Changeset 295

Timestamp:

09/05/11 19:45:44 (14 years ago)

Author:

qipapers

Message:

commit via qipapers

Files:

• qipapers.bib (modified) (1 diff)
• qipapers.html (modified) (1 diff)

qipapers.bib

@@ -10346 +10346 @@
   year = {1994},
   title = {Coupled geometry-driven diffusion equations for low-level vision},
-  booktitle = {Geometry-dr
+  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 Letter},
+  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},
+  journal = {Nature},
+  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,
+  year = {2010},
+  title = {Single-Molecule Redox Blinking of Perylene Diimide
+Derivatives in Water},
+  journal = {Journal of the American Chemical Society},
+  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}
+}
+@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 = {Optimizationofexit-planewavesrestoredfromHRTEMthrough-focalseries},
+  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 = {Quantitativ eanalysis 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, Michael 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, Jan and Furrer, Patrick and Katritch, Vsevolod and Stasiak, Alicja Z. and Dubochet, Jacques and Stasiak, Andrzej}
+}
+@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 de Vries, A.H.B. 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}},
+  journal = {{Physical Review E}},
+  volume = {{73}},
+  author = {Wiggins, Paul A. and Nelson, Philip 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, Daniel and Neumann, Franck R. and Hediger, Florence and Gasser, Susan M. and Unser, Michael}
+}
+@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, Stefan and Axmann, Markus and Sch\\\"utz, Gerhard 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, Yasushi and Sedat, John W. and Agard, David 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 Von Middendorff, C. and Jakobs, S. and Schonle, 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 = {Polariztion 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. v. 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 Von Middendorff, C. 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 von Middendorff, C. 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-Oxford},
+  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},
+  note = {accepted},
+  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},
+  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 = {NanoLetters},
+  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 = {NanoLetters},
+  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{Unser2009,
+  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 van de Ville, D.}
+}
+@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.}
+}

qipapers.html

@@ -14 +14 @@
      (see http://www.lri.fr/~filliatr/bibtex2html/),
      with the following command:
-     /usr/bin/bibtex2html -o - -t qipapers.html -s plain /tmp/tmp4RNmrv.bib  -->
+     /usr/bin/bibtex2html -o - -t qipapers.html -s plain /tmp/tmpF0FAC6.bib  -->
 
 <h1>qipapers.html</h1>