Changeset 789 for qipapers.bib


Ignore:
Timestamp:
05/14/14 11:24:36 (11 years ago)
Author:
qipapers
Message:

commit via qipapers

File:
1 edited

Legend:

Unmodified
Added
Removed
  • qipapers.bib

    r788 r789  
    1571415714  pages = {{131-135}},
    1571515715  journal = {{Biomedical Papers}},
    15716   volume = {{147}
     15716  volume = {{147}},
     15717  author = {Dvor\\\'ak, Zdenek and Pascussi, Jean-Marc and Modriansk\\\'y, Martin}
     15718}
     15719@article{Medalion2010,
     15720  number = {{4}},
     15721  year = {2010},
     15722  title = {{Coupling of twist and writhe in short DNA loops
     15723 }},
     15724  pages = {{045101}},
     15725  journal = {{The Journal of Chemical Physics}},
     15726  volume = {{132}},
     15727  author = {Medalion, Shlomi and Rappaport, Shay M. and Rabin, Yitzhak}
     15728}
     15729@article{Cherif2006,
     15730  number = {{2}},
     15731  year = {2006},
     15732  title = {{Clinically Related Protein-Peptide Interactions Monitored in Real Time on Novel Peptide Chips by Surface Plasmon Resonance Imaging}},
     15733  pages = {{255-262}},
     15734  journal = {{Clinical Chemistry}},
     15735  volume = {{52}},
     15736  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}
     15737}
     15738@article{Gibson1991,
     15739  number = {{10}},
     15740  year = {1991},
     15741  title = {{Experimental test of an analytical model of aberration in an oil-immersion objective lens used in three-dimensional light microscopy}},
     15742  pages = {{1601-1613}},
     15743  journal = {{Journal of the Optical Society of America A}},
     15744  volume = {{8}},
     15745  author = {Gibson, Sarah Frisken and Lanni, Frederick}
     15746}
     15747@misc{Bouchiat2007,
     15748  year = {2007},
     15749  title = {{Spatial Constraint Corrections to the Elasticity of dsDNA Measured with Magnetic Tweezers}},
     15750  author = {Bouchiat, C.}
     15751}
     15752@article{Bouchiat2006,
     15753  number = {{03}},
     15754  year = {2006},
     15755  title = {{Entropic elasticity of double-strand DNA subject to simple spatial constraints}},
     15756  pages = {{P03019}},
     15757  journal = {{Journal of Statistical Mechanics: Theory and Experiment}},
     15758  author = {Bouchiat, C.}
     15759}
     15760@article{Yoshinaga2002,
     15761  number = {{22}},
     15762  year = {2002},
     15763  title = {{Multiscaling in a long semiflexible polymer chain in two dimensions}},
     15764  journal = {{Journal of Chemical Physics}},
     15765  volume = {{116}},
     15766  author = {Yoshinaga, Natsuhiko and Yoshikawa, Kenichi and Kidoaki, Satoru}
     15767}
     15768@article{Sottas1999,
     15769  year = {1999},
     15770  title = {{Brownian Dynamics Simulation of DNA Condensation}},
     15771  pages = {{1858-1870}},
     15772  journal = {{Biophysical Journal}},
     15773  volume = {{77}},
     15774  author = {Sottas, Pierre-Edouard and Larquet, Eric and Stasiak, Andrzej and Dubochet, Jacques}
     15775}
     15776@article{Yamakawa1976a,
     15777  number = {{12}},
     15778  year = {1976},
     15779  title = {{Statistical mechanics of helical wormlike chains. I. Differential equations and moments}},
     15780  pages = {{5222-5228}},
     15781  journal = {{The Journal of Chemical Physics}},
     15782  volume = {{64}},
     15783  author = {Yamakawa, Hiromi and Fujii, Motoharu}
     15784}
     15785@article{Odijk1979,
     15786  year = {1979},
     15787  title = {{On the Ionic-Strength Dependence of the Intrinsic Viscosity of DNA}},
     15788  pages = {{3111-3113}},
     15789  journal = {{Biopolymers}},
     15790  volume = {{18}},
     15791  author = {Odijk, Theo}
     15792}
     15793@article{Sheppard1997,
     15794  number = {{3}},
     15795  year = {1997},
     15796  title = {{Effects of specimen refractive index on confocal imaging}},
     15797  pages = {{366-374}},
     15798  journal = {{Journal of Microscopy}},
     15799  volume = {{185}},
     15800  author = {Sheppard, C. J. R. and T\\\"or\\\"ok, P.}
     15801}
     15802@article{Vologodskii1994,
     15803  number = {{20}},
     15804  year = {1994},
     15805  title = {{DNA Extension under the Action of an External Force}},
     15806  pages = {{5623-5625}},
     15807  journal = {{Macromolecules}},
     15808  volume = {{27}},
     15809  author = {Vologodskii, Alexander}
     15810}
     15811@article{Rayleigh1919,
     15812  year = {1919},
     15813  title = {{On the problem of random vibrations, and of random flights in one, two, or three dimensions}},
     15814  pages = {{321-347}},
     15815  journal = {{Philosophical Magazine}},
     15816  volume = {{37}},
     15817  author = {Rayleigh, Lord}
     15818}
     15819@article{Lukic2007,
     15820  year = {2007},
     15821  title = {{Motion of a colloidal particle in an optical trap}},
     15822  pages = {{011112}},
     15823  journal = {{Physical Review E}},
     15824  volume = {{76}},
     15825  author = {{Luki\c{c}}, B. and Jeney, S. and Sviben, Z. and Kulik, A. and Florin, E.-L. and {Forr\'o}, L.}
     15826}
     15827@article{Storm2003a,
     15828  number = {{5}},
     15829  year = {2003},
     15830  title = {{The bend stiffness of S-DNA}},
     15831  pages = {{760-766}},
     15832  journal = {{Europhysics Letters (EPL)}},
     15833  volume = {{62}},
     15834  author = {Storm, C. and Nelson, P. C.}
     15835}
     15836@article{Odijk1977,
     15837  year = {1977},
     15838  title = {{Polyelectrolytes near the Rod Limit}},
     15839  pages = {{477-483}},
     15840  journal = {{Journal of Polymer Science: Polymer Physics Edition}},
     15841  volume = {{15}},
     15842  author = {Odijk, Theo}
     15843}
     15844@article{Beausang2007b,
     15845  year = {2007},
     15846  title = {{Diffusive hidden Markov model characterization of DNA looping dynamics in tethered particle experiments}},
     15847  journal = {{Physical Biology}},
     15848  author = {Beausang, John F. and Nelson, Philip C.}
     15849}
     15850@article{Fixman1973,
     15851  number = {{4}},
     15852  year = {1973},
     15853  title = {{Polymer conformational statistics. I. Probability distribution}},
     15854  pages = {{1553-1558}},
     15855  journal = {{The Journal of Chemical Physics}},
     15856  volume = {{58}},
     15857  author = {Fixman, Marshall and Alben, Richard}
     15858}
     15859@article{Gupta1993,
     15860  number = {{2}},
     15861  year = {1993},
     15862  title = {{Mean-field theory of phase transitions in liquid-crystalline polymers}},
     15863  pages = {{1588-1596}},
     15864  journal = {{Journal of Chemical Physics}},
     15865  volume = {{98}},
     15866  author = {Gupta, Anshu M. and Edwards, Sam F.}
     15867}
     15868@article{Butler2005,
     15869  year = {2005},
     15870  title = {{Brownian dynamics simulations of a flexible polymer chain which includes continuous resistance and multibody hydrodynamic interactions}},
     15871  journal = {{The Journal of Chemical Physics}},
     15872  volume = {{122}},
     15873  author = {Butler, Jason E. and Shaqfeh, Eric S.G.}
     15874}
     15875@article{Csiszar1991,
     15876  number = {{4}},
     15877  year = {1991},
     15878  title = {{Why Least Squares and Maximum Entropy? An Axiomatic Approach to Inference for Linear Inverse Problems}},
     15879  pages = {{2032-2066}},
     15880  journal = {{The Annals of Statistics}},
     15881  volume = {{19}},
     15882  author = {Csiszar, Imre}
     15883}
     15884@inproceedings{Dietrich2006,
     15885  year = {2006},
     15886  title = {{Advances in the Development of a Novel Method to be used in Proteomics using Gold Nanobeads}},
     15887  booktitle = {{Ultrasensitive and Single-Molecule Detection Technologies}},
     15888  editor = {Enderlein, J\\\"org and Gryczynski, Zygmunt K.},
     15889  volume = {{6092}},
     15890  publisher = {{Proceedings of SPIE}},
     15891  author = {Dietrich, Heidelinde R.C. and Young, Ian T. and Garini, Yuval}
     15892}
     15893@inproceedings{Dietrich2007,
     15894  year = {2007},
     15895  title = {A New Optical Method for Characterizing Single Molecule Interactions based on Dark Field Microscopy},
     15896  booktitle = {{Ultrasensitive and Single-Molecule Detection Technologies II}},
     15897  pages = {644403-1 - 64403-8},
     15898  editor = {Enderlein, J. and Gryczynski, Z.K.},
     15899  volume = {{6444}},
     15900  publisher = {{Proceedings of SPIE}},
     15901  author = {Dietrich, Heidelinde R.C. and Vermolen, Bart J. and Rieger, Bernd and Young, Ian T. and Garini, Yuval}
     15902}
     15903@article{Torok1996,
     15904  number = {{3}},
     15905  year = {1996},
     15906  title = {{Dark-field and differential phase contrast imaging modes in confocal microscopy using a half-aperture stop}},
     15907  pages = {{101-106}},
     15908  journal = {{Optik}},
     15909  volume = {{103}},
     15910  author = {T\\\"or\\\"ok, P. and Sheppard, C. J. R. and Laxzik, Z.}
     15911}
     15912@article{Dietrich2002,
     15913  number = {{1}},
     15914  year = {2002},
     15915  title = {{Relationship of Lipid Rafts to Transient Confinement Zones Detected by Single Particle Tracking}},
     15916  pages = {{274-284}},
     15917  journal = {{Biophysical Journal}},
     15918  volume = {{82}},
     15919  author = {Dietrich, Chrisian and Yang, Bing and Fujiwara, Takahiro and Kusumi, Akihiro and Jacobson, Ken}
     15920}
     15921@article{Schafer1991,
     15922  number = {{6334}},
     15923  year = {1991},
     15924  title = {{Transcription by single molecules of RNA polymerase observed by light microscopy}},
     15925  pages = {{444-448}},
     15926  journal = {{Nature}},
     15927  volume = {{352}},
     15928  author = {Schafer, Dorothy A. and Gelles, Jeff and Sheetz, Michael P. and Landick, Robert}
     15929}
     15930@book{Mazo2002,
     15931  series = {{International series of monographs on physics}},
     15932  year = {2002},
     15933  title = {{Brownian Motion: fluctuations, dynamics, and applications}},
     15934  address = {{Oxford}},
     15935  publisher = {{Clarendon Press}},
     15936  author = {Mazo, Robert M.}
     15937}
     15938@article{Deng2009,
     15939  number = {{10}},
     15940  year = {2009},
     15941  title = {{Effect of aberration on height calibration in three-dimensional localization-base microscoyp and particle tracking}},
     15942  pages = {{1886-1890}},
     15943  journal = {{Applied Optics}},
     15944  volume = {{48}},
     15945  author = {Deng, Yi. and Shaevitz, Joshua W.}
     15946}
     15947@article{Han2006,
     15948  year = {2006},
     15949  title = {{Brownian Motion of an Ellipsoid}},
     15950  journal = {{Science}},
     15951  volume = {{314}},
     15952  author = {Han, Y. and Alsayed, A.M. and Nobili, M. and Zhang, J. and Lubensky, T.C. and Yodh, A.G.}
     15953}
     15954@article{Dietrich2009,
     15955  year = {2009},
     15956  title = {Tethered Particle Motion Mediated by Scattering from Gold Nanoparticles and Darkfield Microscopy},
     15957  pages = {{031795}},
     15958  journal = {{Journal of Nanophotonics}},
     15959  volume = {{3}},
     15960  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}
     15961}
     15962@article{Shaevitz2007,
     15963  number = {{9}},
     15964  year = {2007},
     15965  title = {{Enhanced three-dimensional deconvolution microscopy using a measured depth-varying point-spread function}},
     15966  pages = {{2622-2627}},
     15967  journal = {{Journal of the Optical Society of America A}},
     15968  volume = {{24}},
     15969  author = {Shaevitz, Joshua W. and Fletcher, Daniel A.}
     15970}
     15971@book{Doi1986,
     15972  year = {1986},
     15973  title = {{The Theory of Polymer Dynamics}},
     15974  address = {{New York}},
     15975  publisher = {{Oxford University Press}},
     15976  author = {Doi, M. and Edwards, S.F. }
     15977}
     15978@article{Dhar2002,
     15979  number = {{6}},
     15980  year = {2002},
     15981  title = {{Triple Minima in the Free Energy of Semiflexible Polymers}},
     15982  pages = {{065502}},
     15983  journal = {{Physical Review Letters}},
     15984  volume = {{89}},
     15985  author = {Dhar, Abhishek and Chaudhuri, Debasish}
     15986}
     15987@article{Watkins2004,
     15988  number = {{6}},
     15989  year = {2004},
     15990  title = {{Information Bounsd and Optimal Analysis of Dynamic Single Molecule Measurements}},
     15991  pages = {{4015-4029}},
     15992  journal = {{Biophysical Journal}},
     15993  volume = {{86}},
     15994  author = {Watkins, Lucas P. and Yang, Haw}
     15995}
     15996@article{Elburg2007,
     15997  number = {{1}},
     15998  year = {2007},
     15999  title = {{Improved correction of axial geometrical distortion in index-mismatched fluorescent confocal microscopic images using high-aperture objective lenses}},
     16000  pages = {{45-54}},
     16001  journal = {{Journal of Microscopy}},
     16002  volume = {{228}},
     16003  author = {Elburg, H.J. van and Kuypers, L.C. and Decraemer, W.F. and Dirckx, J.J.J.}
     16004}
     16005@phdthesis{Li2006,
     16006  year = {2006},
     16007  title = {{DNA entropic elasticity for short molecules attached to beads}},
     16008  author = {Li, Jinyu and Nelson, Philip C. and Betterton, M.D.}
     16009}
     16010@book{Cohen1988,
     16011  series = {{Statistics: Textbooks and monographs}},
     16012  year = {1988},
     16013  title = {{Parameter estimation in reliability and life span models}},
     16014  volume = {{96}},
     16015  address = {{New York}},
     16016  publisher = {{Marcel Dekker, Inc}},
     16017  author = {Cohen, A. Clifford and Whitten, Betty Jones}
     16018}
     16019@article{Cocco2002,
     16020  year = {2002},
     16021  title = {{Theoretical models for single-molecule DNA and RNA experiments: from elasticity to unzipping}},
     16022  pages = {{569-584}},
     16023  journal = {{Comptes rendus de l'Academie des Sciences Physique}},
     16024  volume = {{3}},
     16025  author = {Cocco, S. and Marko, J.F. and Monasson, R.}
     16026}
     16027@article{Cocco2003,
     16028  year = {2003},
     16029  title = {{Force-extension behavior of folding polymers}},
     16030  pages = {{249-263}},
     16031  journal = {{The European Physical Journal E}},
     16032  volume = {{10}},
     16033  author = {Cocco, S. and Marko, J.F. and Monasson, R. and Sarkar, A. and Yan, J.}
     16034}
     16035@article{Hughes2001,
     16036  year = {2001},
     16037  title = {{DNA microarrays for expression profiling}},
     16038  pages = {{21-25}},
     16039  journal = {{Current Opinion in Chemical Biology}},
     16040  volume = {{5}},
     16041  author = {Hughes, Timothy R. and Shoemaker, Daniel D.}
     16042}
     16043@article{Tinland1997,
     16044  number = {{19}},
     16045  year = {1997},
     16046  title = {{Persistence Length of Single-Stranded DNA}},
     16047  pages = {{5763-5765}},
     16048  journal = {{Macromolecules}},
     16049  volume = {{30}},
     16050  author = {Tinland, Bernard and Pluen, Alain and Sturm, Jean and Weill, Gilbert}
     16051}
     16052@article{Massey1951,
     16053  year = {1951},
     16054  title = {{The Kolmogorov-Smirnov test for goodness of fit}},
     16055  pages = {{68-78}},
     16056  journal = {{Journal of the American Statistical Association}},
     16057  volume = {{46}},
     16058  author = {Massey, Frank J., Jr.}
     16059}
     16060@article{Burkhardt1993,
     16061  year = {1993},
     16062  title = {{Semiflexible polymer in the half plane and statistics of the integral of a Brownian curve}},
     16063  pages = {{L1157-L1162}},
     16064  journal = {{Journal of Physics A: Mathematical and General}},
     16065  volume = {{26}},
     16066  author = {Burkhardt, Theodore W.}
     16067}
     16068@article{Stepanow2002,
     16069  number = {{4}},
     16070  year = {2002},
     16071  title = {{The distribution function of a semiflexible polymer and random walks with constraints}},
     16072  pages = {{546-551}},
     16073  journal = {{Europhysics Letters (EPL)}},
     16074  volume = {{60}},
     16075  author = {Stepanow, S. and Sch\\\"utz, G. M.}
     16076}
     16077@article{Smith1992,
     16078  number = {{5085}},
     16079  year = {1992},
     16080  title = {{Direct Mechanical Measurement of the Elasticity of Single DNA Molecules by Using Magnetic Beads}},
     16081  pages = {{1122-1126}},
     16082  journal = {{Science}},
     16083  volume = {{258}},
     16084  author = {Smith, Steven B. and Finzi, Laura and Bustamante, Carlos}
     16085}
     16086@article{Bao2002,
     16087  number = {{8}},
     16088  year = {2002},
     16089  title = {{High-Sensitivity Detection of DNA Hybridization on Microarrays Using Resonance Light Scattering}},
     16090  pages = {{1792-1979}},
     16091  journal = {{Analytical Chemistry}},
     16092  volume = {{74}},
     16093  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}
     16094}
     16095@article{Baumann1997,
     16096  year = {1997},
     16097  title = {{Ionic effects on the elasticity of single DNA molecules}},
     16098  pages = {{6185-6190}},
     16099  journal = {{Proceedings of the National Academy of Sciences of the USA}},
     16100  volume = {{94}},
     16101  author = {Baumann, Christoph G. and Smith, Steven B. and Bloomfield, Victor A. and Bustamante, Carlos}
     16102}
     16103@article{Vandenberg1991,
     16104  number = {{1}},
     16105  year = {1991},
     16106  title = {{Structure of 3-aminopropyl triethoxy silane on silicon oxide}},
     16107  pages = {{103-118}},
     16108  journal = {{Journal of Colloid and Interface Science}},
     16109  volume = {{147}},
     16110  author = {Vandenberg, Elaine T. and Bertilsson, Lars and Liedberg, Bo and Uvdal, Kajsa and Erlandsson, Ragnar and Elwing, Hans and Lundstrom, Ingemar}
     16111}
     16112@article{Blumberg2005,
     16113  year = {2005},
     16114  title = {{Three-Dimensional Characterization of Tethered Microspheres by Total Internal Reflection Fluorescence Microscopy}},
     16115  pages = {{1272-1281}},
     16116  journal = {{Biophysical Journal}},
     16117  volume = {{89}},
     16118  author = {Blumberg, Seth and Gajraj, Arivalagan and Pennington, Matthew W.}
     16119}
     16120@misc{Neumann2001,
     16121  month = {January 22, 2001},
     16122  year = {2001},
     16123  title = {{Entropic Elasticity of Weakly Perturbed Polymers}},
     16124  pages = {11},
     16125  publisher = {{The Energy Institute, The Pennsylvania State University}},
     16126  author = {Neumann, Richard M.}
     16127}
     16128@article{Ommering2010,
     16129  number = {{15}},
     16130  year = {2010},
     16131  title = {{Mobility and height detection of particle labels in an optical evanescent wave biosensor with single-label resolution}},
     16132  pages = {{155501}},
     16133  journal = {{Journal of Physics D: Applied Physics}},
     16134  volume = {{43}},
     16135  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.}
     16136}
     16137@article{Heaton2001,
     16138  number = {{7}},
     16139  year = {2001},
     16140  title = {{Electrostatic surface plasmon resonance: Direct electric field-induced hybridization and denaturation in monolayer nucleic acid films and label-free discrimination of base mismatches}},
     16141  pages = {{3701-3704}},
     16142  journal = {{Proceedings of the National Academy of Sciences of the USA}},
     16143  volume = {{98}},
     16144  author = {Heaton, Richard J. and Peterson, Alexander W. and Georgiadis, Rosina M.}
     16145}
     16146@article{Gobush1972,
     16147  number = {{7}},
     16148  year = {1972},
     16149  title = {{Statistical Mechanics of Wormlike Chains. I. Asymptotic Behavior}},
     16150  pages = {{2839-2843}},
     16151  journal = {{The Journal of Chemical Physics}},
     16152  volume = {{57}},
     16153  author = {Gobush, William and Yamakawa, Hiromi and Stockmayer, W. H. and Magee, W. S.}
     16154}
     16155@article{Henderson2001,
     16156  number = {{4}},
     16157  year = {2001},
     16158  title = {{Exploring the Confidence Interval for a Binomial Parameter in a First Course in Statistical Computing}},
     16159  pages = {{337-344}},
     16160  journal = {{The American Statistician}},
     16161  volume = {{55}},
     16162  author = {Henderson, Michael and Meyer, Mary C.}
     16163}
     16164@article{Winkler1994,
     16165  number = {{9}},
     16166  year = {1994},
     16167  title = {{Models and equilibrium properties of stiff molecular chains}},
     16168  pages = {{8119-8129}},
     16169  journal = {{journal of Chemical Physics}},
     16170  volume = {{101}},
     16171  author = {Winkler, Roland G. and Reineker, Peter and Harnau, Ludger}
     16172}
     16173@article{William1972,
     16174  number = {{7}},
     16175  year = {1972},
     16176  title = {{Statistical Mechanics of Wormlike Chains. I. Asymptotic Behavior}},
     16177  pages = {{2839-2843}},
     16178  journal = {{The Journal of Chemical Physics}},
     16179  volume = {{57}},
     16180  author = {William, Gobush and Hiromi, Yamakawa and Stockmayer, W. H. and Magee, W. S.}
     16181}
     16182@article{Peterlinz1997,
     16183  year = {1997},
     16184  title = {{Observation of Hybridization and Dehybridization of Thiol-Tethered DNA Using Two-Color Surface Plasmon Resonance Spectroscopy}},
     16185  pages = {{3401-3402}},
     16186  journal = {{Journal of the American Chemical Society}},
     16187  volume = {{119}},
     16188  author = {Peterlinz, Kevin A. and Georgiadis, Rosina M. and Herne, Tonya M. and Tarlov, Michael J.}
     16189}
     16190@article{Morriss2010,
     16191  number = {{3}},
     16192  year = {2010},
     16193  title = {{A systematically coarse-grained model for DNA and its predictions for persistence length, stacking, twist, and chirality}},
     16194  pages = {{035105}},
     16195  journal = {{The Journal of Chemical Physics}},
     16196  volume = {{132}},
     16197  author = {Morriss-Andrews, Alex and Rottler, Joerg and Plotkin, Steven S.}
     16198}
     16199@article{Chandrasekhar1943,
     16200  number = {{1}},
     16201  year = {1943},
     16202  title = {{Stochastic Problems in Physics and Astronomy}},
     16203  pages = {{2-87}},
     16204  journal = {{Revieuws of Modern Physics}},
     16205  volume = {{15}},
     16206  author = {Chandrasekhar, S.}
     16207}
     16208@inproceedings{Ram2005,
     16209  series = {{Proceedings of SPIE}},
     16210  year = {2005},
     16211  title = {{How accurately can a single molecule be localized in three dimensions using a fluorescence microscope?}},
     16212  booktitle = {{Imaging, Manipulation and Analysis of Biomolecule and Cells: Fundamentals and Applications III}},
     16213  pages = {426-435},
     16214  volume = {{5699}},
     16215  author = {Ram, Sripad and Ward, E. Sally and Ober, Raimond J.}
     16216}
     16217@book{Papoulis1991,
     16218  series = {{McGraw-Hill series in electrical engineering, Communications and signal processing}},
     16219  edition = {{Third edition}},
     16220  year = {1991},
     16221  title = {{Probability, random variables, and stochastic processes}},
     16222  address = {{Singapore}},
     16223  publisher = {{McGraw-Hill}},
     16224  author = {Papoulis, Athanasios}
     16225}
     16226@inproceedings{Ram2007,
     16227  year = {2007},
     16228  title = {{A novel approach to determining the three-dimensional location of microscopic objects with applications to 3D particle tracking}},
     16229  booktitle = {{Three-Dimensional and Multidimensional Microscopy: Image Acquisition and Processing XIV}},
     16230  pages = {64430D},
     16231  editor = {Conchello, Jose-Angel and Cogswell, Carol J. and Wilson, Tony},
     16232  volume = {{6443}},
     16233  publisher = {{Proceedings of SPIE}},
     16234  author = {Ram, Sripad and Chao, Jerry and Prabhat, Prashant and Ward, E. Sally and Ober, Raimond J.}
     16235}
     16236@article{Wu2005,
     16237  year = {2005},
     16238  title = {{Three-dimensional fluorescent particle tracking at micron-scale using a single camera}},
     16239  pages = {{461-465}},
     16240  journal = {{Experiments in Fluids}},
     16241  volume = {{38}},
     16242  author = {Wu, Mingming and Roberts, John W. and Buckley, Mark}
     16243}
     16244@article{Maier2000,
     16245  number = {{22}},
     16246  year = {2000},
     16247  title = {{Replication by a single DNA polymerase of a stretched single-stranded DNA}},
     16248  pages = {{12002-12007}},
     16249  journal = {{Proceedings of the National Academy of Sciences of the USA}},
     16250  volume = {{97}},
     16251  author = {Maier, Berenike and Bensimon, David and Croquette, Vincent}
     16252}
     16253@misc{Odijk2005,
     16254  month = {August 4, 2005},
     16255  year = {2005},
     16256  title = {{Note on DNA grafted to a surface (experiments Heidi Dietrich, TU Delft)}},
     16257  author = {Odijk, Theo}
     16258}
     16259@article{Zimm1956,
     16260  number = {{2}},
     16261  year = {1956},
     16262  title = {{Dynamics of Polymer Molecules in Dilute Solution: Viscoelasticity, Flow Birefringence and Dielectric Loss}},
     16263  pages = {{269-278}},
     16264  journal = {{The Journal of Chemical Physics}},
     16265  volume = {{24}},
     16266  author = {Zimm, Bruno H.}
     16267}
     16268@article{Sadr2007,
     16269  year = {2007},
     16270  title = {{Diffusion-induced bias in near-wall velocimetry}},
     16271  pages = {{443-456}},
     16272  journal = {{Journal of Fluid Mechanics}},
     16273  volume = {{577}},
     16274  author = {Sadr, Reza and Hohenegger, Christel and Li, Haifeng and Mucha, Peter J. and Yoda, Minami}
     16275}
     16276@article{Qian2000b,
     16277  number = {{1}},
     16278  year = {2000},
     16279  title = {{Single-Particle Tracking: Brownian Dynamics of Viscoelastic Materials}},
     16280  pages = {{137-143}},
     16281  journal = {{Biophysical Journal}},
     16282  volume = {{79}},
     16283  author = {Qian, Hong}
     16284}
     16285@article{Pirrung2002,
     16286  number = {{8}},
     16287  year = {2002},
     16288  title = {{How to Make a DNA Chip}},
     16289  pages = {{1276-1289}},
     16290  journal = {{Angewandte Chemie International Edition}},
     16291  volume = {{41}},
     16292  author = {Pirrung, Michael C.}
     16293}
     16294@article{Marko2003,
     16295  number = {{3}},
     16296  year = {2003},
     16297  title = {{The micromechanics of DNA}},
     16298  journal = {{Physics World}},
     16299  volume = {{16}},
     16300  author = {Marko, John F. and Cocco, Simona}
     16301}
     16302@article{Qian2000a,
     16303  number = {{4}},
     16304  year = {2000},
     16305  title = {{A mathematical analysis for the Brownian dynamics of a DNA tether}},
     16306  pages = {{331-340}},
     16307  journal = {{Journal of Mathematical Biology}},
     16308  volume = {{41}},
     16309  author = {Qian, Hong}
     16310}
     16311@misc{Marko2005,
     16312  month = {June 2, 2005},
     16313  year = {2005},
     16314  title = {{Introduction to Single-DNA Micromechanics}},
     16315  pages = {63},
     16316  publisher = {{Department of Physics, University of Illinois at Chicago}},
     16317  author = {Marko, J.F.}
     16318}
     16319@article{Schaefer1980,
     16320  number = {{5}},
     16321  year = {1980},
     16322  title = {{Dynamics of Semiflexible Polymers in Solution}},
     16323  pages = {{1280-1289}},
     16324  journal = {{Macromolecules}},
     16325  volume = {{13}},
     16326  author = {Schaefer, D.W. and Joanny, J.F. and Pincus, P.}
     16327}
     16328@article{Zurla2006,
     16329  year = {2006},
     16330  title = {{Novel tethered particle motion analysis of CI protein-mediated DNA looping in the regulation of bacteriophage lambda}},
     16331  pages = {{S225-S234}},
     16332  journal = {{Journal of Physics: Condensed Matter}},
     16333  volume = {{18}},
     16334  author = {Zurla, C. and Franzini, A. and Galli, G. and Dunlap, D. D. and Lewis, D. E. A. and Adhya, S. and Finzi, L.}
     16335}
     16336@article{Prabhat2007,
     16337  number = {{14}},
     16338  year = {2007},
     16339  title = {{Elucidation of intracellular recycling pathways leading to exocytosis of the Fc receptor, FcRn, by using multifocal plane microscopy}},
     16340  pages = {{5889-5894}},
     16341  journal = {{Proceedings of the National Academy of Sciences of the USA}},
     16342  volume = {{104}},
     16343  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}
     16344}
     16345@inproceedings{Prabhat2006,
     16346  year = {2006},
     16347  title = {{Simultaneous imaging of several focal planes in fluorescence microscopy for the study of cellular dynamics in 3D}},
     16348  booktitle = {{Three-Dimensional and Multidimensional Microscopy: Image Acquisition and Processing XIII}},
     16349  pages = {60900L},
     16350  editor = {Conchello, Jose-Angel and Cogswell, Carol J. and Wilson, Tony},
     16351  volume = {{6090}},
     16352  publisher = {{Proceedings of SPIE}},
     16353  author = {Prabhat, Prashant and Ram, Sripad and Ward, E. Sally and Ober, Raimond J.}
     16354}
     16355@article{Marko1994,
     16356  number = {{5171}},
     16357  year = {1994},
     16358  title = {{Fluctuations and Supercoiling of DNA}},
     16359  pages = {{506-508}},
     16360  journal = {{Science}},
     16361  volume = {{265}},
     16362  author = {Marko, John F. and Siggia, Eric D.}
     16363}
     16364@article{Marko1995,
     16365  number = {{26}},
     16366  year = {1995},
     16367  title = {{Stretching DNA}},
     16368  pages = {{8759-8770}},
     16369  journal = {{Macromolecules}},
     16370  volume = {{28}},
     16371  author = {Marko, John F. and Siggia, Eric D.}
     16372}
     16373@article{Winkler1992,
     16374  number = {{24}},
     16375  year = {1992},
     16376  title = {{Finitie Size Distribution and Partition Functions of Gaussian Chains: Maximum Entropy Approach}},
     16377  pages = {{6891-6896}},
     16378  journal = {{Macromolecules}},
     16379  volume = {{25}},
     16380  author = {Winkler, R.G. and Reineker, P.}
     16381}
     16382@article{Berciaud2005,
     16383  number = {{3}},
     16384  year = {2005},
     16385  title = {{Observation of Intrinsic Size Effects in the Optical Response of Individual Gold Nanoparticles}},
     16386  pages = {{515-518}},
     16387  journal = {{Nano Letters}},
     16388  volume = {{5}},
     16389  author = {Berciaud, St\\\'ephane and Cognet, Laurent and Tamarat, Philippe and Lounis, Brahim}
     16390}
     16391@article{Lahtinen2001,
     16392  year = {2001},
     16393  title = {{Diffusion of hard disks and rodlike molecules on surfaces}},
     16394  journal = {{Physical Review E}},
     16395  volume = {{64}},
     16396  author = {Lahtinen, J.M. and Hjelt, T. and Ala-Nissila, T. and Chvoj, Z.}
     16397}
     16398@article{Wong2006,
     16399  number = {{25}},
     16400  year = {2006},
     16401  title = {{The effect of integration time on fluctuation measurements: calibrating an optical trap in the presence of motion blur}},
     16402  pages = {{12517-12531}},
     16403  journal = {{Optics Express}},
     16404  volume = {{14}},
     16405  author = {Wong, Wesley P. and Halvorsen, Ken}
     16406}
     16407@article{Perkins1994,
     16408  year = {1994},
     16409  title = {{Relaxation of a Single DNA Molecule Observed by Optical Microscopy}},
     16410  pages = {{822-826}},
     16411  journal = {{Science}},
     16412  volume = {{264}},
     16413  author = {Perkins, Thomas T. and Quake, Stephern R. and Smith, Douglas E. and Chu, Steven}
     16414}
     16415@article{Lu2002,
     16416  year = {2002},
     16417  title = {{DNA Persistencde Length Revisited}},
     16418  pages = {{261-275}},
