live Cell {STED} Microscopy
Using Genetically Encoded Markers},
  address = {{G\"ottingen}, Germany},
  school = {Georg-August-{Universit\"at} {G\"ottingen} },
  author = {Hein, B.}
}
@article{Grunwald2010,
  year = {2010},
  title = {In vivo imaging of labelled endogenous b-actin
{mRNA} during nucleocytoplasmic transport},
  pages = {604-609},
  journal = {Nature},
  volume = {467},
  author = {{Gr\"unwald}, D. and Singer, R.H.}
}
@article{Delber2008,
  year = {2008},
  title = {A Fence-like Coat for the Nuclear Pore Membrane},
  pages = {815-826},
  journal = {Molecular Cell},
  volume = {32},
  author = {Delber, E.W. and Ma, Y. and Seo, H.-S. and Hsia, K.-C. and Noriega, T.R. and Blobel, G. and Hoelz, A.}
}
@article{Churchman2005,
  number = {5},
  year = {2005},
  title = {Single molecule high-resolution colocalization of {Cy3}
and {Cy5} attached to macromolecules measures
intramolecular distances through time},
  pages = {1419-1423},
  journal = {Proceedings of the National Academy of Science},
  volume = {102},
  author = {Churchman, L.S. and {\"Oktem}, Z. and Rock, R.S. and Dawson, J.F. and Spudich, J.A.}
}
@article{Brohawn2009,
  year = {2008},
  title = {Structural Evidence for Common Ancestry of the Nuclear Pore Complex and Vesicle Coats},
  pages = {1369-1373},
  journal = {Science},
  volume = {322},
  author = {Brohawn, S.G. and Leksa, N.C. and Spear, E.D. and Rajashankar, K.R. and Schwartz, T.U.}
}
@article{Beck2007,
  year = {2007},
  title = {Snapshots of nuclear pore complexes in action
captured by cryo-electron tomography},
  pages = {611-615},
  journal = {Nature},
  volume = {449},
  author = {Beck, M. and Lucic, V. and {F\"orster}, F. and Baumeister, W. and Medalia, O.}
}
@article{Alber2007,
  year = {2007},
  title = {The molecular architecture of the nuclear
pore complex},
  pages = {695-701},
  journal = {Nature},
  volume = {450},
  author = {Alber, F. and Dokudovskaya, S. and Veenhoff, L.M. and Zhang, W. and Kipper, J. nad Devos, D. and Suprapto, A. and Karni-Schmidt, O. and Williams, R. and Chait, B.T. and Sali, A. and Rout, M.P.}
}
@article{Varbioiu2006,
  number = {466-469},
  year = {2006},
  title = {Structural insight into yeast septin organizaiton from polarized fluorescent micrsocopy},
  journal = {Nature},
  volume = {443},
  author = {Varabioiu, A.M. and Mitchison, T.J.}
}
@article{Mattheyses2010,
  year = {2010},
  title = {Fluorescence anisotropy reveals order and disorder of protein domains in the nuclear pore complex},
  pages = {1706-1717},
  journal = {Biophysical Journal},
  volume = {99},
  author = {Mattheyes, A.L. and Kampmann, M. and Aktinson, C.E. and Simon, S.M.}
}
@article{Voortman2012,
  year = {2012},
  title = {Fast, spatially varying {CTF} correction in {TEM}},
  pages = {26-34},
  journal = {Ultramicroscopy},
  volume = {118},
  author = {Voortman, L.M. and Franken, E.M. and Vliet, L.J. van and Rieger, B.}
}
@article{Hell2003a,
  year = {2003},
  title = {Imaging and writing at the nanoscale with focused visible light through saturable optical transitions},
  pages = {859-860},
  journal = {Applied Physics A},
  volume = {77},
  author = {Hell, S.W. and Jakobs, S. and Kastrup, L.}
}
@article{Huang2011,
  number = {5},
  year = {2011},
  title = {Simultaneous multiple-emitter fitting for single molecule super-resolution imaging},
  pages = {1377-1393},
  journal = {Biomedical Optics Express },
  volume = {2},
  author = {Huang, F. and  Schwartz, S.L. and  Byars, J.M. and Lidke, K.A. }
}
@article{Bader2011,
  year = {2011},
  title = {Homo-FRET Imaging as a Tool to Quantify Protein and
Lipid Clustering},
  pages = {475-483},
  journal = {ChemPhysChem},
  volume = {12},
  author = {Bader,A.N. and  Hoetzl, S. and Hofman, E.G. and   Voortman, J. and Bergen en Henegouwen,  
P.M.P. van and  Meer, G. van and Gerritsen, H.C.}
}
@article{Bader2009,
  year = {2009},
  title = {Homo-FRET Imaging Enables Quantification of Protein Cluster Sizes
with Subcellular Resolution},
  pages = {2613-2622},
  journal = {Biophysical Journal},
  volume = {97},
  author = {Bader,A.N. and Hofmann, E.G. and Voortman, J. and Bergen en Henegouwen, P.M.P. van and Gerritsen, H.C.}
}
@article{Bader2007,
  number = {11},
  year = {2007},
  title = {Imaging of protein cluster sizes by means of
confocal time-gated fluorescence anisotropy
microscopy},
  pages = {6934-6945},
  journal = {Optics Express},
  volume = {15},
  author = {Bader, A.N. and  Hofman,  E.G. and  Bergen en Henegouwen, P.M.P. van and
 Gerritsen,H.C.}
}
@article{Dange208,
  number = {1},
  year = {2008},
  title = {Autonomy and robustness of thranslocation through the nuclear pore complex: a single molecule study},
  pages = {77-86},
  journal = {Journal of Cell Biology},
  volume = {183},
  author = {Dange, T. and {Gr\"unwald}, D. and {Gr\"unwald}, A. and Peters, R. and Kubitscheck, U.}
}
@article{Kubitscheck2005,
  number = {2},
  year = {2005},
  title = {Nuclear transport of single molecules: dwell times at the nuclear pore complex},
  pages = {233-243},
  journal = {Journal of Cell Biology},
  volume = {168},
  author = {Kubitscheck, U. and {Gr\"unwald}, D. and Hoekstra, A. and Rohleder, D. and Kues, T. and Siebrasse, J.P. and Peters, R.}
}
@article{Arhel2006,
  number = {10},
  year = {2006},
  title = {Quantitative four-dimensional tracking of cytoplasmic and nuclear {HIV-1} complexes},
  pages = {817-824},
  journal = {Nature methods},
  volume = {3},
  author = {Arhel, N. and Genovesio, A. and Kim, K.A. and Miko, S. and Perret, E. and Olvio-Marin, J.C. and Shorte, S. and Charneau, P.}
}
@article{Rout2000,
  year = {2000},
  title = {The yeast nuclear pore complex: Composition, architecture, and transport mechanism},
  pages = {635-651},
  journal = {Journal of Cell Biology},
  volume = {148},
  author = {Rout,M.P. and Aitchison, J.D. and Suprapto, A. and Hjertaas, K. and Zhao, Y.M. and  Chait, B.T.}
}
@article{Alber2007b,
  year = {2007},
  title = {Determining the architectures of
macromolecular assemblies},
  pages = {683-694},
  journal = {Nature},
  volume = {450},
  author = {Alber, F. and Dokudovskaya2, S. and Veenhoff, L.M. and  Zhang, W. and  Kipper, J. and 
Devos, D. and Suprapto, A. and Karni-Schmidt, O. and  Williams, R. and  Chait, B.T. and 
Rout, M.P. and Sali,A.}
}
@article{Brohawn2009b,
  number = {11},
  year = {2009},
  title = {Molecular architecture of the {Nup84-Nup145C-Sec13} edge element in the nuclear pore complex lattice},
  pages = {1173-1178},
  journal = {Nature structural & molecular biology},
  volume = {16},
  author = {Brohawn, S.G. and  Schwartz, T.U.}
}
@article{Lewis2007,
  year = {2007},
  title = {A nuclear envelope protein linking nuclear pore basket assembly, {SUMO} protease regulation, and {mRNA} surveillance},
  pages = {813-827},
  journal = {Journal of Cell Biology},
  volume = {178},
  author = {Lewis, A. and Felberbaum, R. and Hochstrasser, M.}
}
@article{Jovanovic2008,
  year = {2008},
  title = {Artificial nanopores that mimic the transport selectivity of the nuclear pore complex },
  pages = {1023-1027},
  journal = {Nature},
  volume = {457},
  author = {Jovanovic-Talisman, T. and Tetenbaum-Novatt, J. and McKenney, A.S. and Zilman, A. and Peters, R. and Rout, M.P. and Chait, B.T.}
}
@article{Kim2008,
  year = {2008},
  title = {A structure-permeability relationship of ultrathin nanoporous silicon membrane: a comparison with the nuclear envelope},
  pages = {4230-4231},
  journal = {Journal of the American Chemical Society},
  volume = {130},
  author = {Kim, E. and Xiong, H. and Striemer, C.C. and Fang, D.Z. and Fauchet, P.M. and McGrath, J.L. and Amemiya, S.}
}
@article{Debler2008,
  year = {2008},
  title = {A fence-like coat for the nuclear pore membrane},
  pages = {815-826},
  journal = {Molecular Cell},
  volume = {32},
  author = {Debler, E.W. and Ma, Y. and Seo, H.S. and Hsia, K.C. and Noriega, T.R. and Blobel, G. and Hoelz, A.}
}
@article{Rout2007,
  year = {2007},
  title = {Virtual gating and nuclear transport: the hole picture},
  pages = {622-628},
  journal = {Trends in Cell Biology},
  volume = {13},
  author = {Rout, M.P. and Aitchison, J.D. and Magnasco, M.O. and Chait, B.T.}
}
@article{Qu2004,
  number = {31},
  year = {2004},
  title = {Nanometer-localized multiple single-molecule fluorescence microscopy},
  pages = {11298-11303},
  journal = {Proceedings of the National Academy of Science USA},
  volume = {101},
  author = {Qu, X. and Wu, D. and Mets, L. and Scherer, N.F.}
}
@article{Hsia2007,
  year = {2007},
  title = {Architecture of a coat for the nuclear pore membrane},
  pages = {1313-1326},
  journal = {Cell},
  volume = {131},
  author = {Hsia, K. C. and Savropoulos, P. and Blobel, G. and Hoelz, A.}
}
@article{Daigle2001,
  year = {2001},
  title = {Nuclear pore complexes from immobile networks and have a very low turnover in mammalian cells},
  pages = {71-84},
  journal = {Journal of Cell Biology},
  volume = {154},
  author = {Daigle, N. and Beaudouin, J. and Hartnell, L. and Imreh, G. and Hallberg, E. and Lippincott-Schwartz, J. and Ellenberg, J.}
}
@article{Roberti2011,
  year = {2011},
  title = {Confocal fluorescence anisotropy and FRAP imaging of alpha-synuclein amyloid aggregates in living cells},
  pages = {e23338},
  journal = {PLoS ONE},
  volume = {6},
  author = {Roberti, M.J. and  Jovin, T.M. and Jares-Erijman, E.}
}
@article{Roberti2007,
  year = {2007},
  title = {Fluorescence imaging of amyloid formation in living cells by a functional, tetracysteine-tagged alpha-synuclein},
  pages = {345-351},
  journal = {Nature Methods},
  volume = {4},
  author = {Roberti, M.J. and Bertoncini, C.W. and  Klement, R. and Jares-Erijman, E.A. and Jovin, T.M.}
}
@article{Dudkina2011,
  number = {37},
  year = {2011},
  title = {Interaction of complexes {I, III}, and {IV} within
the bovine respirasome by single particle
cryoelectron tomography},
  pages = {15196-15200},
  journal = {Proceedings of the National Academy of Science USA},
  volume = {108},
  author = {Dudkina, N. and Kudryashev, M. and Stahlberg, H. and Boekema, E.J.}
}
@article{Rudnaya2011,
  year = {2011},
  title = {Defocus and twofold astigmatism correction in {HAADF-STEM}},
  pages = {1043-1054},
  journal = {Ultramicroscopy},
  volume = {111},
  author = {Rudnaya, M.E. and Broek, W. van den and Doornbos, R.M.P. and Mattheij, R.M.M. and Maubach, J.M.L.}
}
@article{Verdoold2011,
  year = {2011},
  title = {Femtomolar {DNA} detection by parallel colorimetric darkfield microscopy of functionalized gold nanoparticles},
  pages = {77-81},
  journal = {Biosensors and Bioelectronics},
  volume = {27},
  author = {Verdoold, R. and Gill, R. and Ungureanu, F. and Molenaar, R. and Kooyman, R.P.H.}
}
@article{Putten2011,
  year = {2011},
  title = {Scattering Lens Resolves Sub-100 nm Structures with Visible Light},
  pages = {193905},
  journal = {Physical Review Letters},
  volume = {106},
  author = {Putten, E.G. van and Akbulut, D. and Bertolotti, J. and Vos, W.L. and Lagendijk, A. and Mosk, A.P.}
}
@article{Foreman2011,
  year = {2011},
  title = {Fundamental limits in single-molecule orientation measurements},
  pages = {093013},
  journal = {New Journal of Physics},
  volume = {13},
  author = {Foreman, M.R. and {T\"or\"ok}, P.}
}
@article{Kendrick1994,
  number = {27},
  year = {1994},
  title = {Phase-diversity wave-front sensor for imaging systems},
  pages = {6533-6546},
  journal = {Applied Optics},
  volume = {33},
  author = {Kendrick, R.L. and Acton, D.S. and Duncan, A.L.}
}
@article{Olivier2009,
  number = {20},
  year = {1009},
  title = {Dynamic aberration correction for multiharmonic microscopy},
  pages = {3145-3147},
  journal = {Optics Letters},
  volume = {34},
  author = {Olivier, N. and Debarre, D. and Beaurepaire, E.}
}
@article{Coene1991,
  year = {1991},
  title = {Improved methods for the determination of the spherical aberration coefficient in high-resolution electron microscopy from micrographs of an amorphous object},
  pages = {225-233},
  journal = {Ultramicroscopy},
  volume = {38},
  author = {Coene, W.M.J. and Denteneer, T.J.J.}
}
@article{Saxton2000,
  year = {2000},
  title = {A new way of measuring microscope aberrations},
  pages = {41-45},
  journal = {Ultramicroscopy},
  volume = {81},
  author = {Saxton, W.O.}
}
@article{Steinecker2000,
  year = {2000},
  title = {Measurement of lens aberrations by means of image
displacements in beam-tilt series},
  pages = {149-161},
  journal = {Ultramicroscopy},
  volume = {81},
  author = {Steinecker, A. and Mader, W.}
}
@phdthesis{Brinkers2011,
  month = {October},
  year = {2011},
  title = {All that glitters is gold: },
  address = {Delft, The Netherlands},
  school = {Delft University of Technology},
  author = {Brinkers, S.}
}
@article{Thust1992,
  year = {1992},
  title = {Quantitative high-speed matching of high-resolution electron microscopy images},
  pages = {23-45},
  journal = {Ultramicroscopy},
  volume = {45},
  author = {Thust, A. and Urban, K.}
}
@article{Holden2011,
  number = {4},
  year = {2011},
  title = {{DAOSTORM}: an algorithm for high-density
super-resolution microscopy},
  pages = {279-280},
  journal = {Nature Methods},
  volume = {8},
  author = {Holden, S.J. and Uphoff, S. and Kapanidis, A.N.}
}
@article{Tejada2011,
  year = {2011},
  title = {The role of {Poisson's} binomial distribution in the analysis of {TEM} images},
  pages = {1553-1556},
  journal = {Ultramicroscopy},
  volume = {111},
  author = {Tejada, A. and Dekker, A.J. den}
}
@article{Nejadasl2011,
  year = {2011},
  title = {Defocus estimationfromstroboscopiccryo-electronmicroscopydata},
  pages = {1592-1598},
  journal = {Ultramicroscopy},
  volume = {111},
  author = {Nejadasl, F. Karimi and Karuppasamy, M. and Koster, A.J. and Ravelli, R.B.G.}
}
@article{Barton2011,
  year = {2011},
  title = {In-focus electron microscopy of frozen-hydrated biological samples with a
Boersch phase plate},
  pages = {1696-1705},
  journal = {Ultramicroscopy},
  volume = {111},
  author = {Barton, B. and Rhinow, D. and Walter, A. and {Schr\"oder}, R. and Benner, G. and Majorovits, E. and Matijevic, M.}
}
@article{Adelson1992,
  number = {2},
  year = {1992},
  title = {Single lens stereo with a plenoptic camera},
  pages = {99-106},
  journal = {IEEE Transactions on Pattern Analysis and Machine Intelligence},
  volume = {14},
  author = {Adelson, E.H. and Wang, J.Y.A.}
}
@article{Deschout2012,
  number = {1},
  year = {2012},
  title = {The influence of movement on the localization precision of sub-resolution particles in fluorescence microscopy},
  pages = {97-109},
  journal = {Journal of Biophotonics},
  volume = {5},
  author = {Deschout, H. and Neyts, K. and Breaeckmans, K.}
}
@article{Zhou2011,
  number = {12},
  year = {2011},
  title = {Computational Cameras: Convergence of Optics and Processing},
  pages = {3322-3340},
  journal = {IEEE Transactions on Image Processing},
  volume = {20},
  author = {Zhou, C. and Nayar, S.K.}
}
@misc{patentappPAM,
  month = {29 Septemeber},
  year = {2011},
  title = {Optical Modulator device and spatio-temporally light modulated imaging system},
  howpublished = {WO 2011/116904},
  author = {Jovin, T.M. and Caarls, W. and Vries, A. de}
}
@article{Piestun2010,
  number = {19},
  month = {October},
  year = {2010},
  title = {Performance limits on three-dimensional particle localization in photon-limited microscopy},
  pages = {3306-3308},
  journal = {{Optics letters}},
  volume = {35},
  author = {Grover, G. and Pavani, S.R.P. and Piestun, R.}
}
@article{Schonle2008,
  number = {25},
  month = {December},
  year = {2008},
  title = {Isotropic {3D} Nanoscopy based on single emitter switching},
  pages = {20774-20788},
  journal = {Optics Express},
  volume = {16},
