Index: /qipapers.bib =================================================================== --- /qipapers.bib (revision 314) +++ /qipapers.bib (revision 315) @@ -14784,3 +14784,4859 @@ pages = {121-160}, journal = {Advances in Imaging and Electron Physics}, - volume + 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.} +} +@article{Knowles2011, + number = {36}, + year = {2011}, + title = {Observation of spatial propagation of amyloid +assembly from single nuclei}, + pages = {14746-14751}, + journal = {Proceedings of the National Academy of Science USA}, + volume = {108}, + author = {Knowles, T.P.J. and White, D.A. and Abate, A.A. and Agresti, J.J. and Cohen, S.I.A. and Sperling, R.A. and Genst, E.J. de and Dobson, C.M. and Weitz, D.A.} +} +@article{Kampmannetal2011, + number = {6}, + year = {2011}, + title = {Mapping the orientation of nuclear pore proteins in living cells with polarized fluorescence microscopy}, + pages = {643-650}, + journal = {Nature structural & molecular biology}, + volume = {18}, + author = {Kampmann, M. and Atkinson, C.E. and Mattheyses, A.L. and Simon, S.M.} +} +@article{Nature08-2011, + year = {2011}, + title = {Suppression of the coffee-ring effect by +shape-dependent capillary interactions}, + pages = {308-311}, + journal = {Nature}, + volume = {476}, + author = {Yunker, P.J. and Still, T. and Lohr, M.A. Yodh, A.G.} +} +@article{Park2004, + number = {3}, + year = {2004}, + title = {Nanometre localization of single {ReAsH} molecules}, + pages = {199-205}, + journal = {Journal of Microscopy}, + volume = {216}, + author = {Park, H. and Hanson, T. and Duff, S.R. and Selvin, P.R.} +} +@article{Martin2005, + number = {10}, + year = {2005}, + title = {Mammalian cell-based optimization of the biarsenical binding tetracysteine motif for improved fluorescence and affinity}, + pages = {1308-1314}, + journal = {Nature biotechnology}, + volume = {23}, + author = {Martin, B.R. and Giepmanns, B.N.G. and Adams, S.R. and Tsien, R.Y.} +} +@article{Kampmann2008, + number = {7}, + year = {2008}, + title = {Three-dimensional structure and flexibility of a membrane-coating module of the nuclear pore complex}, + pages = {782-789}, + journal = {Nature structural & molecular biology}, + volume = {16}, + author = {Kampmann, M. and Blobel, G.} +} +@phdthesis{Hein2009, + year = {2009}, + title = {Live Cell {STED} Microscopy +Using Genetically Encoded Markers}, + address = {{G\"ottingen}, Germany}, + school = {Georg-August-{Universit\"at} {G\"ottingen} }, + author = {Hein, B.} +} +@article{Grunwald2010, + year = {2010}, + title = {In vivo imaging of labelled endogenous b-actin +{mRNA} during nucleocytoplasmic transport}, + pages = {604-609}, + journal = {Nature}, + volume = {467}, + author = {{Gr\"unwald}, D. and Singer, R.H.} +} +@article{Delber2008, + year = {2008}, + title = {A Fence-like Coat for the Nuclear Pore Membrane}, + pages = {815-826}, + journal = {Molecular Cell}, + volume = {32}, + author = {Delber, E.W. and Ma, Y. and Seo, H.-S. and Hsia, K.-C. and Noriega, T.R. and Blobel, G. and Hoelz, A.} +} +@article{Churchman2005, + number = {5}, + year = {2005}, + title = {Single molecule high-resolution colocalization of {Cy3} +and {Cy5} attached to macromolecules measures +intramolecular distances through time}, + pages = {1419-1423}, + journal = {Proceedings of the National Academy of Science}, + volume = {102}, + author = {Churchman, L.S. and {\"Oktem}, Z. and Rock, R.S. and Dawson, J.F. and Spudich, J.A.