     16419  journal = {{Biopolymers}},
     16420  volume = {{61}},
     16421  author = {Lu, Yongjun and Weers, Brock and Stellwagen, Nancy C.}
     16422}
     16423@article{Laurens2009,
     16424  year = {2009},
     16425  title = {{Dissecting protein-induced DNA looping dynamics in real time}},
     16426  journal = {{Nucleic Acids Research}},
     16427  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.}
     16428}
     16429@article{Yguerabide1998b,
     16430  year = {1998},
     16431  title = {{Light-Scattering Submicroscopic Particles as Highly Fluorescent Analogs and Their Use as Tracer Labels in Clinical and Biological Applications. II. Experimental Characterization}},
     16432  pages = {{157-176}},
     16433  journal = {{Analytical Biochemistry}},
     16434  volume = {{262}},
     16435  author = {Yguerabide, Juan and Yguerabide, Evangelina E.}
     16436}
     16437@article{Capitanio2004,
     16438  year = {2004},
     16439  title = {{Exploring Molecular Motors and Switches at the Single-Molecule Level}},
     16440  pages = {{194-204}},
     16441  journal = {{Microscopy Research and Technique}},
     16442  volume = {{65}},
     16443  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.}
     16444}
     16445@article{Sheppard2004,
     16446  number = {{22}},
     16447  year = {2004},
     16448  title = {{Annular pupils, radial polarization, and superresolution}},
     16449  pages = {{4322-4327}},
     16450  journal = {{Applied Optics}},
     16451  volume = {{43}},
     16452  author = {Sheppard, Colin J.R.}
     16453}
     16454@article{Zhu2006,
     16455  number = {{5}},
     16456  year = {2006},
     16457  title = {{Direct Numerical Simulation of Single-Molecule DNA by Cable Dynamics}},
     16458  pages = {{1078-1087}},
     16459  journal = {{Journal of Microelectromechanical Systems}},
     16460  volume = {{15}},
     16461  author = {Zhu, Qiang and Zeng, Jun and Triantafyllou, Michael S. and Yue, Dick K.P.}
     16462}
     16463@article{Strick1998,
     16464  year = {1998},
     16465  title = {{Behavior of Supercoiled DNA}},
     16466  pages = {{2016-2028}},
     16467  journal = {{Biophysical Journal}},
     16468  volume = {{74}},
     16469  author = {Strick, T.R. and Allemand, J.-F. and Bensimon, D. and Croquette, V.}
     16470}
     16471@article{Pouget2004,
     16472  number = {{9}},
     16473  year = {2004},
     16474  title = {{Single-particle tracking for DNA tether length monitoring}},
     16475  journal = {{Nucleic Acids Research}},
     16476  volume = {{32}},
     16477  author = {Pouget, Noelle and Dennis, Cynthia and Turlan, Catherine and Grigoriev, Mikhail and Chandler, Michael and Salome, Laurence}
     16478}
     16479@article{Saito1967,
     16480  number = {{1}},
     16481  year = {1967},
     16482  title = {{The Statistical Mechanical Theory of Stiff Chains}},
     16483  pages = {{219-226}},
     16484  journal = {{Journal of the Physical Society of Japan}},
     16485  volume = {{22}},
     16486  author = {Saito, Nobuhiko and Takahashi, Kunihiko and Yunoki, Yasuo}
     16487}
     16488@article{Smith1996,
     16489  number = {{5250}},
     16490  year = {1996},
     16491  title = {{Overstretching B-DNA: The Elastic Response of Individual Double-Stranded and Single-Stranded DNA Molecules}},
     16492  pages = {{795-799}},
     16493  journal = {{Science}},
     16494  volume = {{271}},
     16495  author = {Smith, Steven B. and Cui, Yujia and Bustamante, Carlos}
     16496}
     16497@article{Roeffaers2007,
     16498  number = {{31}},
     16499  year = {2007},
     16500  title = {{Single-molecule fluorescence spectroscopy in (bio)catalysis}},
     16501  pages = {{12603-12609}},
     16502  journal = {{Proceedings of the National Academy of Sciences of the USA}},
     16503  volume = {{104}},
     16504  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}
     16505}
     16506@book{Pluta1989,
     16507  year = {1989},
     16508  title = {{Advanced Light Microscopy}},
     16509  volume = {{2: Specialized Methods}},
     16510  address = {{Amsterdam}},
     16511  publisher = {{Elsevier}},
     16512  author = {Pluta, Maksymilian}
     16513}
     16514@book{Pluta1988,
     16515  year = {1988},
     16516  title = {{Advanced Light Microscopy}},
     16517  volume = {{1: Principles and Basic Properties}},
     16518  address = {{Amsterdam}},
     16519  publisher = {{Elsevier}},
     16520  author = {Pluta, Maksymilian}
     16521}
     16522@article{Broek2006,
     16523  number = {{1}},
     16524  year = {2006},
     16525  title = {{Real-time observation of DNA looping dynamics of Type IIE restriction enzymes NaeI and NarI}},
     16526  pages = {{167-174}},
     16527  journal = {{Nucleic Acids Research}},
     16528  volume = {{34}},
     16529  author = {Broek, Bram van den and Vanzi, Francesco and Normanno, Davide and Pavone, Francesco S. and Wuite, Gijs J. L.}
     16530}
     16531@article{Braslavsky2003,
     16532  number = {{7}},
     16533  year = {2003},
     16534  title = {{Sequence Information can be Obtained from Single DNA Molecules}},
     16535  pages = {{3960-3964}},
     16536  journal = {{Proceedings of the National Academy of Sciences of the USA}},
     16537  volume = {{100}},
     16538  author = {Braslavsky, Ido and Hebert, Benedict and Kartalov, Emil and Quake, Stephern R.}
     16539}
     16540@article{Ariel2003,
     16541  number = {{1}},
     16542  year = {2003},
     16543  title = {{Persistence length of a strongly charged rodlike polyelectrolyte in the presence of salt}},
     16544  pages = {{011805-1-011805-11}},
     16545  journal = {{Physical Review E}},
     16546  volume = {{67}},
     16547  author = {Ariel, Gil and Andelman, David}
     16548}
     16549@article{Yamakawa1972,
     16550  number = {{7}},
     16551  year = {1972},
     16552  title = {{Statistical Mechanics of Wormlike Chains. II. Excluded Volume Effects}},
     16553  pages = {{2843-2854}},
     16554  journal = {{The Journal of Chemical Physics}},
     16555  volume = {{57}},
     16556  author = {Yamakawa, Hiromi and Stockmayer, W. H.}
     16557}
     16558@article{Davidson1995,
     16559  year = {1995},
     16560  title = {{Arrays of Uniform Latex Spheres as Test Objects in Optical Microscopy}},
     16561  pages = {{173-178}},
     16562  journal = {{Particle and Particle Systems Characterization}},
     16563  volume = {{12}},
     16564  author = {Davidson, John A.}
     16565}
     16566@article{Huisken2004,
     16567  number = {{5686}},
     16568  year = {2004},
     16569  title = {{Optical Sectioning Deep Inside Live Embryos by Selective Plane Illumination Microscopy}},
     16570  pages = {{1007-1009}},
     16571  journal = {{Science}},
     16572  volume = {{305}},
     16573  author = {Huisken, Jan and Swoger, Jim and Del Bene, Filippo and Wittbrodt, Joachim and Stelzer, Ernst H. K.}
     16574}
     16575@article{Goldman1967,
     16576  number = {{4}},
     16577  year = {1967},
     16578  title = {{Slow viscous motion of a sphere parallel to a plane wall - I Motion through a quiescent fluid}},
     16579  pages = {{637-651}},
     16580  journal = {{Chemical Engineering Science}},
     16581  volume = {{22}},
     16582  author = {Goldman, A.J. and Cox, R.G. and Brenner, H.}
     16583}
     16584@article{Maher2007,
     16585  year = {2007},
     16586  title = {{Spring theory}},
     16587  pages = {{984-986}},
     16588  journal = {{Nature}},
     16589  volume = {{448}},
     16590  author = {Maher, Brendan}
     16591}
     16592@article{Cui2008,
     16593  number = {{31}},
     16594  year = {2008},
     16595  title = {{Lensless high-resolution on-chip optrofluidic microscopes for Caenorhabditis elegans and cell imaging}},
     16596  pages = {{10670-10675}},
     16597  journal = {{Proceedings of the National Academy of Sciences of the USA}},
     16598  volume = {{105}},
     16599  author = {Cui, Xiquan and Lee, Lap Man and Heng, Xin and Zhong, Weiwei and Sternberg, Paul W. and Psaltis, Demetri and Yang, Changhuei}
     16600}
     16601@article{Hagerman1988,
     16602  year = {1988},
     16603  title = {{Flexibility of DNA}},
     16604  pages = {{265-286}},
     16605  journal = {{Annual Review of Biophysics and BioEngineering}},
     16606  volume = {{17}},
     16607  author = {Hagerman, P.J.}
     16608}
     16609@article{Vanzi2006,
     16610  number = {{12}},
     16611  year = {2006},
     16612  title = {{Lac repressor hinge flexibility and DNA looping: single molecule kinetics by tethered particle motion}},
     16613  pages = {{3409-3420}},
     16614  journal = {{Nucleic Acids Research}},
     16615  volume = {{34}},
     16616  author = {Vanzi, Francesco and Broggio, Chiara and Sacconi, Leonardo and Pavone, Francesco Saverio}
     16617}
     16618@article{Bronstein2009,
     16619  number = {{1}},
     16620  year = {2009},
     16621  title = {{Transient Anomalous Diffusion of Telomeres in the Nucleus of Mammalian Cells}},
     16622  pages = {{018102}},
     16623  journal = {{Physical Review Letters}},
     16624  volume = {{103}},
     16625  author = {Bronstein, I. and Israel, Y. and Kepten, E. and Mai, S. and Shav-Tal, Y. and Barkai, E. and Garini, Y.}
     16626}
     16627@article{Bawendi1985,
     16628  number = {{5}},
     16629  year = {1985},
     16630  title = {{A Wiener integral model for stiff polymer chains}},
     16631  pages = {{2491}},
     16632  journal = {{Journal of Chemical Physics}},
     16633  volume = {{83}},
     16634  author = {Bawendi, M.G. and Freed, Karl F.}
     16635}
     16636@article{Martin2002,
     16637  number = {{4}},
     16638  year = {2002},
     16639  title = {{Apparent Subdiffusion Inherent to Single Particle Tracking}},
     16640  pages = {{2109-2117}},
     16641  journal = {{Biophysical Journal}},
     16642  volume = {{83}},
     16643  author = {Martin, Douglas S. and Forstner, Martin B. and K\\\"as, Josef A.}
     16644}
     16645@article{Savelkoul2006,
     16646  number = {{1}},
     16647  year = {2006},
     16648  title = {{Detection of Mycobacterium tuberculosis complex with Real Time PCR: Comparison of different primer-probe sets based on the IS6110 element}},
     16649  pages = {{177-180}},
     16650  journal = {{Journal of Microbiological Methods}},
     16651  volume = {{66}},
     16652  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.}
     16653}
     16654@article{Bustamante2000,
     16655  number = {{3}},
     16656  year = {2000},
     16657  title = {{Single-molecule studies of DNA mechanics}},
     16658  pages = {{279-285}},
     16659  journal = {{Current Opinion in Structural Biology}},
     16660  volume = {{10}},
     16661  author = {Bustamante, Carlos and Smith, Steven B. and Liphardt, Jan and Smith, Doug}
     16662}
     16663@article{Bustamante2003,
     16664  year = {2003},
     16665  title = {{Ten years of tension: single-molecule DNA mechanics}},
     16666  pages = {{423-427}},
     16667  journal = {{Nature}},
     16668  volume = {{421}},
     16669  author = {Bustamante, Carlos and Bryant, Zev and Smith, Steven B.}
     16670}
     16671@article{Holtzer2007,
     16672  year = {2007},
     16673  title = {Nanometric three-dimensional tracking of individual quantom dots in cells},
     16674  pages = {053902},
     16675  journal = { Applied Physics Letters},
     16676  volume = {90},
     16677  author = {Holtzer, L. and Meckel, T. and Schmidt, T.}
     16678}
     16679@article{Huang2008,
     16680  year = {2008},
     16681  title = {Three-Dimensional Super-Resolution Imaging by Stochastic Optical Reconstruction Microscopy},
     16682  pages = {810-813},
     16683  journal = {Science},
     16684  volume = {319},
     16685  author = {Huang, B. and Wang, W. and Bates, M. and Zhuang, X.}
     16686}
     16687@article{Lindner2009,
     16688  year = {2009},
     16689  title = {{Studies of Single Molecules in their Natural Form}},
     16690  pages = {{283-291}},
     16691  journal = {{Israel Journal of Chemistry}},
     16692  volume = {{49}},
     16693  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}
     16694}
     16695@article{Wilhelm1996,
     16696  number = {{12}},
     16697  year = {1996},
     16698  title = {{Radial Distribution Function of Semiflexible Polymers}},
     16699  pages = {{2581}},
     16700  journal = {{Physical Review Letters}},
     16701  volume = {{77}},
     16702  author = {Wilhelm, Jan and Frey, Erwin}
     16703}
     16704@article{Clercx1992,
     16705  number = {{4}},
     16706  year = {1992},
     16707  title = {{Brownian particles in shear flow and harmonic potentials: A study of long-time tails}},
     16708  pages = {{1942-1950}},
     16709  journal = {{Physical Review A}},
     16710  volume = {{46}},
     16711  author = {Clercx, H.J.H. and Schram, P.P.J.M.}
     16712}
     16713@inproceedings{Subotic2004,
     16714  year = {2004},
     16715  title = {{On the Feasability of Axial Tracking of a Fluorescent Nano-Particle Using a Defocusing Model}},
     16716  booktitle = {{Proceedings IEEE International Symposium on Biomedical Imaging: From Macro to Nano}},
     16717  pages = {1231-1234},
     16718  volume = {{2}},
     16719  author = {Subotic, Nadja and van de Ville, Dimitri and Unser, Michael}
     16720}
     16721@article{Ebenstein2009,
     16722  number = {{4}},
     16723  year = {2009},
     16724  title = {Lighting Up Individual {DNA} Binding Proteins with Quantum Dots},
     16725  pages = {{1598-1603}},
     16726  journal = {{Nano Letters}},
     16727  volume = {{9}},
     16728  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.}
     16729}
     16730@article{Harlepp2004,
     16731  number = {{17}},
     16732  year = {2004},
     16733  title = {{Subnanometric measurements of evanescent wave penetration depth using total internal reflection microscopy combined with fluorescent correlation spectroscopy}},
     16734  journal = {{Applied Physics Letters}},
     16735  volume = {{85}},
     16736  author = {Harlepp, S. and Robert, J. and Darnton, N.C. and Chateney, D.}
     16737}
     16738@inproceedings{Nguyen2000,
     16739  year = {2000},
     16740  title = {{Magnification Corrected Optical Image Splitting for Simultaneous Multiplanar Acquisition}},
     16741  booktitle = {{Optical Diagnostics of Living Cells III}},
     16742  pages = {31-40},
     16743  editor = {Farkas, Daniel L. and Leif, Robert C.},
     16744  volume = {{3921}},
     16745  publisher = {{Proceedings of SPIE}},
     16746  author = {Nguyen, Lam K. and Bravo-Zanoguera, Miguel and Kellner, Albert L. and Price, Jeffrey H.}
     16747}
     16748@article{Braslavsky2001,
     16749  number = {{31}},
     16750  year = {2001},
     16751  title = {{Objective-type dark-field illumination for scattering from microbeads}},
     16752  pages = {{5650-5667}},
     16753  journal = {{Applied Optics}},
     16754  volume = {{40}},
     16755  author = {Braslavsky, Ido and Amit, Roee and Jaffar Ali, B.M. and Gileadi, Opher and Oppenheim, Amos and Stavans, Joel}
     16756}
     16757@article{Stepanow2004,
     16758  number = {{4}},
     16759  year = {2004},
     16760  title = {{Statistical mechanics of semiflexible polymers}},
     16761  pages = {{499-512}},
     16762  journal = {{The European Physical Journal B}},
     16763  volume = {{39}},
     16764  author = {Stepanow, S.}
     16765}
     16766@article{Gelles1988,
     16767  number = {{6155}},
     16768  year = {1988},
     16769  title = {{Tracking kinesin-driven movements with nanometric-scale precision}},
     16770  pages = {{450-453}},
     16771  journal = {{Nature}},
     16772  volume = {{331}},
     16773  author = {Gelles, Jeff and Schnapp, Bruce J. and Sheetz, Michael P.}
     16774}
     16775@book{Rubinstein2006,
     16776  year = {2006},
     16777  title = {{Polymer Physics}},
     16778  address = {{New York}},
     16779  publisher = {{Oxford University Press Inc.}},
     16780  author = {Rubinstein, Michael and Colby, Ralph H.}
     16781}
     16782@article{Seol2007,
     16783  number = {{12}},
     16784  year = {2007},
     16785  title = {{Elasticity of Short DNA Molecules: Theory and Experiment for Contour Lengths of 0.6-7 um}},
     16786  pages = {{4360-4373}},
     16787  journal = {{Biophysical Journal}},
     16788  volume = {{93}},
     16789  author = {Seol, Yeonee and Li, Jinyu and Nelson, Philip C. and Perkins, Thomas T. and Betterton, M.D.}
     16790}
     16791@article{Cohen2007,
     16792  number = {{31}},
     16793  year = {2007},
     16794  title = {{Principle-component analysis of shape fluctuations of single DNA molecules}},
     16795  pages = {{12622-12627}},
     16796  journal = {{Proceedings of the National Academy of Sciences of the USA}},
     16797  volume = {{104}},
     16798  author = {Cohen, Adam E. and Moerner, W.E.}
     16799}
     16800@article{Saxton2007,
     16801  number = {{4}},
     16802  year = {2007},
     16803  title = {{A Biological Interpretation of Transient Anomalous Subdiffusion. I. Qualitative Model}},
     16804  pages = {{1178-1191}},
     16805  journal = {{Biophysical Journal}},
     16806  volume = {{92}},
     16807  author = {Saxton, M.J.}
     16808}
     16809@article{Otto1994,
     16810  number = {{3}},
     16811  year = {1994},
     16812  title = {{Persistence lengths of semiflexible chains - Methods and approximations}},
     16813  pages = {{543-555}},
     16814  journal = {{Macromolecular Theory and Simulations}},
     16815  volume = {{3}},
     16816  author = {Otto, Matthias and Eckert, Jochen and Vilgis, Thomas A.}
     16817}
     16818@article{Vennemann2007,
     16819  number = {{3}},
     16820  year = {2007},
     16821  title = {{In vivo whole-field blood velocity measurement techniques}},
     16822  pages = {{495-511}},
     16823  journal = {{Experiments in Fluids}},
     16824  volume = {{42}},
     16825  author = {Vennemann, Peter and Lindken, Ralph and Westerweel, Jerry}
     16826}
     16827@article{Vosch2007,
     16828  number = {{31}},
     16829  year = {2007},
     16830  title = {{Strongly emissive individual DNA-encapsulated Ag nanoclusters as single-molecule fluorophores}},
     16831  pages = {{12616-12621}},
     16832  journal = {{Proceedings of the National Academy of Sciences of the USA}},
     16833  volume = {{104}},
     16834  author = {Vosch, Tom and Antoku, Yasuko and Hsiang, Jung-Cheng and Richards, Chris I. and Gonzalez, Jose I. and Dickson, Robert M.}
     16835}
     16836@article{Galletto2006,
     16837  number = {{7113}},
     16838  year = {2006},
     16839  title = {{Direct observation of individual RecA filaments assembling on single DNA molecules}},
     16840  pages = {{875-878}},
     16841  journal = {{Nature}},
     16842  volume = {{443}},
     16843  author = {Galletto, Roberto and Amitani, Ichiro and Baskin, Ronald J. and Kowalczykowski, Stephen C.}
     16844}
     16845@article{Singh-Zocchi2003,
     16846  number = {{13}},
     16847  year = {2003},
     16848  title = {{Single-molecule detection of DNA hybridization}},
     16849  pages = {{7605-7610}},
     16850  journal = {{Proceedings of the National Academy of Sciences of the USA}},
     16851  volume = {{100}},
     16852  author = {Singh-Zocchi, Mukta and Dixit, Sanhita and Ivanov, Vassili and Zocchi, Giovanni}
     16853}
     16854@article{Frej1993,
     16855  number = {{9}},
     16856  year = {1993},
     16857  title = {{Hindered diffusion of a single sphere very near a wall in a nonuniform force field}},
     16858  pages = {{7552-7564}},
     16859  journal = {{Journal of Chemical Physics}},
     16860  volume = {{98}},
     16861  author = {Frej, Nasser A. and Prieve, Dennis C.}
     16862}
     16863@article{Lagowski1991,
     16864  number = {{2}},
     16865  year = {1991},
     16866  title = {{Stiff chain model-functional integral approach}},
     16867  pages = {{1266-1296}},
     16868  journal = {{Journal of Chemical Physics}},
     16869  volume = {{95}},
     16870  author = {Lagowski, Jolanta B. and Noolandi, Jaan and Nickel, Bernie}
     16871}
     16872@article{Bednar1995,
     16873  number = {{4}},
     16874  year = {1995},
     16875  title = {Determination of {DNA} Persistence Length by Cryo-electron Microscopy. Separation of the Static and Dynamic Contributions to the Apparent Persistence Length of {DNA}},
     16876  pages = {{579-594}},
     16877  journal = {{Journal of Molecular Biology}},
     16878  volume = {{254}},
     16879  author = {Bednar, J. and Furrer, P. and Katritch, V. and Stasiak, A.Z. and Dubochet, J. and Stasiak, A.}
     16880}
     16881@article{McIntosh2009,
     16882  number = {{4}},
     16883  year = {2009},
     16884  title = {{Detailed scaling analysis of low-force polyelectrolyte elasticity}},
     16885  pages = {{041803}},
     16886  journal = {{Physical Review E}},
     16887  volume = {{80}},
     16888  author = {McIntosh, D.B. and Ribeck, N. and Saleh, O.A.}
     16889}
     16890@article{Hyeon2006b,
     16891  number = {{3}},
     16892  year = {2006},
     16893  title = {{Size, shape, and flexibility of RNA structures}},
     16894  pages = {{194905}},
     16895  journal = {{The Journal of Chemical Physics}},
     16896  volume = {{125}},
     16897  author = {Hyeon, Changbong and Dima, Ruxandra I. and Thirumalai, D.}
     16898}
     16899@article{Caarls2011,
     16900  number = {1},
     16901  year = {2011},
     16902  title = {Minimizing light exposure with the programmable array microscope},
     16903  pages = {101-110},
     16904  journal = {Journal of Microscopy},
     16905  volume = {241},
     16906  author = {Caarls, W. and Rieger, B and Vries, A.H.B. de and Arndt-Jovin, D.J. and Jovin, T.M.}
     16907}
     16908@article{Jacobsen2006,
     16909  number = {{1}},
     16910  year = {2006},
     16911  title = {{Interferometric optical detection and tracking of very small gold nanoparticles at a water-glass interface}},
     16912  pages = {{405}},
     16913  journal = {{Optics Express}},
     16914  volume = {{14}},
     16915  author = {Jacobsen, Volker and Stoller, Patrick and Brunner, Christian and Vogel, Viola and Sandoghdar, Vahid}
     16916}
     16917@article{Crut2007,
     16918  number = {{29}},
     16919  year = {2007},
     16920  title = {{Fast dynamics of supercoiled DNA revealed by single-molecule experiments}},
     16921  pages = {{11957-11962}},
     16922  journal = {{Proceedings of the National Academy of Sciences of the USA}},
     16923  volume = {{104}},
     16924  author = {Cut, Aur\\\'elien and Koster, Daniel A. and Seidel, Ralf and Wiggins, Chris H. and Dekker, Nynke H.}
     16925}
     16926@article{Yguerabide1998a,
     16927  year = {1998},
     16928  title = {{Light-Scattering Submicroscopic Particles as Highly Fluorescent Analogs and Their Use as Tracer Labels in Clinical and Biological Applications. I. Theory}},
     16929  pages = {{137-156
     16930 }},
     16931  journal = {{Analytical Biochemistry}},
     16932  volume = {{262}},
     16933  author = {Yguerabide, Juan and Yguerabide, Evangelina E.}
     16934}
     16935@article{Strick1998b,
     16936  number = {{3-4}},
     16937  year = {1998},
     16938  title = {{Physical Approaches to the Study of DNA}},
     16939  pages = {{647-672}},
     16940  journal = {{Journal of Statistical Physics}},
     16941  volume = {{93}},
     16942  author = {Strick, T.R. and Allemand, J.-F. and Croquette, V. and Bensimon, D.}
     16943}
     16944@article{Rechendorff2009,
     16945  number = {{9}},
     16946  year = {2009},
     16947  title = {{Persistence length and scaling properties of single-stranded DNA adsorbed on modified graphite}},
     16948  pages = {{095103}},
     16949  journal = {{Journal of Chemical Physics}},
     16950  volume = {{131}},
     16951  author = {Rechendorff, Kristian and Witz, Guillaume and Adamcik, Jozef and Dietler, Giovanni}
     16952}
     16953@article{Graff2006,
     16954  number = {{1}},
     16955  year = {2006},
     16956  title = {{Resonance Light Scattering (RLS) Detection of Nanoparticle Separations in a Microelectrical Field-Flow Fractionation System}},
     16957  pages = {{8-13}},
     16958  journal = {{IEEE Transactions on Nanotechnology}},
     16959  volume = {{5}},
     16960  author = {Graff, Mason and Frazier, A. Bruno}
     16961}
     16962@article{Kao1994,
     16963  number = {{3}},
     16964  year = {1994},
     16965  title = {{Tracking of single fluorescent particles in three dimensions: use of cylindrical optics to encode particle position}},
     16966  pages = {{1291-1300}},
     16967  journal = {{Biophysical Journal}},
     16968  volume = {{67}},
     16969  author = {Kao, H.P. and Verkman, A.S.}
     16970}
     16971@article{Jo2007,
     16972  number = {{8}},
     16973  year = {2007},
     16974  title = {{A single-molecule barcoding system using nanoslits for DNA analysis}},
     16975  pages = {{2673-2678}},
     16976  journal = {{Proceedings of the National Academy of Sciences of the USA}},
     16977  volume = {{104}},
     16978  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.}
     16979}
     16980@article{Speidel2003,
     16981  number = {{2}},
     16982  year = {2003},
     16983  title = {{Three-dimensional tracking of fluorescent nanoparticles with subnanometer precision by use of off-focus imaging}},
     16984  pages = {{69-71}},
     16985  journal = {{Optics Letters}},
     16986  volume = {{28}},
     16987  author = {Speidel, Michael and Jonas, Alexandr and Florin, Ernst-Ludwig}
     16988}
     16989@article{Pounder2006,
     16990  number = {{3}},
     16991  year = {2006},
     16992  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 }},
     16993  pages = {{217-222}},
     16994  journal = {{Diagnostic Microbiology and Infectious Disease}},
     16995  volume = {{54}},
     16996  author = {Pounder, June I. and Aldous, Wade K. and Woods, Gail L.}
     16997}
     16998@article{Harris1966,
     16999  number = {{7}},
     17000  year = {1966},
     17001  title = {{On Polymer Dynamics}},
     17002  pages = {{2595}},
     17003  journal = {{The Journal of Chemical Physics}},
     17004  volume = {{44}},
     17005  author = {Harris, R.A. and Hearst, J.E.}
     17006}
     17007@article{Willert1992,
     17008  year = {1992},
     17009  title = {{Three-dimensional particle imaging with a single camera}},
     17010  pages = {{353-358}},
     17011  journal = {{Experiments in Fluids}},
     17012  volume = {{12}},
     17013  author = {Willert, C. E. and Gharib, M.}
     17014}
     17015@article{Oberholzer1997,
     17016  number = {21},
     17017  year = {1997},
     17018  title = {Grand canonical Brownian dynamics simulation of colloidal adsorption},
     17019  pages = {9157-9167},
     17020  journal = {Journal of Chemical Physics},
     17021  volume = {107},
     17022  author = {Oberholzer, M.R. and Wagner, N.J. and Lenhoff, Abraham M.}
     17023}
     17024@article{Wiggins2006,
     17025  year = {2006},
     17026  title = {Generalized theory of semiflexible polymers},
     17027  pages = {031906},
     17028  journal = {Physical Review E},
     17029  volume = {73},
     17030  author = {Wiggins, P.A. and Nelson, P.C.}
     17031}
     17032@article{Brenner1961,
     17033  number = {{3-4}},
     17034  year = {1961},
     17035  title = {{The slow motion of a sphere through a viscous fluid towards a plane surface}},
     17036  pages = {{242-251}},
     17037  journal = {{Chemical Engineering Science}},
     17038  volume = {{16}},
     17039  author = {Brenner, Howard}
     17040}
     17041@article{Bhattacharjee1987,
     17042  number = {{1}},
     17043  year = {1987},
     17044  title = {{Statistical mechanics of solutions of semiflexible chains: A path integral formulation}},
     17045  pages = {{411-418}},
     17046  journal = {{the Journal of Chemical Physics}},
     17047  volume = {{86}},
     17048  author = {Bhattacharjee, Somendra M. and Muthukumar, M.}
     17049}
     17050@article{Armani2007,
     17051  year = {2007},
     17052  title = {{Label-Free, Single-Molecule Detection with Optical Microcavities}},
     17053  journal = {{Sciencexpress}},
     17054  author = {Armani, Andrea M. and Kulkarni, Rajan P. and Fraser, Scott E. and Flagan, Richard C. and Vahala, Kerry J.}
     17055}
     17056@article{Hegner1999,
     17057  number = {{18}},
     17058  year = {1999},
     17059  title = {{Polymerization and mechanical properties of single RecA-DNA filaments}},
     17060  pages = {{10109-10114}},
     17061  journal = {{Proceedings of the National Academy of Sciences of the USA}},
     17062  volume = {{96}},
     17063  author = {Hegner, Martin and Smith, Steven B. and Bustamante, Carlos}
     17064}
     17065@article{Zhu2001,
     17066  number = {{1}},
     17067  year = {2001},
     17068  title = {{Protein arrays and microarrays}},
     17069  pages = {{40-45}},
     17070  journal = {{Current Opinion in Chemical Biology}},
     17071  volume = {{5}},
     17072  author = {Zhu, Heng and Snyder, Michael}
     17073}
     17074@article{Wiggins2006b,
     17075  year = {2006},
     17076  title = {{High flexibility of DNA on short length scales probed by atomic force microscopy}},
     17077  pages = {{137-141}},
     17078  journal = {{Nature Nanotechnology}},
     17079  volume = {{1}},
     17080  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.}
     17081}
     17082@article{Zhang2007,
     17083  number = {{10}},
     17084  year = {2007},
     17085  title = {{Gaussian approximations of fluorescence microscope point-spread function models}},
     17086  pages = {{1819-1829}},
     17087  journal = {Applied Optics},
     17088  volume = {{46}},
     17089  author = {Zhang, B. and Zerubia, J. and Olivio-Marin, J.-C.}
     17090}
     17091@article{Scott1979,
     17092  number = {{3}},
     17093  year = {1979},
     17094  title = {{On optimal and data-based histograms}},
     17095  pages = {{605-610}},
     17096  journal = {{Biometrika}},
     17097  volume = {{66}},
     17098  author = {Scott, David W.}
     17099}
     17100@article{Mlodzianoski2009,
     17101  number = {{10}},
     17102  year = {2009},
     17103  title = {Experimental characterization of 3D localization techniques for particle-tracking and super-resolution microscopy},
     17104  pages = {{8264-8277}},
     17105  journal = {{Optics Express}},
     17106  volume = {{17}},
     17107  author = {Mlodzianoski, M.J. and Juette, M.F. and Beane, G.L. and Bewersdorf, J.}
     17108}
     17109@article{Carre2003,
     17110  year = {2003},
     17111  title = {{Molecular interactions between DNA and an aminated glass substrate}},
     17112  pages = {{49-55}},
     17113  journal = {{Journal of Colloid and Interface Science}},
     17114  volume = {{260}},
     17115  author = {Carr\\\'e, Alain and Lacarri\\\`ere, Val\\\'erie and Birch, William}
     17116}
     17117@article{Sage2005,
     17118  number = {9},
     17119  year = {2005},
     17120  title = {Automatic Tracking of Individual Fluorescence Particles: Application to the Study of Chromosome Dynamics},
     17121  pages = {1372-1383},
     17122  journal = {IEEE Transactions on Image Processing},
     17123  volume = {14},
     17124  author = {Sage, D. and Neumann, F.R. and Hediger, F. and Gasser, S.M. and Unser, M.}
     17125}
     17126@article{Dohoney2001,
     17127  year = {2001},
     17128  title = {{Chi-Sequence recognition and DNA translocation by single RecBCD helicase/nuclease molecules}},
     17129  pages = {{370-374}},
     17130  journal = {{Nature}},
     17131  volume = {{409}},
     17132  author = {Dohoney, Kathleen M. and Gelles, Jeff}
     17133}
     17134@article{Saleh2009,
     17135  number = {{6}},
     17136  year = {2009},
     17137  title = {{Nonlinear Low-Force Elasticity of Single-Stranded DNA Molecules}},
     17138  pages = {{068301}},
     17139  journal = {{Physical Review Letters}},
     17140  volume = {{102}},