  author = {Middendorff, C. von and Egner, A. and Geisler, C. and Hell, S.W. and {Sch\"onle}, A.}
}
@article{Moerner2010,
  number = {16},
  month = {October},
  year = {2010},
  title = {Three-dimensional localization precision of the double-helix point spread function versus astigmatism and biplane},
  journal = {Applied Physics Letters},
  volume = {97},
  author = {Badieirostami, M. and Lew, M.D. and Thompson, M.A. and Moerner, W.E.}
}
@inproceedings{DeBeule2011,
  year = {2011},
  title = {Generation-3 programmable array microscope {(PAM)} with digital micro-mirror device {(DMD)}},
  booktitle = {SPIE Proceeding Conference 7932 Session 4},
  pages = {7932-15},
  author = {Beule, P.A.A. de and Vried, A.H.B. de and Arndt-Jovin, D.J. and Jovin, T.M.}
}
@article{Greenaway2011,
  year = {2011},
  title = {Nanometric depth resolution from multi-focal images in microscopy},
  pages = {942-951},
  journal = {Journal of the royal society},
  volume = {8},
  author = {Dalgarno, H.I.C. and Dalgarno, P.A. and Dada, A.C. and Towers, C.E. and Gibson, G.J. and Parton, R.M. and Davis, I. and Warburton R.J. and Greenaway, A.H.}
}
@article{Cherny2010,
  year = {2010},
  title = {Stoichiometry of a regulatory splicing complex
revealed by single-molecule analyses},
  journal = {The EMBO Journal},
  author = {Cherny, D.I. and Gooding, C. and Eperon, G.E. and Coelho, M.B. and Bagshaw, C.R. and Smith, C.W.J. and Eperon, I.C. }
}
@article{Xu2012,
  number = {2},
  year = {2012},
  title = {Dual-objective {STORM} reveals three-dimensional filament organization in the actin cytoskeleton},
  pages = {185-190},
  journal = {Nature Methods},
  volume = {9},
  author = {Xu, K. and Babcock, H.P. and Zhuang, X.}
}
@article{Cox2012,
  number = {2},
  year = {2012},
  title = {Bayesian localization microscopy reveals nanoscale
podosome dynamics},
  pages = {195-200},
  journal = {Nature Methods},
  volume = {9},
  author = {Cox, S. and Rosten, E. and Monypenny, J. and Jovanoivc-Talisman, T. and Burnette, D.T. and Lippincott-Schwartz, J. and Jones, G.E. and Heintzmann, R.}
}
@article{Stallinga2012,
  number = {6},
  year = {2012},
  title = {Position and orientation estimation of fixed dipole emitters using an effective Hermite point spread function model},
  pages = {5896-5921},
  journal = {Optics Express},
  volume = {20},
  author = {Stallinga, S. and Rieger, B.}
}
@article{Loeschberger2012,
  number = {3},
  year = {2012},
  title = {Super-resolution imaging visualizes the eightfold symmetry of gp210 proteins around the nuclear pore complex and resolves the central channel with nanometer resolution},
  pages = {570-575},
  journal = {Journal of Cell Sciences},
  volume = {125},
  author = {{L\"oschberger}, A. and Linde, S. van de and Dabauvalle, M.C. and Rieger, B. and Heilemann, M. and Krohne, G. and Sauer, M.}
}
@article{Broek2012,
  year = {2012},
  title = {Fully Automated Measurement of the Modulation Transfer Function of Charge-Coupled Devices above the Nyquist Frequency},
  journal = {Microscopy and Microanalysis},
  author = {Broek, W. van den and Aert, A. van and Dyck, D. van}
}
@article{Humphry2012,
  year = {2012},
  title = {Ptychographic electron microscopy using high-angle dark-field scattering for sub-nanometre resolution imaging},
  pages = {730-736},
  note = {DOI: 10.1038/ncomms1733},
  journal = {Nature communications},
  volume = {3},
  author = {Humphry, M.J. and Kraus, B. and Hurst, A.C. and Maiden, A.M. and Rodenburg, J.M.}
}
@article{Zhang2012,
  number = {1},
  year = {2012},
  title = {{IPET} and {FETR}: Experimental Approach for Studying Molecular Structure Dynamics by Cryo-Electron Tomography of a Single-Molecule Structure},
  pages = {e30249},
  journal = {PLOS one},
  volume = {7},
  author = {Zhang, L. and ren, G.}
}
@mastersthesis{Nieuwenhuizen2011,
  month = {March},
  year = {2011},
  title = {Resolution in localization microscopy},
  address = {Delft, The Netherlands},
  school = {Delft University of Technology},
  author = {R.P.J. Nieuwenhuizen}
}
@book{Penczek2010,
  year = {2010},
  title = {Resolution Measures in Molecular Electron Microscopy},
  note = {p 73-100},
  volume = {482},
  publisher = {Academic Press},
  author = {Penczek, P.A.}
}
@article{Beckmann1997,
  number = {5346},
  year = {1997},
  title = {Alignment of conduits for the nascent polypeptide chain in the ribosome-sec61 complex},
  pages = {213-2126},
  journal = {Science},
  volume = {278},
  author = {Beckmann, R. and Bubeck, D. and Grassucci, R. and Penczek, P.A. and Verschoor, A. and Blobel, G. and Frank, J.}
}
@article{Bottcher1997,
  number = {6620},
  year = {1997},
  title = {Determination of the fold of the core protein of
hepatitis {B} virus by electron cryomicroscopy},
  pages = {88-91},
  journal = {Nature},
  volume = {386},
  author = {{B\"ottcher}, B. and Wynne, S.A. and Crowther, R.A.}
}
@article{SheppardOptikVol72No4_1986,
  number = {4},
  year = {1986},
  title = {The spatial frequency cut-off in three-dimensional imaging},
  pages = {131--133},
  journal = {Optik},
  volume = {72},
  author = {Sheppard, C.J.R.}
}
@article{SheppardOptikVol74No3_1986,
  number = {3},
  year = {1986},
  title = {The spatial frequency cut-off in three-dimensional imaging II},
  pages = {128--129},
  journal = {Optik},
  volume = {74},
  author = {Sheppard, C.J.R.}
}
@book{Saxton1978,
  year = {1978},
  title = {Computer Techniques for Image Processing of Electron Microscopy},
  address = {New York},
  publisher = {Academic Press},
  author = {Saxton, W.O.}
}
@article{Orlova1997,
  number = {3},
  year = {1997},
  title = {Structure of Keyhole Limpet Hemocyanin Type 1 (KLH1) at 15 A Resolution by Electron Cryomicroscopy and Angular Reconstitution},
  pages = {417-437},
  journal = {Journal of Molecular Biology},
  volume = {271},
  author = {Orlova, E.V. and Dube, P. and Harris, J.R. and Beckman, E. and Zemlin, F. and Markl, J. and  Heel, M. van}
}
@article{Corless1996,
  number = {1},
  year = {1996},
  title = {On the Lambert-W function},
  pages = {329-359},
  journal = {Advances in Computational Mathematics},
  volume = {5},
  author = {Corless, R. and Gonnet, G. and Hare, D. and Jeffrey, D. and Knuth, D.}
}
@article{Barry2000,
  number = {1-2},
  year = {2000},
  title = {Analytical approximations for real values of the {Lambert W-function}},
  pages = {95-103},
  journal = {Mathematics and Computers in Simulation},
  volume = {53},
  author = {Barry,D.A.  and  Parlange, J.-Y. and  Li, L. and  Prommer, H. and Cunningham, C.J. and Stagnitti, F.}
}
@article{Ram2009,
  number = {8},
  year = {2009},
  title = {Improved single particle localization accuracy with dual objective multifocal plane mircoscopy},
  pages = {6881-6898},
  journal = {Optics Express},
  volume = {17},
  author = {Ram, S. and Prabhat, P. and Ward, E.S. and Ober, R.J.}
}
@article{Wong2011,
  number = {3},
  year = {2011},
  title = {Limit of the Accuracy of Parameter Estimation for Moving Single Molecules Imaged by Fluorescence Microscopy},
  pages = {895-911},
  journal = {IEEE Transactions on Signal Processing},
  volume = {59},
  author = {Wong, Y. and Lin, Z. and Ober, R.J.}
}
@article{Chao2012,
  year = {2012},
  title = {Fisher information matrix for branching processes
with application to electron-multiplying charge-coupled devices},
  pages = {349-379},
  journal = {Multidimensional System and Signal Processing},
  volume = {23},
  author = {Chao, J. and Ward, E.S. and Ober, R.J.}
}
@article{Dempsey2011,
  number = {12},
  year = {2011},
  title = {Evaluation of fluorophores for optimal performance in localization-based super-resolution imaging},
  pages = {1027-1031},
  journal = {Nature Methods},
  volume = {8},
  author = {Dempsey, G.T. and Vaughan, J.C. and Chen, K.H. and Bates, M. and Zhuang, X.}
}
@article{Manely2008,
  number = {2},
  year = {2008},
  title = {High-density mapping of single-molecule trajectories with photoactivated localization microscopy},
  pages = {156-158},
  journal = {Nature Methods},
  volume = {5},
  author = {Manely, S. and Gilette, J.M. and Patterson, G.H. and Shroff, H. and Hess, H.F. and Betzig, E. and Lippincott-Schwarz, J.}
}
@article{Wicker2010a,
  year = {2010},
  title = {Single-shot optical sectioning using polarization-coded structured illumination},
  pages = {084010},
  journal = {Journal of Optics},
  author = {Wicker, K. and Heintzmann, R.}
}
@article{Schoen2011,
  year = {2011},
  title = {Binding-Activated Localization Microscopy of {DNA} Structures},
  journal = {Nano Letters},
  author = {Schoen, I. and Ries, J. and Klotzsch, E. and Ewers, H. and Vogel, V.}
}
@article{Vrabioiu2006,
  number = {28},
  year = {2006},
  title = {Structural insights into yeast septin organization
from polarized fluorescence microscopy},
  pages = {446-449},
  journal = {Nature},
  volume = {443},
  author = {Vrabioiu, A.M. and Mitschison, T.J.}
}
@article{Lukosz1962a,
  number = {4},
  year = {1962},
  title = {{\"Ubertragung} nicht-negativer Signale durch lineare Filter},
  pages = {335-364},
  journal = {Journal of Modern Optics},
  volume = {9},
  author = {Lukosz, W.}
}
@article{Fitzhugh1983,
  year = {1983},
  title = {Statistical Properties of the Asymmetric Random Telegraph Signal, with Applications to Single-Channel Analysis},
  pages = {75-89},
  journal = {Mathematical Biosciences},
  volume = {64},
  author = {R. Fitzhugh}
}
@article{Bobroff1986,
  number = {6},
  year = {1986},
  title = {Position measurement with a resolution and noiselimited instrument},
  pages = {1152-1157},
  journal = {Review of Scientifric Instruments},
  volume = {57},
  author = {N. Bobroff}
}
@article{Heintzmann2007,
  year = {2007},
  title = {Estimating missing information by maximum likelihood deconvolution},
  pages = {136-144},
  journal = {Micron},
  volume = {38},
  author = {Heintzmann, R.}
}
@article{Annibale2011,
  number = {7},
  year = {2011},
  title = {Identification of clustering artifacts in
photoactivated localization microscopy},
  pages = {527-528},
  journal = {Nature Methods},
  volume = {8},
  author = {Annibale, P. and Vanni, S. and Scarelli, M. and Rothlisberger, U. and Radenovic, A.}
}
@article{Ta2010,
  number = {1},
  year = {2010},
  title = {An Extended Scheme for Counting Fluorescent Molecules by Photon- Antibunching},
  pages = {119-124},
  journal = {Laser Physics},
  volume = {20},
  author = {Ta, H. and Wolfrum, J. and Herten, D.-P.}
}
@article{Tian2012,
  number = {8},
  year = {2012},
  title = {Experimental compressive phase space tomography},
  pages = {8296-8308},
  journal = {Optics Express},
  volume = {20},
  author = {Tian, L. and Lee, J. and Oh, S.B. and Barbastathis, G.}
}
@article{Waller2011,
  number = {3},
  year = {2011},
  title = {Phase and amplitude imaging from noisy images by Kalman filtering},
  pages = {2805-2815},
  journal = {Optics Express},
  volume = {19},
  author = {Waller, L. and Tsang, M. and Ponda, S. and Young Yang, S. and Barbastathis, G.}
}
@inproceedings{Kurz2012,
  series = {SPIE},
  year = {2012},
  title = {Quantification of fluorescent samples by photon-antibunching},
  booktitle = {Single Molecule Spectroscopy and Superresolution Imaging V},
  pages = {82280K-1},
  editor = {Enderlein, J. and Karol, Z. and Erdmann, R. and Koberling, F. and Gregor, I.},
  author = {Kurz, A. and Schwering, M. and Herten, D.-P.}
}
@article{Harms1999,
  year = {1999},
  title = {Single-Molecule Anisotropy Imaging},
  pages = {2864-2870},
  journal = {Bipphysical Journal},
  volume = {77},
  author = {Harms, G.S. and Sonnleitner, M. and {Sch\"utz}, G.J. and Gruber, H.J. and Schmidt, T.}
}
@article{Uji2006,
  year = {2006},
  title = {Visualizing spatial and temporal heterogeneity of single molecule rotational diffusion in a  glassy polymer by defocused wide-field imaging},
  pages = {2511-2518},
  journal = {Polymer},
  volume = {47},
  author = {Uij-i, H. and Melnikov, S.M. and Deres, A. Bergamini, G. and Schryver, F. de and Herrmann, A. and {M\"ullen}, K. and Enderlein, J. and Hofkens, J.}
}
@article{Ruiter1997,
  year = {1997},
  title = {Single Molecule Rotational and Translational Diffusion Observed by Near-Field Scanning Optical Microscopy},
  pages = {7318-7323},
  journal = {Journal of Physical Chemistry},
  volume = {101},
  author = {Ruiter, A.G.T. and Veerman, J.A. and Garcia-Parajo, M.F. and Hulst, N.F. van}
}
@article{Pieper2011,
  year = {2011},
  title = {Fluorescence correlation spectroscopy as a tool  for measuring the rotational diffusion of macromolecules},
  pages = {1-11},
  journal = {Chemical Physics Letters},
  volume = {516},
  author = {Pieper, C.M. and Enderlein, J.}
}
@article{Loman2011,
  year = {2010},
  title = {Measuring rotational diffusion of macromolecules by fluorescence correlation spectroscopy},
  pages = {627-636},
  journal = {Photochem. Photobiol. Sci.},
  volume = {9},
  author = {Loman, A. and Gergor, I. and Stutz, C. and Mund, M. and Enderlein, J.}
}
@article{Adhikarietal2011,
  year = {2011},
  title = {Temperature dependent single molecule rotational dynamics in {PMA}},
  pages = {1849-1856},
  journal = {Phys. Chem. Chem. Phys.},
  volume = {13},
  author = {Adhikari, S. and Selmke, M. and Cichos, F.}
}
@article{Malkusch2012,
  year = {2012},
  title = {Coordinate-based colocalization analysis of single-molecule localization microscopy data},
  pages = {1-10},
  journal = {Histochemistry and Cell Biology},
  volume = {137},
  author = {Malkusch, S. and Endesfelder, U. and Mondry, J. and Helleri, M. and Verveer, P.J. and Heilemann, M.}
}
@article{Kazantsev2010,
  year = {2010},
  title = {Fully three-dimensional defocus-gradient corrected backprojection in cryoelectron microscopy},
  pages = {1128-1142},
  journal = {Ultramicroscopy},
  volume = {110},
  author = {Kazantsev, I. and Klukowska, J. and Herman, G.T. and Cernetic, L.}
}
@article{Mariani2011,
  year = {2011},
  title = {Simulation and correction of electron images of tilted planar weak-phase samples},
  pages = {259-268},
  journal = {Journal of Structural Biology},
  volume = {174},
  author = {Mariani, V. and Schenk, A.D. and Philippsen, A. and Engel, A.}
}
@inproceedings{Studer2012,
  series = {Proceedings of the SPIE},
  year = {2012},
  title = {Hyperspectral fluorescence microscopy based on compressed sensing },
  booktitle = {Three-Dimensional and Multidimensional Microscopy: Image Acquisition and Processing XIX},
  note = {doi: 10.1117/12.908532},
  editor = {Conchello, J.-A. and Cogswell, C.J. and  Wilson, T. and  Brown, T.G.},
  author = {Studer, V. and Bobin, J. and Chahid, M. and Moussavi, H. and Candes, E. and Dahan, M.}
}
@article{Gabor1946b,
  year = {1946},
  title = {Theory of Communication: Part II: The analysis of hearing},
  pages = {442-445},
  journal = {Journal of the Institution of Electrical Engineers},
  volume = {93},
  author = {Gabor, D.}
}
@article{Gabor1946c,
  year = {1946},
  title = {Theory of Communication: Part III: Frequency Compression and Expansion},
  pages = {445-457},
  journal = {Journal of the Institution of Electrical Engineers},
  volume = {93},
  author = {Gabor, D.}
}
@article{Chruchmann2012,
  year = {2012},
  title = {Colocalization of fluorescent probes: accurate and precise registration with  nanometer resolution},
  pages = {141-150},
  note = {doi:10.1101/pdb.top067918},
  journal = {Cold Spring Harbor Protocolls},
  author = {Churchmann, L.S. and Spudich, J.A.}
}
@article{Dedecker2009,
  year = {2012},
  title = {Defocused Wide-field Imaging Unravels Structural and Temporal Heterogeneity in Complex Systems},
  pages = {1079-1090},
  journal = {Advanced Materials},
  volume = {21},
  author = {Dedecker, P. and Muls, B. and Deres, A. and Uji-i, H. and Hotta, J. and Sliwa, M. and Soumillion, J.-P. and {M\"ullen}, K. and Enderlein, J. and Hofkens, J.}