} +} +@article{Brohawn2009, + year = {2008}, + title = {Structural Evidence for Common Ancestry of the Nuclear Pore Complex and Vesicle Coats}, + pages = {1369-1373}, + journal = {Science}, + volume = {322}, + author = {Brohawn, S.G. and Leksa, N.C. and Spear, E.D. and Rajashankar, K.R. and Schwartz, T.U.} +} +@article{Beck2007, + year = {2007}, + title = {Snapshots of nuclear pore complexes in action +captured by cryo-electron tomography}, + pages = {611-615}, + journal = {Nature}, + volume = {449}, + author = {Beck, M. and Lucic, V. and {F\"orster}, F. and Baumeister, W. and Medalia, O.} +} +@article{Alber2007, + year = {2007}, + title = {The molecular architecture of the nuclear +pore complex}, + pages = {695-701}, + journal = {Nature}, + volume = {450}, + author = {Alber, F. and Dokudovskaya, S. and Veenhoff, L.M. and Zhang, W. and Kipper, J. nad Devos, D. and Suprapto, A. and Karni-Schmidt, O. and Williams, R. and Chait, B.T. and Sali, A. and Rout, M.P.} +} +@article{Varbioiu2006, + number = {466-469}, + year = {2006}, + title = {Structural insight into yeast septin organizaiton from polarized fluorescent micrsocopy}, + journal = {Nature}, + volume = {443}, + author = {Varabioiu, A.M. and Mitchison, T.J.} +} +@article{Mattheyses2010, + year = {2010}, + title = {Fluorescence anisotropy reveals order and disorder of protein domains in the nuclear pore complex}, + pages = {1706-1717}, + journal = {Biophysical Journal}, + volume = {99}, + author = {Mattheyes, A.L. and Kampmann, M. and Aktinson, C.E. and Simon, S.M.} +} +@article{Loschberger2011, + year = {2011}, + title = {Super-resolution imaging reveals eightfold symmetry of gp210 proteins around the nuclear pore complex and resolves the central channel with nanometer resolution}, + note = {accepted}, + journal = {Journal of Cell Science}, + author = {{L\"oschberger}, A. and Linde, S. van de and Dabauvalle, M.-C. and Rieger, B. and Heilemann, M. and Krohne, G. and Sauer, M.} +} +@article{Huang2011, + number = {5}, + year = {2011}, + title = {Simultaneous multiple-emitter fitting for single molecule super-resolution imaging}, + pages = {1377-1393}, + journal = {Biomedical Optics Express }, + volume = {2}, + author = {Huang, F. and Schwartz, S.L. and Byars, J.M. and Lidke, K.A. } +} +@article{Bader2011, + year = {2011}, + title = {Homo-FRET Imaging as a Tool to Quantify Protein and +Lipid Clustering}, + pages = {475-483}, + journal = {ChemPhysChem}, + volume = {12}, + author = {Bader,A.N. and Hoetzl, S. and Hofman, E.G. and Voortman, J. and Bergen en Henegouwen, +P.M.P. van and Meer, G. van and Gerritsen, H.C.} +} +@article{Bader2009, + year = {2009}, + title = {Homo-FRET Imaging Enables Quantification of Protein Cluster Sizes +with Subcellular Resolution}, + pages = {2613-2622}, + journal = {Biophysical Journal}, + volume = {97}, + author = {Bader,A.N. and Hofmann, E.G. and Voortman, J. and Bergen en Henegouwen, P.M.P. van and Gerritsen, H.C.} +} Index: /qipapers.html =================================================================== --- /qipapers.html (revision 314) +++ /qipapers.html (revision 315) @@ -14,5 +14,5 @@ (see http://www.lri.fr/~filliatr/bibtex2html/), with the following command: - /usr/bin/bibtex2html -o - -t qipapers.html -s plain /tmp/tmpscWhDI.bib --> + /usr/bin/bibtex2html -o - -t qipapers.html -s plain /tmp/tmp97Guh5.bib -->

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