     17141  author = {Saleh, O.A. and McIntosh, D.B. and Pincus, P. and Ribeck, N.}
     17142}
     17143@article{Moerner2007,
     17144  number = {{31}},
     17145  year = {2007},
     17146  title = {{New directions in single-molecule imaging and analysis}},
     17147  pages = {{12596-12602}},
     17148  journal = {{Proceedings of the National Academy of Sciences of the USA}},
     17149  volume = {{104}},
     17150  author = {Moerner, W.E.}
     17151}
     17152@article{Spakowitz2005,
     17153  year = {2005},
     17154  title = {{End-to-end distance vector distribution with fixed end orientations for the wormlike chain model}},
     17155  journal = {{Physical Review E}},
     17156  volume = {{72}},
     17157  author = {Spakowitz, Andrew J. and Wang, Zhen-Gang}
     17158}
     17159@article{Spakowitz2004,
     17160  year = {2004},
     17161  title = {{Exact Results for a Semiflexible Polymer Chain in an Aligning Field}},
     17162  pages = {{5814-5823}},
     17163  journal = {{Macromolecules}},
     17164  volume = {{37}},
     17165  author = {Spakowitz, Andrew J. and Wang, Zhen-Gang}
     17166}
     17167@article{Spakowitz2006,
     17168  number = {{5}},
     17169  year = {2006},
     17170  title = {{Wormlike chain statistics with twist and fixed ends}},
     17171  pages = {{684-690}},
     17172  journal = {{Europhysics Letters (EPL)}},
     17173  volume = {{73}},
     17174  author = {Spakowitz, A. J.}
     17175}
     17176@article{Wieser2008,
     17177  number = {12},
     17178  year = {2008},
     17179  title = {Versatile Analysis of Single-Molecule Tracking Data by Comprehensive Testing against {Monte Carlo} Simulations},
     17180  pages = {5988-6001},
     17181  journal = {Biophysical Journal},
     17182  volume = {95},
     17183  author = {Wieser, S. and Axmann, M. and {Sch\"utz}, G.J.}
     17184}
     17185@phdthesis{Sarkar2002,
     17186  year = {2002},
     17187  title = {{Theoretical micromechanics of DNA and DNA-protein complexes}},
     17188  school = {{University of Illinois at Chicago}},
     17189  author = {Sarkar, Abhijit}
     17190}
     17191@article{Ha1995,
     17192  number = {{21}},
     17193  year = {1995},
     17194  title = {{A mean-field model for semiflexible chains}},
     17195  pages = {{9408-9412}},
     17196  journal = {{Journal of Chemical Physics}},
     17197  volume = {{103}},
     17198  author = {Ha, B.-Y. and Thirumalai, D.}
     17199}
     17200@misc{Beausang2006,
     17201  month = {October 1, 2006},
     17202  year = {2006},
     17203  title = {{Elementary simulation of tethered Brownian motion}},
     17204  author = {Beausang, John F. and Zurla, Chiara and Sullivan, Luke and Finzi, Laura and Nelson, Philip C.}
     17205}
     17206@article{Beausang2007,
     17207  number = {{6}},
     17208  year = {2007},
     17209  title = {{Elementary simulation of tethered Brownian motion}},
     17210  pages = {{520-523}},
     17211  journal = {{American Journal of Physics}},
     17212  volume = {{75}},
     17213  author = {Beausang, John F. and Zurla, Chiara and Finzi, Laura and Sullivan, Luke and Nelson, Philip C.}
     17214}
     17215@phdthesis{Guasto2008,
     17216  year = {2008},
     17217  title = {{Micro- and Nano-scale Colloidal Dynamics Near Surfaces}},
     17218  school = {{Brown University}},
     17219  author = {Guasto, Jeffrey S.}
     17220}
     17221@misc{Nelson2001,
     17222  year = {2001},
     17223  title = {{Dynamical Theories of Brownian Motion}},
     17224  volume = {Second edition},
     17225  publisher = {{Princeton University Press}},
     17226  author = {Nelson, Edward}
     17227}
     17228@article{Shivashankar1998,
     17229  number = {{3}},
     17230  year = {1998},
     17231  title = {{Backscattering from a tethered bead as a probe of DNA flexibility}},
     17232  pages = {{291-293}},
     17233  journal = {{Applied Physics Letters}},
     17234  volume = {{73}},
     17235  author = {Shivashankar, G.V. and Stolovitzky, G. and Libchaber, A.}
     17236}
     17237@phdthesis{Niu2004,
     17238  year = {2004},
     17239  title = {{A Label-free, Fluorescence Based Assay for Microarray}},
     17240  school = {{Virginia Polytechnic Institute and State University}},
     17241  author = {Niu, Sanjun}
     17242}
     17243@article{Hiraoka1987,
     17244  year = {1987},
     17245  title = {The Use of a Charge-Coupled Device for Quantitative Optical Microscopy of Biological Structures},
     17246  pages = {{36-41}},
     17247  journal = {Science},
     17248  volume = {{238}},
     17249  author = {Hiraoka, Y. and Sedat, J.W. and Agard, D.A.}
     17250}
     17251@article{Yamakawa1976,
     17252  number = {{6}},
     17253  year = {1976},
     17254  title = {{Statistical mechanics of helical wormlike chains. II. Operational method and moments}},
     17255  pages = {{2371-2376}},
     17256  journal = {{The Journal of Chemical Physics}},
     17257  volume = {{65}},
     17258  author = {Yamakawa, Hiromi and Fujii, Motoharu and Shimada, Jiro}
     17259}
     17260@article{Nelson2007,
     17261  year = {2007},
     17262  title = {{Colloidal particle motion as a diagnostic of DNA conformational transitions}},
     17263  journal = {{Current Opinion in Colloid & Interface Science}},
     17264  author = {Nelson, Philip C.}
     17265}
     17266@article{Allemand2003,
     17267  year = {2003},
     17268  title = {{Stretching DNA and RNA to probe their interactions with proteins}},
     17269  pages = {{266-274}},
     17270  journal = {{Current Opinion in Structural Biology}},
     17271  volume = {{13}},
     17272  author = {Allemand, Jean-Francois and Bensimon, David and Croquette, Vincent}
     17273}
     17274@article{Liu2007,
     17275  number = {{12}},
     17276  year = {2007},
     17277  title = {{Quantized plasmon quenching dips nanospectroscopy via plasmon resonance energy transfer}},
     17278  pages = {{1015-1017}},
     17279  journal = {{Nature Methods}},
     17280  volume = {{4}},
     17281  author = {Liu, Gang Logan and Long, Yi-Tao and Choi, Yeonho and Kang, Taewook and Lee, Luke P.}
     17282}
     17283@article{Prieve1990,
     17284  number = {{2}},
     17285  year = {1990},
     17286  title = {{Total Internal Reflection Microscopy: a Tool for Measuring Colloidal Forces}},
     17287  pages = {{396-403}},
     17288  journal = {{Langmuir}},
     17289  volume = {{6}},
     17290  author = {Prieve, Dennis C. and Frej, Nasser A.}
     17291}
     17292@article{Strick1996,
     17293  number = {{5257}},
     17294  year = {1996},
     17295  title = {{The Elasticity of a Single Supercoiled DNA Molecule}},
     17296  pages = {{1835-1837}},
     17297  journal = {{Science}},
     17298  volume = {{271}},
     17299  author = {Strick, T.R. and Allemand, J.-F. and Bensimon, D. and Bensimon, A. and Croquette, V.}
     17300}
     17301@article{Prieve1993,
     17302  number = {{9}},
     17303  year = {1993},
     17304  title = {{Scattering of an evanescent surface wave by a microscopic dielectric sphere}},
     17305  journal = {{Applied Optics}},
     17306  volume = {{32}},
     17307  author = {Prieve, Dennis C. and Walz, John Y.}
     17308}
     17309@article{Montanari2001,
     17310  number = {{10}},
     17311  year = {2001},
     17312  title = {{Hairpin Formation and Elongation of Biomolecules}},
     17313  pages = {{2178-2181}},
     17314  journal = {{Physical Review Letters}},
     17315  volume = {{86}},
     17316  author = {Montanari, Andrea and M\\\'ezard, Marc}
     17317}
     17318@article{Storm2003b,
     17319  number = {{5}},
     17320  year = {2003},
     17321  title = {{Theory of high-force DNA stretching and overstretching}},
     17322  pages = {{051906}},
     17323  journal = {{Physical Review E}},
     17324  volume = {{67}},
     17325  author = {Storm, C. and Nelson, P. C.}
     17326}
     17327@article{Bouchiat1999,
     17328  year = {1999},
     17329  title = {{Estimating the Persistence Length of a Worm-Like Chain Molecule from Force-Extension Measurements}},
     17330  pages = {{409-413}},
     17331  journal = {{Biophysical Journal}},
     17332  volume = {{76}},
     17333  author = {Bouchiat, C. and Wang, M. D. and Allemand, J.-F. and Strick, T. and Block, S. M. and Croquette, V.}
     17334}
     17335@article{Cady2007,
     17336  year = {2007},
     17337  title = {{Optimized linkage and quenching strategies for quantum dot molecular beacons}},
     17338  pages = {{116-124}},
     17339  journal = {{Molecular and Cellular Probes}},
     17340  volume = {{21}},
     17341  author = {Cady, Nathaniel C. and Strickland, Aaron D. and Batt, Carl A.}
     17342}
     17343@article{Fraden1993,
     17344  number = {{4}},
     17345  year = {1993},
     17346  title = {{Angular correlations and the isotropic-nematic phase transition in suspensions of tobacco mosaic virus}},
     17347  pages = {{2816-2838}},
     17348  journal = {{Physical Review E}},
     17349  volume = {{48}},
     17350  author = {Fraden, Seth and Maret, Georg}
     17351}
     17352@article{Bustamante1994,
     17353  number = {{5178}},
     17354  year = {1994},
     17355  title = {{Entropic Elasticity of lambda-Phage DNA}},
     17356  pages = {{1599-1601}},
     17357  journal = {{Science}},
     17358  volume = {{265}},
     17359  author = {Bustamante, C. and Marko, J.F. and Siggia, E.D. and Smith, S.}
     17360}
     17361@article{Rouse1953,
     17362  number = {{7}},
     17363  year = {1953},
     17364  title = {{A Theory of the Linear Viscoelastic Properties of Dilute Solutions of Coiling Polymers}},
     17365  pages = {{1272-1280}},
     17366  journal = {{The Journal of Chemical Physics}},
     17367  volume = {{21}},
     17368  author = {Rouse, Prince E.}
     17369}
     17370@article{Vanzi2003,
     17371  number = {{10}},
     17372  year = {2003},
     17373  title = {{Protein synthesis by single ribosomes}},
     17374  pages = {{1174-1179}},
     17375  journal = {{RNA}},
     17376  volume = {{9}},
     17377  author = {Vanzi, Francesco and Vladimirov, Serguei and Knudsen, Charlotte R. and Goldman, Yale E. and Cooperman, Barry S.}
     17378}
     17379@article{Lambert2006,
     17380  year = {2006},
     17381  title = {{Mg2+-Induced Compaction of Single RNA Molecules Monitored by Tethered Particle Microscopy}},
     17382  pages = {{3672-3685}},
     17383  journal = {{Biophysical Journal}},
     17384  volume = {{90}},
     17385  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.}
     17386}
     17387@article{Kessler2004,
     17388  number = {{2}},
     17389  year = {2004},
     17390  title = {{Distribution functions for filaments under tension}},
     17391  pages = {{1155-1164}},
     17392  journal = {{Journal of Chemical Physics}},
     17393  volume = {{121}},
     17394  author = {Kessler, David A. and Rabin, Yitzhak}
     17395}
     17396@article{Edwards1970,
     17397  year = {1970},
     17398  title = {{Theory of the Single Chain}},
     17399  pages = {{43}},
     17400  journal = {{Discussions of the Faraday Society}},
     17401  volume = {{49}},
     17402  author = {Edwards, S.F.}
     17403}
     17404@article{Bouzigues2008,
     17405  number = {{11}},
     17406  year = {2008},
     17407  title = {{Nanofluidics in the Debye Layer at Hydrophilic and Hydrophobic Surfaces}},
     17408  pages = {{114503}},
     17409  journal = {{Physical Review Letters}},
     17410  volume = {{101}},
     17411  author = {Bouzigues, C. I. and Tabeling, P. and Bocquet, L.}
     17412}
     17413@misc{Odijk2008,
     17414  month = {05 September 2008},
     17415  year = {2008},
     17416  title = {{Private communication}},
     17417  author = {Odijk, Theo}
     17418}
     17419@article{Kirkpatrick2008,
     17420  number = {{1}},
     17421  year = {2008},
     17422  title = {{Performance of a gradient-based shift estimator in a spatially sparse data environment: tracking the sub-pixel motion of fluorescent particles}},
     17423  pages = {{64-72}},
     17424  journal = {{Journal of Microscopy}},
     17425  volume = {{212}},
     17426  author = {Kirkpatrick, S.J. and Duncan, D.D.}
     17427}
     17428@article{Visnapuu2009,
     17429  number = {{10}},
     17430  year = {2009},
     17431  title = {{Single-molecule imaging of DNA curtains reveals intrinsic energy landscapes for nucleosome deposition}},
     17432  pages = {{1056-1062}},
     17433  journal = {{Nature Structural & Molecular Biology}},
     17434  volume = {{16}},
     17435  author = {Visnapuu, Mari-Liis and Greene, Eric C.}
     17436}
     17437@book{Conover1980,
     17438  series = {{Wiley series in probability and mathematical statistics}},
     17439  edition = {{Second edition}},
     17440  year = {1980},
     17441  title = {{Practical Nonparametric Statistics}},
     17442  address = {{New York}},
     17443  publisher = {{Wiley}},
     17444  author = {Conover, W.J.}
     17445}
     17446@article{Snyder1992,
     17447  number = {{5}},
     17448  year = {1992},
     17449  title = {{Deblurring Subject to Nonnegativity Constraints}},
     17450  pages = {{1143-1150}},
     17451  journal = {{IEEE Transactions on Signal Processing}},
     17452  volume = {{40}},
     17453  author = {Snyder, Donald L. and Schulz, Timothy H. and O'Sullivan, Joseph A.}
     17454}
     17455@article{DiMarzio1965b,
     17456  number = {{2}},
     17457  year = {1965},
     17458  title = {{One-Dimensional Model of Polymer Adsorption}},
     17459  journal = {{The Journal of Chemical Physics}},
     17460  volume = {{43}},
     17461  author = {DiMarzio, Edmund A. and McCrackin, Frank L.}
     17462}
     17463@article{DiMarzio1965a,
     17464  number = {{6}},
     17465  year = {1965},
     17466  title = {{Proper Accounting of Conformations of a Polymer Near a Surface}},
     17467  pages = {{2101-2106}},
     17468  journal = {{The Journal of Chemical Physics}},
     17469  volume = {{42}},
     17470  author = {DiMarzio, Edmund A.}
     17471}
     17472@article{Netopilik1990,
     17473  year = {1990},
     17474  title = {{Orientation-dependent rotational diffusion coefficient of rod-like macromolecules in semi-dilute solution}},
     17475  pages = {{172-173}},
     17476  journal = {{Rheologica Acta}},
     17477  volume = {{29}},
     17478  author = {Netopil\\\'{\\\i}k, M.}
     17479}
     17480@article{Hamaker1937,
     17481  number = {{10}},
     17482  year = {1937},
     17483  title = {{The London-Van Der Waals Attraction Between Spherical Particles}},
     17484  pages = {{1058-1072}},
     17485  journal = {{Physica }},
     17486  volume = {{4}},
     17487  author = {Hamaker, H.C.}
     17488}
     17489@article{Cheezum2001,
     17490  number = {{4}},
     17491  year = {2001},
     17492  title = {{Quantitative Comparison of Algorithms for Tracking Single Fluorescent Particles}},
     17493  pages = {{2378-2388}},
     17494  journal = {{Biophysical Journal}},
     17495  volume = {{81}},
     17496  author = {Cheezum, Michael K. and Walker, William F. and Guilford, William H.}
     17497}
     17498@article{Ritchie2005,
     17499  number = {{3}},
     17500  year = {2005},
     17501  title = {{Detection of Non-Brownian Diffusion in the Cell Membrane in Single Molecule Tracking}},
     17502  pages = {{2266-2277}},
     17503  journal = {{Biophysical Journal}},
     17504  volume = {{88}},
     17505  author = {Ritchie, Ken and Sha, Xiao-Yuan and Kondo, Junko and Iwasawa, Kokoro and Fujiwara, Takahiro and Kusumi, Akihiro}
     17506}
     17507@incollection{Han2009,
     17508  series = {{The IMA Volumes in Mathematics and its Applications}},
     17509  year = {2009},
     17510  title = {{Calibration of Tethered Particle Motion Experiments}},
     17511  booktitle = {{Mathematics of DNA Structure, Funcion and Interactions}},
     17512  editor = {Benham, C.J. and Harvey, S. and Olson, W.K. and Sumners, D.W. and Swigon, D.},
     17513  volume = {150},
     17514  publisher = {{Springer}},
     17515  author = {Han, Lin and Lui, Bertrand and Blumberg, Seth and Beausang, John F. and Nelson, Philip C. and Philips, Rob}
     17516}
     17517@article{Towles2009,
     17518  year = {2009},
     17519  title = {{First-principles calculation of DNA looping in tethered particle experiments}},
     17520  pages = {{025001}},
     17521  journal = {{Physical Biology}},
     17522  volume = {{6}},
     17523  author = {Towles, Kevin B. and Beausang, John F. and Garcia, H.G. and Philips, Rob and Nelson, Philip C.}
     17524}
     17525@article{Pralle1999,
     17526  number = {{5}},
     17527  year = {1999},
     17528  title = {{Three-Dimensional High-resolution Particle Tracking for Optical Tweezers by Forward Scattered Light}},
     17529  pages = {{378-386}},
     17530  journal = {{Microscopy Research and Technique}},
     17531  volume = {{44}},
     17532  author = {Pralle, A. and Prummer, M. and Florin, E.-L and Stelzer, E.H.K. and H\\\"orber, J.K.H.}
     17533}
     17534@article{Wrobel2003,
     17535  number = {{12}},
     17536  year = {2003},
     17537  title = {{Optimization of high-density cDNA-microarray protocols by 'design of experiments'}},
     17538  journal = {{Nucleic Acids Research}},
     17539  volume = {{131}},
     17540  author = {Wrobel, Gunnar and Schlingemann, Joerg and Hummerich, Lars and Kramer, Heidi and Lichter, Peter and Hahn, Meinhard}
     17541}
     17542@article{Gibson1989,
     17543  number = {{9}},
     17544  year = {1989},
     17545  title = {{Diffraction by a Circular Aperture as a Model for Three-Dimensional Microscopy}},
     17546  pages = {{1357-1367}},
     17547  journal = {{Journal of the Optical Society of America A}},
     17548  volume = {{6}},
     17549  author = {Gibson, Sarah Frisken and Lanni, Frederick}
     17550}
     17551@article{Destainville2006,
     17552  number = {{2}},
     17553  year = {2006},
     17554  title = {{Quantification and Correction of Systematic Erros Due to Detector Time-Averaging in Single-Molecule Tracking Experiments}},
     17555  pages = {{L17-L19}},
     17556  journal = {{Biophysical Journal}},
     17557  volume = {{90}},
     17558  author = {Destainville, Nicolas and Salom\\\'e, Laurence}
     17559}
     17560@article{Sader1997,
     17561  number = {{2}},
     17562  year = {1997},
     17563  title = {{Accurate Analytic Formulae for the Far Field Effective Potential and Surface Charge Density of a Uniformly Charged Sphere}},
     17564  pages = {{508-510}},
     17565  journal = {{Journal of Colloid and Interface Science}},
     17566  volume = {{188}},
     17567  author = {Sader, John Elie}
     17568}
     17569@article{Durnin1987,
     17570  number = {{15}},
     17571  year = {1987},
     17572  title = {{Diffraction-Free Beams}},
     17573  pages = {{1499-1501}},
     17574  journal = {{Physical Review Letters}},
     17575  volume = {{58}},
     17576  author = {Durnin, J. and Miceli, J.J., Jr. and Eberly, J.H.}
     17577}
     17578@article{Moroz1998,
     17579  year = {1998},
     17580  title = {{Entropic Elasticity of Twist-Storing Polymers}},
     17581  pages = {{6333-6347}},
     17582  journal = {{Macromolecules}},
     17583  volume = {{31}},
     17584  author = {Moroz, J. David and Nelson, Philip}
     17585}
     17586@article{Peters1998,
     17587  number = {{7}},
     17588  year = {1998},
     17589  title = {{Three dimensional single-particle tracking with nanometer resolution}},
     17590  pages = {{2762-2766}},
     17591  journal = {{Review of Scientific Instruments}},
     17592  volume = {{69}},
     17593  author = {Peters, Inge M. and de Grooth, Bart G. and Schins, Juleon M. and Figdor, Carl G. and Greve, Jan}
     17594}
     17595@article{Kessler1991,
     17596  year = {1991},
     17597  title = {{The digoxigenin:anti-digoxigening (DIG) technology - a survey on the concept and realization of a novel bioanalytical indicator system}},
     17598  pages = {{161-205}},
     17599  journal = {{Molecular and Cellular Probes}},
     17600  volume = {{5}},
     17601  author = {Kessler, Christoph}
     17602}
     17603@article{Hyeon2006a,
     17604  number = {{10}},
     17605  year = {2006},
     17606  title = {{Kinetics of interior loop formation in semiflexible chains}},
     17607  pages = {{104905}},
     17608  journal = {{The Journal of Chemical Physics}},
     17609  volume = {{124}},
     17610  author = {Hyeon, Changbong and Thirumalai, D.}
     17611}
     17612@article{Moroz1997,
     17613  number = {{26}},
     17614  year = {1997},
     17615  title = {{Torsional directed walks, entropic elasticity, and DNA twist stiffness}},
     17616  pages = {{14418-14422}},
     17617  journal = {{Proceedings of the National Academy of Sciences of the USA}},
     17618  volume = {{94}},
     17619  author = {Moroz, J. David and Nelson, Philip}
     17620}
     17621@article{Massart2005,
     17622  number = {{4}},
     17623  year = {2005},
     17624  title = {{Visual Presentation of Data by Means of Box Plots}},
     17625  pages = {{215-218}},
     17626  journal = {{LC-GC Europe}},
     17627  volume = {{18}},
     17628  author = {Massart, D.L. and Smeyers-Verbeke, J. and Capron, X. and Schlesier, Karin}
     17629}
     17630@article{Hynes2001,
     17631  number = {3},
     17632  year = {2001},
     17633  title = {The ErbB receptor tyrosine family as signal integrators},
     17634  pages = {151-9},
     17635  journal = {Endocr Relat Cancer},
     17636  volume = {8},
     17637  author = {Hynes, N. E. and Horsch, K. and Olayioye, M. A. and Badache, A.}
     17638}
     17639@article{Michalet2001,
     17640  number = {4},
     17641  year = {2001},
     17642  title = {Properties of fluorescent semiconductor nanocrystals and their application to biological labeling},
     17643  pages = {261-276},
     17644  journal = {Single Molecules},
     17645  volume = {2},
     17646  author = {Michalet, X. and Pinaud, F. and Lacoste, T. D. and Dahan, M. and Bruchez, M. P. and Alivisatos, A. P. and Weiss, S.}
     17647}
     17648@article{Kuno2001,
     17649  number = {2},
     17650  year = {2001},
     17651  title = {"On"/"off" fluorescence intermittency of single semiconductor quantum dots},
     17652  pages = {1028-1040},
     17653  journal = {Journal of Chemical Physics},
     17654  volume = {115},
     17655  author = {Kuno, M. and Fromm, D. P. and Hamann, H. F. and Gallagher, A. and Nesbitt, D. J.}
     17656}
     17657@article{Martinez2003,
     17658  number = {4},
     17659  year = {2003},
     17660  title = {Identification and removal of contaminating fluorescence from commercial and in-house printed DNA microarrays},
     17661  pages = {e18},
     17662  journal = {Nucleic Acids Research},
     17663  volume = {31},
     17664  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.}
     17665}
     17666@article{Stauffer1997,
     17667  number = {6},
     17668  year = {1997},
     17669  title = {Compartmentalized IgE receptor-mediated signal transduction in living cells},
     17670  pages = {1447-54},
     17671  journal = {J Cell Biol},
     17672  volume = {139},
     17673  author = {Stauffer, T. P. and Meyer, T.}
     17674}
     17675@article{Hebert2005,
     17676  number = {5},
     17677  year = {2005},
     17678  title = {Spatiotemporal image correlation Spectroscopy (STICS) theory, verification, and application to protein velocity mapping in living CHO cells},
     17679  pages = {3601-3614},
     17680  journal = {Biophysical Journal},
     17681  volume = {88},
     17682  author = {Hebert, B. and Costantino, S. and Wiseman, P. W.}
     17683}
     17684@article{Pyenta2003,
     17685  year = {2003},
     17686  title = {Lateral diffusion of membrane lipid-anchored probes before and after aggregation of cell surface IgE-receptors},
     17687  pages = {8310-8318},
     17688  journal = {J. Phys. Chem. A},
     17689  volume = {107},
     17690  author = {Pyenta, P. and Schwille, P. and Webb, W. and Holowka, D. and Baird, B.}
     17691}
     17692@misc{CUDA,
     17693  year = {2007},
     17694  title = {Compute Unified Device Architecture (CUDA)},
     17695  note = {{http://www.nvidia.com}},
     17696  author = {NVIDIA}
     17697}
     17698@article{Petersen1993,
     17699  year = {1993},
     17700  title = {Quantitation of membrane receptor distributions by image correlation spectroscopy: concept and application},
     17701  pages = {1135-1146},
     17702  journal = {Biophys. J.},
     17703  volume = {65},
     17704  author = {Petersen, N. and Hoddelius, P.L. and Wiseman, P. and Seger, O. and Magnusson, K.}
     17705}
     17706@article{Hess2006,
     17707  number = {11},
     17708  year = {2006},
     17709  title = {Ultra-high resolution imaging by fluorescence photoactivation localization microscopy},
     17710  pages = {4258-4272},
     17711  journal = {Biophysical Journal},
     17712  volume = {91},
     17713  author = {Hess, S.T. and Girirajan, T.P.K. and Mason, M.D.}
     17714}
     17715@article{Kotula2004,
     17716  year = {2004},
     17717  title = {Automated analysis of SEM X-Ray spectral images: a powerful new microanalysis tool},
     17718  pages = {1-17},
     17719  journal = {Microscopy and Microanalysis },
     17720  volume = {9},
     17721  author = {Kotula, P. G. and Keenan, M. R. and Michael, J. R. }
     17722}
     17723@article{Yarden2001,
     17724  number = {2},
     17725  year = {2001},
     17726  title = {Untangling the ErbB signalling network},
     17727  pages = {127-37},
     17728  journal = {Nat Rev Mol Cell Biol},
     17729  volume = {2},
     17730  author = {Yarden, Y. and Sliwkowski, M. X.}
     17731}
     17732@article{MinGW,
     17733  year = {2008},
     17734  title = {Minimalist GNU for Windows},
     17735  url = {http://www.mingw.org/},
     17736  author = {MinGW}
     17737}
     17738@article{Shroff2008,
     17739  number = {5},
     17740  year = {2008},
     17741  title = {Live-cell photoactivated localization microscopy of nanoscale adhesion dynamics},
     17742  pages = {417-423},
     17743  journal = {Nature Methods},
     17744  volume = {5},
     17745  author = {Shroff, H. and Galbraith, C. G. and Galbraith, J. A. and Betzig, E.}
     17746}
     17747@book{Jain1988,
     17748  year = {1988},
     17749  title = {Algorithms for Clustering Data},
     17750  publisher = {Prentice Hall},
     17751  author = {Jain, A. and Dubes, R.}
     17752}
     17753@article{Grecco2004,
     17754  number = {4-5},
     17755  year = {2004},
     17756  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},
     17757  pages = {169-179},
     17758  journal = {Microscopy Research and Technique},
     17759  volume = {65},
     17760  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.}
     17761}
     17762@article{VanBenthem2002,
     17763  year = {2002},
     17764  title = {Application of equality constraints on variables during alternating least squares procedures},
     17765  pages = {613-622},
     17766  journal = {Journal of Chemometrics},
     17767  volume = {16},
     17768  author = {Van Benthem, M. H. and Keenan, M. R. and Haaland, D. M. }
     17769}
     17770@article{Manley2008,
     17771  number = {2},
     17772  year = {2008},
     17773  title = {High-density mapping of single-molecule trajectories with photoactivated localization microscopy},
     17774  pages = {155-157},
     17775  journal = {Nature Methods},
     17776  volume = {5},
     17777  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.}
     17778}
     17779@article{Wilson2000,
     17780  number = {5},
     17781  year = {2000},
     17782  title = {Observing FcepsilonRI signaling from the inside of the mast cell membrane},
     17783  pages = {1131-1142},
     17784  journal = {Journal of Cell Biology},
     17785  volume = {149},
     17786  author = {Wilson, B. S. and Pfeiffer, J. R. and Oliver, J. M.}
     17787}
     17788@article{Wilson2004,
     17789  number = {6},
     17790  year = {2004},
     17791  title = {Markers for detergent-resistant lipid rafts occupy distinct and dynamic domains in native membranes},
     17792  pages = {2580-2592},
     17793  journal = {Molecular Biology of the Cell},
     17794  volume = {15},
     17795  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.}
     17796}
     17797@article{Timlin2005,
     17798  number = {1},
     17799  year = {2005},
     17800  title = {Hyperspectral microarray scanning: impact on the accuracy and reliability of gene expression data},
     17801  pages = {72},
     17802  journal = {BMC Genomics},
     17803  volume = {6},
     17804  author = {Timlin, J. A. and Haaland, D. M. and Sinclair, M. B. and Aragon, A. D. and Martinez, M. J. and Werner-Washburne, M.}
     17805}
     17806@article{Forney1973,
     17807  number = {3},
     17808  year = {1973},
     17809  title = {Viterbi Algorithm},
     17810  pages = {268-278},
     17811  journal = {Proceedings of the Ieee},
     17812  volume = {61},
     17813  author = {Forney, G. D.}
     17814}
     17815@article{Szent-Gyorgyi2008,
     17816  number = {4},
     17817  year = {2008},
     17818  title = {Fluorogen-activating single-chain antibodies for imaging cell surface proteins (vol 26, pg 235, 2008)},
     17819  pages = {470-470},
     17820  journal = {Nature Biotechnology},
     17821  volume = {26},
     17822  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.}
     17823}
     17824@article{Andrews2008,
     17825  number = {8},
     17826  year = {2008},
     17827  title = {Actin restricts {Fc}$\epsilon${RI} diffusion and facilitates antigen-induced receptor immobilization},
     17828  pages = {955-963},
     17829  journal = {Nature Cell Biology},
     17830  volume = {10},
     17831  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.}
     17832}
     17833@inproceedings{Lidke2007ieee,
     17834  year = {2007},
     17835  title = {Localization fluorescence microscopy using quantum dot blinking},
     17836  booktitle = {4th IEEE International Symposium on Biomedical Imaging},
     17837  pages = {936-939},
     17838  address = {Metro Washington DC, USA. },
     17839  author = {Lidke, K. A. and Heintzmann, R.}
     17840}
     17841@article{Jinschek2010,
     17842  year = {2010},
     17843  title = {Quantitative atomic 3-D imaging of single/double sheet graphene structure},
     17844  journal = {Carbon},
     17845  author = {Jinschek, J.R. and Yucelen, E. and Calderon, H.A. and Freitag, B.}
     17846}
     17847@article{Bates2007,
     17848  number = {5845},
     17849  year = {2007},
     17850  title = {Multicolor super-resolution imaging with photo-switchable fluorescent probes},
     17851  pages = {1749-53},
     17852  journal = {Science},
     17853  volume = {317},
     17854  author = {Bates, M. and Huang, B. and Dempsey, G. T. and Zhuang, X.}
     17855}
     17856@book{Bos2007,
     17857  year = {2007},
     17858  title = {Parameter Estimation for Scientists and Engineers},
     17859  address = {New Jersey},
     17860  publisher = {Wiley \& Sons},
     17861  author = {A. van den Bos}
     17862}
     17863@article{Wolter2009,
     17864  number = {1},
     17865  year = {2010},
     17866  title = {Real-time computation of subdiffraction-resolution fluorescence images},
     17867  pages = {12-22},
     17868  journal = {Journal of Microscopy},
     17869  volume = {237},
     17870  author = {Wolter, S. and Schuttpelz, M. and Tescherepanow, M. and Linde, van de S. and Heilemann, M. and Sauer, M.}
     17871}
     17872@article{Bock2007,
     17873  number = {2},
     17874  year = {2007},
     17875  title = {Two-color far-field fluorescence nanoscopy based on photoswitchable emitters},
     17876  pages = {161-165},
     17877  journal = {Applied Physics B - Lasers and Optics},
     17878  volume = {88},
     17879  author = {Bock, H. and Geisler, C. and Wurm, C. A. and  Middendorff, C. von and Jakobs, S. and {Sch\"onle}, A. and Egner, A. and Hell, S. W. and Eggeling, C.}