}
@article{Ha1998,
  number = {10},
  year = {1998},
  title = {Hindered Rotational Diffusion and Rotational Jumps of Single Molecules},
  pages = {2093-2096},
  journal = {Physical Review Letters},
  volume = {80},
  author = {Ha, T. and Glass, J. and Enderle, T. and Chemla, D.S. and Weiss, S.}
}
@article{Bartko2002,
  number = {2},
  year = {2002},
  title = {Three-Dimensional Single Molecule Rotational Diffusion in Glassy State Polymer Films},
  pages = {026101},
  journal = {Physical Review Letters},
  volume = {89},
  author = {Bartko, A.P. and Xu, K. and Dickson, R.M.}
}
@article{Gould2008,
  number = {12},
  year = {2008},
  title = {Nanoscale imaging of molecular positions and anisotropies},
  pages = {1027-1031},
  journal = {Nature Methods},
  volume = {5},
  author = {Gould, T.J. and Gunewardene, M.S. and Gudheti, M.V. and Verkhusha, V.V. and Yin, S.-R. and Gosse, J.A. and Hess, S.T.}
}
@article{Hernando2006,
  year = {2006},
  title = {Effect of Disorder on Ultrafast Exciton Dynamics Probed by Single Molecule Spectroscopy},
  pages = {216403},
  journal = {Physical Review Letters},
  volume = {97},
  author = {Hernando, J. and Dijk, E.M.H.P. van and Hoogenboom, J.P. and Garcia-Lopez, J.-J. and Reinhoudt, D.N. and Crego-Calama, M. and Garcia-Parajo, M.F. and Hulst, N.F. van}
}
@article{Simmonds2011,
  number = {24},
  year = {2011},
  title = {Three dimensional laser microfabrication in diamond using a dual adaptive optics system},
  pages = {24122-24128},
  journal = {Optics Express},
  volume = {19},
  author = {Simmonds, R.D. and Salter, P.S. and Jesacher, A. and Booth, M.J.}
}
@article{Cumming2011,
  number = {10},
  year = {2011},
  title = {Adaptive aberration compensation for three-dimensional micro-fabrication of photonic crystals in lithium niobate},
  pages = {9419-9426},
  journal = {Optics Express},
  volume = {19},
  author = {Cumming, B.P. and Jesacher, A. and Booth, M.J. and Wilson, T. and Gu, M.}
}
@article{Marshall2011,
  number = {5},
  year = {2011},
  title = {Three-dimensional imaging of direct-written photonic structures},
  pages = {695-697},
  journal = {Optics Letters},
  volume = {36},
  author = {Marshall, G.D. and Jesacher, A. and Thayil, A. and Withford, M.J. and Booth, M.}
}
@article{Chizhik2011,
  year = {2011},
  title = {Probing the Radiative Transition of Single m olecules with a Tunable Microresonator},
  pages = {1700-1703},
  journal = {Nano Letters},
  volume = {11},
  author = {Chizihik, A.I. and Chizhik, A.M. and Khoptyar, D. and {B\"ar}, S. and Meixner, A.J. and Enderlein, J.}
}
@article{Kalaidzidis2007,
  year = {2007},
  title = {Intracelluar objects tracking},
  pages = {569-578},
  journal = {European Journal of Cell Biology},
  volume = {86},
  author = {Kalaidzidis, Y.}
}
@article{Kalaidzidis2009,
  year = {2009},
  title = {Multiple objects tracking in fluorescence microscopy},
  pages = {57-80},
  journal = {Journal of Mathematical Biology},
  volume = {58},
  author = {Kalaidzidis, Y.}
}
@article{Rink2005,
  year = {2005},
  title = {Rab Conversion as a Mechanism of Progression
from Early to Late Endosomes},
  pages = {735-749},
  journal = {Cell},
  volume = {122},
  author = {Rink, J. and Ghigo, E. and Kalaidzidis, Y. and Zerial, M.}
}
@inproceedings{Bryne2012,
  month = {May 2-5},
  year = {2012},
  title = {MODELS FOR BIOMEDICAL IMAGE RECONSTRUCTION
BASED ON INTEGRAL APPROXIMATION METHODS},
  booktitle = {IEEE International Symposium on Biomedical Imaging},
  pages = {70-73},
  address = {Barcelona, Spain},
  author = {Bryne, C. and Gordon, D. and Heilper, D.},
  organization = {IEEE}
}
@inproceedings{Becker2012,
  month = {May 2-5},
  year = {2012},
  title = {FROM TIMELAPSE-DATA TO GENEALOGIC TREES: USING DIFFERENT CONTRAST
MECHANISMS TO IMPROVE CELL TRACKING},
  booktitle = {IEEE International Symposium on Biomedical Imaging},
  pages = {386-389},
  address = {Barcelona, Spain},
  author = {Becker, T. and Rapoport, D.H. and Mamlouk, A.M.},
  organization = {IEEE}
}
@inproceedings{Wang2012,
  month = {May 2-5},
  year = {2012},
  title = {A HYBRID TOTAL-VARIATION MINIMIZATION APPROACH TO COMPRESSED SENSING},
  booktitle = {IEEE International Symposium on Biomedical Imaging},
  pages = {74-77},
  address = {Barcelona, Spain},
  author = {Wang, Y. and Liang, D. and Chang, Y. and Ying, L.},
  organization = {IEEE}
}
@inproceedings{Cohen2012,
  month = {May 2-5},
  year = {2012},
  title = {IMAGE REGISTRATION ERROR ANALYSIS WITH APPLICATIONS IN SINGLE MOLECULE MICROSCOPY},
  booktitle = {IEEE International Symposium on Biomedical Imaging},
  pages = {966-969},
  address = {Barcelona, Spain},
  author = {Cohen, E.A.K. and Ober, R.J.},
  organization = {IEEE}
}
@inproceedings{Hu2012,
  month = {May 2-5},
  year = {2012},
  title = {MITOSIS DETECTION OF HEMATOPOIETIC STEM CELL POPULATIONS IN TIME-LAPSE PHASE-CONTRAST MICROSCOPY IMAGES},
  booktitle = {IEEE International Symposium on Biomedical Imaging},
  pages = {390-393},
  address = {Barcelona, Spain},
  publisher = {IEEE},
  author = {Huh, S. and Eom, S. and Elmer Ker, D.F. and Weiss, L. and Kanade, T.}
}
@inproceedings{Stallinga2012a,
  month = {May 2-5},
  year = {2012},
  title = {THE EFFECT OF BACKGROUND ON LOCALIZATION UNCERTAINTY IN SINGLE EMITTER IMAGING},
  booktitle = {IEEE International Symposium on Biomedical Imaging},
  pages = {988-991},
  address = {Barcelona, Spain},
  publisher = {IEEE},
  author = {Stallinga, S. and Rieger, B.}
}
@inproceedings{Wong2012,
  month = {May 2-5},
  year = {2012},
  title = {Effect of Time Discretization on the Limit of the
Accuracy of Parameter Estimation for Moving
Single Molecules Imaged by Fluorescence
Microscopy},
  booktitle = {IEEE International Symposium on Biomedical Imaging },
  pages = {1228-1231},
  address = {Barcelona, Spain},
  author = {Wong, Y. and Lin, Z. and Ober, R.J.}
}
@inproceedings{Ducroz2012,
  month = {May 2-5},
  year = {2012},
  title = {CHARACTERIZATION OF CELL SHAPE AND DEFORMATION IN 3D USING SPHERICAL HARMONICS},
  booktitle = {IEEE International Symposium on Biomedical Imaging },
  address = {Barcelona, Spain},
  author = {Ducroz, C. and Olivio-Marin, J.-C. and Dufor, A.},
  organization = {IEEE}
}
@techreport{hassanich2012,
  month = {Jan},
  year = {2012},
  title = {Nearly Optimal Sparse Fourier Transform},
  address = {arXiv:1201.2501v1 [cs.DS] },
  institution = {Massachusetts Institute of Technology, USA},
  author = {Hassanieh, H. and Indyk, P. and Katabi, D. and Price, E.}
}
@inproceedings{Levet2012,
  month = {May 2-5},
  year = {2012},
  title = {AUTOMATIC NON-PARAMETRIC CAPSID SEGMENTATION USING WAVELETS TRANSFORM AND GRAPH},
  booktitle = {IEEE International Symposium on Biomedical Imaging},
  address = {Barcelona, Spain},
  author = {Levert, F. and Cassany, A. and Kann, M. and Sibarita, J.-B.},
  organization = {IEEE}
}
@inproceedings{Jezierska2012,
  month = {May 2-5},
  year = {2012},
  title = {POISSON-GAUSSIAN NOISE PARAMETER ESTIMATION IN FLUORESCENCE MICROSCOPY IMAGING},
  booktitle = {IEEE International Symposium on Biomedical Imaging},
  pages = {1663-1666},
  address = {Barcelona, Spain},
  author = {Jezierska, A. and Talbot, H. and Chaux, C. and Pesquet, J.-C. and Engler, G.},
  organization = {IEEE}
}
@article{Vulovic2012,
  year = {2012},
  title = {Precise and unbiased estimation of astigmatism and defocus in transmission electron microscopy},
  pages = {115-134},
  journal = {Ultramicroscopy},
  volume = {116},
  author = {Vulovic, M. and Franken, E. and Ravelli, R.B.G. and Vliet, L.J. van and Rieger, B.}
}
@article{Mukamel2012,
  year = {2012},
  title = {Statistical Deconvolution for Superresolution Fluorescence Microscopy},
  pages = {2391-2400},
  journal = {Biophysical Journal},
  volume = {102},
  author = {Mukamel, E.A. and Babcock, H. and Zhuang, X.}
}
@article{Fernandez2012,
  number = {10},
  year = {2012},
  title = {Computational Methods for Electron Tomography},
  pages = {1010-1030},
  journal = {Micron},
  volume = {43},
  author = {Fernandez, J.-J.}
}
@article{Kopek2012,
  number = {16},
  year = {2012},
  title = {Correlative 3D superresolution fluorescence and
electron microscopy reveal the relationship of
mitochondrial nucleoids to membranes},
  pages = {6136-6141},
  journal = {Proceedings of the National Academy of Science USA},
  volume = {109},
  author = {Kopek, B.G. and Shtengel, G. and Shan Xu, C. and Clayton, D.A. and Hess, H.F.}
}
@article{Shtengel2009,
  number = {9},
  year = {2009},
  title = {Interferometric fluorescent super-resolution
microscopy resolves 3D cellular ultrastructure},
  pages = {3125-3130},
  journal = {Proceeding of the National Academy of Science USA},
  volume = {106},
  author = {Shtengel, G. and Galbraith, J.A. and Galbraith, C.G. and Lippincott-Schwartz, J. and Gillette, J.M. and Manely, S. and Sougrat, R. and Waterman, C.M. and Knachanawong, P. and Davidson, M.W. and Fetter, R.D. and Hess, H.F.}
}
@misc{materialsmethods,
  title = {Materials and methods are available as supplementary material on {Science Online}.}
}
@article{Pavani2008,
  number = {26},
  year = {2008},
  title = {Three dimensional tracking of fluorescent microparticles using a photon-limited double-helix response system},
  pages = {22048-22057},
  journal = {Optics Express},
  volume = {16},
  author = {Pavani, S.R.P. and Piestun, R.}
}
@article{Mlodzianoski2011,
  number = {16},
  year = {2011},
  title = {Sample drift correction in 3D fluorescence photoactivation localization microscopy},
  pages = {15009-15019},
  journal = {Optics Express},
  volume = {19},
  author = {Mlodzianoski, M.J. and Schreiner, J.M. and Callahan, S.P. and Smolkova, K. and Dlaskova, A. and Santorova, J. and Jezek, P. and Bewersdorf, J.}
}
@article{Heilemann2005,
  number = {11},
  year = {2005},
  title = {Carbocyanine dyes as efficient reversible single-molecule optical switch},
  pages = {3801-3806},
  journal = {Journal of the American Chemical Society},
  volume = {127},
  author = {Heilemann, M. and Margeat, E. and Kasper, R. and Sauer, M. and Tinnefeld, P. }
}
@inbook{Frank1980,
  year = {1980},
  title = {Computer Processing of Electron Microscope Images},
  pages = {197-233},
  editor = {Hawkes, P.W.},
  chapter = {The Role of Correlation Techniques in Computer Image Processing},
  publisher = {Springer Verlag},
  author = {Frank, J.}
}
@article{Bolte2006,
  number = {3},
  year = {2006},
  title = {A guided tour into subcellular colocalization analysis in light microscopy},
  pages = {213-232},
  journal = {Journal of Microscopy},
  volume = {224},
  author = {Bolte, S. and Cordelieres, F.P.}
}
@article{Adler2008,
  number = {1},
  year = {2008},
  title = {Replicate-based noise corrected correlation for accurate measurements of colocalization},
  pages = {121-133},
  journal = {Journal of Microscopy},
  volume = {230},
  author = {Adler, J. and Pagakis, S.N. and Parmryd, I.}
}
@article{Ries2012,
  number = {6},
  year = {2012},
  title = {A simple, versatile method for {GFP-based} super-resolution microscopy via nanobodies},
  pages = {582-587},
  journal = {Nature Methods},
  volume = {9},
  author = {Ries, J. and Kaplan, C. and Platonova, E. and Eghlidi, H. and Ewers, H.}
}
@article{Neumuller2010,
  number = {11},
  year = {2010},
  title = {Photounbinding of Calmodulin from a Family of {CaM} Binding Peptides},
  pages = {14050},
  journal = {PlOS one},
  volume = {5},
  author = {{Neum\"uller}, K.G. and Elsayad, K. and Reisecker, J.M. and Waxham, M.N. and Heinze, K.G.}
}
@article{Mourik2012,
  year = {2012},
  title = {Signatures of Majorana Fermions in
Hybrid Superconductor-Semiconductor
Nanowire Devices},
  pages = {1003-1008},
  journal = {Science},
  volume = {336},
  author = {Mourik, V. and Zuo, K. and Frolov, S.M. and Plissard, S.R. and Bakkers, E.P.A.M. and Kouwenhouven, L.P.}
}
@article{Loenhout2012,
  number = {10},
  year = {2012},
  title = {Non-Bias-Limited Tracking of Spherical Particles, Enabling Nanometer Resolution at Low Magnification},
  pages = {2362-2371},
  journal = {Biophysical Journal},
  volume = {102},
  author = {Loenhout, M.T.J. van and Kerssemakers, J.W.J. and Vlaminck, I. De and Dekker, C.}
}
@article{Hofmann2005,
  number = {49},
  year = {2005},
  title = {Breaking the diffraction barrier in fluorescence microscopy at low light intensities by using reversibly photoswitchable proteins},
  pages = {17565-17569},
  journal = {Proceedings of the National Academy of Sciences USA},
  volume = {102},
  author = {Hofmann, M. and Eggeling, C. and Jakobs, S. and Hell, S.W.}
}
@article{Clifford2007,
  number = {6987-69991},
  year = {2007},
  title = {Fluorescence of Single Molecules in Polymer Films: Sensitivity of Blinking to Local Environment},
  journal = {The Journal of Physical Chemistry B Letters},
  volume = {111},
  author = {Clifford, J.N. and Bell, T.D.M. and Tinnefeld, P. and Heilemann, M. and Melnikov, S.M. and Hotta, J.-I. and Sliwa, M. and Dedecker, P. and Sauer, M. and Hofkens, J. and Yeow, E.K.L.}
}
@article{Isack2012,
  year = {2012},
  title = {Energy-Based Geometric Multi-model Fitting},
  pages = {123-147},
  journal = {International Journal of Computer Vision},
  volume = {97},
  author = {Isack, H. and Boybov, Y.}
}
@article{Rullgrad2011,
  number = {3},
  year = {2011},
  title = {Simulation of transmission electron microscope images of biological specimens},
  pages = {234-256},
  journal = {Journal of Microscopy},
  volume = {243},
  author = {{Rullgr\aad}, H. and {\"Ofverstedt}, L.-G. and Masich, S. and Daneholt, B. and {\"Oktem}, O.}
}
@article{York2012,
  number = {7},
  year = {2012},
  title = {Resolution doubling in live, multicellular organisms via multifocal structured illumination microscopy},
  pages = {749-754},
  journal = {Nature Methods},
  volume = {9},
  author = {York, A.G. and Parekh, S.H. and Nogare, D.D. and Fischer, R.S. and Temprine, K. and Mione, M. and Chitnis, A.B. and Combs, C.A. and Shroff, H.}
}
@article{Cleveland1979,
  number = {368},
  month = {Dec.},
  year = {1979},
  title = {Robust Locally Weighted Regression and Smoothing Scatterplots},
  pages = {829-836},
  journal = {Journal of the American Statistical Association},
  volume = {74},
  author = {Cleveland, W.S.}
}
@book{Erni2010a,
  year = {2010},
  title = {Aberration-Corrected Imaging in Transmission Electron Microscopy},
  address = {London, UK},
  publisher = {Imperial College Press},
  author = {Erni, R.}
}
@article{Saghi2012,
  year = {2012},
  title = {Electron Tomography in the {(S)TEM}: From Nanoscale
Morphological Analysis to {3D} Atomic Imaging},
  pages = {59-79},
  journal = {Annu. Rev. Mater. Res.},
  volume = {42},
  author = {Saghi,  A. and Midgley, P.A.}
}
@article{Midgley2009,
  year = {2009},
  title = {Electron tomography and holography in materials science},
  pages = {271-280},
  journal = {Nature Materials},
  volume = {8},
  author = {Midgley, P.A. and Dunin-Borkowski, R.E.}
}
@article{Midgley2003,
  year = {2003},
  title = {{3D} electron microscopy in the physical sciences: the development of {Z-contrast} and {EFTEM} tomography},
  pages = {413-431},
  journal = {Ultramicroscopy},
  volume = {96},
  author = {Midgley, P.A. and Weyland, M.}
}
@article{Spontak1988,
  year = {1988},
  title = {Three-dimensional study of cylindrical morphology in a styrene-butadiene-styrene block copolymer},
  pages = {387-395},
  journal = {Polymer},
  volume = {29},
  author = {Spontak, R.J. and Williams, M.C. and Agard, D.A.}
}
@article{Friedrich2005,
  year = {2005},
  title = {Comparison of intensity distributions in tomograms from {BF TEM, ADF TEM, HAADF STEM}, and calculated tilt series},
  pages = {18-27},
  journal = {Ultramicroscopy},
  volume = {106},