     17880}
     17881@article{Rust2006,
     17882  number = {10},
     17883  year = {2006},
     17884  title = {Sub-diffraction-limit imaging by stochastic optical reconstruction microscopy {(STORM)}},
     17885  pages = {793-795},
     17886  journal = {Nature Methods},
     17887  volume = {3},
     17888  author = {Rust, M.J. and Bates, M. and Zhuang, X.W.}
     17889}
     17890@article{Enderlein2006,
     17891  number = {18},
     17892  year = {2006},
     17893  title = {Polariztion effect on position accuracy of fluorophore localization},
     17894  pages = {8112-8120},
     17895  journal = {Optics Express},
     17896  volume = {14},
     17897  author = {Enderlein, J. and Toprak, E. and Selvin, P.R.}
     17898}
     17899@article{Enderlein2000,
     17900  number = {9},
     17901  year = {2000},
     17902  title = {Theoretical Study of detection of a dipole emitter through an objective with high numerical aperture},
     17903  pages = {634-636},
     17904  journal = {Optics Letters},
     17905  volume = {25},
     17906  author = {Enderlein, J.}
     17907}
     17908@article{Dahan2003,
     17909  number = {5644},
     17910  year = {2003},
     17911  title = {Diffusion dynamics of glycine receptors revealed by single-quantum dot tracking},
     17912  pages = {442-445},
     17913  journal = {Science},
     17914  volume = {302},
     17915  author = {Dahan, M. and Levi, S. and Luccardini, C. and Rostaing, P. and Riveau, B. and Triller, A.}
     17916}
     17917@misc{OberEstimationtool,
     17918  year = {2009},
     17919  title = {Estimation tool},
     17920  note = {University of Texas, Southwestern {http://www4.utsouthwestern.edu/wardlab}},
     17921  author = {Ober, R.J. and Ward, E.S.}
     17922}
     17923@article{Jin2007,
     17924  number = {3},
     17925  year = {2007},
     17926  title = {Single-particle tracking of membrane protein diffusion in a potential: Simulation, detection, and application to confined diffusion of CFTR Cl- channels},
     17927  pages = {1079-1088},
     17928  journal = {Biophysical Journal},
     17929  volume = {93},
     17930  author = {Jin, S. and Haggie, P. M. and Verkman, A. S.}
     17931}
     17932@article{Jin2007b,
     17933  number = {14},
     17934  year = {2007},
     17935  title = {Single particle tracking of complex diffusion in membranes: Simulation and detection of barrier, raft, and interaction phenomena},
     17936  pages = {3625-3632},
     17937  journal = {Journal of Physical Chemistry B},
     17938  volume = {111},
     17939  author = {Jin, S. and Verkman, A. S.}
     17940}
     17941@article{Rasnik2006,
     17942  number = {11},
     17943  year = {2006},
     17944  title = {Nonblinking and longlasting single-molecule fluorescence imaging},
     17945  pages = {891-893},
     17946  journal = {Nature Methods},
     17947  volume = {3},
     17948  author = {Rasnik, I. and McKinney, S. A. and Ha, T.}
     17949}
     17950@article{Hell1992,
     17951  number = {5-6},
     17952  year = {1992},
     17953  title = {Fundamental Improvement of Resolution with a 4Pi-Confocal Fluorescence Microscope Using 2-Photon Excitation},
     17954  pages = {277-282},
     17955  journal = {Optics Communications},
     17956  volume = {93},
     17957  author = {Hell, S. and Stelzer, E. H. K.}
     17958}
     17959@article{LidkeDS2007,
     17960  year = {2007},
     17961  title = {Exploring membrane protein dynamics by multicolor single quantum dot imaging using wide field, TIRF, and hyperspectral microscopy},
     17962  pages = {6448Y1-8},
     17963  journal = {Proc. of SPIE},
     17964  volume = {6448},
     17965  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.}
     17966}
     17967@article{Warren1997,
     17968  number = {4},
     17969  year = {1997},
     17970  title = {Compact prism spectrographs based on aplanatic principles},
     17971  pages = {1174-1182},
     17972  journal = {Optical Engineering},
     17973  volume = {36},
     17974  author = {Warren, D. W. and Hackwell, J. A. and Gutierrez, D. J.}
     17975}
     17976@article{Schlessinger2002,
     17977  number = {6},
     17978  year = {2002},
     17979  title = {Ligand-induced, receptor-mediated dimerization and activation of EGF receptor},
     17980  pages = {669-72},
     17981  journal = {Cell},
     17982  volume = {110},
     17983  author = {Schlessinger, J.}
     17984}
     17985@article{Arndt-Jovin2006,
     17986  year = {2006},
     17987  title = {In vivo cell imaging with semiconductor quantum dots and noble-metal nanodots},
     17988  journal = {Proc. of SPIE},
     17989  volume = {6096, 60960P},
     17990  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.}
     17991}
     17992@article{Ehrensperger2007,
     17993  number = {10},
     17994  year = {2007},
     17995  title = {Multiple association states between glycine receptors and gephyrin identified by SPT analysis},
     17996  pages = {3706-3718},
     17997  journal = {Biophysical Journal},
     17998  volume = {92},
     17999  author = {Ehrensperger, M. V. and Hanus, C. and Vannier, C. and Triller, A. and Dahan, M.}
     18000}
     18001@article{Gilfillan2006,
     18002  number = {3},
     18003  year = {2006},
     18004  title = {Integrated signalling pathways for mast-cell activation},
     18005  pages = {218-30},
     18006  journal = {Nat Rev Immunol},
     18007  volume = {6},
     18008  author = {Gilfillan, A. M. and Tkaczyk, C.}
     18009}
     18010@article{Eggeling2009,
     18011  year = {2009},
     18012  title = {Direct observation of the nanoscale dynamics of membrane lipids in a living cell},
     18013  pages = {1159-1163},
     18014  journal = {Nature},
     18015  volume = {457},
     18016  author = {Eggeling, C. and Ringemann, C. and Medda, R. and
     18017Schwarzmann, G. and Sandhoff, K. and Polyakova, S. and Belov, V.N. and Hein, B. and Middendorff, C. von and {Sch\"onle}, A. and  Hell, S. W.}
     18018}
     18019@article{Huang2008a,
     18020  number = {12},
     18021  year = {2008},
     18022  title = {Whole-cell {3D STORM} reveals interactions between cellular structures with nanometer-scale resolution},
     18023  pages = {1047-1053},
     18024  journal = {Nature Methods},
     18025  volume = {5},
     18026  author = {Huang, B. and Jones, S.A. and Brandenburg, B. and Zhuang, X.}
     18027}
     18028@article{Hess2007,
     18029  number = {44},
     18030  year = {2007},
     18031  title = {Dynamic clustered distribution of hemagglutinin resolved at 40 nm in living cell membranes discriminates between raft theories},
     18032  pages = {17370-17375},
     18033  journal = {Proceedings of the National Academy of Sciences},
     18034  volume = {104},
     18035  author = {Hess, S.T. and Gould, T.J. and Gudhetl, M.V. and Maas, S.A. and Mills, K.D. and Zimmerberg, J.}
     18036}
     18037@article{Gustafsson2005,
     18038  number = {37},
     18039  year = {2005},
     18040  title = {Nonlinear structured-illumination microscopy: Wide-field fluorescence imaging with theoretically unlimited resolution},
     18041  pages = {13081-13086},
     18042  journal = {Proceedings of the National Academy of Sciences of the United States of America},
     18043  volume = {102},
     18044  author = {Gustafsson, M. G. L.}
     18045}
     18046@article{Egner2007,
     18047  number = {9},
     18048  year = {2007},
     18049  title = {Fluorescence nanoscopy in whole cells by asynchronous localization of photoswitching emitters},
     18050  pages = {3285-3290},
     18051  journal = {Biophysical Journal},
     18052  volume = {93},
     18053  author = {Egner, A. and Geisler, C. and Middendorff, C. von and Bock, H. and Wenzel, D. and Medda, R. and Andresen, M. and Stiel, A.C. and Jakobs, S. and Eggeling, C. and {Sch\"onle}, A. and Hell, S.W.}
     18054}
     18055@article{Bates2005,
     18056  number = {10},
     18057  year = {2005},
     18058  title = {Short-range spectroscopic ruler based on a single-molecule optical switch},
     18059  pages = {-},
     18060  journal = {Physical Review Letters},
     18061  volume = {94},
     18062  author = {Bates, M. and Blosser, T. R. and Zhuang, X. W.}
     18063}
     18064@article{Sinclair2006,
     18065  number = {24},
     18066  year = {2006},
     18067  title = {Hyperspectral confocal microscope},
     18068  pages = {6283-91},
     18069  journal = {Appl Opt},
     18070  volume = {45},
     18071  author = {Sinclair, M. B. and Haaland, D. M. and Timlin, J. A. and Jones, H. D.}
     18072}
     18073@article{Sinclair2004,
     18074  number = {10},
     18075  year = {2004},
     18076  title = {Design, construction, characterization, and application of a hyperspectral microarray scanner},
     18077  pages = {2079-2088},
     18078  journal = {Applied Optics},
     18079  volume = {43},
     18080  author = {Sinclair, M. B. and Timlin, J. A. and Haaland, D. M. and Werner-Washburne, M.}
     18081}
     18082@article{Sark2002,
     18083  number = {10},
     18084  year = {2002},
     18085  title = {Blueing, bleaching, and blinking of single CdSe/ZnS quantum dots},
     18086  pages = {871-879},
     18087  journal = {Chemphyschem},
     18088  volume = {3},
     18089  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.}
     18090}
     18091@book{Haaland2003,
     18092  series = {In Spectral Imaging: Instrumentation, Applications, and Analysis},
     18093  year = {2003},
     18094  title = {Multivariate curve resolution for hyperspectral image analysis: applications to microarray technology},
     18095  volume = {4959},
     18096  address = {San Jose, CA.},
     18097  publisher = {International Society for Optical Engineering},
     18098  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.}
     18099}
     18100@article{Geisler2007,
     18101  number = {2},
     18102  year = {2007},
     18103  title = {Resolution of lambda/10 in fluorescence microscopy using fast single molecule photo-switching},
     18104  pages = {223-226},
     18105  journal = {Applied Physics A - Materials Science and Processing},
     18106  volume = {88},
     18107  author = {Geisler, C. and Schonle, A. and Middendorff, C. von and Bock, H. and Eggeling, C. and Egner, A. and Hell, S. W.}
     18108}
     18109@article{Metzger1992,
     18110  year = {1992},
     18111  title = {Transmembrane signalling: the joy of aggregation},
     18112  pages = {1477-1487},
     18113  journal = {Journal of Immunology },
     18114  volume = {149},
     18115  author = {Metzger, H.}
     18116}
     18117@article{Hanser2004,
     18118  year = {2004},
     18119  title = {Phase-retrieved pupil functions in wide-field fluorescence microscopy},
     18120  pages = {32-48},
     18121  journal = {Journal of Microscopy},
     18122  volume = {216},
     18123  author = {Hanser, B.M. and Gustafsson, M.G.L. and Agard, D.A. and Sedat, J.W.}
     18124}
     18125@book{Bharucha-Reid1960,
     18126  year = {1960},
     18127  title = {Elements of the Theory of Markov Processes and Their Applications},
     18128  publisher = {New York: McGraw-Hill},
     18129  author = {Bharucha-Reid, A. T}
     18130}
     18131@article{Herring2010,
     18132  year = {2010},
     18133  title = {Coherent electron interference from amorphous
     18134TEM specimens},
     18135  journal = {Journal of Electron Microscopy},
     18136  author = {Herring, R.A. and Saitoh, K. and Tanaka, N. and Tanji, T.}
     18137}
     18138@article{Schmidt2008,
     18139  number = {6},
     18140  year = {2008},
     18141  title = {Spherical nanosized focal spots unravels the interior of cells},
     18142  pages = {539-544},
     18143  journal = {Nature Methods},
     18144  volume = {5},
     18145  author = {Schmidt, R. and Wurm, C.A. and Jakobs, S. and Engelhardt, J. and Egner, A. and Hell, S.W.}
     18146}
     18147@article{Kner2009,
     18148  number = {5},
     18149  year = {2009},
     18150  title = {Super-resolution video microscopy of live cells by structured illumination},
     18151  pages = {339-344},
     18152  journal = {Nature Methods},
     18153  volume = {6},
     18154  author = {Kner, P. and Chhun, B.B. and Griffs, E.R. and Winoto, L. and Gustafsson, M.G.L.}
     18155}
     18156@article{Heintzmann2009,
     18157  year = {2009},
     18158  title = {Subdiffraction resolution in continuous samples},
     18159  pages = {362-364},
     18160  journal = {Nature Photonics},
     18161  volume = {3},
     18162  author = {Heintzmann, R. and Gustafsson, M.G.L.}
     18163}
     18164@article{Boulanger2010,
     18165  number = {2},
     18166  year = {2010},
     18167  title = {Patch-Based Nonlocal Functional for Denoising
     18168Fluorescence Microscopy Image Sequences},
     18169  pages = {442-454},
     18170  journal = {IEEE Transactions on Medical Image Processing},
     18171  volume = {29},
     18172  author = {Boulanger, J. and Kervrann, C. and Bouthemy, P. and Elbau, P. and Sibarita, J.-B. and Salamero, J.}
     18173}
     18174@article{Carlton2010,
     18175  year = {2010},
     18176  title = {Fast live simultaneous multiwavelength four-dimensional optical microscopy},
     18177  journal = {Proceedings of the National Academy of Sciences},
     18178  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.}
     18179}
     18180@article{Grabenbauer2005,
     18181  year = {2005},
     18182  title = {Correlative microscopy and electron tomography of GFP through photooxidation},
     18183  pages = {857-862},
     18184  journal = {Nature Methods},
     18185  volume = {2},
     18186  author = {Grabenbauer, M. and Geerts, W.J. and Fernadez-Rodriguez, J. and Hoenger, A. and Koster, A.J. and Nilsson, T.}
     18187}
     18188@article{Folling2008,
     18189  year = {2008},
     18190  title = {Fluorescence nanoscopy by ground-state depletion and single-molecule return},
     18191  pages = {943-945},
     18192  journal = {Nature Methods},
     18193  volume = {5},
     18194  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.}
     18195}
     18196@article{Agronskaia2008,
     18197  number = {2},
     18198  year = {2008},
     18199  title = {Integrated fluorescence and transmission electron microscopy},
     18200  pages = {183-189},
     18201  journal = {Journal of Structural Biology},
     18202  volume = {164},
     18203  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.}
     18204}
     18205@article{Aguet2009,
     18206  number = {8},
     18207  year = {2009},
     18208  title = {Super-resolution orientation estimation and localization of fluorescent dipoles using 3-D steerable filters},
     18209  pages = {6829},
     18210  journal = {Optics Express},
     18211  volume = {17},
     18212  author = {Aguet, F. and Geissbuhler, S. and Marki, I. and Lasser, T. and Unser, M.}
     18213}
     18214@article{Giepmans2005,
     18215  year = {2005},
     18216  title = {Correlated light and electron microscopic imaging of multiple endogenous proteins using quantum dots},
     18217  pages = {743-749},
     18218  journal = {Nature Methods},
     18219  volume = {10},
     18220  author = {Giepmans, B.N.G. and Deerinck, T.J. and Smarr, B.L. and Jones, Y.Z. and Ellisman, M.H.}
     18221}
     18222@article{Stallinga2004,
     18223  number = {9},
     18224  year = {2004},
     18225  title = {Light distribution close to focus in biaxially       birefringent media
     18226},
     18227  pages = {1785-1788},
     18228  journal = {Journal of the Optical Society of America A},
     18229  volume = {21},
     18230  author = {Stallinga, S.}
     18231}
     18232@article{Wang2010,
     18233  number = {4},
     18234  year = {2010},
     18235  title = {In vitro and in vivo imaging with quantum dots },
     18236  pages = {1397-1415},
     18237  journal = {Analytical and Bioanalytical Chemistry },
     18238  volume = {397},
     18239  author = {Wang, C. and Gao, X. and Su, X.}
     18240}
     18241@article{Jamieson2007,
     18242  number = {31},
     18243  year = {2007},
     18244  title = {Biological applications of quantum dots },
     18245  pages = {4717-4732},
     18246  journal = {Biomaterials},
     18247  volume = {28},
     18248  author = {Jamieson, T. and Bakhshi, R. and Petrova, D. and Pocock, R. and Imani, M. and Seifalian, A.M.}
     18249}
     18250@article{Abraham2009,
     18251  number = {26},
     18252  year = {2009},
     18253  title = {Quantitative study of single molecule location estimation techniques },
     18254  pages = {23352-23373},
     18255  journal = {Optics Express},
     18256  volume = {17},
     18257  author = {Abraham, A.V. and Ram, S. and Chao, J. and Ward, E.S. and Ober, R.J.}
     18258}
     18259@article{Chao2009,
     18260  number = {26},
     18261  year = {2009},
     18262  title = {A comparative study of high resolution microscopy imaging modalities using a three-dimensional resolution measure},
     18263  pages = {24377-24401},
     18264  journal = {Optics Express},
     18265  volume = {17},
     18266  author = {Chao, J. and Ram, S. and Ward, E.S. and Ober, R.J.}
     18267}
     18268@article{Ram2008,
     18269  number = {12},
     18270  year = {2008},
     18271  title = {High accuracy 3D quantum dot tracking with multifocal plane microscopy for the study of fast intracellular dynamics in live cells },
     18272  pages = {6025-6043},
     18273  journal = {Biophysical Journal},
     18274  volume = {95},
     18275  author = {Ram, S. and Prabhar, P. and Chao, J. and Ward, E.S. and Ober, R.J.}
     18276}
     18277@article{Wilson1997,
     18278  year = {1997},
     18279  title = {The imaging of dielectric point scatterers in conventional and confocal polarisation microscopes},
     18280  pages = {298-313},
     18281  journal = {Optics Communications},
     18282  volume = {141},
     18283  author = {Wilson, T. and Juskaitis, R. and Higdon, P.D.}
     18284}
     18285@article{Stallinga2010,
     18286  number = {24},
     18287  year = {2010},
     18288  title = {Accuracy of the {Gaussian} Point Spread Function model in {2D} localization microscopy
     18289},
     18290  pages = {24461-24476},
     18291  journal = {Optics Express},
     18292  volume = {18},
     18293  author = {Stallinga, S. and Rieger, B.}
     18294}
     18295@article{Barrett1995,
     18296  number = {5},
     18297  year = {1995},
     18298  title = {Objective assessment of image quality. II. Fisher information, Fourier crosstalk, and
     18299figures of merit for task performance},
     18300  pages = {834-853},
     18301  journal = {Journal of the Optical Society of America A},
     18302  volume = {12},
     18303  author = {Barrett, H. H. and Denny, J.L. and Wagner, R.F. and Myers, K.J.}
     18304}
     18305@article{Foreman2007,
     18306  number = {21},
     18307  year = {2007},
     18308  title = {Photon statistics in single molecule
     18309orientational imaging},
     18310  pages = {13597-13606},
     18311  journal = {Optics Express},
     18312  volume = {15},
     18313  author = {Foreman, M.R. and Sherif, S.S. and {T\"or\"ok}, P.}
     18314}
     18315@article{Haeberle2003,
     18316  number = {22},
     18317  year = {2003},
     18318  title = {Point spread function of optical microscopes
     18319imaging through stratified media},
     18320  pages = {2964-2969},
     18321  journal = {Optics Express},
     18322  volume = {11},
     18323  author = {{Haeberl\'e}, O. and Ammar, M. and Furukawa, H. and Tenjimbayashi, K. and {T\"or\"ok}, P.}
     18324}
     18325@article{McGuire1994,
     18326  number = {22},
     18327  year = {1994},
     18328  title = {Polarization aberrations.
     183291. Rotationally symmetric optical systems},
     18330  pages = {5080-5100},
     18331  journal = {Applied Optics},
     18332  volume = {33},
     18333  author = {McGuire, J.P. Jr. and Chipman, R.A.}
     18334}
     18335@article{McGuire1994a,
     18336  number = {22},
     18337  year = {1994},
     18338  title = {Polarization aberrations.
     183392. Tilted and decentered optical systems},
     18340  pages = {5101-5107},
     18341  journal = {Applied Optics},
     18342  volume = {33},
     18343  author = {McGuire, J.P. Jr. and Chipman, R.A.}
     18344}
     18345@article{Muller2005,
     18346  year = {2005},
     18347  title = {Measures of performance in nonlinear estimation
     18348tasks: prediction of estimation performance at low signal-to-noise ratio},
     18349  pages = {3697-3715},
     18350  journal = {Physics in Medicine and Biology},
     18351  volume = {50},
     18352  author = {{M\"uller}, S.P. and Abbey, C.K. and Rybicki, F.J. and Moore, S.C. and Kijewski, M.F.}
     18353}
     18354@article{Ji2010,
     18355  number = {2},
     18356  year = {2010},
     18357  title = {Adaptive optics via pupil segmentation for
     18358high-resolution imaging in biological tissues},
     18359  pages = {141-150},
     18360  journal = {Nature Methods},
     18361  volume = {7},
     18362  author = {Ji, N. and Milkie, D.E. and Betzig, E.}
     18363}
     18364@article{Wombacher2010,
     18365  number = {9},
     18366  year = {2010},
     18367  title = {Live-cell super-resolution imaging with trimethoprim conjugates},
     18368  pages = {717-722},
     18369  journal = {Nature Methods},
     18370  volume = {7},
     18371  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.}
     18372}
     18373@article{Henriques2010,
     18374  number = {5},
     18375  year = {2010},
     18376  title = {Quick{PALM}: 3D real-time photoactivation nanoscopy image processing in {ImageJ}},
     18377  pages = {339-340},
     18378  journal = {Nature Methods},
     18379  volume = {7},
     18380  author = {Henriques, R. and Lelek, M. and Fornasiero, E.F. and Valtorta, F. and Zimmer, C. and Mhlanga, M.M.}
     18381}
     18382@article{Dertinger2009,
     18383  number = {52},
     18384  year = {2009},
     18385  title = {Fast, background-free, {3D} super-resolution optical fluctuation imaging {(SOFI)}},
     18386  pages = {22287-22292},
     18387  journal = {Proceedings of the National Academy of Sciences USA},
     18388  volume = {106},
     18389  author = {Dertinger, T. and Colyer, R. and Iyer, G. and Weiss, S. and Enderlein, J.}
     18390}
     18391@article{Dertinger2010,
     18392  number = {18},
     18393  year = {2010},
     18394  title = {Achieving increased resolution and more pixels
     18395with Superresolution Optical Fluctuation
     18396Imaging {(SOFI)}},
     18397  pages = {18875-11885},
     18398  journal = {Optics Express},
     18399  volume = {18},
     18400  author = {Dertinger, T. and Colyer, R. and Vogel, R. and  Enderlein, J. and Weiss, S.}
     18401}
     18402@article{Landau1967,
     18403  number = {1},
     18404  year = {1967},
     18405  title = {Necessary  density conditions for sampling and interpolation of certain entire function},
     18406  pages = {37-52},
     18407  journal = {Acta Mathematica},
     18408  volume = {117},
     18409  author = {Landau, H.}
     18410}
     18411@article{Heilemann2008,
     18412  number = {33},
     18413  year = {2008},
     18414  title = {Subdiffraction-Resolution Fluorescence Imaging with Conventional Fluorescent Probes},
     18415  pages = {6172-6176},
     18416  journal = {Angewannte Chemie},
     18417  volume = {47},
     18418  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.}
     18419}
     18420@article{Gustafsson2000,
     18421  number = {2},
     18422  year = {2000},
     18423  title = {Surpassing the lateral resolution limit by a factor of two using structured illumination microscopy},
     18424  pages = {82-87},
     18425  journal = {Journal of Microscopy},
     18426  volume = {198},
     18427  author = {Gustafsson, M.G.L.}
     18428}
     18429@article{Dedecker2007,
     18430  year = {2007},
     18431  title = {Orientational effects in the excitation
     18432and de-excitation of single molecules interacting with donut-mode laser beams},
     18433  pages = {3372-3383},
     18434  journal = {Optics Express},
     18435  volume = {15},
     18436  author = {Dedecker, P. and Muls, B. and Hofkens, J. and  Enderlein, J. and Hotta, J. }
     18437}
     18438@article{Smal2010,
     18439  year = {2010},
     18440  title = {Quantitative Comparison of Spot Detection Methods in Fluorescence Microscopy},
     18441  pages = {282-301},
     18442  journal = {IEEE Transactions on Medical Imaging},
     18443  volume = {29},
     18444  author = {Smal, I. and Loog, M. and Niessen, W.J.  and  Meijering, E.}
     18445}
     18446@article{Akhmanova2008,
     18447  year = {2008},
     18448  title = {Tracking the ends: a dynamic protein network controls the fate of microtubule tips},
     18449  pages = {309-322},
     18450  journal = {Nature Reviews Molecular Cell Biology},
     18451  volume = {9},
     18452  author = {Akhmanova, A. and  Steinmetz, M.O.}
     18453}
     18454@article{Heuvel2008,
     18455  year = {2008},
     18456  title = {Single-Molecule Observation of Anomalous Electrohydrodynamic Orientation of Microtubules
     18457},
     18458  pages = {118301},
     18459  journal = {Physical Review Letters},
     18460  volume = {101},
     18461  author = {Heuvel, M.G.L. van den and Bondesan, R. and Cosentino Langomarsino, M. and Dekker, C.}
     18462}
     18463@article{Lupini2008,
     18464  number = {6},
     18465  year = {2008},
     18466  title = {Rapid autotuning for crystalline specimens from an inline hologram},
     18467  pages = {195-201},
     18468  journal = {Journal of Electron Microscopy},
     18469  volume = {57},
     18470  author = {Lupini, A.R. and Pennycook, S.J.}
     18471}
     18472@article{Hell2009a,
     18473  year = {2009},
     18474  title = {Diffraction-unlimited three-dimensional optical
     18475nanoscopy with opposing lenses},
     18476  pages = {381-387},
     18477  journal = {Nature Photonics},
     18478  volume = {3},
     18479  author = {Hell, S.W. and Schmidt, R. and Egner, A.}
     18480}
     18481@article{Manghi2010,
     18482  year = {2010},
     18483  title = {Probing {DNA} conformational changes
     18484with high temporal resolution by tethered
     18485particle motion},
     18486  pages = {046003},
     18487  journal = {Physical Biology},
     18488  volume = {7},
     18489  author = {Manghi, M. and Tardin, C. and Baglio, J. and Rousseau, P. and Salome, L. and Destainville, N.}
     18490}
     18491@article{Destainville2009,
     18492  number = {11},
     18493  year = {2009},
     18494  title = {Microscopic Mechanism for Experimentally Observed Anomalous Elasticity of DNA in Two Dimensions},
     18495  pages = {4464-4469},
     18496  journal = {Biophysical Journal},
     18497  volume = {96},
     18498  author = {Destainville, Nicolas and Manghi, Manoel and Palmeri, John}
     18499}
     18500@article{Barthel2010,
     18501  year = {2010},
     18502  title = {Aberration measurement in {HRTEM}: {Implementation} and diagnostic use of numerical procedures for the highly precise recognition of diffractogram patterns},
     18503  pages = {27-46},
     18504  journal = {Ultramicroscopy},
     18505  volume = {111},
     18506  author = {Barthel, J. and Thust, A.}
     18507}
     18508@article{Perfetti2010,
     18509  year = {2010},
     18510  title = {X-ray micro tomography and image analysis as complementary methods for morphological characterization and coating thickness measurement
     18511of coated particles},
     18512  pages = {663-675},
     18513  journal = {Advanced Powder Technology},
     18514  volume = {21},
     18515  author = {Perfetti, G. and Casteele, E. van de and Rieger, B. and Wildeboer, W.J. and Meesters, G.M.H.}
     18516}
     18517@article{Stallinga2005,
     18518  year = {2005},
     18519  title = {Compact description of substrate-related aberrations in high numerical aperture optical disk readout},
     18520  pages = {949-958},
     18521  journal = {Applied Optics},
     18522  volume = {44},
     18523  author = {Stallinga, S.}
     18524}
     18525@article{Muhlich2009,
     18526  number = {7},
     18527  year = {2009},
     18528  title = {Analysis of Multiple Orientations},
     18529  pages = {1424-1437},
     18530  journal = {IEEE Transactions on Image Processing},
     18531  volume = {18},
     18532  author = {M{\"u}hlich, M. and Aach, T.}
     18533}
     18534@inproceedings{Franken2007,
     18535  series = {4485},
     18536  year = {2007},
     18537  title = {Nonlinear diffusion on the 2D Euclidean Motion group},
     18538  booktitle = {LNCS},
     18539  pages = {461-472},
     18540  author = {Franken, E.M. and Duits, R. and Haar Romenij, B.M. ter}
     18541}
     18542@inproceedings{Franken2006,
     18543  series = {3954},
     18544  year = {2006},
     18545  title = {An Efficient Method for Tensor Voting using Steerable Filters},
     18546  booktitle = {LNCS},
     18547  pages = {228-240},
     18548  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}
     18549}
     18550@inproceedings{Faas2007,
     18551  series = {4678},
     18552  year = {2007},
     18553  title = {A crossing detector based on the structure tensor},
     18554  booktitle = {LNCS},
     18555  pages = {212-220},
     18556  editor = {Blanc-Talon, J.},
     18557  author = {Faas, F.G.A. and Vliet, L.J. van}
     18558}
     18559@inproceedings{Herberthsson2006,
     18560  series = {SSBA},
     18561  month = {March},
     18562  year = {2006},
     18563  title = {Pairs of Orientation in the Plane},
     18564  booktitle = {Proceedings of the {SSBA} Symposium on Image Analysis},
     18565  author = {Herberthsson, M. and Brun, A. and Knutsson, H.}
     18566}
     18567@book{Stein1971,
     18568  year = {1971},
     18569  title = {Introduction to Fourier Analysis on Euclidean Spaces},
     18570  publisher = {Princeton University Press},
     18571  author = {Stein, E. and Stein, E.M. and Weiss, G.}
     18572}
     18573@article{Cordes2010a,
     18574  year = {2010},
     18575  title = {Resolving Single-Molecule Assembled Patterns with Superresolution Blink-Microscopy},
     18576  pages = {645-651},
     18577  journal = {Nano Letters},
     18578  volume = {10},
     18579  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.}
     18580}
     18581@article{Luengo2010,
     18582  number = {6},
     18583  year = {2010},
     18584  title = {Constrained and Dimensionality-Independent Path Openings},
     18585  pages = {1587-1595},
     18586  journal = {IEEE Transactions on Image Processing},
     18587  volume = {19},
     18588  author = {Luengo Hendriks, C.L.}
     18589}
     18590@article{Luengo2007a,
     18591  year = {2007},
     18592  title = {Improving the accuracy of isotropic granulometries},
     18593  pages = {865-872},
     18594  journal = {Pattern Recognition Letters},
     18595  volume = {28},
     18596  author = {Luengo Hendriks, C.L. and Kempen, G.M.P. and Vliet, L.J. van}
     18597}
     18598@article{Luengo2007,
     18599  number = {19},
     18600  year = {2007},
     18601  title = {Automatic channel unmixing for high-throughput quantitative analysis of fluorescence images},
     18602  pages = {12306-123117},
     18603  journal = {Optics Express},
     18604  volume = {15},
     18605  author = {Luengo Hendriks, C.L. and {Ker\"a}nen, S.V.E. and Biggin, M.D. and Knowles, D.W.}
     18606}
     18607@article{Caarls2010,
     18608  year = {2010},
     18609  title = {Characterization of Coupled Ground State and Excited State Equilibria by Fluorescence Spectral Deconvolution},
     18610  pages = {181-190},
     18611  journal = {Journal of Fluorescence},
     18612  volume = {20},
     18613  author = {Caarls, W. and Celej, M.S. and Demchenko, A.P. and Jovin, T.M.}
     18614}
     18615@article{Celej2009,
     18616  year = {2009},
     18617  title = {A Triple-Emission Fluorescent Probe Reveals Distinctive Amyloid Fibrillar Polymorphism of Wild-Type R-Synuclein and Its Familial Parkinson's Disease Mutants},
     18618  pages = {7465-7472},
     18619  journal = {Biochemistry},
     18620  volume = {48},
     18621  author = {Celej, M.S. and Caarls, W. and Demchenko, A.P. and Jovin, T.M.}
     18622}
     18623@article{Nagy2010,
     18624  number = {38},
     18625  year = {2010},
     18626  title = {Distribution of resting and ligand-bound {ErbB1} and {ErbB2} receptor tyrosine kinases in living cells using number and brightness analysis},
     18627  pages = {16524-16529},
     18628  journal = {Proceedings of the National Academy of Sciences of the United States of America},
     18629  volume = {107},
     18630  author = {Nagy, P. and Claus, J. and Jovin, T.M. and Arndt-Jovin, D.J.}
     18631}
     18632@article{Finzi2010,
     18633  number = {25},
     18634  year = {2010},
     18635  title = {Single-molecule Approaches to Probe the Structure, Kinetics, and Thermodynamics of Nucleoprotein Complexes That Regulate Transcription},
     18636  pages = {18973-18978},
     18637  journal = {JOURNAL OF BIOLOGICAL CHEMISTRY},
     18638  volume = {285},
     18639  author = {Finzi, L. and Dunlap, D.D.}
     18640}
     18641@article{Engelhardt2011,
     18642  year = {2010},
     18643  title = {Molecular Orientation Affects Localization Accuracy in Superresolution Far-Field Fluorescence Microscopy},
     18644  pages = {209-213},
     18645  journal = {Nano Letters},
     18646  volume = {11},
     18647  author = {Engelhardt, J. and Keller, J. and Hoyer, P. and Reuss, M. and Staudt, T. and Hell, S.W.}
     18648}
     18649@article{Lindner2011,
     18650  year = {2011},
     18651  title = {Force-free measurements of the conformations of {DNA} molecules tethered to a wall},
     18652  pages = {011916},
     18653  journal = {Physical Review E},
     18654  volume = {83},
     18655  author = {Lindner, M. and Nir, G. and Medalion, S. and Dietrich, H.R.C. and Rabin, Y. and Garini, Y.}
     18656}
     18657@article{Beleggia2004,
     18658  year = {2004},
     18659  title = {On the transport of intensity technique for phase retrieval},
     18660  pages = {37-49},
     18661  journal = {Ultramicroscopy},
     18662  volume = {102},
     18663  author = {Beleggia, M. and Schofield, M.A. and Volkov, V.V. and Zhu, Y.}
     18664}
     18665@article{Bronnikov2002,
     18666  year = {2002},
     18667  title = {Theory of quatitative phase-contrast computed tomography},
     18668  pages = {472-480},
     18669  journal = {Journal of the Optical Society of America A},
     18670  volume = {19},
     18671  author = {Bronnikov, A.V.}
     18672}
     18673@article{Donoho2006,
     18674  number = {4},
     18675  year = {2006},
     18676  title = {Compressed Sensing},
     18677  pages = {1289-1306},
     18678  journal = {IEEE Transactions of Information Theory},
     18679  volume = {52},
     18680  author = {Donoho, D.L.}
     18681}
     18682@article{Jesacher2005,
     18683  year = {2005},
     18684  title = {Shadow Effects in Spiral Phase Contrast Microscopy},
     18685  pages = {233902},
     18686  journal = {Physics Review Letters},
     18687  volume = {94},
     18688  author = {Jesacher, A. and {F\"urhapter}, S. and Bernet, S. and Ritsch-Marte, M.}
     18689}
     18690@article{Furhapter2005,
     18691  number = {15},
     18692  year = {2005},
     18693  title = {Spiral interferometry},
     18694  pages = {1953-1955},
     18695  journal = {Optics Letters},
     18696  volume = {30},
     18697  author = {{F\"urhapter}, S. and Jesacher, A. and Bernet, S. and Ritsch-Marte, M.}
     18698}
     18699@article{Aarts2011,
     18700  year = {2011},
     18701  title = {Three-dimensional atomic imaging of crystalline
     18702nanoparticles},
     18703  journal = {Nature},
     18704  author = {Aaarts, S. van and Batenburg, K.J. and Rossell, M.D. and Erni, R. and Tendeloo, G. van}
     18705}
     18706@article{jensen_helium,
     18707  year = {2006},
     18708  title = {A comparison of liquid nitrogen and liquid helium as cryogens for electron cryotomography},
     18709  pages = {231-240},
     18710  journal = {Journal of Structural Biology},
     18711  volume = {153},
     18712  author = {Iancu, C.V. and Wright, E.R. and Heymann, J.B. and Jensen, G.J.}
     18713}
     18714@inproceedings{Noorden2010,
     18715  series = {LNCS 6362},
     18716  month = {September 20-24},
     18717  year = {2010},
     18718  title = {A Comparison of the Cingulum in Amyotrophic Lateral Sclerosis using Kernel Matchin},
     18719  booktitle = {Medical Image Computing and Computer-Assisted Intervention - MICCAI 2010},
     18720  pages = {249-256},
     18721  editor = {T. Jiang, T. and Navab, N. and Pluim, J.P.W. and  Viergever, M.A.},
     18722  address = {Beijing, China},
     18723  publisher = {Springer},
     18724  author = {Noorden, S. van and Caan, M.W.A. and Graaf, M. van der and Vliet, L.J. van and Vos, F.M.}
     18725}
     18726@article{McMorran2011,
     18727  year = {2011},
     18728  title = {Electron Vortex Beams with High Quanta of Orbital Angular Momentum},
     18729  pages = {192-195},
     18730  journal = {Science},
     18731  volume = {331},
     18732  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.}
     18733}
     18734@article{Voortman2011,
     18735  year = {2011},
     18736  title = {A fast algorithm for computing and correcting the
     18737{CTF} for tilted, thick specimens in {TEM}},
     18738  pages = {1029-1036},
     18739  journal = {Ultramicroscopy},
     18740  volume = {111},
     18741  author = {Voortman, L.M. and Stallinga, S. and Schoenmakers, R.H.M. and Vliet, L.J. van and Rieger, B.}
     18742}
     18743@article{Karuppasamy2011,
     18744  year = {2011},
     18745  title = {Radiation damage in single-particle cryo-electron
     18746microscopy: effects of dose and dose rate},
     18747  pages = {398-412},
     18748  journal = {Journal of Synchrotron Radiation},
     18749  volume = {18},
     18750  author = {Karuppasamy, M. and Karimi Nejadasl, F and Vulovic, M. and Koster, A.J. and Ravelli, R.B.G. }
     18751}
     18752@article{Krysting2011,
     18753  year = {2011},
     18754  title = {Heat Profiling of Three-Dimensionally Optically Trapped Gold Nanoparticles using Vesicle Cargo Release},
     18755  pages = {888-892},
     18756  journal = {Nano Letters},
     18757  volume = {11},
     18758  author = {Krysting, A. and Bendix, P.M. and Stamou, D.G. and Oddershede, L.B.}
     18759}
     18760@article{Schutz2001,
     18761  number = {2},
     18762  year = {2001},
     18763  title = {Imaging Single Molecules in Three Dimensions},
     18764  pages = {69-74},
     18765  journal = {Single Molecules},
     18766  volume = {2},
     18767  author = {{Sch\"utz}, G.J. and Axman M. and Schindler, H.}
     18768}
     18769@article{vanElburg2007,
     18770  number = {1},
     18771  year = {2007},
     18772  title = {Improved correction of axial geometrical distortion in index-mismatched fluorescent confocal            microscopic images using high-aperture objective lenses},
     18773  pages = {45-54},
     18774  journal = {Journal of Microscopy},
     18775  volume = {228},
     18776  author = {van Elburg, H.J. and Kuypers, L.C. and Decraemer, W.F. and Dirckx, J.J.J.}
     18777}
     18778@article{vandenBroek2006,
     18779  number = {1},
     18780  year = {2006},
     18781  title = {Real-time observation of {DNA} looping dynamics of Type {IIE} restriction enzymes {NaeI} and {NarI}},
     18782  pages = {167-174},
     18783  journal = {Nucleic Acids Research},
     18784  volume = {34},
     18785  author = {van den Broek, B. and Vanzi, F. and Normanno, D. and Pavone, F.S. and Wuite, G.J.L.}
     18786}
     18787@article{Finzi1995,
     18788  number = {5196},
     18789  year = {1995},
     18790  title = {Measurement of Lactose Repressor-Mediated Loop Formation and Breakdown in Single DNA Molecules},
     18791  pages = {378-380},
     18792  journal = {Science},
     18793  volume = {267},
     18794  author = {Finzi, L. and Gelles, J.}
     18795}
     18796@article{deGennes1976a,
     18797  number = {4},
     18798  year = {1976},
     18799  title = {Dynamics of Entangled Polymer Solutions. {I.} The Rouse Model},
     18800  pages = {587-593},
     18801  journal = {Macromolecules},
     18802  volume = {9},
     18803  author = {De Gennes, P.G.}
     18804}
     18805@article{deGennes1976b,
     18806  number = {4},
     18807  year = {1976},
     18808  title = {Dynamics of Entangled Polymer Solutions. {II.} Inclusion of Hydrodynamic Interactions},
     18809  pages = {594-598},
     18810  journal = {Macromolecules},
     18811  volume = {9},
     18812  author = {De Gennes, P.G.}
     18813}
     18814@article{Robertson2006,
     18815  number = {19},
     18816  year = {2006},
     18817  title = {Diffusion of isolated DNA molecules: {Dependence} on length and topology},
     18818  pages = {7310-7314},
     18819  journal = {Proceedings of the National Academy of Sciences of the USA},
     18820  volume = {103},
     18821  author = {Robertson, R.M.}
     18822}
     18823@article{Derjaguin1941,
     18824  year = {1941},
     18825  title = {Theory of the stability of strongly charged lyophobic sols and of the adhesion of strongly charged      particles in solutions of electrolytes.},
     18826  journal = {Acta Physico Chimica URSS},
     18827  volume = {14},
     18828  author = {Derjaguin, B. and Landau, L.}
     18829}
     18830@book{Verwey1948,
     18831  year = {1948},
     18832  title = {Theory of the stability of lyophobic colloids},
     18833  publisher = {Elsevier},
     18834  author = {Verwey, E.J.W. and Overbeek, J.Th.G.}
     18835}
     18836@article{Debye1923,
     18837  year = {1923},
     18838  title = {The theory of electrolytes. {I.} Lowering of freezing point and related phenomena},
     18839  pages = {185-206},
     18840  journal = {Physikalische Zeitschrift},
     18841  volume = {24},
     18842  author = {Debye, P. and {H\"uckel}, E.}
     18843}
     18844@book{Lyklema1991,
     18845  year = {1991},
     18846  title = {Fundamentals of Interface and Colloid Science},
     18847  volume = {Volume I: Fundamentals},
     18848  address = {London, UK},
     18849  publisher = {Academic Press Limited},
     18850  author = {Lyklema, J. and van Leeuwen, H.P. and van Vliet, T. and Cazabat, A.-M}
     18851}
     18852@book{Happel1973,
     18853  edition = {2nd edition},
     18854  year = {1973},
     18855  title = {Low Reynolds number hydrodynamics},
     18856  address = {Leyden, The Netherlands},
     18857  publisher = {Noordhoff},
     18858  author = {Happel, John}
     18859}
     18860@article{Bevan2000,
     18861  number = {3},
     18862  year = {2000},
     18863  title = {Hindered diffusion of colloidal particles very near to a wall: Revisited},
     18864  pages = {1128-1236},
     18865  journal = {Journal of Chemical Physics},
     18866  volume = {113},
     18867  author = {Bevan, Michael A. and Prieve, Dennis C.}
     18868}
     18869@article{Stallinga2005a,
     18870  year = {2005},
     18871  title = {Finite conjugate spherical aberration compensation in high numerical-aperture optical disc read-out},
     18872  pages = {7307-7312},
     18873  journal = {Applied Optics},
     18874  volume = {44},
     18875  author = {Stallinga, S.}
     18876}
     18877@article{Fan2009,
     18878  number = {5},
     18879  year = {2009},
     18880  title = {Studying {RecBCD} Helicase Translocation Along {chi-DNA} Using Tethered Particle Motion with a Stretching Force},
     18881  pages = {1875-1883},
     18882  journal = {Biophysical Journal},
     18883  volume = {96},
     18884  author = {Fan, Hsiu-Fang and Li, Hung-Wen}
     18885}
     18886@article{Geggier2010,
     18887  number = {35},
     18888  year = {2010},
     18889  title = {Sequence dependence of {DNA} bending rigidity},
     18890  pages = {15421-15426},
     18891  journal = {Proceedings of the National Academy of Sciences of the USA},
     18892  volume = {107},
     18893  author = {Geggier, Stephanie and Vologodskii, Alexander}
     18894}
     18895@article{Smith1996b,
     18896  number = {4},
     18897  year = {1996},
     18898  title = {Dynamical Scaling of {DNA} Diffusion Coefficients},
     18899  pages = {1372-1373},
     18900  journal = {Macromolecules},
     18901  volume = {29},
     18902  author = {Smith, Douglas E. and Perkins, Thomas T. and Chu, Steven}
     18903}
     18904@article{Hodgson1991,
     18905  number = {10},
     18906  year = {1991},
     18907  title = {Dilute solution behavior of cyclic and linear polyelectrolytes},
     18908  pages = {7653-7663},
     18909  journal = {Journal of Chemical Physics},
     18910  volume = {95},
     18911  author = {Hodgson, Donald F. and Amis, Eric J.}
     18912}
     18913@inproceedings{Rieger2011,
     18914  series = {LNCS 6688},
     18915  month = {May 23-27},
     18916  year = {2011},
     18917  title = {Continuous orientation representation for arbitrary dimensions - a generalized Knutsson mapping},
     18918  booktitle = {Proceedings of the 17th Scandinavian Conference on Image Analysis, SCIA 2011},
     18919  pages = {774-783},
     18920  editor = {Heyden, A. and Kahl, F.},
     18921  address = {Heidelberg},
     18922  publisher = {Springer},
     18923  author = {Rieger, B. and Vliet, L.J. van and Verbeek, P.W.}
     18924}
     18925@book{FundFluidMech,
     18926  edition = {3rd},
     18927  year = {1998},
     18928  title = {Fundamentals of Fluid Mechanics},
     18929  address = {New York},
     18930  publisher = {John Wiley \& Sons, Inc},
     18931  author = {Munson, Bruce R. and Young, Donald F. and Okiishi, Theodore H.}
     18932}
     18933@article{Rosenthal2003,
     18934  number = {4},
     18935  year = {2003},
     18936  title = {Optimal Determination of Particle Orientation,
     18937Absolute Hand, and Contrast Loss in Single-particle Electron Cryomicroscopy},
     18938  pages = {721-745},
     18939  journal = {Journal of Molecular Biology},
     18940  volume = {333},
     18941  author = {Rosenthal, P.B. and Henderson, R.}
     18942}
     18943@article{Wicker2009,
     18944  number = {18},
     18945  year = {2009},
     18946  title = {Characterisation of a resolution enhancing image inversion interferometer},
     18947  pages = {15491-15501},
     18948  journal = {Optics Express},
     18949  volume = {17},
     18950  author = {Wicker, K. and Sindbert, S. and Heintzmann, R.}
     18951}
     18952@article{Wicker2007,
     18953  number = {19},
     18954  year = {2007},
     18955  title = {Interferometric resolution improvement for confocal microscopes},
     18956  pages = {12206-12216},
     18957  journal = {Optics Express},
     18958  volume = {15},
     18959  author = {Wicker, K. and Heintzmann, R.}
     18960}
     18961@article{Schermelleh2010,
     18962  number = {2},
     18963  year = {2010},
     18964  title = {A guide to super-resolution fluorescence microscopy},
     18965  pages = {165-175},
     18966  journal = {The journal of cell biology},
     18967  volume = {190},
     18968  author = {Schermelleh, L. and Heintzmann, R. and Leonhardt, H.}
     18969}
     18970@article{Ruckstuhl2004,
     18971  number = {18},
     18972  year = {2004},
     18973  title = {Supercritical angle fluorescence {(SAF)} microscopy},
     18974  pages = {4246-4254},
     18975  journal = {Optics Express},
     18976  volume = {12},
     18977  author = {Ruckstuhl, T. and Verdes, D.}
     18978}
     18979@article{Rohrbach2009,
     18980  number = {19},
     18981  year = {2009},
     18982  title = {Artifacts resulting from imaging in scattering media: a theoretical prediction},
     18983  pages = {3041-3043},
     18984  journal = {Optics Letters},
     18985  volume = {34},
     18986  author = {Rohrbach, A.}
     18987}
     18988@article{Murdy2010,
     18989  year = {2010},
     18990  title = {Isotropic Diffraction-Limited Focusing Using a Single Objective Lens},
     18991  pages = {203903},
     18992  journal = {Physical Review Letters},
     18993  volume = {105},
     18994  author = {Murdy, E. and Moral, E. le and Ferrand, P. and Chaumet, P.C. and Sentenac, A. }
     18995}
     18996@article{Min2009,
     18997  number = {22},
     18998  year = {2009},
     18999  title = {Imaging chromophores with undetectable fluorescence by stimulated emission microscopy},
     19000  pages = {1105-1109},
     19001  journal = {Nature},
     19002  volume = {461},
     19003  author = {Min, W. and Lu, S. and Chong, S. and Roy, R. and Holtom, G.R. and Xie, X.S.}
     19004}
     19005@inbook{Manley2010,
     19006  series = {Methods in Enzymology},
     19007  year = {2010},
     19008  title = {Single-Particle Tracking Photoactivated Localization
     19009Microscopy for Mapping Single-Molecule Dynamics},
     19010  pages = {109-120},
     19011  volume = {475},
     19012  chapter = {5},
     19013  publisher = {Elsevier},
     19014  author = {Manely, S. and Gillette, J.M. and Lippincott-Schwartz, J.}
     19015}
     19016@article{Luisier2007,
     19017  number = {3},
     19018  year = {2007},
     19019  title = {A New {SURE} Approach to Image Denoising:
     19020Interscale Orthonormal Wavelet Thresholding},
     19021  pages = {593-606},
     19022  journal = {IEEE Transactions on Image Processing},
     19023  volume = {16},
     19024  author = {Luisier, F. and Blu, T. and Unser, M.}
     19025}
     19026@article{Krizek2011,
     19027  number = {4},
     19028  year = {2011},
     19029  title = {Minimizing detection errors in single molecule localization microscopy},
     19030  pages = {3226-3235},
     19031  journal = {Optics Express},
     19032  volume = {19},
     19033  author = {Krizek, P. and Raska, I. and Hagen, G.M}
     19034}
     19035@article{Kaufmann2011a,
     19036  year = {2011},
     19037  title = {Imaging label-free intracellular structures by localisation microscopy},
     19038  pages = {348-352},
     19039  journal = {Micron},
     19040  volume = {42},
     19041  author = {Kaufmann, R. and {M\"uller}, P. and Hausmann, M. and Cremer, C.}
     19042}
     19043@article{Kaufmann2011,
     19044  number = {1},
     19045  year = {2011},
     19046  title = {Analysis of {Her2/neu} membrane protein clusters in different types of breast cancer cells using localization microscopy},
     19047  pages = {46-54},
     19048  journal = {Journal of Microscopy},
     19049  volume = {242},
     19050  author = {Kaufmann, R. and {M\"uller}, P. and Hildenbrand, G. and Hausmann, M. and Cremer, C.}
     19051}
     19052@article{Fujita2007,
     19053  year = {2007},
     19054  title = {High-Resolution Confocal Microscopy by Saturated Excitation of Fluorescence},
     19055  pages = {228105},
     19056  journal = {Physical Review Letters},
     19057  volume = {99},
     19058  author = {Fujita, K. and Kobayashi, M. and Kawano, S. and YTamanaka, M. and Kawata, S.}
     19059}
     19060@article{Fahrbach2010,
     19061  year = {2010},
     19062  title = {Microscopy with self-reconstructing beams},
     19063  note = {DOI: 10.1038/NPHOTON.2010.204},
     19064  journal = {Nature photonics},
     19065  author = {Fahrbach, F.O. and Simon, P. and Rohrbach, A.}
     19066}
     19067@article{Debarre2007,
     19068  number = {13},
     19069  year = {2007},
     19070  title = {Image based adaptive optics through optimisation of low spatial frequencies},
     19071  pages = {8176-8190},
     19072  journal = {Optics Express},
     19073  volume = {15},
     19074  author = {Debarre, D. and Booth, M.J. and Wilson, T.}
     19075}
     19076@article{Cox2004,
     19077  year = {2004},
     19078  title = {Practical Limits of Resolution in Confocal and Non-Linear Microscopy},
     19079  pages = {18-22},
     19080  journal = {MICROSCOPY RESEARCH AND TECHNIQUE},
     19081  volume = {63},
     19082  author = {Cox, G. and Sheppard, C.J.R.}
     19083}
     19084@article{Cox1982,
     19085  number = {5},
     19086  year = {1982},
     19087  title = {Improvement in resolution by nearly confocal microscopy},
     19088  pages = {778-781},
     19089  journal = {Applied Optics},
     19090  volume = {21},
     19091  author = {Cox, I.J. and Sheppard, C.J.R. and Wilson, T.}
     19092}
     19093@article{Dobrucki2007,
     19094  year = {2007},
     19095  title = {Scattering of Exciting Light by Live Cells in Fluorescence Confocal Imaging: Phototoxic Effects and Relevance for {FRAP} Studies},
     19096  pages = {1778-1786},
     19097  journal = {Biophysical Journal},
     19098  volume = {93},
     19099  author = {Dobrucki, J.W. and Feret, D. and Noatynska, A.}
     19100}
     19101@phdthesis{Wicker2010,
     19102  month = {October},
     19103  year = {2010},
     19104  title = {Increasing resolution and light efficiency
     19105in fluorescence microscopy},
     19106  address = {United Kingdom},
     19107  school = {King's College London},
     19108  author = {Wicker, K.}
     19109}
     19110@article{PoissonNoise,
     19111  number = {1},
     19112  year = {1965},
     19113  title = {Noise in Photoemission Current},
     19114  pages = {79-80},
     19115  journal = {Applied Optics},
     19116  volume = {4},
     19117  author = {Fried, D.L.}
     19118}
     19119@article{Kiel2007,
     19120  year = {2007},
     19121  title = {Direct Monitoring of Formation and Dissociation of Individual Metal Complexes by Single-Molecule Fluorescence Spectroscopy},
     19122  pages = {3363-3366},
     19123  journal = {Angewandte Chemie Interational Edition},
     19124  volume = {46},
     19125  author = {Kiel, A. and Kovacs, J. and Mokhir, A. and {Kr\"amer}, R. and Herten, D.-P.}
     19126}
     19127@article{Schwering2011,
     19128  year = {2011},
     19129  title = {Far-Field Nanoscopy with Reversible Chemical Reactions},
     19130  pages = {2940-2945},
     19131  journal = {Angewandte Chemie International Edition},
     19132  volume = {50},
     19133  author = {Schwering, M. and Kiel, A. and Kurz, A. and Lymperopoulos,K. and {Spr\"odefeld}, A. and {Kr\"amer}, R. and Herten, D.-P. }
     19134}
     19135@article{Rossow2010,
     19136  number = {11},
     19137  year = {2010},
     19138  title = {Raster image correlation spectroscopy in live cells},
     19139  pages = {1761-1773},
     19140  journal = {Nature Protocols},
     19141  volume = {5},
     19142  author = {Rossow, M.J. and Sasaki, J.M. and Digmann, M.A. and Gratton, E.}
     19143}
     19144@inproceedings{Knutsson1987,
     19145  month = {September},
     19146  year = {1987},
     19147  title = {A tensor representation of 3-D structure},
     19148  booktitle = {5th IEEE-ASSP and EURASIP Workshop on Multidimensional Signal Processing},
     19149  address = {Noorwijkerhoudt, Netherlands},
     19150  author = {Knutsson, H.}
     19151}
     19152@inproceedings{Serino2011,
     19153  series = {Lecture Notes in Computer Science 6688},
     19154  year = {2011},
     19155  title = {Using the Skeleton for 3D Object Decomposition},
     19156  booktitle = {Image Analysis},
     19157  pages = {447-456},
     19158  editor = {Heyden, A. and Kahl, F.},
     19159  address = {Heidelberg},
     19160  publisher = {Springer},
     19161  author = {Serino, L. and Sanniti di Baja, G. and Arcelli, C.}
     19162}
     19163@inproceedings{Schlager2011,
     19164  series = {Lecture Notes in Computer Science 6688},
     19165  year = {2011},
     19166  title = {Coherence Probe Microscopy Imaging and
     19167Analysis for Fiber-Reinforced Polymers},
     19168  booktitle = {Image Analysis},
     19169  pages = {424-434},
     19170  editor = {Heyden, A. and Kahl, F.},
     19171  address = {Heidelberg},
     19172  publisher = {Springer},
     19173  author = {Schlager1, V. and Schausberger, S.E. and Stifter, D. and Heise1, B.}
     19174}
     19175@inproceedings{Malmberg2011,
     19176  series = {Lecture Notes in Computer Science 6688},
     19177  year = {2011},
     19178  title = {Generalized Hard Constraints for Graph
     19179Segmentation},
     19180  booktitle = {Image Analysis},
     19181  pages = {36-47},
     19182  editor = {Heyden, A. and Kahl, F.},
     19183  address = {Heidelberg},
     19184  publisher = {Springer},
     19185  author = {Malmberg, F. and Strand, R. and {Nystr\"om}, I.}
     19186}
     19187@inproceedings{Larsson2011,
     19188  series = {Lecture Notes in Computer Science 6688},
     19189  year = {2011},
     19190  title = {Using Fourier Descriptors and Spatial Models
     19191for Traffic Sign Recognition},
     19192  booktitle = {Image Analysis},
     19193  pages = {238-249},
     19194  editor = {Heyden, A. and Kahl, F.},
     19195  address = {Heidelberg},
     19196  publisher = {Springer},
     19197  author = {Larsson, F. and Felsberg, M.}
     19198}
     19199@inproceedings{Landstrom2011,
     19200  series = {Lecture Notes in Computer Science 6688},
     19201  year = {2011},
     19202  title = {Image Reconstruction by Prioritized
     19203Incremental Normalized Convolution},
     19204  booktitle = {Image Analysis},
     19205  pages = {176-185},
     19206  editor = {Heyden, A. and Kahl, F.},
     19207  address = {Heidelberg},
     19208  publisher = {Springer},
     19209  author = {{Landstr\"om}, A. and Nellros, F. and Jonsson, H. and Thurley, M.}
     19210}
     19211@inproceedings{Knutsson2011,
     19212  series = {Lecture Notes in Computer Science 6688},
     19213  year = {2011},
     19214  title = {Representing Local Structure Using Tensors {II}},
     19215  booktitle = {Image Analysis},
     19216  pages = {545-556},
     19217  editor = {Heyden, A. and Kahl, F.},
     19218  address = {Heidelberg},
     19219  publisher = {Springer},
     19220  author = {Knutsson, H. and Westin, C.-F. and Andersson, M.}
     19221}
     19222@inproceedings{Josth2011,
     19223  series = {Lecture Notes in Computer Science 6688},
     19224  year = {2011},
     19225  title = {Real-Time Line Detection Using Accelerated
     19226High-Resolution Hough Transform},
     19227  booktitle = {Image Analysis},
     19228  pages = {784-793},
     19229  editor = {Heyden, A. and Kahl, F.},
     19230  address = {Heidelberg},
     19231  publisher = {Springer},
     19232  author = {Josth, R. and Dubska, M. and Herout, A. and Havel, J.}
     19233}
     19234@inproceedings{Eklund2011,
     19235  series = {Lecture Notes in Computer Science 6688},
     19236  year = {2011},
     19237  title = {Using the Local Phase of the Magnitude of the
     19238Local Structure Tensor for Image Registration},
     19239  booktitle = {Image Analysis},
     19240  pages = {414-423},
     19241  editor = {Heyden, A. and Kahl, F.},
     19242  address = {Heidelberg},
     19243  publisher = {Springer},
     19244  author = {Eklund, A. and Forsberg, D. and Andersson, M. and Knutsson, H.}
     19245}
     19246@inproceedings{Astrom2011,
     19247  series = {Lecture Notes in Computer Science 6688},
     19248  year = {2011},
     19249  title = {Color Persistent Anisotropic Diffusion of Images},
     19250  booktitle = {Image Analysis},
     19251  pages = {262-272},
     19252  editor = {Heyden, A. and Kahl, F.},
     19253  address = {Heidelberg},
     19254  publisher = {Springer},
     19255  author = {{\AAstr\"om}, F. and Felsberg, M. and Lenz, R.}
     19256}
     19257@article{Unser2011,
     19258  number = {11},
     19259  year = {2011},
     19260  title = {Multiresolution Monogenic Signal Analysis Using
     19261the {Riesz-Laplace} Wavelet Transform},
     19262  pages = {2402-2418},
     19263  journal = {IEEE TRANSACTIONS ON IMAGE PROCESSING},
     19264  volume = {18},
     19265  author = {Unser, M. and Sage, D. and Ville, D. van de}
     19266}
     19267@article{Frank1976,
     19268  year = {1975},
     19269  title = {Signal to noise ratio of electron micrographs obtained by cross correlation},
     19270  pages = {376-379},
     19271  journal = {Nature},
     19272  volume = {256},
     19273  author = {Frank, J. and Al-Ali, L.}
     19274}
     19275@article{Patra2005,
     19276  year = {2005},
     19277  title = {Defocused imaging of quantum-dot angular distribution of radiation},
     19278  pages = {101103},
     19279  journal = {Applied Physics Letters},
     19280  volume = {87},
     19281  author = {Patra, D. and Gergor, I. and Enderlein, J.}
     19282}
     19283@article{Toprak2006,
     19284  number = {17},
     19285  year = {2006},
     19286  title = {Defocused orientation and position imaging
     19287{(DOPI)} of myosin {V}},
     19288  pages = {6495-6499},
     19289  journal = {Proceedings of the National Academy of Sciences USA},
     19290  volume = {103},
     19291  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.}
     19292}
     19293@article{Geissbuehler2011,
     19294  number = {3},
     19295  year = {2011},
     19296  title = {Comparison between {SOFI} and {STORM}},
     19297  pages = {408-420},
     19298  journal = {BIOMEDICAL OPTICS EXPRESS},
     19299  volume = {2},
     19300  author = {Geissbuehler, S. and Dellagiacoma, C. and Lasser, T.}
     19301}
     19302@article{Enderlein2005,
     19303  year = {2005},
     19304  title = {Performance of Fluorescence Correlation
     19305Spectroscopy for Measuring Diffusion and
     19306Concentration},
     19307  pages = {2324-2336},
     19308  journal = {ChemPhysChem},
     19309  volume = {6},
     19310  author = {Enderlein, J. and Gregor, I. and Patra, D. and Dertinger, T. and Kaupp, U.B.}
     19311}
     19312@article{Dertinger2007,
     19313  year = {2007},
     19314  title = {Two-Focus Fluorescence Correlation
     19315Spectroscopy: A New Tool for Accurate and
     19316Absolute Diffusion Measurements},
     19317  pages = {433-443},
     19318  journal = {ChemPhysChem},
     19319  volume = {8},
     19320  author = {Dertinger, T. and Pacheco, V. and Hocht, I. van der and Hartmann, R. and Gregor, I. and Enderlein, J.}
     19321}
     19322@article{Pusey2011,
     19323  year = {2011},
     19324  title = {Brownian Motion Goes Ballistic},
     19325  pages = {802-803},
     19326  journal = {Science},
     19327  volume = {332},
     19328  author = {Pusey, P.N.}
     19329}
     19330@article{Maye2010,
     19331  year = {2010},
     19332  title = {Switching binary states of nanoparticle
     19333superlattices and dimer clusters by {DNA} strands},
     19334  pages = {116},
     19335  journal = {Nature Nanotechnology},
     19336  volume = {5},
     19337  author = {Maye, M.M. and Kumara, M.T. and Nykypanchuk, D. and Sherman, W.B. and Gang, O.}
     19338}
     19339@article{Leunissen2011,
     19340  year = {2011},
     19341  title = {Numerical study of {DNA}-functionalized microparticles and nanoparticles: Explicit pair potentials and their implications for phase behavior},
     19342  pages = {084702},
     19343  journal = {Journal of Chemical Physics},
     19344  volume = {134},
     19345  author = {Leunissen, M.E. and Frenkel, D.}
     19346}
     19347@article{Chan2001,
     19348  number = {2},
     19349  year = {2001},
     19350  title = {Active Contours Without Edges},
     19351  pages = {266-277},
     19352  journal = {IEEE TRANSACTIONS ON IMAGE PROCESSING},
     19353  volume = {10},
     19354  author = {Chan, T.T. and Vese, L.A.}
     19355}
     19356@article{Yen1995,
     19357  number = {3},
     19358  year = {1995},
     19359  title = {A new criterion for automatic multilevel thresholding},
     19360  pages = {370-378},
     19361  journal = {IEEE Transactions on Image Processing},
     19362  volume = {4},
     19363  author = {Yen, J.-C. and Chang, F.-J. and Chang, S.}
     19364}
     19365@article{Kapur1985,
     19366  number = {3},
     19367  year = {1985},
     19368  title = {A new method for gray-level picture thresholding using the entropy of the histogram},
     19369  pages = {273-285},
     19370  journal = {Computer Vision, Graphics, and Image Processing},