  author = {Friedrich, H. and McCartney, M.R. and Buseck, P.R.}
}
@article{Kubel2005,
  number = {5},
  year = {2005},
  title = {Recent Advances in Electron Tomography: {TEM} and {HAADF-STEM} Tomography for Materials Science and Semiconductor Applications},
  pages = {378-400},
  journal = {Microscopy and Microanalysis},
  volume = {11},
  author = {{K\"ubel}, C. and Voigt, A. and Schoenmakers, R. and Otten, M. and Su, D. and Lee, T.-C. and Carlsson, A. and Bradley, J.}
}
@article{Rose1975,
  year = {1975},
  title = {Zur Theorie der Bildentstehung im Elektronenmikroskop},
  pages = {217-244},
  journal = {Optik},
  volume = {42},
  author = {Rose, H.}
}
@article{Freitag1981,
  year = {1981},
  title = {Resolution and contrast of crystalline objects in high-resolution scanning electron microscopy},
  pages = {407-429},
  journal = {Optik},
  volume = {59},
  author = {Freitag, J. and Rose, H.}
}
@incollection{Nellist2000a,
  series = {113},
  year = {2000},
  title = {The principle and interpretation of annular dark-field Z-contrast imaging},
  booktitle = {Advances in Imaging and Electron Physics},
  pages = {147-203},
  author = {Nellist, P.D. and Pennycook, S.J.}
}
@article{Zhu2012,
  number = {7},
  year = {2012},
  title = {Faster {STORM} using compressed sensing},
  pages = {721-726},
  journal = {Nature Methods},
  volume = {9},
  author = {Zhu, L. and Zhang, W. and Elnatan, D. and Huang, B.}
}
@article{Zecevic2012,
  number = {17},
  year = {2012},
  title = {Mesoporosity of Zeolite {Y}: Quantitative Three-Dimensional Study by Image Analysis of Electron Tomograms},
  pages = {4213-4217},
  journal = {Angewandte Chemie Int. Ed.},
  volume = {51},
  author = {Zecevic, J. and Gommes, C.J. and Friedrich, H. and
Jongh, P.E. de and Jong, K.P. de}
}
@article{Brilot2012,
  year = {2012},
  title = {Beam-induced motion of vitrified specimen on holey carbon film},
  pages = {630-637},
  journal = {Journal of Structural Biology},
  volume = {177},
  author = {Brilot, A.F. and Chen, J.Z. and Cheng, A. and Pan, J. and Harrison, S.C .and Potter, C.S. and Carragher, B. and Henderson, R. and Grigorieff, N.}
}
@article{Brettschneider2007,
  year = {2007},
  title = {Breaking the Diffraction Barrier in Fluorescence Microscopy by Optical Shelving},
  pages = {218103},
  journal = {Physical Review Letters},
  author = {Bretschneider, S. and Eggeling, C. and Hell, S.W.}
}
@article{Testa2008,
  number = {25},
  year = {2008},
  title = {Nanoscale separation of molecular species based
on their rotational mobility},
  pages = {21094-21105},
  journal = {Optics Express},
  volume = {16},
  author = {Testa, I. and {Sch\"onle}, A. and Middendoff, C. von and Geisler, C. and Medda, R. and Wurm, C.A. and Stiel, A.C. and Jakobs, S. and Bossi, M. and Eggeling, C. and Hell, S.W. and Egner, A.}
}
@article{Baddeley2011,
  number = {5},
  year = {2011},
  title = {{4D} Super-Resolution Microscopy with Conventional
Fluorophores and Single Wavelength Excitation in
Optically Thick Cells and Tissues},
  pages = {e20645},
  journal = {PLOS one},
  volume = {6},
  author = {Baddeley, D. and Crossman, D. and Rossberger, S. and Cheyne, J.E. and Montgomery, J.M. and Jayasinghe, I.D. and Cremer, C. and Cannell, M.B. and {S\"oller}, C.}
}
@article{Testa2011,
  year = {2010},
  title = {Multicolor Fluorescence Nanoscopy in Fixed and  Living Cells by Exciting Conventional Fluorophores with a Single Wavelength},
  pages = {2686-2694},
  journal = {Biophysical Journal},
  volume = {99},
  author = {Testa, I. and Wurm, C.A. and Medda, R. and Rothermel, E. and Middendorf, C. von and {F\"olling}, J. and Jakobs, S. and {Sch\"onle}, A. and Hell, S.W. and Eggeling, C.}
}
@article{Gunawerdene2011,
  year = {2011},
  title = {Superresolution Imaging of Multiple Fluorescent Proteins with Highly Overlapping Emission Spectra in Living Cells},
  pages = {1522-1528},
  journal = {Biophysical Journal},
  volume = {101},
  author = {Gunewardene, M.S. and Subach, F.V. and Gould, T.J. and Penoncello, G.P. and Gudheti, M.V. and Verkhusha, V.V. and Hess, S.T.}
}
@article{Bohmer2003,
  number = {3},
  year = {2003},
  title = {Orientation imaging of single molecules by wide-field epifluorescence microscopy},
  pages = {554-559},
  journal = {Journal of the Optical Society of America B},
  volume = {20},
  author = {{B\"ohmer}, M. and Enderlein, J.}
}
@article{Fitzgerald2012,
  year = {2012},
  title = {Estimation Theoretic Measure of Resolution for Stochastic Localization Microscopy},
  pages = {048102},
  journal = {Physical Review Letters},
  volume = {109},
  author = {Fitzgerald, J.E. and Lu, J. and Schnitzer, M.J.}
}
@article{Test2012,
  year = {2012},
  title = {Test},
  journal = {bladievla},
  author = {Ronald}
}
@article{Wolter2011,
  number = {8},
  month = {April},
  year = {2011},
  title = {Measuring localization performance of super-resolution algorithms on very active samples},
  pages = {7020-7033},
  journal = {Optics Express},
  volume = {19},
  author = {Wolter,S. and Endesfelder, U. and Linde, S. van de and Heilemann, M. and Sauer, M.}
}
@article{Bates2012,
  year = {2012},
  title = {Multicolor Super-Resolution Fluorescence Imaging via
Multi-Parameter Fluorophore Detection},
  pages = {99-107},
  journal = {ChemPhysChem},
  volume = {13},
  author = {Bates, M. and Dempsey, G.T. and Chen, K.H. and Zhuang, X.}
}
@article{Linde2010,
  year = {2010},
  title = {The effect of photoswitching kinetics and labeling densities on super-resolution
fluorescence imaging},
  pages = {260-266},
  journal = {Journal of Biotechnology},
  volume = {149},
  url = {http://dx.doi.org/10.1016/j.bbr.2011.03.031},
  author = {Linde, S. van de and Wolter, S. and Heilemann, M. and Sauer, M.}
}
@article{Wang2012b,
  number = {14},
  year = {2012},
  title = {PALMER: a method capable of parallel localization of multiple emitters for high-density localization microscopy
},
  pages = {16039-16049},
  journal = {Optics Express},
  volume = {20},
  url = {http://www.opticsinfobase.org/oe/abstract.cfm?uri=oe-20-14-16039},
  author = {Wang, Y. and Quan, T. and Zeng, S. and Huang, Z.-L.}
}
@article{Eibauer2012,
  year = {2012},
  title = {Unraveling the structure of membrane proteins in situ by transfer function corrected cryo-electron tomography},
  journal = {Journal of Structural Biology},
  author = {Eibauer, M. and Hoffmann, C. and Plitzko, J.M. and  Baumeister, W. and Nickell, S. and
Engelhardt, H.}
}
@inbook{Tukey1967,
  year = {1967},
  title = {Analysis of time series},
  pages = {25-46},
  editor = {Harris, B.},
  address = {New York},
  chapter = {An introduction to the calculations of numerical spectrum analysis},
  publisher = {Wiley},
  author = {Tukey, J. W.}
}
@article{Ghosh1994,
  number = {5},
  month = {May},
  year = {1994},
  title = {Automated detection and tracking of individual and clustered cell surface low density lipoprotein receptor molecules},
  pages = {1301-1318},
  journal = {Biophysical Journal},
  volume = {66},
  author = {Ghosh, R.N. and Webb, W.W.}
}
@article{Lee1991,
  number = {14},
  month = {July},
  year = {1991},
  title = {Direct observation of brownian motion of lipids in a membrane},
  pages = {6274-6278},
  journal = {Proceedings of the National Academy of Sciences of the USA},
  volume = {88},
  author = {Lee, G.M. and Ishihara, A. and Jacobson, K.A.}
}
@article{Niessen1996,
  month = {July},
  year = {1996},
  title = {Deficiency of the $\beta$4 subunit in junctional epidermolysis bullosa with pyloric atresia: consequences for hemidesmosome formation and adhesion properties},
  pages = {1695-1706},
  journal = {Journal of Cell Science},
  volume = {109},
  author = {Niessen, C.M. and Raaij-Helmer, L.M.H. van der and Hulsman, E.H.M. and Neut, R. van der and Jonkman, M.F. and Sonnenberg, A.}
}
@article{Schaapveld1998,
  number = {1},
  month = {July},
  year = {1998},
  title = {Hemidesmosome formation is initiated by the $\beta$4 integrin subunit, requires complex formation of  $\beta$4 and H.D1/plectin, and involves a direct interaction between $\beta$4 and the bullous pemphigoid antigen},
  pages = {271-284},
  journal = {Journal of Cell Biology},
  volume = {142},
  author = {Schaapveld, R.Q.J. and Borradori, L. and Geerts, D. and Leusden, M.R. van and Kuikman, I. and Nievers, M.G. and Niessen, C.M. and Steenbergen, R.D.M. and Snijders, P.J.F. and Sonnenberg, A.}
}
@article{Rojo2006,
  number = {553-560},
  year = {2006},
  title = {A METHOD TO REMOVE FRINGES FROM IMAGES USING WAVELETS},
  journal = {The Astrophysical Journal},
  volume = {649},
  author = {Rojo, P.M. and Harrington, J.}
}
@article{Donnert2006,
  number = {31},
  year = {2006},
  title = {Macromolecular-scale resolution in biological
fluorescence microscopy},
  pages = {11440-11445},
  journal = {Proceedings of the National Academy of Sciences USA},
  volume = {103},
  author = {Donnert, G. and Keller, J. and Medda, R. and Andrei, M.A. and Rizzoli, S.O. and {L\"uhrmann}, R. and Jahn, R. and Eggeling, C. and Hell, S.W.}
}
@article{Faas2012,
  number = {3},
  year = {2012},
  title = {Virtual nanoscopy: Generation of ultra-large high
resolution electron microscopy maps},
  pages = {457-469},
  journal = {Journal of Cell Biology},
  volume = {198},
  author = {Faas, F.G.A. and Avramut, M.C. and Berg, B.M. van den and Mommaas, M.A. and Koster, A.J. and Ravelli, R.B.G.}
}
@inbook{Bates2011,
  year = {2011},
  title = {Imaging: A Laboratory Manual},
  note = {ISBN  978-0-879699-36-9 },
  editor = {Yuste, R.},
  chapter = {Stochastic Optical Reconstruction Microscopy (STORM): a method for super-resolution fluorescence imaging},
  publisher = {Cold Spring Harbor Laboratory Press},
  author = {Bates, M. and Jones, S.A. and Zhuang, X.}
}
@article{Izeddin2012,
  number = {3},
  year = {2012},
  title = {Wavelet analysis for single molecule localization
microscopy},
  pages = {2081-2095},
  journal = {Optics Express},
  volume = {20},
  author = {Izeddin, I. and Boulanger, J. and Racine, V. and Specht, C.G. and Kechkar, A. and Nair, D. and Triller, A. and Choquet, D. and Dahan, M. and Sibarita, J.B.}
}
@article{Parthasarathy2012,
  number = {7},
  year = {2012},
  title = {Rapid, accurate particle tracking by calculation of radial symmetry centers},
  pages = {724-726},
  journal = {Nature Methods},
  volume = {9},
  author = {Parthasarathy, R.}
}
@article{Mukamel2012a,
  year = {2012},
  title = {Unified Resolution Bounds for Conventional and Stochastic Localization Fluorescence Microscopy},
  pages = {168102},
  journal = {Physical Review Letters},
  volume = {109},
  author = {Mukamel, E.A. and Schnitzer, M.J.}
}
@article{Lippincott2009,
  number = {1},
  year = {2009},
  title = {Putting super-resolution fluorescence microscopy to
work},
  pages = {21},
  journal = {Nature Methods},
  volume = {6},
  author = {Lippincott-Schwartz, J. and Manley, S.}
}
@article{Veatch2012,
  number = {2},
  month = {February},
  year = {2012},
  title = {Correlation functions quantify super-resolution images and estimate apparent clustering due to over-counting},
  pages = {e31457},
  journal = {Plos ONE},
  volume = {7},
  author = {Veatch, S.L. and Machta, B.B. and Shelby, S.A. and Chiang, E.N. and Holowka, D.A. and Baird, B.A.}
}
@article{Huang2010,
  year = {2010},
  title = {Breaking the Diffraction Barrier:
Super-Resolution Imaging of Cells},
  pages = {1047-1058},
  journal = {Cell},
  volume = {143},
  author = {Huang, B. and Babcock, H. and Zhuang, X.}
}
@article{Anselmi2011,
  number = {49},
  year = {2011},
  title = {Three-dimensional imaging and photostimulation by
remote-focusing and holographic light patterning},
  pages = {19504-19509},
  journal = {Proceedings of the National Academy of Sciences U.S.A.},
  volume = {108},
  author = {Anselmi, F. and Ventalon, C. and Begue, Ogden, D. and Emiliani, V.}
}
@article{Botcherby2007,
  number = {14},
  year = {2007-2009},
  title = {Aberration-free optical refocusing in high
numerical aperture microscopy},
  pages = {2007},
  journal = {Optics Letters},
  volume = {32},
  author = {Botcherby, E.J. and juskaitis, R. and Booth, M.J. and Wilson, T.}
}
@article{Wolter2012,
  number = {11},
  year = {2012},
  title = {{rapidSTORM}: accurate, fast open-source software for localization microscopy},
  pages = {1040-1041},
  journal = {Nature Methods},
  volume = {9},
  author = {Wolter, S. and {L\"oschberger}, A. and Holm, T. and Aufmkolk, S. and Dabauvalle, M.-C. and Linde, S. van de and Sauer, M.}
}
@article{Manders1992,
  year = {1992},
  title = {Dynamics of three-dimensional replication patterns during the S-phase, analysed by double labelling of DNA and confocal microscopy},
  pages = {857-862},
  journal = {Journal of Cell Science},
  volume = {103},
  author = {Manders, E.M.M. and Stap, J. and Brakenhoff, G.J. and Driel, R. van and Aten, J.A.}
}
@article{Adler2010,
  number = {8},
  year = {2010},
  title = {Quantifying Colocalization by Correlation: The Pearson Correlation Coefficient is Superior to the Mander's Overlap Coefficient},
  pages = {733-742},
  journal = {Cytometry Part A},
  volume = {77A},
  author = {Adler, J. and Parmryd, I.}
}
@article{Annibale2012_OpticalNanoscopy,
  number = {9},
  year = {2012},
  title = {Identification of the factors affecting co-localization precision for quantitative multicolor localization microscopy},
  journal = {Optical Nanoscopy},
  volume = {1},
  author = {Annibale, P. and Scarselli, M. and Greco, M. and Radenovic, A.}
}
@article{Parmryd2003,
  number = {1},
  year = {2003},
  title = {Imaging metabolism of phosphatidylinositol 4,5-bisphosphate in T-cell
GM1-enriched domains containing Ras proteins},
  pages = {27-38},
  journal = {Experimental Cell Research},
  volume = {285},
  author = {Parmryd, I. and Adler, J. and Patel, R. and Magee, A.I.}
}
@article{Bergholm2010,
  number = {3},
  year = {2010},
  title = {Analysis of Bias in the Apparent Correlation Coefficient Between Image Pairs Corrupted by Severe Noise},
  pages = {204-219},
  journal = {Journal of Mathematical Imaging and Vision},
  volume = {37},
  author = {Bergholm, F. and Adler, J. and Parmryd, I.}
}
@article{Helmuth2010,
  number = {372},
  year = {2010},
  title = {Beyond co-localization: inferring spatial
interactions between sub-cellular structures from
microscopy images},
  journal = {BMC Bioinformatics},
  volume = {11},
  author = {Helmuth, J.A. and Paul, G. and Sbalzarini, I. F.}
}
@article{Dunn2011,
  number = {4},
  year = {2011},
  title = {A practical guide to evaluating colocalization in biological microscopy},
  pages = {C723-C742},
  journal = {American Journal of Physiology: Cell Physiology},
  volume = {300},
  author = {Dunn, K.W. and Kamocka, M.M. and McDonald, J.H.}
}
@article{Li2004a,
  number = {16},
  year = {2004},
  title = {A Syntaxin 1, G$\alpha_{0}$, and N-Type Calcium Channel Complex at a Presynaptic Nerve Terminal: Analysis by Quantitative Immunocolocalization},
  pages = {4070-4081},
  journal = {Journal of Neuroscience},
  volume = {24},
  author = {Li, Q. and Lau, A. and Morris, T.J. and Guo, L. and Fordyce, C.B. and Stanley, E.F.}
}
@inproceedings{Zhang2008a,
  month = {May},
  year = {2008},
  title = {Statistical colocalization in biological imaging with false discovery control},
  booktitle = {Biomedical Imaging: From Nano to Macro, 2008. ISBI 2008. 5th IEEE International Symposium on},
  pages = {1327 - 1330 },
  author = {Zhang, B. and Chenouard, N. and Olivo-Marin, J.-C. and Meas-Yedid, V.}
}
@article{Jaskolski2005,
  number = {1},
  year = {2005},
  title = {An automated method to quantify and visualize
colocalized fluorescent signals},
  pages = {42-49},
  journal = {Journal of Neuroscience Methods},
  volume = {146},
  author = {Jaskolski, F. and Mulle, C. and Manzoni, O.J.}