     19371  volume = {29},
     19372  author = {Kapur, J.N. and Sahdoo, P.K. and Wong, A.K.C.}
     19373}
     19374@article{Sezgin2004,
     19375  number = {1},
     19376  year = {2004},
     19377  title = {Survey over image thresholding techniques
     19378and quantitative performance evaluation},
     19379  pages = {146-165},
     19380  journal = {Journal of Electronic Imaging},
     19381  volume = {13},
     19382  author = {Sezgin, M. and Sankur, B.}
     19383}
     19384@article{Kittler1986,
     19385  number = {1},
     19386  year = {1986},
     19387  title = {Minimum error thresholding},
     19388  pages = {41-47},
     19389  journal = {Pattern Recognition},
     19390  volume = {19},
     19391  author = {Kittler, J. and Illingworth, J.}
     19392}
     19393@article{Otsu1979,
     19394  year = {1979},
     19395  title = {A threshold selection method from gray-level histograms},
     19396  pages = {62-66},
     19397  journal = {IEEE Transactions on Systems, Man and Cybernetics },
     19398  volume = {9},
     19399  author = {Otsu, N.}
     19400}
     19401@article{Zeskind2007,
     19402  number = {7},
     19403  year = {2007},
     19404  title = {Nucleic acid and protein mass mapping by live-cell deep-ultraviolet microscopy},
     19405  pages = {567-569},
     19406  journal = {Nature Methos},
     19407  volume = {4},
     19408  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.}
     19409}
     19410@article{Dorenbos2008,
     19411  year = {2008},
     19412  title = {Low noise superconducting single photon detectors on silicon},
     19413  pages = {131101},
     19414  journal = {Applied Physics Letters},
     19415  volume = {93},
     19416  author = {Dorenbos, S.N. and Reiger, E.M. and Perinetti, U. and Zwiller, V. and Zijlstra, T. and Klapwijk, T.M.}
     19417}
     19418@article{Goltsman2001,
     19419  number = {6},
     19420  year = {2001},
     19421  title = {Picosecond superconduction single-photon optical detector},
     19422  pages = {705-707},
     19423  journal = {Applied Physics Letters},
     19424  volume = {79},
     19425  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.}
     19426}
     19427@article{Shore2011,
     19428  number = {2},
     19429  year = {2011},
     19430  title = {Optimal acquisition scheme for subwavelength localization microscopy of bleachable fluorophores},
     19431  pages = {289-291},
     19432  journal = {Optics Letters},
     19433  volume = {36},
     19434  author = {Shore, E. and Small, A.}
     19435}
     19436@article{Stallinga2011,
     19437  year = {2011},
     19438  title = {Optical trapping at low numerical aperture},
     19439  pages = {11027},
     19440  journal = {Journal of the European Optical Society},
     19441  volume = {6},
     19442  author = {Stallinga, S.}
     19443}
     19444@article{Ulbrich2007,
     19445  number = {4},
     19446  year = {2007},
     19447  title = {Subunit counting in membrane-bound proteins},
     19448  pages = {319-321},
     19449  journal = {Nature Methods},
     19450  volume = {4},
     19451  author = {Ulbrich, M.H. and Isacoff, E.Y.}
     19452}
     19453@article{Ulbrich2007-S3,
     19454  number = {4},
     19455  year = {2007},
     19456  title = {Subunit counting in membrane-bound proteins},
     19457  pages = {319-321},
     19458  note = {Supplementary Methods},
     19459  journal = {Nature Methods},
     19460  volume = {4},
     19461  author = {Ulbrich, M.H. and Isacoff, E.Y.}
     19462}
     19463@article{Grunwald2011,
     19464  year = {2011},
     19465  title = {Nuclear export dynamics of {RNA}-protein complexes},
     19466  pages = {333-341},
     19467  journal = {Nature},
     19468  volume = {475},
     19469  author = {{Gr\"unwald}, D. and Singer, R.H. and Rout, M.}
     19470}
     19471@inbook{Luengo2011,
     19472  series = {Biological and Medical Physics, Biomedical Engineering Series},
     19473  year = {2011},
     19474  title = {Medical Image Processing: Techniques and Applications},
     19475  note = {ISBN 978-1-4419-9769-2},
     19476  editor = {Dougherty, G.},
     19477  chapter = {Rapid prototyping of image analysis applications},
     19478  publisher = {Springer},
     19479  author = {Luengo Hendriks, C. L. and Malm, P. and  Bengtsson, E.}
     19480}
     19481@article{Knowles2011,
     19482  number = {36},
     19483  year = {2011},
     19484  title = {Observation of spatial propagation of amyloid
     19485assembly from single nuclei},
     19486  pages = {14746-14751},
     19487  journal = {Proceedings of the National Academy of Science USA},
     19488  volume = {108},
     19489  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.}
     19490}
     19491@article{Kampmannetal2011,
     19492  number = {6},
     19493  year = {2011},
     19494  title = {Mapping the orientation of nuclear pore proteins in living cells with polarized fluorescence microscopy},
     19495  pages = {643-650},
     19496  journal = {Nature structural & molecular biology},
     19497  volume = {18},
     19498  author = {Kampmann, M. and Atkinson, C.E. and Mattheyses, A.L. and Simon, S.M.}
     19499}
     19500@article{Nature08-2011,
     19501  year = {2011},
     19502  title = {Suppression of the coffee-ring effect by
     19503shape-dependent capillary interactions},
     19504  pages = {308-311},
     19505  journal = {Nature},
     19506  volume = {476},
     19507  author = {Yunker, P.J. and Still, T. and Lohr, M.A. Yodh, A.G.}
     19508}
     19509@article{Park2004,
     19510  number = {3},
     19511  year = {2004},
     19512  title = {Nanometre localization of single {ReAsH} molecules},
     19513  pages = {199-205},
     19514  journal = {Journal of Microscopy},
     19515  volume = {216},
     19516  author = {Park, H. and Hanson, T. and Duff, S.R. and Selvin, P.R.}
     19517}
     19518@article{Martin2005,
     19519  number = {10},
     19520  year = {2005},
     19521  title = {Mammalian cell-based optimization of the biarsenical binding tetracysteine motif for improved fluorescence and affinity},
     19522  pages = {1308-1314},
     19523  journal = {Nature biotechnology},
     19524  volume = {23},
     19525  author = {Martin, B.R. and Giepmanns, B.N.G. and Adams, S.R. and Tsien, R.Y.}
     19526}
     19527@article{Kampmann2009,
     19528  number = {7},
     19529  year = {2009},
     19530  title = {Three-dimensional structure and flexibility of a membrane-coating module of the nuclear pore complex},
     19531  pages = {782-789},
     19532  journal = {Nature structural & molecular biology},
     19533  volume = {16},
     19534  author = {Kampmann, M. and Blobel, G.}
     19535}
     19536@phdthesis{Hein2009,
     19537  year = {2009},
     19538  title = {Live Cell {STED} Microscopy
     19539Using Genetically Encoded Markers},
     19540  address = {{G\"ottingen}, Germany},
     19541  school = {Georg-August-{Universit\"at} {G\"ottingen} },
     19542  author = {Hein, B.}
     19543}
     19544@article{Grunwald2010,
     19545  year = {2010},
     19546  title = {In vivo imaging of labelled endogenous b-actin
     19547{mRNA} during nucleocytoplasmic transport},
     19548  pages = {604-609},
     19549  journal = {Nature},
     19550  volume = {467},
     19551  author = {{Gr\"unwald}, D. and Singer, R.H.}
     19552}
     19553@article{Delber2008,
     19554  year = {2008},
     19555  title = {A Fence-like Coat for the Nuclear Pore Membrane},
     19556  pages = {815-826},
     19557  journal = {Molecular Cell},
     19558  volume = {32},
     19559  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.}
     19560}
     19561@article{Churchman2005,
     19562  number = {5},
     19563  year = {2005},
     19564  title = {Single molecule high-resolution colocalization of {Cy3}
     19565and {Cy5} attached to macromolecules measures
     19566intramolecular distances through time},
     19567  pages = {1419-1423},
     19568  journal = {Proceedings of the National Academy of Science},
     19569  volume = {102},
     19570  author = {Churchman, L.S. and {\"Oktem}, Z. and Rock, R.S. and Dawson, J.F. and Spudich, J.A.}
     19571}
     19572@article{Brohawn2009,
     19573  year = {2008},
     19574  title = {Structural Evidence for Common Ancestry of the Nuclear Pore Complex and Vesicle Coats},
     19575  pages = {1369-1373},
     19576  journal = {Science},
     19577  volume = {322},
     19578  author = {Brohawn, S.G. and Leksa, N.C. and Spear, E.D. and Rajashankar, K.R. and Schwartz, T.U.}
     19579}
     19580@article{Beck2007,
     19581  year = {2007},
     19582  title = {Snapshots of nuclear pore complexes in action
     19583captured by cryo-electron tomography},
     19584  pages = {611-615},
     19585  journal = {Nature},
     19586  volume = {449},
     19587  author = {Beck, M. and Lucic, V. and {F\"orster}, F. and Baumeister, W. and Medalia, O.}
     19588}
     19589@article{Alber2007,
     19590  year = {2007},
     19591  title = {The molecular architecture of the nuclear
     19592pore complex},
     19593  pages = {695-701},
     19594  journal = {Nature},
     19595  volume = {450},
     19596  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.}
     19597}
     19598@article{Varbioiu2006,
     19599  number = {466-469},
     19600  year = {2006},
     19601  title = {Structural insight into yeast septin organizaiton from polarized fluorescent micrsocopy},
     19602  journal = {Nature},
     19603  volume = {443},
     19604  author = {Varabioiu, A.M. and Mitchison, T.J.}
     19605}
     19606@article{Mattheyses2010,
     19607  year = {2010},
     19608  title = {Fluorescence anisotropy reveals order and disorder of protein domains in the nuclear pore complex},
     19609  pages = {1706-1717},
     19610  journal = {Biophysical Journal},
     19611  volume = {99},
     19612  author = {Mattheyes, A.L. and Kampmann, M. and Aktinson, C.E. and Simon, S.M.}
     19613}
     19614@article{Voortman2012,
     19615  year = {2012},
     19616  title = {Fast, spatially varying {CTF} correction in {TEM}},
     19617  pages = {26-34},
     19618  journal = {Ultramicroscopy},
     19619  volume = {118},
     19620  author = {Voortman, L.M. and Franken, E.M. and Vliet, L.J. van and Rieger, B.}
     19621}
     19622@article{Hell2003a,
     19623  year = {2003},
     19624  title = {Imaging and writing at the nanoscale with focused visible light through saturable optical transitions},
     19625  pages = {859-860},
     19626  journal = {Applied Physics A},
     19627  volume = {77},
     19628  author = {Hell, S.W. and Jakobs, S. and Kastrup, L.}
     19629}
     19630@article{Huang2011,
     19631  number = {5},
     19632  year = {2011},
     19633  title = {Simultaneous multiple-emitter fitting for single molecule super-resolution imaging},
     19634  pages = {1377-1393},
     19635  journal = {Biomedical Optics Express },
     19636  volume = {2},
     19637  author = {Huang, F. and  Schwartz, S.L. and  Byars, J.M. and Lidke, K.A. }
     19638}
     19639@article{Bader2011,
     19640  year = {2011},
     19641  title = {Homo-FRET Imaging as a Tool to Quantify Protein and
     19642Lipid Clustering},
     19643  pages = {475-483},
     19644  journal = {ChemPhysChem},
     19645  volume = {12},
     19646  author = {Bader,A.N. and  Hoetzl, S. and Hofman, E.G. and   Voortman, J. and Bergen en Henegouwen, 
     19647P.M.P. van and  Meer, G. van and Gerritsen, H.C.}
     19648}
     19649@article{Bader2009,
     19650  year = {2009},
     19651  title = {Homo-FRET Imaging Enables Quantification of Protein Cluster Sizes
     19652with Subcellular Resolution},
     19653  pages = {2613-2622},
     19654  journal = {Biophysical Journal},
     19655  volume = {97},
     19656  author = {Bader,A.N. and Hofmann, E.G. and Voortman, J. and Bergen en Henegouwen, P.M.P. van and Gerritsen, H.C.}
     19657}
     19658@article{Bader2007,
     19659  number = {11},
     19660  year = {2007},
     19661  title = {Imaging of protein cluster sizes by means of
     19662confocal time-gated fluorescence anisotropy
     19663microscopy},
     19664  pages = {6934-6945},
     19665  journal = {Optics Express},
     19666  volume = {15},
     19667  author = {Bader, A.N. and  Hofman,  E.G. and  Bergen en Henegouwen, P.M.P. van and
     19668 Gerritsen,H.C.}
     19669}
     19670@article{Dange208,
     19671  number = {1},
     19672  year = {2008},
     19673  title = {Autonomy and robustness of thranslocation through the nuclear pore complex: a single molecule study},
     19674  pages = {77-86},
     19675  journal = {Journal of Cell Biology},
     19676  volume = {183},
     19677  author = {Dange, T. and {Gr\"unwald}, D. and {Gr\"unwald}, A. and Peters, R. and Kubitscheck, U.}
     19678}
     19679@article{Kubitscheck2005,
     19680  number = {2},
     19681  year = {2005},
     19682  title = {Nuclear transport of single molecules: dwell times at the nuclear pore complex},
     19683  pages = {233-243},
     19684  journal = {Journal of Cell Biology},
     19685  volume = {168},
     19686  author = {Kubitscheck, U. and {Gr\"unwald}, D. and Hoekstra, A. and Rohleder, D. and Kues, T. and Siebrasse, J.P. and Peters, R.}
     19687}
     19688@article{Arhel2006,
     19689  number = {10},
     19690  year = {2006},
     19691  title = {Quantitative four-dimensional tracking of cytoplasmic and nuclear {HIV-1} complexes},
     19692  pages = {817-824},
     19693  journal = {Nature methods},
     19694  volume = {3},
     19695  author = {Arhel, N. and Genovesio, A. and Kim, K.A. and Miko, S. and Perret, E. and Olvio-Marin, J.C. and Shorte, S. and Charneau, P.}
     19696}
     19697@article{Rout2000,
     19698  year = {2000},
     19699  title = {The yeast nuclear pore complex: Composition, architecture, and transport mechanism},
     19700  pages = {635-651},
     19701  journal = {Journal of Cell Biology},
     19702  volume = {148},
     19703  author = {Rout,M.P. and Aitchison, J.D. and Suprapto, A. and Hjertaas, K. and Zhao, Y.M. and  Chait, B.T.}
     19704}
     19705@article{Alber2007b,
     19706  year = {2007},
     19707  title = {Determining the architectures of
     19708macromolecular assemblies},
     19709  pages = {683-694},
     19710  journal = {Nature},
     19711  volume = {450},
     19712  author = {Alber, F. and Dokudovskaya2, S. and Veenhoff, L.M. and  Zhang, W. and  Kipper, J. and
     19713Devos, D. and Suprapto, A. and Karni-Schmidt, O. and  Williams, R. and  Chait, B.T. and
     19714Rout, M.P. and Sali,A.}
     19715}
     19716@article{Brohawn2009b,
     19717  number = {11},
     19718  year = {2009},
     19719  title = {Molecular architecture of the {Nup84-Nup145C-Sec13} edge element in the nuclear pore complex lattice},
     19720  pages = {1173-1178},
     19721  journal = {Nature structural & molecular biology},
     19722  volume = {16},
     19723  author = {Brohawn, S.G. and  Schwartz, T.U.}
     19724}
     19725@article{Lewis2007,
     19726  year = {2007},
     19727  title = {A nuclear envelope protein linking nuclear pore basket assembly, {SUMO} protease regulation, and {mRNA} surveillance},
     19728  pages = {813-827},
     19729  journal = {Journal of Cell Biology},
     19730  volume = {178},
     19731  author = {Lewis, A. and Felberbaum, R. and Hochstrasser, M.}
     19732}
     19733@article{Jovanovic2008,
     19734  year = {2008},
     19735  title = {Artificial nanopores that mimic the transport selectivity of the nuclear pore complex },
     19736  pages = {1023-1027},
     19737  journal = {Nature},
     19738  volume = {457},
     19739  author = {Jovanovic-Talisman, T. and Tetenbaum-Novatt, J. and McKenney, A.S. and Zilman, A. and Peters, R. and Rout, M.P. and Chait, B.T.}
     19740}
     19741@article{Kim2008,
     19742  year = {2008},
     19743  title = {A structure-permeability relationship of ultrathin nanoporous silicon membrane: a comparison with the nuclear envelope},
     19744  pages = {4230-4231},
     19745  journal = {Journal of the American Chemical Society},
     19746  volume = {130},
     19747  author = {Kim, E. and Xiong, H. and Striemer, C.C. and Fang, D.Z. and Fauchet, P.M. and McGrath, J.L. and Amemiya, S.}
     19748}
     19749@article{Debler2008,
     19750  year = {2008},
     19751  title = {A fence-like coat for the nuclear pore membrane},
     19752  pages = {815-826},
     19753  journal = {Molecular Cell},
     19754  volume = {32},
     19755  author = {Debler, E.W. and Ma, Y. and Seo, H.S. and Hsia, K.C. and Noriega, T.R. and Blobel, G. and Hoelz, A.}
     19756}
     19757@article{Rout2007,
     19758  year = {2007},
     19759  title = {Virtual gating and nuclear transport: the hole picture},
     19760  pages = {622-628},
     19761  journal = {Trends in Cell Biology},
     19762  volume = {13},
     19763  author = {Rout, M.P. and Aitchison, J.D. and Magnasco, M.O. and Chait, B.T.}
     19764}
     19765@article{Qu2004,
     19766  number = {31},
     19767  year = {2004},
     19768  title = {Nanometer-localized multiple single-molecule fluorescence microscopy},
     19769  pages = {11298-11303},
     19770  journal = {Proceedings of the National Academy of Science USA},
     19771  volume = {101},
     19772  author = {Qu, X. and Wu, D. and Mets, L. and Scherer, N.F.}
     19773}
     19774@article{Hsia2007,
     19775  year = {2007},
     19776  title = {Architecture of a coat for the nuclear pore membrane},
     19777  pages = {1313-1326},
     19778  journal = {Cell},
     19779  volume = {131},
     19780  author = {Hsia, K. C. and Savropoulos, P. and Blobel, G. and Hoelz, A.}
     19781}
     19782@article{Daigle2001,
     19783  year = {2001},
     19784  title = {Nuclear pore complexes from immobile networks and have a very low turnover in mammalian cells},
     19785  pages = {71-84},
     19786  journal = {Journal of Cell Biology},
     19787  volume = {154},
     19788  author = {Daigle, N. and Beaudouin, J. and Hartnell, L. and Imreh, G. and Hallberg, E. and Lippincott-Schwartz, J. and Ellenberg, J.}
     19789}
     19790@article{Roberti2011,
     19791  year = {2011},
     19792  title = {Confocal fluorescence anisotropy and FRAP imaging of alpha-synuclein amyloid aggregates in living cells},
     19793  pages = {e23338},
     19794  journal = {PLoS ONE},
     19795  volume = {6},
     19796  author = {Roberti, M.J. and  Jovin, T.M. and Jares-Erijman, E.}
     19797}
     19798@article{Roberti2007,
     19799  year = {2007},
     19800  title = {Fluorescence imaging of amyloid formation in living cells by a functional, tetracysteine-tagged alpha-synuclein},
     19801  pages = {345-351},
     19802  journal = {Nature Methods},
     19803  volume = {4},
     19804  author = {Roberti, M.J. and Bertoncini, C.W. and  Klement, R. and Jares-Erijman, E.A. and Jovin, T.M.}
     19805}
     19806@article{Dudkina2011,
     19807  number = {37},
     19808  year = {2011},
     19809  title = {Interaction of complexes {I, III}, and {IV} within
     19810the bovine respirasome by single particle
     19811cryoelectron tomography},
     19812  pages = {15196-15200},
     19813  journal = {Proceedings of the National Academy of Science USA},
     19814  volume = {108},
     19815  author = {Dudkina, N. and Kudryashev, M. and Stahlberg, H. and Boekema, E.J.}
     19816}
     19817@article{Rudnaya2011,
     19818  year = {2011},
     19819  title = {Defocus and twofold astigmatism correction in {HAADF-STEM}},
     19820  pages = {1043-1054},
     19821  journal = {Ultramicroscopy},
     19822  volume = {111},
     19823  author = {Rudnaya, M.E. and Broek, W. van den and Doornbos, R.M.P. and Mattheij, R.M.M. and Maubach, J.M.L.}
     19824}
     19825@article{Verdoold2011,
     19826  year = {2011},
     19827  title = {Femtomolar {DNA} detection by parallel colorimetric darkfield microscopy of functionalized gold nanoparticles},
     19828  pages = {77-81},
     19829  journal = {Biosensors and Bioelectronics},
     19830  volume = {27},
     19831  author = {Verdoold, R. and Gill, R. and Ungureanu, F. and Molenaar, R. and Kooyman, R.P.H.}
     19832}
     19833@article{Putten2011,
     19834  year = {2011},
     19835  title = {Scattering Lens Resolves Sub-100 nm Structures with Visible Light},
     19836  pages = {193905},
     19837  journal = {Physical Review Letters},
     19838  volume = {106},
     19839  author = {Putten, E.G. van and Akbulut, D. and Bertolotti, J. and Vos, W.L. and Lagendijk, A. and Mosk, A.P.}
     19840}
     19841@article{Foreman2011,
     19842  year = {2011},
     19843  title = {Fundamental limits in single-molecule orientation measurements},
     19844  pages = {093013},
     19845  journal = {New Journal of Physics},
     19846  volume = {13},
     19847  author = {Foreman, M.R. and {T\"or\"ok}, P.}
     19848}
     19849@article{Kendrick1994,
     19850  number = {27},
     19851  year = {1994},
     19852  title = {Phase-diversity wave-front sensor for imaging systems},
     19853  pages = {6533-6546},
     19854  journal = {Applied Optics},
     19855  volume = {33},
     19856  author = {Kendrick, R.L. and Acton, D.S. and Duncan, A.L.}
     19857}
     19858@article{Olivier2009,
     19859  number = {20},
     19860  year = {1009},
     19861  title = {Dynamic aberration correction for multiharmonic microscopy},
     19862  pages = {3145-3147},
     19863  journal = {Optics Letters},
     19864  volume = {34},
     19865  author = {Olivier, N. and Debarre, D. and Beaurepaire, E.}
     19866}
     19867@article{Coene1991,
     19868  year = {1991},
     19869  title = {Improved methods for the determination of the spherical aberration coefficient in high-resolution electron microscopy from micrographs of an amorphous object},
     19870  pages = {225-233},
     19871  journal = {Ultramicroscopy},
     19872  volume = {38},
     19873  author = {Coene, W.M.J. and Denteneer, T.J.J.}
     19874}
     19875@article{Saxton2000,
     19876  year = {2000},
     19877  title = {A new way of measuring microscope aberrations},
     19878  pages = {41-45},
     19879  journal = {Ultramicroscopy},
     19880  volume = {81},
     19881  author = {Saxton, W.O.}
     19882}
     19883@article{Steinecker2000,
     19884  year = {2000},
     19885  title = {Measurement of lens aberrations by means of image
     19886displacements in beam-tilt series},
     19887  pages = {149-161},
     19888  journal = {Ultramicroscopy},
     19889  volume = {81},
     19890  author = {Steinecker, A. and Mader, W.}
     19891}
     19892@phdthesis{Brinkers2011,
     19893  month = {October},
     19894  year = {2011},
     19895  title = {All that glitters is gold: },
     19896  address = {Delft, The Netherlands},
     19897  school = {Delft University of Technology},
     19898  author = {Brinkers, S.}
     19899}
     19900@article{Thust1992,
     19901  year = {1992},
     19902  title = {Quantitative high-speed matching of high-resolution electron microscopy images},
     19903  pages = {23-45},
     19904  journal = {Ultramicroscopy},
     19905  volume = {45},
     19906  author = {Thust, A. and Urban, K.}
     19907}
     19908@article{Holden2011,
     19909  number = {4},
     19910  year = {2011},
     19911  title = {{DAOSTORM}: an algorithm for high-density
     19912super-resolution microscopy},
     19913  pages = {279-280},
     19914  journal = {Nature Methods},
     19915  volume = {8},
     19916  author = {Holden, S.J. and Uphoff, S. and Kapanidis, A.N.}
     19917}
     19918@article{Tejada2011,
     19919  year = {2011},
     19920  title = {The role of {Poisson's} binomial distribution in the analysis of {TEM} images},
     19921  pages = {1553-1556},
     19922  journal = {Ultramicroscopy},
     19923  volume = {111},
     19924  author = {Tejada, A. and Dekker, A.J. den}
     19925}
     19926@article{Nejadasl2011,
     19927  year = {2011},
     19928  title = {Defocus estimationfromstroboscopiccryo-electronmicroscopydata},
     19929  pages = {1592-1598},
     19930  journal = {Ultramicroscopy},
     19931  volume = {111},
     19932  author = {Nejadasl, F. Karimi and Karuppasamy, M. and Koster, A.J. and Ravelli, R.B.G.}
     19933}
     19934@article{Barton2011,
     19935  year = {2011},
     19936  title = {In-focus electron microscopy of frozen-hydrated biological samples with a
     19937Boersch phase plate},
     19938  pages = {1696-1705},
     19939  journal = {Ultramicroscopy},
     19940  volume = {111},
     19941  author = {Barton, B. and Rhinow, D. and Walter, A. and {Schr\"oder}, R. and Benner, G. and Majorovits, E. and Matijevic, M.}
     19942}
     19943@article{Adelson1992,
     19944  number = {2},
     19945  year = {1992},
     19946  title = {Single lens stereo with a plenoptic camera},
     19947  pages = {99-106},
     19948  journal = {IEEE Transactions on Pattern Analysis and Machine Intelligence},
     19949  volume = {14},
     19950  author = {Adelson, E.H. and Wang, J.Y.A.}
     19951}
     19952@article{Deschout2012,
     19953  number = {1},
     19954  year = {2012},
     19955  title = {The influence of movement on the localization precision of sub-resolution particles in fluorescence microscopy},
     19956  pages = {97-109},
     19957  journal = {Journal of Biophotonics},
     19958  volume = {5},
     19959  author = {Deschout, H. and Neyts, K. and Breaeckmans, K.}
     19960}
     19961@article{Zhou2011,
     19962  number = {12},
     19963  year = {2011},
     19964  title = {Computational Cameras: Convergence of Optics and Processing},
     19965  pages = {3322-3340},
     19966  journal = {IEEE Transactions on Image Processing},
     19967  volume = {20},
     19968  author = {Zhou, C. and Nayar, S.K.}
     19969}
     19970@misc{patentappPAM,
     19971  month = {29 Septemeber},
     19972  year = {2011},
     19973  title = {Optical Modulator device and spatio-temporally light modulated imaging system},
     19974  howpublished = {WO 2011/116904},
     19975  author = {Jovin, T.M. and Caarls, W. and Vries, A. de}
     19976}
     19977@article{Piestun2010,
     19978  number = {19},
     19979  month = {October},
     19980  year = {2010},
     19981  title = {Performance limits on three-dimensional particle localization in photon-limited microscopy},
     19982  pages = {3306-3308},
     19983  journal = {{Optics letters}},
     19984  volume = {35},
     19985  author = {Grover, G. and Pavani, S.R.P. and Piestun, R.}
     19986}
     19987@article{Schonle2008,
     19988  number = {25},
     19989  month = {December},
     19990  year = {2008},
     19991  title = {Isotropic {3D} Nanoscopy based on single emitter switching},
     19992  pages = {20774-20788},
     19993  journal = {Optics Express},
     19994  volume = {16},
     19995  author = {Middendorff, C. von and Egner, A. and Geisler, C. and Hell, S.W. and {Sch\"onle}, A.}
     19996}
     19997@article{Moerner2010,
     19998  number = {16},
     19999  month = {October},
     20000  year = {2010},
     20001  title = {Three-dimensional localization precision of the double-helix point spread function versus astigmatism and biplane},
     20002  journal = {Applied Physics Letters},
     20003  volume = {97},
     20004  author = {Badieirostami, M. and Lew, M.D. and Thompson, M.A. and Moerner, W.E.}
     20005}
     20006@inproceedings{DeBeule2011,
     20007  year = {2011},
     20008  title = {Generation-3 programmable array microscope {(PAM)} with digital micro-mirror device {(DMD)}},
     20009  booktitle = {SPIE Proceeding Conference 7932 Session 4},
     20010  pages = {7932-15},
     20011  author = {Beule, P.A.A. de and Vried, A.H.B. de and Arndt-Jovin, D.J. and Jovin, T.M.}
     20012}
     20013@article{Greenaway2011,
     20014  year = {2011},
     20015  title = {Nanometric depth resolution from multi-focal images in microscopy},
     20016  pages = {942-951},
     20017  journal = {Journal of the royal society},
     20018  volume = {8},
     20019  author = {Dalgarno, H.I.C. and Dalgarno, P.A. and Dada, A.C. and Towers, C.E. and Gibson, G.J. and Parton, R.M. and Davis, I. and Warburton R.J. and Greenaway, A.H.}
     20020}
     20021@article{Cherny2010,
     20022  year = {2010},
     20023  title = {Stoichiometry of a regulatory splicing complex
     20024revealed by single-molecule analyses},
     20025  journal = {The EMBO Journal},
     20026  author = {Cherny, D.I. and Gooding, C. and Eperon, G.E. and Coelho, M.B. and Bagshaw, C.R. and Smith, C.W.J. and Eperon, I.C. }
     20027}
     20028@article{Xu2012,
     20029  number = {2},
     20030  year = {2012},
     20031  title = {Dual-objective {STORM} reveals three-dimensional filament organization in the actin cytoskeleton},
     20032  pages = {185-190},
     20033  journal = {Nature Methods},
     20034  volume = {9},
     20035  author = {Xu, K. and Babcock, H.P. and Zhuang, X.}
     20036}
     20037@article{Cox2012,
     20038  number = {2},
     20039  year = {2012},
     20040  title = {Bayesian localization microscopy reveals nanoscale
     20041podosome dynamics},
     20042  pages = {195-200},
     20043  journal = {Nature Methods},
     20044  volume = {9},
     20045  author = {Cox, S. and Rosten, E. and Monypenny, J. and Jovanoivc-Talisman, T. and Burnette, D.T. and Lippincott-Schwartz, J. and Jones, G.E. and Heintzmann, R.}
     20046}
     20047@article{Stallinga2012,
     20048  number = {6},
     20049  year = {2012},
     20050  title = {Position and orientation estimation of fixed dipole emitters using an effective Hermite point spread function model},
     20051  pages = {5896-5921},
     20052  journal = {Optics Express},
     20053  volume = {20},
     20054  author = {Stallinga, S. and Rieger, B.}
     20055}
     20056@article{Loeschberger2012,
     20057  number = {3},
     20058  year = {2012},
     20059  title = {Super-resolution imaging visualizes the eightfold symmetry of gp210 proteins around the nuclear pore complex and resolves the central channel with nanometer resolution},
     20060  pages = {570-575},
     20061  journal = {Journal of Cell Sciences},
     20062  volume = {125},
     20063  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.}
     20064}
     20065@article{Broek2012,
     20066  year = {2012},
     20067  title = {Fully Automated Measurement of the Modulation Transfer Function of Charge-Coupled Devices above the Nyquist Frequency},
     20068  journal = {Microscopy and Microanalysis},
     20069  author = {Broek, W. van den and Aert, A. van and Dyck, D. van}
     20070}
     20071@article{Humphry2012,
     20072  year = {2012},
     20073  title = {Ptychographic electron microscopy using high-angle dark-field scattering for sub-nanometre resolution imaging},
     20074  pages = {730-736},
     20075  note = {DOI: 10.1038/ncomms1733},
     20076  journal = {Nature communications},
     20077  volume = {3},
     20078  author = {Humphry, M.J. and Kraus, B. and Hurst, A.C. and Maiden, A.M. and Rodenburg, J.M.}
     20079}
     20080@article{Zhang2012,
     20081  number = {1},
     20082  year = {2012},
     20083  title = {{IPET} and {FETR}: Experimental Approach for Studying Molecular Structure Dynamics by Cryo-Electron Tomography of a Single-Molecule Structure},
     20084  pages = {e30249},
     20085  journal = {PLOS one},
     20086  volume = {7},
     20087  author = {Zhang, L. and ren, G.}
     20088}
     20089@mastersthesis{Nieuwenhuizen2011,
     20090  month = {March},
     20091  year = {2011},
     20092  title = {Resolution in localization microscopy},
     20093  address = {Delft, The Netherlands},
     20094  school = {Delft University of Technology},
     20095  author = {R.P.J. Nieuwenhuizen}
     20096}
     20097@book{Penczek2010,
     20098  year = {2010},
     20099  title = {Resolution Measures in Molecular Electron Microscopy},
     20100  note = {p 73-100},
     20101  volume = {482},
     20102  publisher = {Academic Press},
     20103  author = {Penczek, P.A.}