}
@article{Lachmanovich2003,
  number = {2},
  month = {November},
  year = {2003},
  title = {Co-localization analysis of complex formation among membrane proteins by computerized fluorescence microscopy: application to immunofluorescence co-patching studies},
  pages = {122-131},
  journal = {Journal of Microscopy},
  volume = {212},
  author = {Lachmanovich, E. and Shvartsman, D.E. and Malka, Y. and Botvin, C. and Henis, Y.I. and Weiss, A.M.}
}
@article{VanSteensel1996,
  year = {1996},
  title = {Partial colocalization of glucocorticoid and mineralocorticoid receptors in discrete compartments in nuclei of rat hippocampus neurons},
  pages = {787-792},
  journal = {Journal of Cell Science},
  volume = {109},
  author = {Steensel, B. van and Binnendijk, E.P. van and Hornsby, C.D. Voort, H.T.M. van der and Krozowski, Z. and Kloet, E.R. de and Driel, R. van}
}
@article{Zinchuk2007,
  number = {4},
  year = {2007},
  title = {Quantitative Colocalization Analysis of Multicolor Confocal Immunofluorescence Microscopy Images: Pushing Pixels to Explore Biological Phenomena},
  pages = {101-111},
  journal = {Acta Histochemica et Cytochemica},
  volume = {40},
  author = {Zinchuk, V. and Zinchuk, O. and Okada, T.}
}
@article{Oton2012,
  year = {2012},
  title = {Image formation in cellular {X-ray} microscopy},
  pages = {29-37},
  journal = {Journal of Structural Biology},
  volume = {178},
  author = {Oton, J. and Sorzano, C.O.S. and Pereiro, E. and Cucenca-Alba, J. and Navarro, R. and Carazo, J.M. and Marabini, R.}
}
@article{Sengupta2011,
  number = {11},
  year = {2011},
  title = {Probing protein heterogeneity in the plasma membrane using {PALM} and pair correlation analysis},
  pages = {969-975},
  journal = {Nature Methods},
  volume = {8},
  author = {Sengupta, P. and Jovanovic-Talisman, T. and Skoko, D. and Renz, M. and Veatch, S.L. and Lippincott-Schwartz, J.}
}
@article{Comeau2006,
  number = {12},
  year = {2006},
  title = {A Guide to Accurate Fluorescence Microscopy
Colocalization Measurements},
  pages = {4611-4622},
  journal = {Biophysical Journal},
  volume = {91},
  author = {Comeau, J.W.D. and Constantino, S. and Wiseman, P.W.}
}
@article{Demandolx1997,
  number = {1},
  year = {1997},
  title = {Multicolour analysis of local image correlation in confocal microscopy},
  pages = {21-36},
  journal = {Journal of Microscopy},
  volume = {185},
  author = {Demandolx, D. and Davoust, J.}
}
@article{Piche2012,
  number = {24},
  year = {2012},
  title = {Experimental realization of optical eigenmode super-resolution},
  pages = {26424-26433},
  journal = {Optics Express},
  volume = {20},
  author = {Piche, K. and Leach, J. and Johnson, A.S. and Salvail, J.Z. and Kolobov, M.I. and Boyd, R.W.}
}
@article{Trabesinger2001,
  number = {6},
  month = {March},
  year = {2001},
  title = {Statistical Analysis of Single-Molecule
Colocalization Assays},
  pages = {1100-1105},
  journal = {Analytical Chemistry},
  volume = {73},
  author = {Trabesinger, W. and Hecht, B. and Wild, U.P. and Schuetz, G.J. and Schindler, H. and Schmidt, Th.}
}
@article{Schmeisser2009,
  number = {6},
  year = {2009},
  title = {Parallel, distributed and {GPU} computing technologies in single-particle electron microscopy},
  pages = {659-671},
  journal = {Acta Crystallographica Section D},
  volume = {65},
  author = {Schmeisser, M. and Heisen, B.C. and Luettich, M. and Busche, B. and Hauer, F. and Koske, T. and Knauber, K.-H. and Stark, H.}
}
@book{Frank2006,
  edition = {2},
  year = {2006},
  title = {Three-Dimensional Electron Microscopy of Macromolecular Assemblies},
  publisher = {Oxford University Press},
  author = {Frank, J.}
}
@inproceedings{Chessel2012,
  month = {May},
  year = {2012},
  title = {Spherical spatial statistics for 3D fluorescence video-microscopy},
  booktitle = {Biomedical Imaging (ISBI), 2012 9th IEEE International Symposium on},
  pages = {1747 -1750},
  author = {Chessel, A. and Dodgson, J. and Carazo-Salas, R.E.}
}
@article{Semrau2011,
  number = {7},
  year = {2011},
  title = {Quantification of Biological Interactions with Particle Image Cross-Correlation Spectroscopy (PICCS)},
  pages = {1810-1818},
  journal = {Biophysical Journal},
  volume = {100},
  author = {Semrau, S. and Holtzer, L. and Gonzales-Gaitan, M. and Schmidt, T.}
}
@article{Berro2012,
  number = {6},
  year = {2012},
  title = {Super-resolution Optical Measurement of Nanoscale Photoacid Distribution in Lithographic Materials},
  pages = {9496-9502},
  journal = {ACS Nano},
  volume = {11},
  author = {Berro, A.J. and Berglund, A.J. and Carmichael, P.T. and Kim, J.S. and Liddle, J.A.}
}
@article{Agrawal2012,
  number = {24},
  year = {2012},
  title = {Limits of {3D} dipole localization and orientation estimation for single-molecule imaging: towards {Green's} tensor engineering},
  pages = {26668-26680},
  journal = {Optics Express},
  volume = {20},
  author = {Agrawal, A. and Quirin, S. and Grover, G. and Piestun, R.}
}
@article{Backlund2012,
  number = {47},
  year = {2012},
  title = {Simultaneous, accurate measurement of the {3D}
position and orientation of single molecules},
  pages = {19087-19092},
  journal = {Proceedings of the National Academy of Sciences USA},
  volume = {109},
  author = {Backlund, M.P. and Lew, M.D. and Backer, A.S. and Sahl, S.J. and Grover, G. and Agrawal, A. and Piestun, R. and Moerner, W.E.}
}
@article{Hemmer2012,
  year = {2012},
  title = {The universal scaling laws that determine the achievable resolution in different schemes for super-resolution imaging},
  pages = {083002},
  journal = {Journal of Optics},
  volume = {14},
  author = {Hemmer, P.R. and Zapata, T.}
}
@article{Tokunaga2008,
  number = {2},
  year = {2008},
  title = {Highly inclined thin illumination enables clear single-molecule imaging in cells},
  pages = {159-161},
  journal = {Nature Methods},
  volume = {5},
  author = {Tokunaga, M. and Imamoto, N. and Sakata-Sogawa, K.}
}
@article{Gerchberg1974,
  number = {9},
  year = {1974},
  title = {Super-resolution through error energy reduction},
  pages = {709-720},
  journal = {Optica Acta},
  volume = {21},
  author = {Gerchberg, R.W.}
}
@article{Gerchberg1972,
  number = {2},
  year = {1972},
  title = {A practical algorithm for the determination of phase from image and diffraction plane pictures},
  pages = {237-246},
  journal = {Optik},
  volume = {35},
  author = {Gerchberg, R.W. and Saxton, W.O.}
}
@article{Braun2013,
  number = {52},
  year = {2013},
  title = {Negative Absolute Temperature for Motional Degrees of Freedom},
  pages = {52-54},
  journal = {Science},
  volume = {339},
  author = {Braun, S. and Ronzheimer, J.P. and Schreiber, M. and Hodgaman, S.S. and Rom, T. and Bloch, I. and Schneider, U.}
}
@article{Aert2006,
  number = {9},
  year = {2006},
  title = {Resolution of coherent and incoherent imaging systems reconsidered - Classical criteria and a statistical alternative},
  pages = {3830-3839},
  journal = {Optics Express},
  volume = {14},
  author = {Aert, S. van and Dyck, D. van and Dekker, A.J. den}
}
@article{LowNam2011,
  number = {11},
  year = {2011},
  title = {{ErbB1} dimerization is promoted by domain
co-confinement and stabilized by ligand binding},
  pages = {1244-1252},
  journal = {Nature Structural \& Molecular Biology},
  volume = {18},
  author = {Low-Nam, S.T. and Lidke, K.A. and Cutler, P.J. and Roovers, R.C. and van Bergen en Henegouwen, P.M.P. and Wilson, B.S. and Lidke, D.S.}
}
@misc{Yoshitoshi1987,
  month = {April},
  year = {1987},
  title = {Focusing detection apparatus },
  howpublished = {US Patent 4,823,331},
  author = {Yoshitoshi, Y. and Matsumoto, Y. and Kume, H.}
}
@article{Bricot1976,
  number = {4},
  year = {1976},
  title = {Optical readout of videodisc},
  pages = {304-308},
  journal = {IEEE Transactions on Consumer Electronics},
  volume = {22},
  author = {Bricot, C. and Lehureau, J.C. and Puech, C.}
}
@article{Meddens2013,
  number = {1},
  year = {2013},
  title = {Automated Podosome Identification and Characterization in Fluorescence Microscopy Images},
  pages = {180-189},
  note = {doi:10.1017/S1431927612014018},
  journal = {Microscopy and Microanalysis},
  volume = {19},
  author = {Meddens, M.B.M. and Rieger, B. and Figdor, C.G. and Cambi, A. and Dries, K. van den}
}
@article{Gopinath2012,
  number = {12},
  year = {2012},
  title = {Shape-Based Regularization of Electron Tomographic Reconstruction},
  pages = {2241-2253},
  journal = {IEEE TRANSACTIONS ON MEDICAL IMAGING},
  volume = {31},
  author = {Gopinath, A. and Xu, G. and Ress, D. and {\"Oktem}, O. and Subramaniam, S. and Baja, C.}
}
@article{Scheres2012,
  number = {9},
  month = {July},
  year = {2012},
  title = {Prevention of overfitting in cryo-EM structure determination},
  pages = {853-854},
  journal = {Nature Methods},
  volume = {9},
  author = {Scheres, S.H.W. and Chen, S.}
}
@article{Liao2010,
  number = {7},
  month = {July},
  year = {2010},
  title = {Definition and Estimation of Resolution
in Single-Particle Reconstructions},
  pages = {768-775},
  journal = {Structure},
  volume = {18},
  author = {Liao, H.Y. and Frank, J.}
}
@article{Dani2010,
  year = {2010},
  title = {Superresolution Imaging of Chemical Synapses in the Brain},
  pages = {843-856},
  journal = {Neuron},
  volume = {68},
  author = {Dani, A. and Huang, B. and Bergan, J. and Dulac, C. and Zhuang, X.}
}
@article{Jones2011,
  number = {6},
  year = {2011},
  title = {Fast, three-dimensional super-resolution imaging
of live cells},
  pages = {499-505},
  journal = {Nature Methods},
  volume = {8},
  author = {Jones, S.A. and Shim, S.-H. and He, J. and Zhuang, X.}
}
@article{Kanchanawong2010,
  year = {2010},
  title = {Nanoscale architecture of integrin-based cell adhesions},
  pages = {580-584},
  journal = {Nature},
  volume = {468},
  author = {Kanchanawong, P. and Shtengel, G. and Pasapera, A.M. and Ramko, E.B. and Davidson, M.W. and Hess, H.F. and Waterman, C.M.}
}
@article{Lando2012,
  year = {2012},
  title = {Quantitative single-molecule microscopy reveals that CENP-ACnp1 deposition occurs during G2 in fission yeast},
  pages = {120078},
  journal = {Open Biology},
  volume = {2},
  author = {Lando, D. and Endesfelder, U. and Berger, H. and Subramanian, L. and Dunne, P.D. and McColl, J. and Klenerman, D. and Carr, A.M. and Sauer, M. and Allshire, R. and Heilemann, M. and Laue, E.D.}
}
@article{Shim2012,
  number = {35},
  year = {2012},
  title = {Super-resolution fluorescence imaging of organelles
in live cells with photoswitchable membrane probes},
  pages = {13978-13983},
  journal = {Proceedings of the National Academy of Sciences USA},
  volume = {109},
  author = {Shim, S.H. and Xia, C. and Zhong, G. and Babcock, G. and Vaughan, J.C. and Huang, B. and Wang, X. and Xu, C. and Bi, G.-Q. and Zhuang, X.}
}
@article{Vogelsang2009,
  number = {20},
  month = {May},
  year = {2009},
  title = {Controlling the fluorescence of ordinary oxazine
dyes for single-molecule switching and superresolution microscopy},
  pages = {8107-8112},
  journal = {Proceedings of the National Academy of Sciences of the USA},
  volume = {106},
  author = {Vogelsang, J. and Cordes, T. and Forthmann, C. and Steinhauer, C. and Tinnefeld, P.}
}
@article{Kirshner2013,
  number = {1},
  year = {2013},
  title = {{3-D PSF} fitting for fluorescence microscopy: implementation and localization application},
  pages = {13-25},
  journal = {Journal of Microscopy},
  volume = {249},
  author = {Kirshner, H. and Aguet, F. and Sage, D. and Unser, M.}
}
@article{Dan2013,
  year = {2013},
  title = {{DMD-based} {LED}-illumination Super-resolution and optical sectioning microscopy},
  pages = {1116},
  journal = {Scientific Reports},
  volume = {3},
  author = {Dan, D. and Lei, M. and Yao, B. and Wang, W. and Winterhalder, M. and Zumbusch, A. and Qi, Y. and Xia, L. and Yan, S. and Yang, Y. and Gao, P. and Ye, T. and Zhao, W.}
}
@article{Treacy2012,
  year = {2012},
  title = {A surprise in the first {Born} approximation for electron scattering},
  pages = {57-62},
  journal = {Ultramicroscopy},
  volume = {119},
  author = {Treacy, M.M.J. and Dyck, D. van}
}
@article{Shang2012,
  year = {2012},
  title = {Hydration-layer models for {cryo-EM} image simulation},
  pages = {10-16},
  journal = {Journal of Structural Biology},
  volume = {180},
  author = {Shang, Z. and Sigworth, F.J.}
}
@article{Blab2004,
  number = {7},
  year = {2004},
  title = {Simultaneous wide-field imaging and spectroscopy
of localized fluorophores},
  pages = {727-729},
  journal = {Optics Letters},
  volume = {29},
  author = {Blab, G.A. and Oellerich, S. and Schumm, R. and Schmidt, T.}
}
@article{Han2008,
  year = {2008},
  title = {Spectral imaging of single molecules by transmission grating-based epi-fluorescence microscopy},
  pages = {209-214},
  journal = {Analytica Chimica Acta},
  volume = {619},
  author = {Han, R. and Zhang, Y. and Dong, X .and Gai, H. and Yeung, E.S.}
}
@article{Heider2010,
  number = {1},
  year = {2010},
  title = {Identification of Single Fluorescent Labels Using
Spectroscopic Microscopy},
  pages = {37-45},
  journal = {Applied Spectroscopy},
  volume = {64},
  author = {Heider, E.C. and Barhoum, M. and Peterson, E.M. and Schaefer, J. and Harris, J.M.}
}
@article{Isailovic2011,
  number = {6},
  year = {2011},
  title = {Multimodal Spectral Imaging of Cells Using a Transmission Diffraction Grating on a Light Microscope},
  pages = {575-583},
  journal = {Applied Spectroscopy},
  volume = {65},
  author = {Isailovic, D. and Xu, Y. and Copus, T. and Sarawat, S. and Nauli, S.M. }
}
@article{Li2008,
  year = {2008},
  title = {Tracking single quantum dot and its spectrum in free solution with controllable thermal diffusion suppression},
  pages = {176-181},
  journal = {Analytical Biochemistry},
  volume = {277},
  author = {Li, Q. and Han, R. and Meng, X. and Gai, H. and Yeung, E.S. }
}
@article{Ma2000,
  year = {2000},
  title = {High-Throughput Single-Molecule Spectroscopy in
Free Solution},
  pages = {4640-4645},
  journal = {Analytical Chemistry},
  volume = {72},
  author = {Ma, Y. and Shortreed, M.R. and Yeung, E.S.}
}
@article{Shi2012,
  year = {2012},
  title = {Superlocalization Spectral Imaging Microscopy of a Multicolor Quantum Dot Complex},
  pages = {1504-1509},
  journal = {Analytical Chemistry},
  volume = {84},
  author = {Shi, X. and Xie, Z. and Song, Y. and Tan, Y. and Yeung, E.S. and Gia, H.}
}
@article{Lee2012,
  number = {43},
  year = {2012},
  title = {Counting single photoactivatable fluorescent molecules by photoactivated localization microscopy {(PALM)}},
  pages = {17436-17441},
  journal = {Proceedings of the National Academy of Sciences USA},
  volume = {109},
  author = {Lee, S.-H. and Shin, J.Y. and Lee, A. and Bustamante, C.}
}
@article{Coltharp2012,
  number = {12},
  year = {2012},
  title = {Accurate Construction of Photoactivated Localization Microscopy (PALM) Images for Quantitative Measurements},
  pages = {e51725},
  journal = {PLoS ONE},
  volume = {7},
  author = {Coltharp, C. and Kessler, R.P. and Xiao, J.}
}
@article{Annibale2011_PlosONE,
  number = {7},
  year = {2011},
  title = {Quantitative Photo Activated Localization Microscopy: Unraveling the Effects of Photoblinking},
  pages = {e22678},
  journal = {PLoS ONE},
  volume = {6},
  author = {Annibale, P. and Vanni, S. and Scarselli, M. and Rothlisberger, U. and Radenovic, A.}
}
@article{Nieuwenhuizen2013,
  number = {6},
  month = {June},
  year = {2013},
  title = {Measuring Image Resolution in Optical Nanoscopy},
  pages = {557-562},
  journal = {Nature Methods},
  volume = {10},
  author = {Nieuwenhuizen, R.P.J. and Lidke, K.A. and Bates, M. and Leyton Puig, D. and {Gr\"unwald}, D. and Stallinga, S. and Rieger, B.}
}
@article{Toplak2012,
  year = {2012},
  title = {{STICCS} Reveals Matrix-Dependent Adhesion Slipping and Gripping in Migrating Cells},
  pages = {1672-1682},
  journal = {Biophysical Journal},
  volume = {103},
  author = {Toplak, T. and Pandzic, E. and Chen, L. and Vicente-Manzanares, M. and Horwitz, A.R. and Wiseman, P.W.}
}
@article{Mudry2012,
  year = {2012},
  title = {Structured illumination microscopy using unknown speckle patterns},
  pages = {312-314},
  journal = {Nature Photonics},
  volume = {6},
  author = {Mudry, E. and Belkebir, K. and Girard, J. and Savatier, J. and Le Moal, E. and Nicoletti, C. and Allain, M. and Sentenac, A.}
}
@article{Kromann2012,
  number = {11},
  year = {2012},
  title = {Quantitative pupil analysis in stimulated emission depletion microscopy using phase retrieval},
  pages = {1805-1807},
  journal = {Optics Letters},
  volume = {37},
  author = {Kromann, B. and Gould, T.J. and Juette, M.F. and Wilhjelm, J.E. and Bewersdorf, J.}
}
@article{Levoy2009,
  number = {2},
  year = {2009},
  title = {Recording and controlling the {4D} light field in a microscope using microlens arrays},
  pages = {144-162},
  journal = {Journal of Microscopy},
  volume = {235},
  author = {Levoy, M. and Zhang, Z. and Mcdowall, I.}
}
@article{Kress2011,
  year = {2011},
  title = {Probing Orientational Behvior of {MHC} Class {I} Protein and Lipid Probes in Cell Membranes by Fluorescence Polarization-Resolved Imaging},
  pages = {468-476},
  journal = {Biophysical Journal},
  volume = {101},
  author = {Kress, A. and Ferrand, P. and Rigneault, H. and Trombik, T. and He, H.-T. and Marguet, D. and Brasselet, S.}
}
@article{Hinde2010,
  number = {38},
  year = {2010},
  title = {In vivo pair correlation analysis of {EGFP} intranuclear diffusion reveals {DNA-dependent} molecular flow},
  pages = {16560-16565},
  journal = {Proceedings of the National Academy of Sciences USA},
  volume = {107},
  author = {Hinde, E. and Cardarelli, F. and Digman, M.A. and Gratton, E.}
}
@article{Grotjohann2012,
  year = {2012},
  title = {{rsEGFP2} enables fast {RESOLFT} nanoscopy of living cells},
  pages = {e00248},
  journal = {eLIFE},
  volume = {1},
  author = {Grotjohann, T. and Testa, I. and Reuss, M. and Brakemann, T. and Eggeling, C. and Hell, S.W. and Jakobs, S.}
}
@article{Grotjohann2011,
  year = {2011},
  title = {Diffraction-unlimited all-optical imaging and writing with a photochromic {GFP}},
  pages = {204-208},
  journal = {Nature},
  volume = {478},
  author = {Grotjohann, T. and Testa, T. and Leutenegger, M. and Bock, H. and Urban, N.T. and Lavoie-Cardinal, F. and Willig, K.I. and Eggeling, C. and Hell, S.W.}
}
@article{Gould2012,
  number = {19},
  year = {2012},
  title = {Adaptive optics enables {3D STED} microscopy in aberrating specimens},
  pages = {20998-21009},
  journal = {Optics Express},
  volume = {20},
  author = {Gould, T.J. and Burke, D. and Bewersdorf, J. and Booth, M.J.}
}
@article{Geissbuehler2012,
  number = {4},
  year = {2012},
  title = {Mapping molecular statistics with balanced
super-resolution optical fluctuation
imaging {(bSOFI)}},
  journal = {Optical Nanoscopy},
  volume = {1},
  author = {Geissbuehler, S. and Bocchio, N.L. and Dellagiacoma, C. and Berclaz, C. and Letenegger, M. and Lasser, T.}
}
@article{Dries2013,
  year = {2013},
  title = {Interplay between myosin {IIA}-mediated contractility and actin network integrity orchestrates podosome composition and oscillations},
  pages = {1412},
  journal = {Nature Communications},
  volume = {4},
  author = {Dries, K. van den and Meddens, M.B.M. and Keijzer, S de and Shekhar, S. and Subramaniam, V. and Figdor, C.G. and Cambi,A.}
}
@article{Digman2009,
  year = {2009},
  title = {Detecting Protein Complexes in Living Cells from Laser Scanning Confocal Image Sequences by the Cross Correlation Raster Image Spectroscopy Method},
  pages = {707-716},
  journal = {Biophysical Journal},
  volume = {96},
  author = {Digman, M.A. and Wiseman, P.W. and Horwitz, A.R. and Gratton, E.}
}
@article{Chao2013,
  year = {2013},
  title = {Ultrahigh accuracy imaging modality for super-localization microscopy},
  pages = {335-338},
  journal = {Nature Methods},
  volume = {10},
  author = {Chao, J. and Ram, S. and Ward, E.S. and Ober, R.J.}
}
@article{Bishop2012,
  number = {5},
  year = {2012},
  title = {The Light Field Camera: Extended Depth of Field, Aliasing, and Superresolution},
  pages = {972-986},
  journal = {IEEE Transactions on Pattern Analysis and Machine Intelligence},
  volume = {34},
  author = {Bishop, T.E. and Favaro, P.}
}
@article{Brede2012,
  year = {2012},
  title = {{GraspJ:} an open source, real-time analysis
package for super-resolution imaging},
  pages = {11},
  journal = {Optical Nanoscopy},
  volume = {1},
  author = {Brede, N. and Lakadamyali, M.}
}
@article{Dyck2011,
  year = {2011},
  title = {Persistent misconceptions about incoherence in electron microscopy},
  pages = {894-900},
  journal = {Ultramicroscopy},
  volume = {111},
  author = {Dyck, D. van}
}
@article{Fanelli2008,
  year = {2008},
  title = {Electron tomography: a short overview with an
emphasis on the absorption potential model for the
forward problem},
  pages = {013001},
  journal = {Inverse Problems},
  volume = {24},
  author = {Fanelli, D. and {\"Oktem}, O.}
}
@article{Boothroyd2013,
  year = {2013},
  title = {Comparison of approaches and artefacts in the measurement of detector modulation transfer functions},
  pages = {18-29},
  journal = {Ultramicroscopy},
  volume = {129},
  author = {Boothroyd, C.B. and Kasama, T. and Dunin-Borkowski, R.E.}
}
@article{Adams2013,
  number = {6},
  year = {2013},
  title = {Uncovering Nuclear Pore Complexity with Innovation},
  pages = {1218-1221},
  journal = {Cell},
  volume = {152},
  author = {Adams, R.L. and Wente, S.R.}
}
@article{Vulovic2013,
  number = {1},
  year = {2013},
  title = {Image Formation Modeling in Cryo Electron Microscopy},
  pages = {19-32},
  journal = {Journal of Structural Biology},
  volume = {183},
  author = {Vulovic, M. and Ravelli, R.B.G. and Vliet, L.J. van and Koster, A.J. and Lazic, I. and {L\"ucken}, U. and {Rullg{\aa}rgd}, H. and {\"Oktem}, O. and Rieger, B.}
}
@article{Briege2013,
  year = {2013},
  title = {The challenge of determining handedness in electron tomography and the use of DNA origami gold nanoparticle helices as molecular standards},
  journal = {Journal of Structural Biology},
  author = {Briegel, A. and Pilhofer, M. and Mastronade, D.N. and Jensen, G.J.}
}
@article{Briegel2012,
  year = {2012},
  title = {Bacterial chemoreceptor arrays are hexagonally
packed trimers of receptor dimers networked
by rings of kinase and coupling proteins},
  note = {doi/10.1073/pnas.1115719109},
  journal = {Proceedings of the National Academy of Sciences USA},
  author = {Briegel, A. and Li, X. and Bilwes, A.M. and Hughes, K.T. and Jensen, G.J. and Crane, B.R.}
}
@article{Schlimpert2012,
  year = {2012},
  title = {General protein diffusion barries create compartments within barcterial cells},
  pages = {1270-1282},
  journal = {Cell},
  volume = {151},
  author = {Schimpfert, S. and Klein, E.A. and Briegel, A. and Hughes, V. and Kahnt, J. and Bolte, K. and Maier, U.G. and Brun, Y.V. and Jensen, G.J. and Gitai, Z. and Thanbichler, M.}
}
@article{Briegel2010,
  year = {2010},
  title = {Correlated light and electron cryo-microscopy},
  pages = {317-342},
  journal = {Methods in  Enzymology},
  volume = {481},
  author = {Briegel, A. and Chen, S. and Koster, A.J. and Plitzko, J.M. and Schwartz, C.L. and Jensen, G.J.}
}
@article{Jensen2007,
  year = {2007},
  title = {How electron cryotomography is opening a new window
onto prokaryotic ultrastructure},
  pages = {260-267},
  journal = {Current Opinion in Structural Biology},
  volume = {17},
  author = {Jensen, G.J. and Briegel, A.}
}
@article{Cowley1962,
  number = {supp B-II},
  year = {1962},
  title = {The scattering of electrons by thin crystals},
  pages = {86-91},
  journal = {Journal of the Physical Society of Japan},
  volume = {17},
  author = {Cowely, J.M. and Moodie, A.F. }
}
@article{Dempsey2009,
  number = {51},
  year = {2009},
  title = {Photoswitching Mechanism of Cyanine Dyes},
  pages = {18192-18193},
  journal = {Journal of the American Chemical Society},
  volume = {131},
  author = {Dempsey, G.T. and Bates, M. and Kowtoniuk, W.E. and Liu, D.R. and Tsien, R.Y. and Zhuang, X.}
}
@article{Betzig1995,
  number = {3},
  year = {1995},
  title = {Proposed method for molecular optical imaging},
  pages = {237-239},
  journal = {Optics Letters},
  volume = {20},
  author = {Betzig, E.}
}
@article{Vaughan2012,
  number = {12},
  year = {2012},
  title = {Ultrabright photoactivatable fluorophores created by reductive caging},
  pages = {1181-1184},
  journal = {Nature Methods},
  volume = {9},
  author = {Vaughan, J.C. and Jia, S. and Zhuang, X.}
}
@article{Xu2013,
  year = {2013},
  title = {Actin, Spectrin, and Associated Proteins Form a Periodic Cytoskeletal Structure in Axons},
  pages = {452-456},
  journal = {Science},
  volume = {339},
  author = {Xu, K. and Zhong, G. and Zhuang, X.}
}
@article{Rees2012,
  year = {2012},
  title = {Blind assessment of localisation microscope
image resolution},
  pages = {12},
  journal = {Optical Nanoscopy},
  volume = {1},
  author = {Rees, E.J. and Erdelyi, M. and Pinotsi, D. and Knight, A. and Metcalf, D. and Kaminski, C.F.}
}
@article{Huang2013,
  number = {7},
  year = {2013},
  title = {Video-rate nanoscopy using {sCMOS} camera-specific
single-molecule localization algorithms},
  pages = {653-658},
  journal = {Nature Methods},
  volume = {10},
  author = {Huang, F. and Hartwich, T.M.P. and Rivera-Molina, F.E. and Lin, Y. and Whitney, C. and Long, J.J. and Uchil, P.D. and Myers, J.R. and Baird, M.A. and Mothes, W. and Davidson, M.W. and Toomre, D. and Bewersdorf, J.}
}
@article{Li2013,
  number = {6},
  year = {2013},
  title = {Electron counting and beam-induced motion correction enable near-atomic-resolution single-particle {cryo-EM}},
  pages = {584-590},
  journal = {Nature Methods},
  volume = {10},
  author = {Li, X. and Mooney, P. and Zheng, S.and Booth, C.R. and Braunfeld, M.B. and Gubbens, S. and Agard, D.A. and Yifan, C.}
}
@article{Nellist2008,
  year = {2008},
  title = {Imaging Modes for Scanning Confocal Electron Microscopy in a Double Aberration-Corrected Transmission Electron Microscope},
  pages = {82-88},
  journal = {Microscopy and Microanalysis},
  volume = {14},
  author = {Nellist, P.D. and Cosgriff, E.C. and Behan, G. and Kirkland, A.I.}
}
@article{Cosgriff2008,
  year = {2008},
  title = {Three-dimensional imaging in double aberration-corrected scanning confocal electron microscopy, Part {I}: Elastic scattering},
  journal = {Ultramicroscopy},
  author = {Cosgriff, E.C .and D'Alfonso, A.J. and Alleen, L.J. and Findlay, S.D. and Kirkland, A.I. and Nellist, P.D.}
}
@article{Dalfonso2008,
  year = {2008},
  title = {Three-dimensional imaging in double aberration-corrected scanning confocal electron microscopy, Part {II}: Inelastic scattering},
  pages = {1567-1578},
  journal = {Ultramicroscopy},
  volume = {108},
  author = {D'Alfonso, A.J. and Cosgriff, E.C. and Behan, G. and Kirkland, A.I. and Nellist, P.D.}
}
@article{Wang2008b,
  year = {2008},
  title = {Nanoscale Energy-Filtered Scanning Confocal Electron Microscopy Using a Double-Aberration-Corrected Transmission Electron Microscope},
  pages = {200801},
  journal = {Physical Review Letters},
  volume = {104},
  author = {Wang, P. and Behan, G. and Takeguchi, M. and Hasimoto, A. and Mituishi, K. and Shimojo, M. and Kirkland, A.I. and Nellist, P.D.}
}
@article{Erdelyi2013,
  number = {9},
  month = {May},
  year = {2013},
  title = {Correcting chromatic offset in multicolor superresolution localization microscopy},
  pages = {10978-10988},
  journal = {Optics Express},
  volume = {21},
  author = {Erdelyi, M. and Rees, E. and Metcalf, D. and Kaminski Schierle, G.S. and Dudas, L. and Sinko, J. and Knight, J. and Kaminski, C.F.}
}
@article{Endesfelder2013,
  year = {2013},
  title = {Multiscale Spatial Organization of {RNA} Polymerase in {Escherichia} coli},
  note = {doi.org/10.1016/j.bpj.2013.05.048},
  journal = {Biophysical Journal},
  volume = {105},
  author = {Endesfelder, U. and Finan, K. and Holden, S.J. and Cook, P.R. and Kapanidis, A.N. and Heilemann, M.}
}
@article{Bertolotti2012,
  year = {2012},
  title = {Non-invasive imaging through opaque scattering
layers},
  pages = {232-234},
  journal = {Nature},
  volume = {491},
  author = {Bertolotti, J. and Putten, E.G. van and Blum, C. and Lagendijk, A. and Vos, W.L. and Mosk, A.P.}
}
@article{Kohler2011,
  year = {2011},
  title = {Structure formation in active networks},
  pages = {462-468},
  journal = {Nature Materials},
  volume = {10},
  author = {{K\"ohler}, S. and Schaller, V. and Bausch, A.R.}
}
@article{Matov2010,
  number = {9},
  year = {2010},
  title = {Analysis of microtubule dynamic instability using
a plus-end growth marker},
  pages = {761-768},
  journal = {Nature Methods},
  volume = {7},
  author = {Matov, A. and Applegate, K. and Kumar, P. and Thoma, C. and Krek, W. and Danuser, G. and Wittmann, T.}
}
@article{Smith2010b,
  year = {2010},
  title = {Segmentation and Tracking of Cytoskeletal Filaments
Using Open Active Contours},
  pages = {693-705},
  journal = {Cytoskeleton},
  volume = {67},
  author = {Smith, M.B. and Li, H. and Shen, T. and Huang, X. and Yusuf, E. and Vavylonis, D.}
}
@phdthesis{Vulovic2013a,
  month = {13 June},
  year = {2013},
  title = {Modeling of Image Formation in Cryo Electron Microscopy},
  school = {Delft University of Technology},
  author = {Vulovic, M.}
}
@phdthesis{Karreman2013,
  month = {March},
  year = {2013},
  title = {Light will guide you},
  school = {Utrecht University},
  author = {Karreman, M.A.}
}
@article{Szymborska2013,
  year = {2013},
  title = {Nuclear Pore Scaffold Structure Analyzed by Super-Resolution Microscopy and Particle Averaging},
  pages = {655-658},
  journal = {Science },
  volume = {341},
  author = {Szymborska, A. and Marco, A de. Daigle, N. and Cordes, V.C. and Briggs, J.A.G. and Elllenberg, J.}
}
@article{Cutler2013,
  number = {5},
  year = {2013},
  title = {Multi-Color Quantum Dot Tracking Using a High-Speed
Hyperspectral Line-Scanning Microscope},
  pages = {e64320},
  journal = {PLOS One},
  volume = {8},
  author = {Culter, P.J. and Malik, M.D. and Sheng, L. and Byars, J.M. and Lidke, D.S. and Lidke, K.A.}
}
@article{Shigematsu2013,
  year = {2013},
  title = {Noise models and cryo-EM drift correction with a direct-electron detector},
  pages = {61-69},
  journal = {Ultramicroscopy},
  volume = {131},
  author = {Shigematsu, H. and Sigworth, F.J.}
}
@article{Genc2013,
  year = {2013},
  title = {XEDS STEM tomography for 3D chemical characterization of nano scale particles},
  pages = {24-32},
  journal = {Ultramicroscopy},
  volume = {131},
  author = {Genc, A. and Kovarik, L. and Gu, M. and Cheng, H. and Plachinda, P. and Pullan, L. and Freitag, B. and Wang, C.}
}
@article{Kechkar2013,
  number = {4},
  month = {04},
  year = {2013},
  title = {Real-Time Analysis and Visualization for Single-Molecule Based Super-Resolution Microscopy},
  pages = {e62918},
  journal = {PLoS ONE},
  volume = {8},
  author = {Kechkar, A. AND Nair, D. AND Heilemann, M. AND Choquet, Da. AND Sibarita, J.-B.}
}
@article{Banterle2013,
  year = {2013},
  title = {Fourier ring correlation as a resolution criterion for super-resolution microscopy},
  journal = {Journal of Structural Biology},
  author = {Banterle, N. and Bui, K.H. and Lemke, E.A. and Beck, M.}
}
@article{Quirin2013,
  number = {13},