     20104}
     20105@article{Beckmann1997,
     20106  number = {5346},
     20107  year = {1997},
     20108  title = {Alignment of conduits for the nascent polypeptide chain in the ribosome-sec61 complex},
     20109  pages = {213-2126},
     20110  journal = {Science},
     20111  volume = {278},
     20112  author = {Beckmann, R. and Bubeck, D. and Grassucci, R. and Penczek, P.A. and Verschoor, A. and Blobel, G. and Frank, J.}
     20113}
     20114@article{Bottcher1997,
     20115  number = {6620},
     20116  year = {1997},
     20117  title = {Determination of the fold of the core protein of
     20118hepatitis {B} virus by electron cryomicroscopy},
     20119  pages = {88-91},
     20120  journal = {Nature},
     20121  volume = {386},
     20122  author = {{B\"ottcher}, B. and Wynne, S.A. and Crowther, R.A.}
     20123}
     20124@article{SheppardOptikVol72No4_1986,
     20125  number = {4},
     20126  year = {1986},
     20127  title = {The spatial frequency cut-off in three-dimensional imaging},
     20128  pages = {131--133},
     20129  journal = {Optik},
     20130  volume = {72},
     20131  author = {Sheppard, C.J.R.}
     20132}
     20133@article{SheppardOptikVol74No3_1986,
     20134  number = {3},
     20135  year = {1986},
     20136  title = {The spatial frequency cut-off in three-dimensional imaging II},
     20137  pages = {128--129},
     20138  journal = {Optik},
     20139  volume = {74},
     20140  author = {Sheppard, C.J.R.}
     20141}
     20142@book{Saxton1978,
     20143  year = {1978},
     20144  title = {Computer Techniques for Image Processing of Electron Microscopy},
     20145  address = {New York},
     20146  publisher = {Academic Press},
     20147  author = {Saxton, W.O.}
     20148}
     20149@article{Orlova1997,
     20150  number = {3},
     20151  year = {1997},
     20152  title = {Structure of Keyhole Limpet Hemocyanin Type 1 (KLH1) at 15 A Resolution by Electron Cryomicroscopy and Angular Reconstitution},
     20153  pages = {417-437},
     20154  journal = {Journal of Molecular Biology},
     20155  volume = {271},
     20156  author = {Orlova, E.V. and Dube, P. and Harris, J.R. and Beckman, E. and Zemlin, F. and Markl, J. and  Heel, M. van}
     20157}
     20158@article{Corless1996,
     20159  number = {1},
     20160  year = {1996},
     20161  title = {On the Lambert-W function},
     20162  pages = {329-359},
     20163  journal = {Advances in Computational Mathematics},
     20164  volume = {5},
     20165  author = {Corless, R. and Gonnet, G. and Hare, D. and Jeffrey, D. and Knuth, D.}
     20166}
     20167@article{Barry2000,
     20168  number = {1-2},
     20169  year = {2000},
     20170  title = {Analytical approximations for real values of the {Lambert W-function}},
     20171  pages = {95-103},
     20172  journal = {Mathematics and Computers in Simulation},
     20173  volume = {53},
     20174  author = {Barry,D.A.  and  Parlange, J.-Y. and  Li, L. and  Prommer, H. and Cunningham, C.J. and Stagnitti, F.}
     20175}
     20176@article{Ram2009,
     20177  number = {8},
     20178  year = {2009},
     20179  title = {Improved single particle localization accuracy with dual objective multifocal plane mircoscopy},
     20180  pages = {6881-6898},
     20181  journal = {Optics Express},
     20182  volume = {17},
     20183  author = {Ram, S. and Prabhat, P. and Ward, E.S. and Ober, R.J.}
     20184}
     20185@article{Wong2011,
     20186  number = {3},
     20187  year = {2011},
     20188  title = {Limit of the Accuracy of Parameter Estimation for Moving Single Molecules Imaged by Fluorescence Microscopy},
     20189  pages = {895-911},
     20190  journal = {IEEE Transactions on Signal Processing},
     20191  volume = {59},
     20192  author = {Wong, Y. and Lin, Z. and Ober, R.J.}
     20193}
     20194@article{Chao2012,
     20195  year = {2012},
     20196  title = {Fisher information matrix for branching processes
     20197with application to electron-multiplying charge-coupled devices},
     20198  pages = {349-379},
     20199  journal = {Multidimensional System and Signal Processing},
     20200  volume = {23},
     20201  author = {Chao, J. and Ward, E.S. and Ober, R.J.}
     20202}
     20203@article{Dempsey2011,
     20204  number = {12},
     20205  year = {2011},
     20206  title = {Evaluation of fluorophores for optimal performance in localization-based super-resolution imaging},
     20207  pages = {1027-1031},
     20208  journal = {Nature Methods},
     20209  volume = {8},
     20210  author = {Dempsey, G.T. and Vaughan, J.C. and Chen, K.H. and Bates, M. and Zhuang, X.}
     20211}
     20212@article{Manely2008,
     20213  number = {2},
     20214  year = {2008},
     20215  title = {High-density mapping of single-molecule trajectories with photoactivated localization microscopy},
     20216  pages = {156-158},
     20217  journal = {Nature Methods},
     20218  volume = {5},
     20219  author = {Manely, S. and Gilette, J.M. and Patterson, G.H. and Shroff, H. and Hess, H.F. and Betzig, E. and Lippincott-Schwarz, J.}
     20220}
     20221@article{Wicker2010a,
     20222  year = {2010},
     20223  title = {Single-shot optical sectioning using polarization-coded structured illumination},
     20224  pages = {084010},
     20225  journal = {Journal of Optics},
     20226  author = {Wicker, K. and Heintzmann, R.}
     20227}
     20228@article{Schoen2011,
     20229  year = {2011},
     20230  title = {Binding-Activated Localization Microscopy of {DNA} Structures},
     20231  journal = {Nano Letters},
     20232  author = {Schoen, I. and Ries, J. and Klotzsch, E. and Ewers, H. and Vogel, V.}
     20233}
     20234@article{Vrabioiu2006,
     20235  number = {28},
     20236  year = {2006},
     20237  title = {Structural insights into yeast septin organization
     20238from polarized fluorescence microscopy},
     20239  pages = {446-449},
     20240  journal = {Nature},
     20241  volume = {443},
     20242  author = {Vrabioiu, A.M. and Mitschison, T.J.}
     20243}
     20244@article{Lukosz1962a,
     20245  number = {4},
     20246  year = {1962},
     20247  title = {{\"Ubertragung} nicht-negativer Signale durch lineare Filter},
     20248  pages = {335-364},
     20249  journal = {Journal of Modern Optics},
     20250  volume = {9},
     20251  author = {Lukosz, W.}
     20252}
     20253@article{Fitzhugh1983,
     20254  year = {1983},
     20255  title = {Statistical Properties of the Asymmetric Random Telegraph Signal, with Applications to Single-Channel Analysis},
     20256  pages = {75-89},
     20257  journal = {Mathematical Biosciences},
     20258  volume = {64},
     20259  author = {R. Fitzhugh}
     20260}
     20261@article{Bobroff1986,
     20262  number = {6},
     20263  year = {1986},
     20264  title = {Position measurement with a resolution and noiselimited instrument},
     20265  pages = {1152-1157},
     20266  journal = {Review of Scientifric Instruments},
     20267  volume = {57},
     20268  author = {N. Bobroff}
     20269}
     20270@article{Heintzmann2007,
     20271  year = {2007},
     20272  title = {Estimating missing information by maximum likelihood deconvolution},
     20273  pages = {136-144},
     20274  journal = {Micron},
     20275  volume = {38},
     20276  author = {Heintzmann, R.}
     20277}
     20278@article{Annibale2011,
     20279  number = {7},
     20280  year = {2011},
     20281  title = {Identification of clustering artifacts in
     20282photoactivated localization microscopy},
     20283  pages = {527-528},
     20284  journal = {Nature Methods},
     20285  volume = {8},
     20286  author = {Annibale, P. and Vanni, S. and Scarelli, M. and Rothlisberger, U. and Radenovic, A.}
     20287}
     20288@article{Ta2010,
     20289  number = {1},
     20290  year = {2010},
     20291  title = {An Extended Scheme for Counting Fluorescent Molecules by Photon- Antibunching},
     20292  pages = {119-124},
     20293  journal = {Laser Physics},
     20294  volume = {20},
     20295  author = {Ta, H. and Wolfrum, J. and Herten, D.-P.}
     20296}
     20297@article{Tian2012,
     20298  number = {8},
     20299  year = {2012},
     20300  title = {Experimental compressive phase space tomography},
     20301  pages = {8296-8308},
     20302  journal = {Optics Express},
     20303  volume = {20},
     20304  author = {Tian, L. and Lee, J. and Oh, S.B. and Barbastathis, G.}
     20305}
     20306@article{Waller2011,
     20307  number = {3},
     20308  year = {2011},
     20309  title = {Phase and amplitude imaging from noisy images by Kalman filtering},
     20310  pages = {2805-2815},
     20311  journal = {Optics Express},
     20312  volume = {19},
     20313  author = {Waller, L. and Tsang, M. and Ponda, S. and Young Yang, S. and Barbastathis, G.}
     20314}
     20315@inproceedings{Kurz2012,
     20316  series = {SPIE},
     20317  year = {2012},
     20318  title = {Quantification of fluorescent samples by photon-antibunching},
     20319  booktitle = {Single Molecule Spectroscopy and Superresolution Imaging V},
     20320  pages = {82280K-1},
     20321  editor = {Enderlein, J. and Karol, Z. and Erdmann, R. and Koberling, F. and Gregor, I.},
     20322  author = {Kurz, A. and Schwering, M. and Herten, D.-P.}
     20323}
     20324@article{Harms1999,
     20325  year = {1999},
     20326  title = {Single-Molecule Anisotropy Imaging},
     20327  pages = {2864-2870},
     20328  journal = {Bipphysical Journal},
     20329  volume = {77},
     20330  author = {Harms, G.S. and Sonnleitner, M. and {Sch\"utz}, G.J. and Gruber, H.J. and Schmidt, T.}
     20331}
     20332@article{Uji2006,
     20333  year = {2006},
     20334  title = {Visualizing spatial and temporal heterogeneity of single molecule rotational diffusion in a  glassy polymer by defocused wide-field imaging},
     20335  pages = {2511-2518},
     20336  journal = {Polymer},
     20337  volume = {47},
     20338  author = {Uij-i, H. and Melnikov, S.M. and Deres, A. Bergamini, G. and Schryver, F. de and Herrmann, A. and {M\"ullen}, K. and Enderlein, J. and Hofkens, J.}
     20339}
     20340@article{Ruiter1997,
     20341  year = {1997},
     20342  title = {Single Molecule Rotational and Translational Diffusion Observed by Near-Field Scanning Optical Microscopy},
     20343  pages = {7318-7323},
     20344  journal = {Journal of Physical Chemistry},
     20345  volume = {101},
     20346  author = {Ruiter, A.G.T. and Veerman, J.A. and Garcia-Parajo, M.F. and Hulst, N.F. van}
     20347}
     20348@article{Pieper2011,
     20349  year = {2011},
     20350  title = {Fluorescence correlation spectroscopy as a tool  for measuring the rotational diffusion of macromolecules},
     20351  pages = {1-11},
     20352  journal = {Chemical Physics Letters},
     20353  volume = {516},
     20354  author = {Pieper, C.M. and Enderlein, J.}
     20355}
     20356@article{Loman2011,
     20357  year = {2010},
     20358  title = {Measuring rotational diffusion of macromolecules by fluorescence correlation spectroscopy},
     20359  pages = {627-636},
     20360  journal = {Photochem. Photobiol. Sci.},
     20361  volume = {9},
     20362  author = {Loman, A. and Gergor, I. and Stutz, C. and Mund, M. and Enderlein, J.}
     20363}
     20364@article{Adhikarietal2011,
     20365  year = {2011},
     20366  title = {Temperature dependent single molecule rotational dynamics in {PMA}},
     20367  pages = {1849-1856},
     20368  journal = {Phys. Chem. Chem. Phys.},
     20369  volume = {13},
     20370  author = {Adhikari, S. and Selmke, M. and Cichos, F.}
     20371}
     20372@article{Malkusch2012,
     20373  year = {2012},
     20374  title = {Coordinate-based colocalization analysis of single-molecule localization microscopy data},
     20375  pages = {1-10},
     20376  journal = {Histochemistry and Cell Biology},
     20377  volume = {137},
     20378  author = {Malkusch, S. and Endesfelder, U. and Mondry, J. and Helleri, M. and Verveer, P.J. and Heilemann, M.}
     20379}
     20380@article{Kazantsev2010,
     20381  year = {2010},
     20382  title = {Fully three-dimensional defocus-gradient corrected backprojection in cryoelectron microscopy},
     20383  pages = {1128-1142},
     20384  journal = {Ultramicroscopy},
     20385  volume = {110},
     20386  author = {Kazantsev, I. and Klukowska, J. and Herman, G.T. and Cernetic, L.}
     20387}
     20388@article{Mariani2011,
     20389  year = {2011},
     20390  title = {Simulation and correction of electron images of tilted planar weak-phase samples},
     20391  pages = {259-268},
     20392  journal = {Journal of Structural Biology},
     20393  volume = {174},
     20394  author = {Mariani, V. and Schenk, A.D. and Philippsen, A. and Engel, A.}
     20395}
     20396@inproceedings{Studer2012,
     20397  series = {Proceedings of the SPIE},
     20398  year = {2012},
     20399  title = {Hyperspectral fluorescence microscopy based on compressed sensing },
     20400  booktitle = {Three-Dimensional and Multidimensional Microscopy: Image Acquisition and Processing XIX},
     20401  note = {doi: 10.1117/12.908532},
     20402  editor = {Conchello, J.-A. and Cogswell, C.J. and  Wilson, T. and  Brown, T.G.},
     20403  author = {Studer, V. and Bobin, J. and Chahid, M. and Moussavi, H. and Candes, E. and Dahan, M.}
     20404}
     20405@article{Gabor1946b,
     20406  year = {1946},
     20407  title = {Theory of Communication: Part II: The analysis of hearing},
     20408  pages = {442-445},
     20409  journal = {Journal of the Institution of Electrical Engineers},
     20410  volume = {93},
     20411  author = {Gabor, D.}
     20412}
     20413@article{Gabor1946c,
     20414  year = {1946},
     20415  title = {Theory of Communication: Part III: Frequency Compression and Expansion},
     20416  pages = {445-457},
     20417  journal = {Journal of the Institution of Electrical Engineers},
     20418  volume = {93},
     20419  author = {Gabor, D.}
     20420}
     20421@article{Chruchmann2012,
     20422  year = {2012},
     20423  title = {Colocalization of fluorescent probes: accurate and precise registration with  nanometer resolution},
     20424  pages = {141-150},
     20425  note = {doi:10.1101/pdb.top067918},
     20426  journal = {Cold Spring Harbor Protocolls},
     20427  author = {Churchmann, L.S. and Spudich, J.A.}
     20428}
     20429@article{Dedecker2009,
     20430  year = {2012},
     20431  title = {Defocused Wide-field Imaging Unravels Structural and Temporal Heterogeneity in Complex Systems},
     20432  pages = {1079-1090},
     20433  journal = {Advanced Materials},
     20434  volume = {21},
     20435  author = {Dedecker, P. and Muls, B. and Deres, A. and Uji-i, H. and Hotta, J. and Sliwa, M. and Soumillion, J.-P. and {M\"ullen}, K. and Enderlein, J. and Hofkens, J.}
     20436}
     20437@article{Ha1998,
     20438  number = {10},
     20439  year = {1998},
     20440  title = {Hindered Rotational Diffusion and Rotational Jumps of Single Molecules},
     20441  pages = {2093-2096},
     20442  journal = {Physical Review Letters},
     20443  volume = {80},
     20444  author = {Ha, T. and Glass, J. and Enderle, T. and Chemla, D.S. and Weiss, S.}
     20445}
     20446@article{Bartko2002,
     20447  number = {2},
     20448  year = {2002},
     20449  title = {Three-Dimensional Single Molecule Rotational Diffusion in Glassy State Polymer Films},
     20450  pages = {026101},
     20451  journal = {Physical Review Letters},
     20452  volume = {89},
     20453  author = {Bartko, A.P. and Xu, K. and Dickson, R.M.}
     20454}
     20455@article{Gould2008,
     20456  number = {12},
     20457  year = {2008},
     20458  title = {Nanoscale imaging of molecular positions and anisotropies},
     20459  pages = {1027-1031},
     20460  journal = {Nature Methods},
     20461  volume = {5},
     20462  author = {Gould, T.J. and Gunewardene, M.S. and Gudheti, M.V. and Verkhusha, V.V. and Yin, S.-R. and Gosse, J.A. and Hess, S.T.}
     20463}
     20464@article{Hernando2006,
     20465  year = {2006},
     20466  title = {Effect of Disorder on Ultrafast Exciton Dynamics Probed by Single Molecule Spectroscopy},
     20467  pages = {216403},
     20468  journal = {Physical Review Letters},
     20469  volume = {97},
     20470  author = {Hernando, J. and Dijk, E.M.H.P. van and Hoogenboom, J.P. and Garcia-Lopez, J.-J. and Reinhoudt, D.N. and Crego-Calama, M. and Garcia-Parajo, M.F. and Hulst, N.F. van}
     20471}
     20472@article{Simmonds2011,
     20473  number = {24},
     20474  year = {2011},
     20475  title = {Three dimensional laser microfabrication in diamond using a dual adaptive optics system},
     20476  pages = {24122-24128},
     20477  journal = {Optics Express},
     20478  volume = {19},
     20479  author = {Simmonds, R.D. and Salter, P.S. and Jesacher, A. and Booth, M.J.}
     20480}
     20481@article{Cumming2011,
     20482  number = {10},
     20483  year = {2011},
     20484  title = {Adaptive aberration compensation for three-dimensional micro-fabrication of photonic crystals in lithium niobate},
     20485  pages = {9419-9426},
     20486  journal = {Optics Express},
     20487  volume = {19},
     20488  author = {Cumming, B.P. and Jesacher, A. and Booth, M.J. and Wilson, T. and Gu, M.}
     20489}
     20490@article{Marshall2011,
     20491  number = {5},
     20492  year = {2011},
     20493  title = {Three-dimensional imaging of direct-written photonic structures},
     20494  pages = {695-697},
     20495  journal = {Optics Letters},
     20496  volume = {36},
     20497  author = {Marshall, G.D. and Jesacher, A. and Thayil, A. and Withford, M.J. and Booth, M.}
     20498}
     20499@article{Chizhik2011,
     20500  year = {2011},
     20501  title = {Probing the Radiative Transition of Single m olecules with a Tunable Microresonator},
     20502  pages = {1700-1703},
     20503  journal = {Nano Letters},
     20504  volume = {11},
     20505  author = {Chizihik, A.I. and Chizhik, A.M. and Khoptyar, D. and {B\"ar}, S. and Meixner, A.J. and Enderlein, J.}
     20506}
     20507@article{Kalaidzidis2007,
     20508  year = {2007},
     20509  title = {Intracelluar objects tracking},
     20510  pages = {569-578},
     20511  journal = {European Journal of Cell Biology},
     20512  volume = {86},
     20513  author = {Kalaidzidis, Y.}
     20514}
     20515@article{Kalaidzidis2009,
     20516  year = {2009},
     20517  title = {Multiple objects tracking in fluorescence microscopy},
     20518  pages = {57-80},
     20519  journal = {Journal of Mathematical Biology},
     20520  volume = {58},
     20521  author = {Kalaidzidis, Y.}
     20522}
     20523@article{Rink2005,
     20524  year = {2005},
     20525  title = {Rab Conversion as a Mechanism of Progression
     20526from Early to Late Endosomes},
     20527  pages = {735-749},
     20528  journal = {Cell},
     20529  volume = {122},
     20530  author = {Rink, J. and Ghigo, E. and Kalaidzidis, Y. and Zerial, M.}
     20531}
     20532@inproceedings{Bryne2012,
     20533  month = {May 2-5},
     20534  year = {2012},
     20535  title = {MODELS FOR BIOMEDICAL IMAGE RECONSTRUCTION
     20536BASED ON INTEGRAL APPROXIMATION METHODS},
     20537  booktitle = {IEEE International Symposium on Biomedical Imaging},
     20538  pages = {70-73},
     20539  address = {Barcelona, Spain},
     20540  author = {Bryne, C. and Gordon, D. and Heilper, D.},
     20541  organization = {IEEE}
     20542}
     20543@inproceedings{Becker2012,
     20544  month = {May 2-5},
     20545  year = {2012},
     20546  title = {FROM TIMELAPSE-DATA TO GENEALOGIC TREES: USING DIFFERENT CONTRAST
     20547MECHANISMS TO IMPROVE CELL TRACKING},
     20548  booktitle = {IEEE International Symposium on Biomedical Imaging},
     20549  pages = {386-389},
     20550  address = {Barcelona, Spain},
     20551  author = {Becker, T. and Rapoport, D.H. and Mamlouk, A.M.},
     20552  organization = {IEEE}
     20553}
     20554@inproceedings{Wang2012,
     20555  month = {May 2-5},
     20556  year = {2012},
     20557  title = {A HYBRID TOTAL-VARIATION MINIMIZATION APPROACH TO COMPRESSED SENSING},
     20558  booktitle = {IEEE International Symposium on Biomedical Imaging},
     20559  pages = {74-77},
     20560  address = {Barcelona, Spain},
     20561  author = {Wang, Y. and Liang, D. and Chang, Y. and Ying, L.},
     20562  organization = {IEEE}
     20563}
     20564@inproceedings{Cohen2012,
     20565  month = {May 2-5},
     20566  year = {2012},
     20567  title = {IMAGE REGISTRATION ERROR ANALYSIS WITH APPLICATIONS IN SINGLE MOLECULE MICROSCOPY},
     20568  booktitle = {IEEE International Symposium on Biomedical Imaging},
     20569  pages = {966-969},
     20570  address = {Barcelona, Spain},
     20571  author = {Cohen, E.A.K. and Ober, R.J.},
     20572  organization = {IEEE}
     20573}
     20574@inproceedings{Hu2012,
     20575  month = {May 2-5},
     20576  year = {2012},
     20577  title = {MITOSIS DETECTION OF HEMATOPOIETIC STEM CELL POPULATIONS IN TIME-LAPSE PHASE-CONTRAST MICROSCOPY IMAGES},
     20578  booktitle = {IEEE International Symposium on Biomedical Imaging},
     20579  pages = {390-393},
     20580  address = {Barcelona, Spain},
     20581  publisher = {IEEE},
     20582  author = {Huh, S. and Eom, S. and Elmer Ker, D.F. and Weiss, L. and Kanade, T.}
     20583}
     20584@inproceedings{Stallinga2012a,
     20585  month = {May 2-5},
     20586  year = {2012},
     20587  title = {THE EFFECT OF BACKGROUND ON LOCALIZATION UNCERTAINTY IN SINGLE EMITTER IMAGING},
     20588  booktitle = {IEEE International Symposium on Biomedical Imaging},
     20589  pages = {988-991},
     20590  address = {Barcelona, Spain},
     20591  publisher = {IEEE},
     20592  author = {Stallinga, S. and Rieger, B.}
     20593}
     20594@inproceedings{Wong2012,
     20595  month = {May 2-5},
     20596  year = {2012},
     20597  title = {Effect of Time Discretization on the Limit of the
     20598Accuracy of Parameter Estimation for Moving
     20599Single Molecules Imaged by Fluorescence
     20600Microscopy},
     20601  booktitle = {IEEE International Symposium on Biomedical Imaging },
     20602  pages = {1228-1231},
     20603  address = {Barcelona, Spain},
     20604  author = {Wong, Y. and Lin, Z. and Ober, R.J.}
     20605}
     20606@inproceedings{Ducroz2012,
     20607  month = {May 2-5},
     20608  year = {2012},
     20609  title = {CHARACTERIZATION OF CELL SHAPE AND DEFORMATION IN 3D USING SPHERICAL HARMONICS},
     20610  booktitle = {IEEE International Symposium on Biomedical Imaging },
     20611  address = {Barcelona, Spain},
     20612  author = {Ducroz, C. and Olivio-Marin, J.-C. and Dufor, A.},
     20613  organization = {IEEE}
     20614}
     20615@techreport{hassanich2012,
     20616  month = {Jan},
     20617  year = {2012},
     20618  title = {Nearly Optimal Sparse Fourier Transform},
     20619  address = {arXiv:1201.2501v1 [cs.DS] },
     20620  institution = {Massachusetts Institute of Technology, USA},
     20621  author = {Hassanieh, H. and Indyk, P. and Katabi, D. and Price, E.}
     20622}
     20623@inproceedings{Levet2012,
     20624  month = {May 2-5},
     20625  year = {2012},
     20626  title = {AUTOMATIC NON-PARAMETRIC CAPSID SEGMENTATION USING WAVELETS TRANSFORM AND GRAPH},
     20627  booktitle = {IEEE International Symposium on Biomedical Imaging},
     20628  address = {Barcelona, Spain},
     20629  author = {Levert, F. and Cassany, A. and Kann, M. and Sibarita, J.-B.},
     20630  organization = {IEEE}
     20631}
     20632@inproceedings{Jezierska2012,
     20633  month = {May 2-5},
     20634  year = {2012},
     20635  title = {POISSON-GAUSSIAN NOISE PARAMETER ESTIMATION IN FLUORESCENCE MICROSCOPY IMAGING},
     20636  booktitle = {IEEE International Symposium on Biomedical Imaging},
     20637  pages = {1663-1666},
     20638  address = {Barcelona, Spain},
     20639  author = {Jezierska, A. and Talbot, H. and Chaux, C. and Pesquet, J.-C. and Engler, G.},
     20640  organization = {IEEE}
     20641}
     20642@article{Vulovic2012,
     20643  year = {2012},
     20644  title = {Precise and unbiased estimation of astigmatism and defocus in transmission electron microscopy},
     20645  pages = {115-134},
     20646  journal = {Ultramicroscopy},
     20647  volume = {116},
     20648  author = {Vulovic, M. and Franken, E. and Ravelli, R.B.G. and Vliet, L.J. van and Rieger, B.}
     20649}
     20650@article{Mukamel2012,
     20651  year = {2012},
     20652  title = {Statistical Deconvolution for Superresolution Fluorescence Microscopy},
     20653  pages = {2391-2400},
     20654  journal = {Biophysical Journal},
     20655  volume = {102},
     20656  author = {Mukamel, E.A. and Babcock, H. and Zhuang, X.}
     20657}
     20658@article{Fernandez2012,
     20659  number = {10},
     20660  year = {2012},
     20661  title = {Computational Methods for Electron Tomography},
     20662  pages = {1010-1030},
     20663  journal = {Micron},
     20664  volume = {43},
     20665  author = {Fernandez, J.-J.}
     20666}
     20667@article{Kopek2012,
     20668  number = {16},
     20669  year = {2012},
     20670  title = {Correlative 3D superresolution fluorescence and
     20671electron microscopy reveal the relationship of
     20672mitochondrial nucleoids to membranes},
     20673  pages = {6136-6141},
     20674  journal = {Proceedings of the National Academy of Science USA},
     20675  volume = {109},
     20676  author = {Kopek, B.G. and Shtengel, G. and Shan Xu, C. and Clayton, D.A. and Hess, H.F.}
     20677}
     20678@article{Shtengel2009,
     20679  number = {9},
     20680  year = {2009},
     20681  title = {Interferometric fluorescent super-resolution
     20682microscopy resolves 3D cellular ultrastructure},
     20683  pages = {3125-3130},
     20684  journal = {Proceeding of the National Academy of Science USA},
     20685  volume = {106},
     20686  author = {Shtengel, G. and Galbraith, J.A. and Galbraith, C.G. and Lippincott-Schwartz, J. and Gillette, J.M. and Manely, S. and Sougrat, R. and Waterman, C.M. and Knachanawong, P. and Davidson, M.W. and Fetter, R.D. and Hess, H.F.}
     20687}
     20688@misc{materialsmethods,
     20689  title = {Materials and methods are available as supplementary material on {Science Online}.}
     20690}
     20691@article{Pavani2008,
     20692  number = {26},
     20693  year = {2008},
     20694  title = {Three dimensional tracking of fluorescent microparticles using a photon-limited double-helix response system},
     20695  pages = {22048-22057},
     20696  journal = {Optics Express},
     20697  volume = {16},
     20698  author = {Pavani, S.R.P. and Piestun, R.}
     20699}
     20700@article{Mlodzianoski2011,
     20701  number = {16},
     20702  year = {2011},
     20703  title = {Sample drift correction in 3D fluorescence photoactivation localization microscopy},
     20704  pages = {15009-15019},
     20705  journal = {Optics Express},
     20706  volume = {19},
     20707  author = {Mlodzianoski, M.J. and Schreiner, J.M. and Callahan, S.P. and Smolkova, K. and Dlaskova, A. and Santorova, J. and Jezek, P. and Bewersdorf, J.}
     20708}
     20709@article{Heilemann2005,
     20710  number = {11},
     20711  year = {2005},
     20712  title = {Carbocyanine dyes as efficient reversible single-molecule optical switch},
     20713  pages = {3801-3806},
     20714  journal = {Journal of the American Chemical Society},
     20715  volume = {127},
     20716  author = {Heilemann, M. and Margeat, E. and Kasper, R. and Sauer, M. and Tinnefeld, P. }
     20717}
     20718@inbook{Frank1980,
     20719  year = {1980},
     20720  title = {Computer Processing of Electron Microscope Images},
     20721  pages = {197-233},
     20722  editor = {Hawkes, P.W.},
     20723  chapter = {The Role of Correlation Techniques in Computer Image Processing},
     20724  publisher = {Springer Verlag},
     20725  author = {Frank, J.}
     20726}
     20727@article{Bolte2006,
     20728  number = {3},
     20729  year = {2006},
     20730  title = {A guided tour into subcellular colocalization analysis in light microscopy},
     20731  pages = {213-232},
     20732  journal = {Journal of Microscopy},
     20733  volume = {224},
     20734  author = {Bolte, S. and Cordelieres, F.P.}
     20735}
     20736@article{Adler2008,
     20737  number = {1},
     20738  year = {2008},
     20739  title = {Replicate-based noise corrected correlation for accurate measurements of colocalization},
     20740  pages = {121-133},
     20741  journal = {Journal of Microscopy},
     20742  volume = {230},
     20743  author = {Adler, J. and Pagakis, S.N. and Parmryd, I.}
     20744}
     20745@article{Ries2012,
     20746  number = {6},
     20747  year = {2012},
     20748  title = {A simple, versatile method for {GFP-based} super-resolution microscopy via nanobodies},
     20749  pages = {582-587},
     20750  journal = {Nature Methods},
     20751  volume = {9},
     20752  author = {Ries, J. and Kaplan, C. and Platonova, E. and Eghlidi, H. and Ewers, H.}
     20753}
     20754@article{Neumuller2010,
     20755  number = {11},
     20756  year = {2010},
     20757  title = {Photounbinding of Calmodulin from a Family of {CaM} Binding Peptides},
     20758  pages = {14050},
     20759  journal = {PlOS one},
     20760  volume = {5},
     20761  author = {{Neum\"uller}, K.G. and Elsayad, K. and Reisecker, J.M. and Waxham, M.N. and Heinze, K.G.}
     20762}
     20763@article{Mourik2012,
     20764  year = {2012},
     20765  title = {Signatures of Majorana Fermions in
     20766Hybrid Superconductor-Semiconductor
     20767Nanowire Devices},
     20768  pages = {1003-1008},
     20769  journal = {Science},
     20770  volume = {336},
     20771  author = {Mourik, V. and Zuo, K. and Frolov, S.M. and Plissard, S.R. and Bakkers, E.P.A.M. and Kouwenhouven, L.P.}
     20772}
     20773@article{Loenhout2012,
     20774  number = {10},
     20775  year = {2012},
     20776  title = {Non-Bias-Limited Tracking of Spherical Particles, Enabling Nanometer Resolution at Low Magnification},
     20777  pages = {2362-2371},
     20778  journal = {Biophysical Journal},
     20779  volume = {102},
     20780  author = {Loenhout, M.T.J. van and Kerssemakers, J.W.J. and Vlaminck, I. De and Dekker, C.}
     20781}
     20782@article{Hofmann2005,
     20783  number = {49},
     20784  year = {2005},
     20785  title = {Breaking the diffraction barrier in fluorescence microscopy at low light intensities by using reversibly photoswitchable proteins},
     20786  pages = {17565-17569},
     20787  journal = {Proceedings of the National Academy of Sciences USA},
     20788  volume = {102},
     20789  author = {Hofmann, M. and Eggeling, C. and Jakobs, S. and Hell, S.W.}
     20790}
     20791@article{Clifford2007,
     20792  number = {6987-69991},
     20793  year = {2007},
     20794  title = {Fluorescence of Single Molecules in Polymer Films: Sensitivity of Blinking to Local Environment},
     20795  journal = {The Journal of Physical Chemistry B Letters},
     20796  volume = {111},
     20797  author = {Clifford, J.N. and Bell, T.D.M. and Tinnefeld, P. and Heilemann, M. and Melnikov, S.M. and Hotta, J.-I. and Sliwa, M. and Dedecker, P. and Sauer, M. and Hofkens, J. and Yeow, E.K.L.}
     20798}
     20799@article{Isack2012,
     20800  year = {2012},
     20801  title = {Energy-Based Geometric Multi-model Fitting},
     20802  pages = {123-147},
     20803  journal = {International Journal of Computer Vision},
     20804  volume = {97},
     20805  author = {Isack, H. and Boybov, Y.}
     20806}
     20807@article{Rullgrad2011,
     20808  number = {3},
     20809  year = {2011},
     20810  title = {Simulation of transmission electron microscope images of biological specimens},
     20811  pages = {234-256},
     20812  journal = {Journal of Microscopy},
     20813  volume = {243},