  year = {2013},
  title = {Instantaneous three-dimensional sensing using spatial light modulator illumination with extended depth of field imaging},
  pages = {16007-16021},
  journal = {Optics Express},
  volume = {21},
  author = {Quirin, S. and  Peterka, D.S. and Yuste, R.}
}
@article{Chmyrov2013,
  number = {8},
  year = {2013},
  title = {Nanoscopy with more than 100,000 'doughnuts'},
  pages = {737-740},
  journal = {Nature Methods},
  volume = {10},
  author = {Chmyrov, A. and Keller, J. and Grotjohann, T. and Ratz, M. and d'Este, E. and Jakobs, S. and Eggeling, C. and Hell, S.W.}
}
@article{Krizek2013,
  number = {22},
  year = {2013},
  title = {Flexible structured illumination microscope with a programmable illumination array},
  pages = {24585-24589},
  journal = {Optics Express},
  volume = {20},
  author = {Krizek, P. and Raska, I. and Hagen, G.M.}
}
@article{Hoebe2007,
  number = {2},
  year = {2007},
  title = {Controlled light-exposure microscopy reduces photobleaching and phototoxicity in fluorescence live-cell imaging},
  pages = {249-253},
  journal = {Nature Biotechnology},
  volume = {25},
  author = {Hoebe, R.A. and Oven, C.H. van and Gadella, T.W. jr and Dhonukshe, P.B. and Noorden, C.J. van and Manders, E.M.M.}
}
@article{Backer2013,
  year = {2013},
  title = {Single-molecule orientation measurements with a quadrated pupil},
  pages = {1521-1523},
  journal = {Optics Letters},
  volume = {38},
  author = {Backer, A.S. and Backlund, M.P. and Lew, M.D. and Moerner, W.E. }
}
@article{Lampe2012,
  year = {2012},
  title = {Multi-colour direct {STORM} with red emitting carbocyanines},
  pages = {1-9},
  journal = {Biology of the Cell},
  volume = {104},
  author = {Lampe, A. and Haucke, V. and Sigrist, S.J. and Heilemann, M. and Schmoranzer, J.}
}
@article{Burnette2011,
  number = {52},
  year = {2011},
  title = {Bleaching/blinking assisted localization microscopy for superresolution imaging using standard fluorescent molecules},
  pages = {21081-6},
  journal = {Proceedings of the National Academy of Sciences USA},
  volume = {108},
  author = {Burnette, D.T. and Sengupta, P. and Dai, Y. and Lippincott-Schwartz, J. and Kachar, B.}
}
@article{Barsic2013,
  year = {2013},
  title = {Super-resolution of dense nanoscale emitters beyond the diffraction limit using spatial and temporal information},
  pages = {231103},
  journal = {Applied Physics Letters},
  volume = {102},
  author = {Barsic, A. and Piestun, R.}
}
@article{Broek2013,
  year = {2013},
  title = {General framework for quantitative three-dimensional reconstruction from arbitrary detection geometries in {TEM}},
  pages = {184108},
  journal = {Physical Review B},
  volume = {87},
  author = {Broek, W. van den and Koch, C.T.}
}
@incollection{Lindeberg2013,
  series = {Volume 178},
  year = {2013},
  title = {Generalized Axiomatic Scale-Space Theory},
  booktitle = {Advances in Imaging and Electron Physics},
  pages = {1-96},
  author = {Lindeberg, T.}
}
@article{Huang2012,
  year = {2012},
  title = {Far-field photostable optical nanoscopy ({PHOTON}) for real-time superresolution single-molecular imaging of signaling pathways of single live cells},
  pages = {2797},
  journal = {Nanoscale},
  volume = {4},
  author = {Huang, T. and Browning, L.M. and Nancy Xu, X.-H.}
}
@article{Vulovic2014,
  year = {2014},
  title = {When to use the projection assumption and the weak-phase object approximation in phase contrast {cryo-EM}},
  pages = {61-66},
  journal = {Ultramircoscopy},
  volume = {136},
  author = {Vulovic, M. and Voortman, L.M. and Vliet, L.J. van and Rieger, B.}
}
@article{Lepiany2013,
  year = {2013},
  title = {Chemical 3D tomography of 28 nm high K metal gate transistor: {STEM XEDS}
experimental method and results},
  pages = {43-49},
  journal = {Micron},
  volume = {47},
  author = {Lepinay, K. and Lorut, F. and Pantel, R. and Epicier, T.}
}
@article{Gittes1993,
  number = {4},
  month = {November},
  year = {1993},
  title = {Flexural rigidity of microtubules and actin filaments measured from thermal fluctuations in shape.},
  pages = {923-934},
  journal = {Journal of Cell Biology},
  volume = {120},
  author = {Gittes, F. and Mickey, B. Nettleton, J. and Howard, J.}
}
@misc{Pengo2013,
  year = {2013},
  title = {{PALM-siever}: {V}isualization and analysis platform for single-molecule localization microscopy},
  note = {[Online; accessed 12-September-2013]},
  url = {http://code.google.com/p/palm-siever/},
  author = {Pengo, T.}
}
@inproceedings{Nieuwenhuizen2013b,
  series = {SPIE Conference vol. 8815},
  month = {Augustus 26-30},
  year = {2013},
  title = {Image resolution in optical nanoscopy },
  booktitle = {Nanoimaging and Nanospectroscopy},
  pages = {881508},
  note = {doi: 10.1117/12.2025352},
  editor = {Verma, P. and Egner, A.},
  address = {San Diego, USA},
  author = {Nieuwenhuizen, R.P.J. and Stallinga, S. and Rieger, B.}
}
@inbook{Nieuwenhuizen2014,
  year = {2014},
  title = {Cell Membrane Nanodomains: from Biochemistry to Nanoscopy},
  editor = {Lidke, D.S. and Cambi, A.},
  chapter = {Visualization and Resolution in Localization Microscopy},
  publisher = {Taylor and Francis},
  author = {Nieuwenhuizen, R.P.J.  and Stallinga, S. and Rieger, B.}
}
@article{Angelo2008,
  number = {10},
  year = {2008},
  title = {Structure, dynamics and function of nuclear pore complexes},
  pages = {456-466},
  journal = {Trends in Cell Biology},
  volume = {18},
  author = {D'Angelo, M.A. and Hetzer, M.W.}
}
@article{Griffis_MolBiolCell_2003,
  year = {2003},
  title = {Nup98 Localizes to Both Nuclear and Cytoplasmic
Sides of the Nuclear Pore and Binds to Two Distinct
Nucleoporin Subcomplexes},
  pages = {600-610},
  journal = {Molecular Biology of the Cell},
  volume = {14},
  author = {Griffs, E.R. and Xu, S. and Powers, M.A.}
}
@article{York2013,
  year = {2013},
  title = {Instant super-resolution imaging in live cells and embryos via analog image processing},
  note = {doi:10.1038/nmeth.2687},
  journal = {Nature Methods},
  author = {York, A.G. and Chandris, P. and Dalle Nogare, D. and Head, J. and Wawrzusin, P. and Fischer, R.S. and Chitnis, A. and Shroff, H. }
}
@inproceedings{Weisenburg2013,
  series = {Proc. of SPIE Vol. 8815},
  month = {22-29 Augustus},
  year = {2013},
  title = {Cryogenic localization of single molecules with Angstrom precision},
  booktitle = {Nanoimaging and Nanospectroscopy},
  pages = {88450D},
  editor = {Prama, V. and Egner, A.},
  address = {San Diego, USA},
  author = {Weisenburger, S. and Jing, B. and Renn, A. and Sandoghdar, V.}
}
@article{Jinschek2012,
  year = {2012},
  title = {Image resolution and sensitivity in an environmental transmission electron microscope},
  pages = {1156-1168},
  journal = {Micron},
  volume = {43},
  author = {Jinscheck, J.R. and Helveg, S.}
}
@article{Faas2013,
  year = {2013},
  title = {Localization of fluorescently labeled structures in frozen-hydrated samples using integrated light electron microscopy},
  pages = {283-290},
  journal = {Journal of Structural Biology},
  volume = {181},
  author = {Faas, F.G.A. and Barcena, M. and Agronskaia, A.V. and Gerritsen, H.C. and Moscicika, K.B. and Diebolder, C.A. and Driel, L.F. van and Limpens, R.W.A.L. and Bos, E. and Ravelli, R.B.G. and Koning, R.I. and Koster, A.J.}
}
@article{Roth2013,
  year = {2013},
  title = {Optical photon reassignment microscopy {(OPRA)}},
  pages = {5},
  note = {doi:10.1186/2192-2853-2-5},
  journal = {Optical nanoscopy},
  volume = {2},
  author = {Roth, S. and Sheppard, C.J.R. and Wicker, K. and Heintzmann, R.}
}
@article{Luca2013,
  number = {11},
  year = {2013},
  title = {Re-scan confocal microscopy: scanning twice for better resolution },
  pages = {2644-2656},
  journal = {Biomedical Optical Express},
  volume = {4},
  author = {Luca, G.M.R. De and Breedijk, R.M.P. and Brandt, R.A.J. and Zeelenberg, C.H.C. and Jong, B.E. de and Timmermanns, W. and Azar, L.N. and Hoebe, R.A. and Stallinga, S. and Manders, E.M.M. }
}
@article{Ruskin2013,
  year = {2013},
  title = {Quantitative characterization of electron detectors for transmission electron microscopy},
  note = {http://dx.doi.org/10.1016/j.jsb.2013.10.016},
  journal = {Journal of Structural Biology},
  author = {Ruskin, R.S. and Yu, Z. and Grigorieff, N.}
}
@article{Righolt2013,
  number = {21},
  year = {2013},
  title = {Image filtering in structured illumination microscopy using the {Lukosz} bound},
  pages = {24431-24451},
  journal = {Optics Express},
  volume = {21},
  author = {Righolt, C.H. and Slotman, J.A. and Young, I.T. and Mai, S. and Vliet, L.J. van and Stallinga, S.}
}
@article{Abrahamsson2013,
  number = {1},
  year = {2013},
  title = {Fast multicolor 3D imaging using aberration corrected multifocus microscopy},
  pages = {60-65},
  journal = {Nature Methods},
  volume = {10},
  author = {Abrahamsson, S. and Chen, J. and Hajj, B. and Stallinga, S. and Katsov, A.Y. and Wisnieski, J. and Mizuguchi, G. and Soule, P. and Mueller, F. and Daugast Darzacq, C. and Darzacq, X. and Wu, C. and Bargmann, C.I. and Agard, D.A. and Dahan, M. and Gustafsson, M.G.L.}
}
@article{Heidari2013,
  year = {2013},
  title = {Quantitative electron tomography: The effect of the three-dimensional point spread function},
  pages = {1-5},
  journal = {Ultramicroscopy},
  volume = {135},
  author = {Heidari, H. and Broek, W. van den and Bals, S.}
}
@article{Fuerstenberg2013,
  number = {36},
  year = {2013},
  title = {Single-molecule localization microscopy -
near-molecular spatial resolution in light
microscopy with photoswitchable fluorophores},
  pages = {14919-14930},
  journal = {Physical Chemistry Chemical Physics},
  volume = {15},
  author = {Fuerstenberg, A. and Heilemann, M.}
}
@article{Sengupta2012,
  number = {6},
  month = {December},
  year = {2012},
  title = {Visualizing Cell Structure and Function
with Point-Localization Superresolution Imaging},
  pages = {1092-1102},
  journal = {Developmental Cell},
  volume = {23},
  author = {Sengupta, P. and Engelenburg, S. van and Lippincott-Schwartz, J.}
}
@article{Kamiyama2012,
  number = {6},
  month = {December},
  year = {2012},
  title = {Development in the STORM},
  pages = {1103-1110},
  journal = {Developmental Cell},
  volume = {23},
  author = {Kamiyama, D. and Huang, B.}
}
@article{Liu2013,
  number = {24},
  year = {2013},
  title = {Three dimensional single molecule localization using a phase retrieved pupil function},
  pages = {29462-29487},
  journal = {Optics Express},
  volume = {21},
  author = {Liu, S. and Kromann, E.B. and Krueger, W.D. and Bewersdorf, J. and Lidke, K.A.}
}
@article{Diebold2013,
  year = {2013},
  title = {Digitally synthesized beat frequency multiplexing
for sub-millisecond fluorescence microscopy},
  pages = {806-810},
  journal = {Nature Photonics},
  volume = {7},
  author = {Diebold, E.D. and Buckley, B.W. and Gossett, D.R. and Jalali, B.}
}
@article{Stennett2014,
  year = {2014},
  title = {Photophysical processes in single molecule organic fluorescent probes},
  note = {DOI: 10.1039/c3cs60211g},
  journal = {Chem Soc Rev},
  author = {Stennett, E.M.S. and Ciuba, M.A. and Levitus, M.}
}
@article{Levitus2011,
  number = {1},
  year = {2011},
  title = {Cyanine dyes inbiophysical research: the
photophysics of polymethine fluorescentdyes
inbiomolecular environments},
  pages = {123-151},
  journal = {Quarterly Reviews of Biophysics},
  volume = {44},
  author = {Levitus, M. and Ranjit, S.}
}
@article{Glaeser2014,
  year = {2014},
  title = {GENERALIZATION OF THE MATSUMOTO-TONOMURA APPROXIMATION FOR THE PHASE SHIFT WITHIN AN OPEN APERTURE},
  note = {http://dx.doi.org/10.1016/j.ultramic.2013.11.009},
  journal = {Ultramicroscopy},
  author = {Glaeser, R.M. and {M\"uller}, H.}
}
@article{Rieger2014,
  number = {4},
  year = {2014},
  title = {The Lateral and Axial Localization Uncertainty in Super-Resolution Light Microscopy},
  pages = {664-670},
  journal = {ChemPhysChem},
  volume = {15},
  author = {Rieger, B. and Stallinga, S.}
}
@article{Shivanandan2013,
  year = {2013},
  title = {MosaicIA: an ImageJ/Fiji plugin for spatial pattern and interaction analysis},
  pages = {349},
  journal = {BMC Bioinformatics},
  volume = {14},
  author = {Shivanandan, A. and Radenovic, A. and Sbalzarini, I.F.}
}
@article{Cardone2013,
  number = {2},
  year = {2013},
  title = {One number does not fit all: Mapping local variations in resolution in cryo-EM reconstructions},
  pages = {226-236},
  journal = {Journal of Structural Biology},
  volume = {184},
  author = {Cardone, G. and Heymann, J.B. and Steven, A.C.}
}
@article{Kucukelbir2013_NatMeth,
  number = {XX},
  year = {2013},
  title = {Quantifying the local resolution of cryo-EM density maps},
  journal = {Nature Methods},
  volume = {XX},
  author = {Kucukelbir, A. and Sigworth, F.J. and Tagare, H.D.}
}
@article{Kudrayashev2013,
  number = {2},
  year = {2012},
  title = {Limiting factors in single particle cryo electron tomography},
  pages = {e201207002},
  journal = {Computational and Structural Biotechnology Journal},
  volume = {1},
  author = {Kudrayashev, M. and Castano-Diez, D. and Stahlberg, H.}
}
@article{Owen2010,
  number = {7},
  year = {2010},
  title = {{PALM} imaging and cluster analysis of protein heterogeneity at the cell surface},
  journal = {Journal of Biophotonics},
  volume = {3},
  author = {Owen, D.M. and Rentero, C. and Rossy, J. and Magenau, A. and Williamson, D. and Rodriguez, M. and Gaus, K.}
}
@article{Sang2014,
  year = {2014},
  title = {Revolving scanning transmission electron microscopy: Correcting sample drift distortion without prior knowledge},
  journal = {Ultramicroscopy},
  author = {Sang, X. and LeBeau, J.M.}
}
@article{Ayuk2013,
  number = {22},
  year = {2013},
  title = {Structured illumination fluorescence microscopy
with distorted excitations using a filtered blind-{SIM} algorithm},
  pages = {4723-4726},
  journal = {Optics Letters},
  volume = {38},
  author = {Ayuk, R. and Giovannini, H. and Jost, A. and Mudry, E. and Girard, J. and Mangeat, T. and Sandeau, N. and Heintzmann, R. and Wicker, K. and Belkebir, K. and Sentenac, A.}
}
@article{Cohen2013,
  number = {24},
  year = {2013},
  title = {Analysis of Point Based Image Registration Errors
With Applications in Single Molecule Microscopy},
  pages = {6291-6306},
  journal = {IEEE Transactions on Signal Processing},
  volume = {61},
  author = {Cohen, E.A.K. and Ober, R.J.}
}
@article{Chizhik2014,
  year = {2014},
  title = {Metal-induced energy transfer for live cell nanoscopy},
  note = {DOI: 10.1038/NPHOTON.2013.345},
  journal = {Nature Photonics},
  author = {Chizhik, A.I. and Rother, J. and Gregor, I. and Janshoff, A. and Enderlein, J.}
}
@article{Schulz2013,
  year = {2013},
  title = {Resolution doubling in fluorescence microscopy with
confocal spinning-disk image scanning microscopy},
  note = {doi/10.1073/pnas.1315858110},
  journal = {Proceedings of the National Academy of Sciences USA},
  author = {Schulz, O. and Pieper, C. and Clever, M. and Pfaff, J. and Ruhlandt, A. and Kehlenbach, R.H. and Wouters, F.S. and Groshans, J. and Bunt, G. and Enderlein, J.}
}
@article{Min2013,
  year = {2013},
  title = {Fluorescent microscopy beyond diffraction limits using speckle illumination and joint support recovery},
  pages = {2075},
  journal = {Scientific Reports},
  volume = {3},
  author = {Min, J. and Jang, J. and Keum, D. and Ryu, S.-W. and Choi, C. and Jeong, K.-H. and Ye, J.-C.}
}
@article{Legros2009,
  number = {1},
  year = {2009},
  title = {High-aperture cryogenic light microscopy},
  pages = {1-8},
  journal = {Journal of Microscopy},
  volume = {235},
  author = {Le Gros, M.A. and McDermott, G. and Uchida, M. and  Knoechel, C.G. and Larabell, C.A.}
}
@article{Kucukelbir2014,
  number = {1},
  year = {2014},
  title = {Quantifying the local resolution of cryo-{EM} density maps},
  pages = {63-65},
  journal = {Nature Methods},
  volume = {11},
  author = {Kucukelbir, A. and Sigworth, F.J. and Tagare, H.D.}
}
@article{McGorty2013,
  year = {2013},
  title = {Active microscope stabilization in three
dimensions using image correlation},
  pages = {3},
  journal = {Optical Nanoscopy},
  volume = {2},
  author = {McGorty, R .and Kamiyama, D. and Huang, B.}
}
@article{Klein2014,
  year = {2014},
  title = {Eight years of single-molecule localization microscopy},
  note = {DOI 10.1007/s00418-014-1184-3},
  journal = {Histochem Cell Biology},
  author = {Klein, T. and Proppert, S. and Sauer, M.}
}
@article{VanDeLinde2011,
  year = {2011},
  title = {Photoinduced formation of reversible dye radicals and their impact on super-resolution imaging},
  pages = {499-506},
  journal = {Photochemical \& Photobiological Sciences},
  volume = {10},
  author = {Linde, S. van de and Krstic, I. and Psisner, T. and Doose, S. and Heilemann, M. and Sauer, M.}
}
@article{Faro2011,
  year = {2011},
  title = {Low-Temperature Chromophore Isomerization Reveals the Photoswitching Mechanism of the Fluorescent Protein Padron},
  pages = {16362-16365},
  journal = {Journal of the American Chemical Society},
  volume = {133},
  author = {Faro, A.R. and Carpentier, P. and Jonasson, G. and Pompidor, G. and Arcizet, D. and Demachy, I. and Bourgeois, D.}
}
@mastersthesis{Pfaff2013,
  year = {2013},
  title = {Cryo Fluorescence Single Molecule Microscopy},
  address = {{W\"urzburg}, Germany},
  school = {Julius-Maximilians-{Universit\"at} {W\"urzburg}},
  author = {Pfaff, D.}
}
@article{Jungmann2014,
  year = {2014},
  title = {Multiplexed {3D} cellular super-resolution imaging with {DNA-PAINT} and Exchange-{PAINT}},
  note = {doi:10.1038/nmeth.2835},
  journal = {Nature Methods},
  author = {Jungmann, R. and Avendano, M. and Woehrstein, J.B. and Dai, M. and Shih, W.M. and Yin, P.}
}
@article{Zhao2011,
  year = {2011},
  title = {Photon budget analysis for fluorescence lifetime imaging microscop},
  pages = {086007},
  journal = {Journal of Biomedical Optics},
  volume = {16},
  author = {Zhao, Q. and Young, I.T. and Sander de Jong, D.G.}
}
@article{Dai2005,
  number = {23},
  year = {2005},
  title = {Measuring large numerical apertures by imaging
the angular distribution of radiation of fluorescing molecules},
  pages = {9409-9414},
  journal = {Optics Express},
  volume = {13},
  author = {Dia, L. and Gergor, I. and Hocht, I. von der, Ruckstuhl, T. and Enderlein, J.}
}
@article{Endesfelder2014,
  month = {February},
  year = {2014},
  title = {A simple method to estimate the average localization precision of a single-molecule localization microscopy experiment},
  journal = {Histochemistry and Cell Biology},
  author = {Endesfelder, U. and Malkusch, S. and Fricke, F. and Heilemann, M.}
}
@article{Duan2014,
  year = {2014},
  title = {Some fast projection methods based on Chan-Vese model for image segmentation},
  pages = {1-6},
  journal = {{EURASIP} Journal on Image and Video Processing},
  volume = {7},
  author = {Duan, J. and Pan, Z. and Yin, X. and Wang, G.}
}
@article{Li2013b,
  number = {6},
  year = {2013},
  title = {Fast and Efficient Molecule
Detection in Localization-Based
Super-Resolution Microscopy by Parallel
Adaptive Histogram Equalization},
  pages = {5207-5214},
  journal = {ACS Nano},
  volume = {7},
  author = {Li, Y. and Ishitsuka, Y. and Hedde, P.E. and Nienhaus, G.U.}
}
@article{Hoogendoorn2014,
  year = {2014},
  title = {The fidelity of stochastic single-molecule
super-resolution reconstructions critically
depends upon robust background
estimation},
  pages = {3854},
  note = {doi:10.1038/srep03854},
  journal = {Scientific Reports},
  volume = {4},
  author = {Hoogendoorn, E. and Crosby, K.C. and Leyton-Puig, D. and Breedijk, R.M.P. and Jalink, K. and Gadella, T.W.J. and Postma, M.}
}
@article{Juette2008,
  number = {6},
  year = {2008},
  title = {Three-dimensional sub 100 nm resolution fluorescence microscopy of thick samples},
  pages = {527-529},
  journal = {Nature Methods},
  volume = {5},
  author = {Juette, M.F. and Gould, T.J. and Lessard, M.D. and Mlodzianoski, M.J. and Nagpure, B.S. and Bennett, B.T. and Hess, S.T. and Bewersdorf, J.}
}
@article{Weisenburger2014,
  year = {2014},
  title = {Cryogenic Colocalization Microscopy for Nanometer-Distance Measurements},
  pages = {763-770},
  journal = {ChemPhysChem},
  volume = {15},
  author = {Weisenburger, S. and Jing, B. and {H\"anni}, D. and Reymond, L. and Schuler, B. and Renn, A. and Sandoghdar, V.}
}
@article{Blythe2014,
  year = {2014},
  title = {Triplet-State-Mediated Super-Resolution Imaging of Fluorophore-Labeled Gold Nanorods},
  pages = {784-793},
  journal = {ChemPhysChem},
  volume = {15},
  author = {Blythe, K.L. and Titus, E.J. and Willets, K.A.}
}
@article{Grussmayer2014,
  number = {734-742},
  year = {2014},
  title = {Single-Molecule Studies on the Label Number Distribution of Fluorescent Markers},
  journal = {ChemPhysChem},
  volume = {15},
  author = {Grussmayer, K.S. and Kurz, A. and Herten, D.-P.}
}
@article{Hafi2014,
  year = {2014},
  title = {Fluorescence nanoscopy by polarization modulation and polarization angle narrowing},
  pages = {579-584},
  journal = {Nature Methods},
  volume = {11},
  author = {Hafi, N. and Grunwald, M. and Heuvel, L.S. van den and Aspelmeier, T. and Chen, J.-H. and Zagrebelsky, M. and {Sch\"utte}, O.M. and Steinem, C. and Korte, M. and Munk, A. and Walla, P.J.}
}
@article{Richards2010,
  number = {1},
  year = {2010},
  title = {Synchronously Amplified Fluorescence Image Recovery {(SAFIRe)}},
  pages = {660-665},
  journal = {Journal of Physical Chemistry B},
  volume = {114},
  author = {Richards, C.I. and Hsiang, J.-C. and Dickson, R.M.}
}
@article{Marriott2008,
  number = {46},
  year = {2008},
  title = {Optical lock-in detection imaging microscopy
for contrast-enhanced imaging in living cells},
  pages = {17789-17794},
  journal = {Proceedings of the National Academy of Sciences USA },
  volume = {105},
  author = {Mariott, G. and Mao, S. and Skata, T. and Ran, J. and Jacksson, D.K. and Petchprayoon, C. and Gomez, T.J. and Warp, E. and Tulyathan, P. and Aaron, H.L. and Isacoff, E.Y. and Yan, Y.}
}
@article{Vicidomini2011,
  number = {7},
  year = {2011},
  title = {Sharper low-power {STED} nanoscopy by time gating},
  pages = {571-573},
  journal = {Nature Methods},
  volume = {8},
  author = {Vicidomini, G. and Moneron, G. and Han, K.Y. and Westphal, V. and Ta, H. and Reuss, M. and Engelhardt, J. and Eggeling, C. and Hell, S.W.}
}
@article{Hettich2002,
  year = {2002},
  title = {Nanometer Resolution and Coherent Optical Dipole Coupling of Two Individual Molecules},
  pages = {385-388},
  journal = {Science},
  volume = {298},
  author = {Hettich, C. and Schmitt, C. and Zitzmann, J. and {K\"uhn}, S. and Gerhardt, I. and Sandoghdar, V.}
}
@article{Schur2013,
  number = {3},
  year = {2013},
  title = {Determination of protein structure at 8.5 {\AA} resolution using cryo-electron tomography and sub-tomogram averaging},
  pages = {394-400},
  journal = {Journal of Structural Biology},
  volume = {184},
  author = {Schur, F.K.M. and  Hagen, W.J.H. and  Marco, A. de and Briggs, J.A.G.}
}
@article{Vogelsang2008,
  number = {29},
  year = {2008},
  title = {A Reducing and Oxidizing System Minimizes Photobleaching and Blinking of Fluorescent Dyes},
  pages = {5465-5469},
  journal = {Angewandte Chemie International Edition},
  volume = {47},
  author = {Vogelsang, J. and Kasper, R. and Steinhauer, C. and Person, B. and Heilemann, M. and Sauer, M. and Tinnefeld, P.}
}
@article{Proppert2014,
  number = {9},
  year = {2014},
  title = {Cubic B-spline calibration for 3D super-resolution measurements using astigmatic imaging},
  pages = {10304-10316},
  journal = {Optics Express},
  volume = {22},
  author = {Proppert, S. and Wolter, S. and Holm, T. and Klein, T. and Linde, S. van de and Sauer, M.}
}
@article{Broeken2014,
  number = {11},
  year = {2014},
  title = {Simultaneous measurement of position and color of single fluorescent emitters using diffractive optics},
  pages = {3352-3355},
  journal = {Optics Letters},
  volume = {39},
  author = {Broeken, J. and Rieger, B. and Stallinga, S.}
}
@phdthesis{Giske2007,
  month = {November},
  year = {2007},
  title = {CryoSTED microscopy: A new spectroscopic approach for improving the resolution of {STED} microscopy using low temperature},
  school = {University of Heidelberg},
  author = {Giske, A.}
}
@article{Gros2009,
  number = {1},
  year = {2009},
  title = {High-aperture cryogenic light microscopy},
  pages = {1-8},
  journal = {Journal of Microscopy},
  volume = {235},
  author = {Gros, M.A. le and McDermott, G. and Uchida, M. and Knoechel, C.G. and Larabell, C.A.}
}
@article{Moerner1999,
  year = {1999},
  title = {Illuminating single molecules in condensed matter},
  pages = {1670-1676},
  journal = {Science},
  volume = {283},
  author = {Moerner, W.E. and Orrit, M.}
}
@article{Ha1996,
  number = {19},
  year = {1996},
  title = {Single Molecule Dynamics studied by Polarization Modulation},
  pages = {3979-3982},
  journal = {Physical Review Letters},
  volume = {77},
  author = {Ha, T. and Enderle, Th. and Chemla, D.S. and Selvin, P.R. and Weiss, S.}
}
@inproceedings{Kuffner2004,
  month = {April },
  year = {2004},
  title = {Effective Sampling and Distance Metrics for 3D Rigid Body Path Planning},
  booktitle = {IEEE International Conference on Robotics and Automation},
  pages = {3993-3998},
  address = {New Orleans, USA},
  author = {Kuffner, J.J.}
}
@article{Geisler2012,
  number = {7},
  year = {2012},
  title = {Drift estimation for single marker switching
based imaging schemes},
  pages = {7274-7289},
  journal = {Optics Express},
  volume = {20},
  author = {Geisler, C. and Hotz, T. and {Sch\"onle}, A. and Hell, S.W. and Munk, A. and Egner, A.}
}
@article{Schonle2014,
  year = {2014},
  title = {Monitoring Triplet State Dynamics With Fluorescence
Correlation Spectroscopy: Bias and Correction},
  journal = {Microscopy Research and Technique},
  author = {{Sch\"onle}, A. and Middendorff, C. von and Ringemann, C. and Hell, S.W. and Eggeling, C.}
}
@article{Donnert2007,
  number = {1},
  year = {2007},
  title = {Major signal increase in fluorescence microscopy
through dark-state relaxation},
  pages = {81-86},
  journal = {Nature Methods},
  volume = {4},
  author = {Donnert, G. and Eggeling, C. and Hell, S.W.}
}
@article{Donnert2009,
  year = {2009},
  title = {Triplet-relaxation microscopy
with bunched pulsed excitation},
  pages = {481-485},
  journal = {Photochemical \& Photobiological Sciences },
  volume = {8},
  author = {Donnert, G. and Eggeling, C. and Hell, S.W.}
}
@article{Zondervan2006,
  year = {2006},
  title = {Laser-Driven Microsecond Temperature Cycles Analyzed by Fluorescence Polarization Microscopy},
  pages = {2958-2969},
  journal = {Biophysical Journal},
  volume = {90},
  author = {Zondervan, R. and Kulzer, R. and  Meer, H. van der and   Disselhorst, J.A.J.M. and Orrit, M.}
}
@article{Briggs2013,
  number = {2},
  year = {2013},
  title = {Structural biology in situ -the potential of subtomogram averaging},
  pages = {261-267},
  journal = {Current Opinion in Structural Biology},
  volume = {23},
  author = {Briggs, J.A.}
}
@article{Cha2007,
  number = {1},
  year = {2007},
  title = {Comprehensive Survey on Distance/Similarity
Measures between Probability Density
Functions },
  pages = {300-307},
  journal = {INTERNATIONAL JOURNAL OF MATHEMATICAL MODELS AND METHODS IN APPLIED SCIENCES},
  volume = {4},
  author = {Cha, S.-H.}
}
@inbook{Wilson2007,
  year = {2007},
  title = {Lipid Rafts},
  pages = {245-261},
  editor = {McIntosh, T.J.},
  chapter = {Exploring Membrane Domains Using Native Membrane Sheets and Transmission Electron Microscopy},
  publisher = {Humana Press},
  author = {Wilson, B.S. and Pfeiffer, J.R. and 
Raymond-Stintz, M.A. and Lidke, D.S. and Andrews, N. and Zhang, J. and Yin, W. and Steinberg, S. and Oliver, J.M. }
}
@article{Papari2011,
  year = {2011},
  title = {Edge and line oriented contour detection: State of the art},
  pages = {79-103},
  journal = {Image and Vision Computing},
  volume = {29},
  author = {Papari, G. and Petkov, N.}
}
@article{Vandewalle2007,
  number = {7},
  year = {2007},
  title = {Super-Resolution From Unregistered and Totally Aliased Signals Using Subspace Methods},
  pages = {3687-3703},
  journal = {IEEE Transactions on Signal Processing},
  volume = {55},
  author = {Vandewalle, P. and Sbaiz, L. and Vandewalle, J. and Vetterli, M.}
}
@article{Ross2013,
  number = {31},
  year = {2013},
  title = {Calculator for conformational statistics of {DNA} and applications to high-curvature bending. },
  pages = {030707},
  journal = {Physical Review E},
  volume = {87},
  author = {Ross, B.C. and Wiggins, P.A.}
}
@article{Engelenburg2014,
  year = {2014},
  title = {Distribution of {ESCRT} Machinery at {HIV} Assembly Sites Reveals Virus Scaffolding of {ESCRT} Subunits},
  pages = {653-656},
  journal = {Science },
  volume = {343},
  author = {Engelenburg, S.B. van and Shtengel, G. and Sengupta, P. and Waki, K. and Jarnik, M. and Ablan, S.D. and Freed, E.O. and Hess, H.F. and Lippincott-Schwartz, J.}
}
@article{Raginsky2010,
  year = {2010},
  title = {Compressed sensing  performance bounds under Poisson noise},
  pages = {3990-4002},
  journal = {IEEE Transactions on Signal Processing },
  volume = {58},
  author = {Raginsky, M. and Willett, R.M. and Harmany, Z.T. and Marcia, R.F.}
}
@article{Small2014,
  number = {3},
  year = {2014},
  title = {Fluorophore localization algorithms for super-resolution microscopy},
  pages = {267-279},
  journal = {Nature Methods},
  volume = {11},
  author = {Small, A. and Stahlheber, S.}
}
@article{Monnier2012,
  number = {3},
  year = {2012},
  title = {Bayesian approach to {MSD-based} analysis of particle motion in live cells.},
  pages = {616-626},
  journal = {Biophysical Journal},
  volume = {103},
  author = {Monnier, N. and Guo, S.M. and Mori, M. and He, J. and Lenart, P. and Bathe, M.}
}
@article{Suzuki1997,
  year = {1997},
  title = {{DNA} Staining for Fluorescence and Laser Confocal Microscopy},
  pages = {49-55},
  journal = {Journal of Histochem Cytochem},
  volume = {45},
  author = {Suzuki, T. and Fujikura, K. and  Higashiyama, T. and Takata, K.}
}
@article{Ober2002,
  number = {3},
  year = {2002},
  title = {The {Fisher} information matrix for linear systems},
  pages = {221-226},
  journal = {Systems and Control Letters},
  volume = {47},
  author = {Ober, R.J.}
}
@article{Persson2013,
  number = {3},
  year = {2013},
  title = {Extracting intracellular diffusive states and transition rates from single-molecule tracking data},
  pages = {265-232},
  journal = {Nature Methods},
  volume = {10},
  author = {Persson, F. and Linden, M. and Unoson, C. and Elf, J.}
}
@article{Albertazzi2014,
  year = {2014},
  title = {Probing Exchange Pathways in One-Dimensional Aggregates with Super-Resolution Microscopy},
  pages = {491-495},
  journal = {Science},
  volume = {334},
  author = {Albertazzi, L. and Zwaag, D. van der and Leenders, C.M.A. and Fitzner, R. and Hofstad, R.W. van der and Meijer, E.W.}
}
@article{Deschout2014,
  number = {3},
  year = {2014},
  title = {Precisely and accurately localizing single emitters in fluorescence microscopy},
  pages = {253-266},
  journal = {Nature Methods},
  volume = {11},
  author = {Deschout, H. and Calla Zanacchi, F. and Mlodzianoski, M. and Diaspro, A. and Bewersdorf, J. and Hess, S.T. and Braeckmans, K.}
}