     20814  author = {{Rullgr\aad}, H. and {\"Ofverstedt}, L.-G. and Masich, S. and Daneholt, B. and {\"Oktem}, O.}
     20815}
     20816@article{York2012,
     20817  number = {7},
     20818  year = {2012},
     20819  title = {Resolution doubling in live, multicellular organisms via multifocal structured illumination microscopy},
     20820  pages = {749-754},
     20821  journal = {Nature Methods},
     20822  volume = {9},
     20823  author = {York, A.G. and Parekh, S.H. and Nogare, D.D. and Fischer, R.S. and Temprine, K. and Mione, M. and Chitnis, A.B. and Combs, C.A. and Shroff, H.}
     20824}
     20825@article{Cleveland1979,
     20826  number = {368},
     20827  month = {Dec.},
     20828  year = {1979},
     20829  title = {Robust Locally Weighted Regression and Smoothing Scatterplots},
     20830  pages = {829-836},
     20831  journal = {Journal of the American Statistical Association},
     20832  volume = {74},
     20833  author = {Cleveland, W.S.}
     20834}
     20835@book{Erni2010a,
     20836  year = {2010},
     20837  title = {Aberration-Corrected Imaging in Transmission Electron Microscopy},
     20838  address = {London, UK},
     20839  publisher = {Imperial College Press},
     20840  author = {Erni, R.}
     20841}
     20842@article{Saghi2012,
     20843  year = {2012},
     20844  title = {Electron Tomography in the {(S)TEM}: From Nanoscale
     20845Morphological Analysis to {3D} Atomic Imaging},
     20846  pages = {59-79},
     20847  journal = {Annu. Rev. Mater. Res.},
     20848  volume = {42},
     20849  author = {Saghi,  A. and Midgley, P.A.}
     20850}
     20851@article{Midgley2009,
     20852  year = {2009},
     20853  title = {Electron tomography and holography in materials science},
     20854  pages = {271-280},
     20855  journal = {Nature Materials},
     20856  volume = {8},
     20857  author = {Midgley, P.A. and Dunin-Borkowski, R.E.}
     20858}
     20859@article{Midgley2003,
     20860  year = {2003},
     20861  title = {{3D} electron microscopy in the physical sciences: the development of {Z-contrast} and {EFTEM} tomography},
     20862  pages = {413-431},
     20863  journal = {Ultramicroscopy},
     20864  volume = {96},
     20865  author = {Midgley, P.A. and Weyland, M.}
     20866}
     20867@article{Spontak1988,
     20868  year = {1988},
     20869  title = {Three-dimensional study of cylindrical morphology in a styrene-butadiene-styrene block copolymer},
     20870  pages = {387-395},
     20871  journal = {Polymer},
     20872  volume = {29},
     20873  author = {Spontak, R.J. and Williams, M.C. and Agard, D.A.}
     20874}
     20875@article{Friedrich2005,
     20876  year = {2005},
     20877  title = {Comparison of intensity distributions in tomograms from {BF TEM, ADF TEM, HAADF STEM}, and calculated tilt series},
     20878  pages = {18-27},
     20879  journal = {Ultramicroscopy},
     20880  volume = {106},
     20881  author = {Friedrich, H. and McCartney, M.R. and Buseck, P.R.}
     20882}
     20883@article{Kubel2005,
     20884  number = {5},
     20885  year = {2005},
     20886  title = {Recent Advances in Electron Tomography: {TEM} and {HAADF-STEM} Tomography for Materials Science and Semiconductor Applications},
     20887  pages = {378-400},
     20888  journal = {Microscopy and Microanalysis},
     20889  volume = {11},
     20890  author = {{K\"ubel}, C. and Voigt, A. and Schoenmakers, R. and Otten, M. and Su, D. and Lee, T.-C. and Carlsson, A. and Bradley, J.}
     20891}
     20892@article{Rose1975,
     20893  year = {1975},
     20894  title = {Zur Theorie der Bildentstehung im Elektronenmikroskop},
     20895  pages = {217-244},
     20896  journal = {Optik},
     20897  volume = {42},
     20898  author = {Rose, H.}
     20899}
     20900@article{Freitag1981,
     20901  year = {1981},
     20902  title = {Resolution and contrast of crystalline objects in high-resolution scanning electron microscopy},
     20903  pages = {407-429},
     20904  journal = {Optik},
     20905  volume = {59},
     20906  author = {Freitag, J. and Rose, H.}
     20907}
     20908@incollection{Nellist2000a,
     20909  series = {113},
     20910  year = {2000},
     20911  title = {The principle and interpretation of annular dark-field Z-contrast imaging},
     20912  booktitle = {Advances in Imaging and Electron Physics},
     20913  pages = {147-203},
     20914  author = {Nellist, P.D. and Pennycook, S.J.}
     20915}
     20916@article{Zhu2012,
     20917  number = {7},
     20918  year = {2012},
     20919  title = {Faster {STORM} using compressed sensing},
     20920  pages = {721-726},
     20921  journal = {Nature Methods},
     20922  volume = {9},
     20923  author = {Zhu, L. and Zhang, W. and Elnatan, D. and Huang, B.}
     20924}
     20925@article{Zecevic2012,
     20926  number = {17},
     20927  year = {2012},
     20928  title = {Mesoporosity of Zeolite {Y}: Quantitative Three-Dimensional Study by Image Analysis of Electron Tomograms},
     20929  pages = {4213-4217},
     20930  journal = {Angewandte Chemie Int. Ed.},
     20931  volume = {51},
     20932  author = {Zecevic, J. and Gommes, C.J. and Friedrich, H. and
     20933Jongh, P.E. de and Jong, K.P. de}
     20934}
     20935@article{Brilot2012,
     20936  year = {2012},
     20937  title = {Beam-induced motion of vitrified specimen on holey carbon film},
     20938  pages = {630-637},
     20939  journal = {Journal of Structural Biology},
     20940  volume = {177},
     20941  author = {Brilot, A.F. and Chen, J.Z. and Cheng, A. and Pan, J. and Harrison, S.C .and Potter, C.S. and Carragher, B. and Henderson, R. and Grigorieff, N.}
     20942}
     20943@article{Brettschneider2007,
     20944  year = {2007},
     20945  title = {Breaking the Diffraction Barrier in Fluorescence Microscopy by Optical Shelving},
     20946  pages = {218103},
     20947  journal = {Physical Review Letters},
     20948  author = {Bretschneider, S. and Eggeling, C. and Hell, S.W.}
     20949}
     20950@article{Testa2008,
     20951  number = {25},
     20952  year = {2008},
     20953  title = {Nanoscale separation of molecular species based
     20954on their rotational mobility},
     20955  pages = {21094-21105},
     20956  journal = {Optics Express},
     20957  volume = {16},
     20958  author = {Testa, I. and {Sch\"onle}, A. and Middendoff, C. von and Geisler, C. and Medda, R. and Wurm, C.A. and Stiel, A.C. and Jakobs, S. and Bossi, M. and Eggeling, C. and Hell, S.W. and Egner, A.}
     20959}
     20960@article{Baddeley2011,
     20961  number = {5},
     20962  year = {2011},
     20963  title = {{4D} Super-Resolution Microscopy with Conventional
     20964Fluorophores and Single Wavelength Excitation in
     20965Optically Thick Cells and Tissues},
     20966  pages = {e20645},
     20967  journal = {PLOS one},
     20968  volume = {6},
     20969  author = {Baddeley, D. and Crossman, D. and Rossberger, S. and Cheyne, J.E. and Montgomery, J.M. and Jayasinghe, I.D. and Cremer, C. and Cannell, M.B. and {S\"oller}, C.}
     20970}
     20971@article{Testa2011,
     20972  year = {2010},
     20973  title = {Multicolor Fluorescence Nanoscopy in Fixed and  Living Cells by Exciting Conventional Fluorophores with a Single Wavelength},
     20974  pages = {2686-2694},
     20975  journal = {Biophysical Journal},
     20976  volume = {99},
     20977  author = {Testa, I. and Wurm, C.A. and Medda, R. and Rothermel, E. and Middendorf, C. von and {F\"olling}, J. and Jakobs, S. and {Sch\"onle}, A. and Hell, S.W. and Eggeling, C.}
     20978}
     20979@article{Gunawerdene2011,
     20980  year = {2011},
     20981  title = {Superresolution Imaging of Multiple Fluorescent Proteins with Highly Overlapping Emission Spectra in Living Cells},
     20982  pages = {1522-1528},
     20983  journal = {Biophysical Journal},
     20984  volume = {101},
     20985  author = {Gunewardene, M.S. and Subach, F.V. and Gould, T.J. and Penoncello, G.P. and Gudheti, M.V. and Verkhusha, V.V. and Hess, S.T.}
     20986}
     20987@article{Bohmer2003,
     20988  number = {3},
     20989  year = {2003},
     20990  title = {Orientation imaging of single molecules by wide-field epifluorescence microscopy},
     20991  pages = {554-559},
     20992  journal = {Journal of the Optical Society of America B},
     20993  volume = {20},
     20994  author = {{B\"ohmer}, M. and Enderlein, J.}
     20995}
     20996@article{Fitzgerald2012,
     20997  year = {2012},
     20998  title = {Estimation Theoretic Measure of Resolution for Stochastic Localization Microscopy},
     20999  pages = {048102},
     21000  journal = {Physical Review Letters},
     21001  volume = {109},
     21002  author = {Fitzgerald, J.E. and Lu, J. and Schnitzer, M.J.}
     21003}
     21004@article{Test2012,
     21005  year = {2012},
     21006  title = {Test},
     21007  journal = {bladievla},
     21008  author = {Ronald}
     21009}
     21010@article{Wolter2011,
     21011  number = {8},
     21012  month = {April},
     21013  year = {2011},
     21014  title = {Measuring localization performance of super-resolution algorithms on very active samples},
     21015  pages = {7020-7033},
     21016  journal = {Optics Express},
     21017  volume = {19},
     21018  author = {Wolter,S. and Endesfelder, U. and Linde, S. van de and Heilemann, M. and Sauer, M.}
     21019}
     21020@article{Bates2012,
     21021  year = {2012},
     21022  title = {Multicolor Super-Resolution Fluorescence Imaging via
     21023Multi-Parameter Fluorophore Detection},
     21024  pages = {99-107},
     21025  journal = {ChemPhysChem},
     21026  volume = {13},
     21027  author = {Bates, M. and Dempsey, G.T. and Chen, K.H. and Zhuang, X.}
     21028}
     21029@article{Linde2010,
     21030  year = {2010},
     21031  title = {The effect of photoswitching kinetics and labeling densities on super-resolution
     21032fluorescence imaging},
     21033  pages = {260-266},
     21034  journal = {Journal of Biotechnology},
     21035  volume = {149},
     21036  url = {http://dx.doi.org/10.1016/j.bbr.2011.03.031},
     21037  author = {Linde, S. van de and Wolter, S. and Heilemann, M. and Sauer, M.}
     21038}
     21039@article{Wang2012b,
     21040  number = {14},
     21041  year = {2012},
     21042  title = {PALMER: a method capable of parallel localization of multiple emitters for high-density localization microscopy
     21043},
     21044  pages = {16039-16049},
     21045  journal = {Optics Express},
     21046  volume = {20},
     21047  url = {http://www.opticsinfobase.org/oe/abstract.cfm?uri=oe-20-14-16039},
     21048  author = {Wang, Y. and Quan, T. and Zeng, S. and Huang, Z.-L.}
     21049}
     21050@article{Eibauer2012,
     21051  year = {2012},
     21052  title = {Unraveling the structure of membrane proteins in situ by transfer function corrected cryo-electron tomography},
     21053  journal = {Journal of Structural Biology},
     21054  author = {Eibauer, M. and Hoffmann, C. and Plitzko, J.M. and  Baumeister, W. and Nickell, S. and
     21055Engelhardt, H.}
     21056}
     21057@inbook{Tukey1967,
     21058  year = {1967},
     21059  title = {Analysis of time series},
     21060  pages = {25-46},
     21061  editor = {Harris, B.},
     21062  address = {New York},
     21063  chapter = {An introduction to the calculations of numerical spectrum analysis},
     21064  publisher = {Wiley},
     21065  author = {Tukey, J. W.}
     21066}
     21067@article{Ghosh1994,
     21068  number = {5},
     21069  month = {May},
     21070  year = {1994},
     21071  title = {Automated detection and tracking of individual and clustered cell surface low density lipoprotein receptor molecules},
     21072  pages = {1301-1318},
     21073  journal = {Biophysical Journal},
     21074  volume = {66},
     21075  author = {Ghosh, R.N. and Webb, W.W.}
     21076}
     21077@article{Lee1991,
     21078  number = {14},
     21079  month = {July},
     21080  year = {1991},
     21081  title = {Direct observation of brownian motion of lipids in a membrane},
     21082  pages = {6274-6278},
     21083  journal = {Proceedings of the National Academy of Sciences of the USA},
     21084  volume = {88},
     21085  author = {Lee, G.M. and Ishihara, A. and Jacobson, K.A.}
     21086}
     21087@article{Niessen1996,
     21088  month = {July},
     21089  year = {1996},
     21090  title = {Deficiency of the $\beta$4 subunit in junctional epidermolysis bullosa with pyloric atresia: consequences for hemidesmosome formation and adhesion properties},
     21091  pages = {1695-1706},
     21092  journal = {Journal of Cell Science},
     21093  volume = {109},
     21094  author = {Niessen, C.M. and Raaij-Helmer, L.M.H. van der and Hulsman, E.H.M. and Neut, R. van der and Jonkman, M.F. and Sonnenberg, A.}
     21095}
     21096@article{Schaapveld1998,
     21097  number = {1},
     21098  month = {July},
     21099  year = {1998},
     21100  title = {Hemidesmosome formation is initiated by the $\beta$4 integrin subunit, requires complex formation of  $\beta$4 and H.D1/plectin, and involves a direct interaction between $\beta$4 and the bullous pemphigoid antigen},
     21101  pages = {271-284},
     21102  journal = {Journal of Cell Biology},
     21103  volume = {142},
     21104  author = {Schaapveld, R.Q.J. and Borradori, L. and Geerts, D. and Leusden, M.R. van and Kuikman, I. and Nievers, M.G. and Niessen, C.M. and Steenbergen, R.D.M. and Snijders, P.J.F. and Sonnenberg, A.}
     21105}
     21106@article{Rojo2006,
     21107  number = {553-560},
     21108  year = {2006},
     21109  title = {A METHOD TO REMOVE FRINGES FROM IMAGES USING WAVELETS},
     21110  journal = {The Astrophysical Journal},
     21111  volume = {649},
     21112  author = {Rojo, P.M. and Harrington, J.}
     21113}
     21114@article{Donnert2006,
     21115  number = {31},
     21116  year = {2006},
     21117  title = {Macromolecular-scale resolution in biological
     21118fluorescence microscopy},
     21119  pages = {11440-11445},
     21120  journal = {Proceedings of the National Academy of Sciences USA},
     21121  volume = {103},
     21122  author = {Donnert, G. and Keller, J. and Medda, R. and Andrei, M.A. and Rizzoli, S.O. and {L\"uhrmann}, R. and Jahn, R. and Eggeling, C. and Hell, S.W.}
     21123}
     21124@article{Faas2012,
     21125  number = {3},
     21126  year = {2012},
     21127  title = {Virtual nanoscopy: Generation of ultra-large high
     21128resolution electron microscopy maps},
     21129  pages = {457-469},
     21130  journal = {Journal of Cell Biology},
     21131  volume = {198},
     21132  author = {Faas, F.G.A. and Avramut, M.C. and Berg, B.M. van den and Mommaas, M.A. and Koster, A.J. and Ravelli, R.B.G.}
     21133}
     21134@inbook{Bates2011,
     21135  year = {2011},
     21136  title = {Imaging: A Laboratory Manual},
     21137  note = {ISBN  978-0-879699-36-9 },
     21138  editor = {Yuste, R.},
     21139  chapter = {Stochastic Optical Reconstruction Microscopy (STORM): a method for super-resolution fluorescence imaging},
     21140  publisher = {Cold Spring Harbor Laboratory Press},
     21141  author = {Bates, M. and Jones, S.A. and Zhuang, X.}
     21142}
     21143@article{Izeddin2012,
     21144  number = {3},
     21145  year = {2012},
     21146  title = {Wavelet analysis for single molecule localization
     21147microscopy},
     21148  pages = {2081-2095},
     21149  journal = {Optics Express},
     21150  volume = {20},
     21151  author = {Izeddin, I. and Boulanger, J. and Racine, V. and Specht, C.G. and Kechkar, A. and Nair, D. and Triller, A. and Choquet, D. and Dahan, M. and Sibarita, J.B.}
     21152}
     21153@article{Parthasarathy2012,
     21154  number = {7},
     21155  year = {2012},
     21156  title = {Rapid, accurate particle tracking by calculation of radial symmetry centers},
     21157  pages = {724-726},
     21158  journal = {Nature Methods},
     21159  volume = {9},
     21160  author = {Parthasarathy, R.}
     21161}
     21162@article{Mukamel2012a,
     21163  year = {2012},
     21164  title = {Unified Resolution Bounds for Conventional and Stochastic Localization Fluorescence Microscopy},
     21165  pages = {168102},
     21166  journal = {Physical Review Letters},
     21167  volume = {109},
     21168  author = {Mukamel, E.A. and Schnitzer, M.J.}
     21169}
     21170@article{Lippincott2009,
     21171  number = {1},
     21172  year = {2009},
     21173  title = {Putting super-resolution fluorescence microscopy to
     21174work},
     21175  pages = {21},
     21176  journal = {Nature Methods},
     21177  volume = {6},
     21178  author = {Lippincott-Schwartz, J. and Manley, S.}
     21179}
     21180@article{Veatch2012,
     21181  number = {2},
     21182  month = {February},
     21183  year = {2012},
     21184  title = {Correlation functions quantify super-resolution images and estimate apparent clustering due to over-counting},
     21185  pages = {e31457},
     21186  journal = {Plos ONE},
     21187  volume = {7},
     21188  author = {Veatch, S.L. and Machta, B.B. and Shelby, S.A. and Chiang, E.N. and Holowka, D.A. and Baird, B.A.}
     21189}
     21190@article{Huang2010,
     21191  year = {2010},
     21192  title = {Breaking the Diffraction Barrier:
     21193Super-Resolution Imaging of Cells},
     21194  pages = {1047-1058},
     21195  journal = {Cell},
     21196  volume = {143},
     21197  author = {Huang, B. and Babcock, H. and Zhuang, X.}
     21198}
     21199@article{Anselmi2011,
     21200  number = {49},
     21201  year = {2011},
     21202  title = {Three-dimensional imaging and photostimulation by
     21203remote-focusing and holographic light patterning},
     21204  pages = {19504-19509},
     21205  journal = {Proceedings of the National Academy of Sciences U.S.A.},
     21206  volume = {108},
     21207  author = {Anselmi, F. and Ventalon, C. and Begue, Ogden, D. and Emiliani, V.}
     21208}
     21209@article{Botcherby2007,
     21210  number = {14},
     21211  year = {2007-2009},
     21212  title = {Aberration-free optical refocusing in high
     21213numerical aperture microscopy},
     21214  pages = {2007},
     21215  journal = {Optics Letters},
     21216  volume = {32},
     21217  author = {Botcherby, E.J. and juskaitis, R. and Booth, M.J. and Wilson, T.}
     21218}
     21219@article{Wolter2012,
     21220  number = {11},
     21221  year = {2012},
     21222  title = {{rapidSTORM}: accurate, fast open-source software for localization microscopy},
     21223  pages = {1040-1041},
     21224  journal = {Nature Methods},
     21225  volume = {9},
     21226  author = {Wolter, S. and {L\"oschberger}, A. and Holm, T. and Aufmkolk, S. and Dabauvalle, M.-C. and Linde, S. van de and Sauer, M.}
     21227}
     21228@article{Manders1992,
     21229  year = {1992},
     21230  title = {Dynamics of three-dimensional replication patterns during the S-phase, analysed by double labelling of DNA and confocal microscopy},
     21231  pages = {857-862},
     21232  journal = {Journal of Cell Science},
     21233  volume = {103},
     21234  author = {Manders, E.M.M. and Stap, J. and Brakenhoff, G.J. and Driel, R. van and Aten, J.A.}
     21235}
     21236@article{Adler2010,
     21237  number = {8},
     21238  year = {2010},
     21239  title = {Quantifying Colocalization by Correlation: The Pearson Correlation Coefficient is Superior to the Mander's Overlap Coefficient},
     21240  pages = {733-742},
     21241  journal = {Cytometry Part A},
     21242  volume = {77A},
     21243  author = {Adler, J. and Parmryd, I.}
     21244}
     21245@article{Annibale2012_OpticalNanoscopy,
     21246  number = {9},
     21247  year = {2012},
     21248  title = {Identification of the factors affecting co-localization precision for quantitative multicolor localization microscopy},
     21249  journal = {Optical Nanoscopy},
     21250  volume = {1},
     21251  author = {Annibale, P. and Scarselli, M. and Greco, M. and Radenovic, A.}
     21252}
     21253@article{Parmryd2003,
     21254  number = {1},
     21255  year = {2003},
     21256  title = {Imaging metabolism of phosphatidylinositol 4,5-bisphosphate in T-cell
     21257GM1-enriched domains containing Ras proteins},
     21258  pages = {27-38},
     21259  journal = {Experimental Cell Research},
     21260  volume = {285},
     21261  author = {Parmryd, I. and Adler, J. and Patel, R. and Magee, A.I.}
     21262}
     21263@article{Bergholm2010,
     21264  number = {3},
     21265  year = {2010},
     21266  title = {Analysis of Bias in the Apparent Correlation Coefficient Between Image Pairs Corrupted by Severe Noise},
     21267  pages = {204-219},
     21268  journal = {Journal of Mathematical Imaging and Vision},
     21269  volume = {37},
     21270  author = {Bergholm, F. and Adler, J. and Parmryd, I.}
     21271}
     21272@article{Helmuth2010,
     21273  number = {372},
     21274  year = {2010},
     21275  title = {Beyond co-localization: inferring spatial
     21276interactions between sub-cellular structures from
     21277microscopy images},
     21278  journal = {BMC Bioinformatics},
     21279  volume = {11},
     21280  author = {Helmuth, J.A. and Paul, G. and Sbalzarini, I. F.}
     21281}
     21282@article{Dunn2011,
     21283  number = {4},
     21284  year = {2011},
     21285  title = {A practical guide to evaluating colocalization in biological microscopy},
     21286  pages = {C723-C742},
     21287  journal = {American Journal of Physiology: Cell Physiology},
     21288  volume = {300},
     21289  author = {Dunn, K.W. and Kamocka, M.M. and McDonald, J.H.}
     21290}
     21291@article{Li2004a,
     21292  number = {16},
     21293  year = {2004},
     21294  title = {A Syntaxin 1, G$\alpha_{0}$, and N-Type Calcium Channel Complex at a Presynaptic Nerve Terminal: Analysis by Quantitative Immunocolocalization},
     21295  pages = {4070-4081},
     21296  journal = {Journal of Neuroscience},
     21297  volume = {24},
     21298  author = {Li, Q. and Lau, A. and Morris, T.J. and Guo, L. and Fordyce, C.B. and Stanley, E.F.}
     21299}
     21300@inproceedings{Zhang2008a,
     21301  month = {May},
     21302  year = {2008},
     21303  title = {Statistical colocalization in biological imaging with false discovery control},
     21304  booktitle = {Biomedical Imaging: From Nano to Macro, 2008. ISBI 2008. 5th IEEE International Symposium on},
     21305  pages = {1327 - 1330 },
     21306  author = {Zhang, B. and Chenouard, N. and Olivo-Marin, J.-C. and Meas-Yedid, V.}
     21307}
     21308@article{Jaskolski2005,
     21309  number = {1},
     21310  year = {2005},
     21311  title = {An automated method to quantify and visualize
     21312colocalized fluorescent signals},
     21313  pages = {42-49},
     21314  journal = {Journal of Neuroscience Methods},
     21315  volume = {146},
     21316  author = {Jaskolski, F. and Mulle, C. and Manzoni, O.J.}
     21317}
     21318@article{Lachmanovich2003,
     21319  number = {2},
     21320  month = {November},
     21321  year = {2003},
     21322  title = {Co-localization analysis of complex formation among membrane proteins by computerized fluorescence microscopy: application to immunofluorescence co-patching studies},
     21323  pages = {122-131},
     21324  journal = {Journal of Microscopy},
     21325  volume = {212},
     21326  author = {Lachmanovich, E. and Shvartsman, D.E. and Malka, Y. and Botvin, C. and Henis, Y.I. and Weiss, A.M.}
     21327}
     21328@article{VanSteensel1996,
     21329  year = {1996},
     21330  title = {Partial colocalization of glucocorticoid and mineralocorticoid receptors in discrete compartments in nuclei of rat hippocampus neurons},
     21331  pages = {787-792},
     21332  journal = {Journal of Cell Science},
     21333  volume = {109},
     21334  author = {Steensel, B. van and Binnendijk, E.P. van and Hornsby, C.D. Voort, H.T.M. van der and Krozowski, Z. and Kloet, E.R. de and Driel, R. van}
     21335}
     21336@article{Zinchuk2007,
     21337  number = {4},
     21338  year = {2007},
     21339  title = {Quantitative Colocalization Analysis of Multicolor Confocal Immunofluorescence Microscopy Images: Pushing Pixels to Explore Biological Phenomena},
     21340  pages = {101-111},
     21341  journal = {Acta Histochemica et Cytochemica},
     21342  volume = {40},
     21343  author = {Zinchuk, V. and Zinchuk, O. and Okada, T.}
     21344}
     21345@article{Oton2012,
     21346  year = {2012},
     21347  title = {Image formation in cellular {X-ray} microscopy},
     21348  pages = {29-37},
     21349  journal = {Journal of Structural Biology},
     21350  volume = {178},
     21351  author = {Oton, J. and Sorzano, C.O.S. and Pereiro, E. and Cucenca-Alba, J. and Navarro, R. and Carazo, J.M. and Marabini, R.}
     21352}
     21353@article{Sengupta2011,
     21354  number = {11},
     21355  year = {2011},
     21356  title = {Probing protein heterogeneity in the plasma membrane using {PALM} and pair correlation analysis},
     21357  pages = {969-975},
     21358  journal = {Nature Methods},
     21359  volume = {8},
     21360  author = {Sengupta, P. and Jovanovic-Talisman, T. and Skoko, D. and Renz, M. and Veatch, S.L. and Lippincott-Schwartz, J.}
     21361}
     21362@article{Comeau2006,
     21363  number = {12},
     21364  year = {2006},
     21365  title = {A Guide to Accurate Fluorescence Microscopy
     21366Colocalization Measurements},
     21367  pages = {4611-4622},
     21368  journal = {Biophysical Journal},
     21369  volume = {91},
     21370  author = {Comeau, J.W.D. and Constantino, S. and Wiseman, P.W.}
     21371}
     21372@article{Demandolx1997,
     21373  number = {1},
     21374  year = {1997},
     21375  title = {Multicolour analysis of local image correlation in confocal microscopy},
     21376  pages = {21-36},
     21377  journal = {Journal of Microscopy},
     21378  volume = {185},
     21379  author = {Demandolx, D. and Davoust, J.}
     21380}
     21381@article{Piche2012,
     21382  number = {24},
     21383  year = {2012},
     21384  title = {Experimental realization of optical eigenmode super-resolution},
     21385  pages = {26424-26433},
     21386  journal = {Optics Express},
     21387  volume = {20},
     21388  author = {Piche, K. and Leach, J. and Johnson, A.S. and Salvail, J.Z. and Kolobov, M.I. and Boyd, R.W.}
     21389}
     21390@article{Trabesinger2001,
     21391  number = {6},
     21392  month = {March},
     21393  year = {2001},
     21394  title = {Statistical Analysis of Single-Molecule
     21395Colocalization Assays},
     21396  pages = {1100-1105},
     21397  journal = {Analytical Chemistry},
     21398  volume = {73},
     21399  author = {Trabesinger, W. and Hecht, B. and Wild, U.P. and Schuetz, G.J. and Schindler, H. and Schmidt, Th.}
     21400}
     21401@article{Schmeisser2009,
     21402  number = {6},
     21403  year = {2009},
     21404  title = {Parallel, distributed and {GPU} computing technologies in single-particle electron microscopy},
     21405  pages = {659-671},
     21406  journal = {Acta Crystallographica Section D},
     21407  volume = {65},
     21408  author = {Schmeisser, M. and Heisen, B.C. and Luettich, M. and Busche, B. and Hauer, F. and Koske, T. and Knauber, K.-H. and Stark, H.}
     21409}
     21410@book{Frank2006,
     21411  edition = {2},
     21412  year = {2006},
     21413  title = {Three-Dimensional Electron Microscopy of Macromolecular Assemblies},
     21414  publisher = {Oxford University Press},
     21415  author = {Frank, J.}
     21416}
     21417@inproceedings{Chessel2012,
     21418  month = {May},
     21419  year = {2012},
     21420  title = {Spherical spatial statistics for 3D fluorescence video-microscopy},
     21421  booktitle = {Biomedical Imaging (ISBI), 2012 9th IEEE International Symposium on},
     21422  pages = {1747 -1750},
     21423  author = {Chessel, A. and Dodgson, J. and Carazo-Salas, R.E.}
     21424}
     21425@article{Semrau2011,
     21426  number = {7},
     21427  year = {2011},
     21428  title = {Quantification of Biological Interactions with Particle Image Cross-Correlation Spectroscopy (PICCS)},
     21429  pages = {1810-1818},
     21430  journal = {Biophysical Journal},
     21431  volume = {100},
     21432  author = {Semrau, S. and Holtzer, L. and Gonzales-Gaitan, M. and Schmidt, T.}
     21433}
     21434@article{Berro2012,
     21435  number = {6},
     21436  year = {2012},
     21437  title = {Super-resolution Optical Measurement of Nanoscale Photoacid Distribution in Lithographic Materials},
     21438  pages = {9496-9502},
     21439  journal = {ACS Nano},
     21440  volume = {11},
     21441  author = {Berro, A.J. and Berglund, A.J. and Carmichael, P.T. and Kim, J.S. and Liddle, J.A.}
     21442}
     21443@article{Agrawal2012,
     21444  number = {24},
     21445  year = {2012},
     21446  title = {Limits of {3D} dipole localization and orientation estimation for single-molecule imaging: towards {Green's} tensor engineering},
     21447  pages = {26668-26680},
     21448  journal = {Optics Express},
     21449  volume = {20},
     21450  author = {Agrawal, A. and Quirin, S. and Grover, G. and Piestun, R.}
     21451}
     21452@article{Backlund2012,
     21453  number = {47},
     21454  year = {2012},
     21455  title = {Simultaneous, accurate measurement of the {3D}
     21456position and orientation of single molecules},
     21457  pages = {19087-19092},
     21458  journal = {Proceedings of the National Academy of Sciences USA},
     21459  volume = {109},
     21460  author = {Backlund, M.P. and Lew, M.D. and Backer, A.S. and Sahl, S.J. and Grover, G. and Agrawal, A. and Piestun, R. and Moerner, W.E.}
     21461}
     21462@article{Hemmer2012,
     21463  year = {2012},
     21464  title = {The universal scaling laws that determine the achievable resolution in different schemes for super-resolution imaging},
     21465  pages = {083002},
     21466  journal = {Journal of Optics},
     21467  volume = {14},
     21468  author = {Hemmer, P.R. and Zapata, T.}
     21469}
     21470@article{Tokunaga2008,
     21471  number = {2},
     21472  year = {2008},
     21473  title = {Highly inclined thin illumination enables clear single-molecule imaging in cells},
     21474  pages = {159-161},
     21475  journal = {Nature Methods},
     21476  volume = {5},
     21477  author = {Tokunaga, M. and Imamoto, N. and Sakata-Sogawa, K.}
     21478}
     21479@article{Gerchberg1974,
     21480  number = {9},
     21481  year = {1974},
     21482  title = {Super-resolution through error energy reduction},
     21483  pages = {709-720},
     21484  journal = {Optica Acta},
     21485  volume = {21},
     21486  author = {Gerchberg, R.W.}
     21487}
     21488@article{Gerchberg1972,
     21489  number = {2},
     21490  year = {1972},
     21491  title = {A practical algorithm for the determination of phase from image and diffraction plane pictures},
     21492  pages = {237-246},
     21493  journal = {Optik},
     21494  volume = {35},
     21495  author = {Gerchberg, R.W. and Saxton, W.O.}
     21496}
     21497@article{Braun2013,
     21498  number = {52},
     21499  year = {2013},
     21500  title = {Negative Absolute Temperature for Motional Degrees of Freedom},
     21501  pages = {52-54},
     21502  journal = {Science},
     21503  volume = {339},
     21504  author = {Braun, S. and Ronzheimer, J.P. and Schreiber, M. and Hodgaman, S.S. and Rom, T. and Bloch, I. and Schneider, U.}
     21505}
     21506@article{Aert2006,
     21507  number = {9},
     21508  year = {2006},
     21509  title = {Resolution of coherent and incoherent imaging systems reconsidered - Classical criteria and a statistical alternative},
     21510  pages = {3830-3839},
     21511  journal = {Optics Express},
     21512  volume = {14},
     21513  author = {Aert, S. van and Dyck, D. van and Dekker, A.J. den}
     21514}
     21515@article{LowNam2011,
     21516  number = {11},
     21517  year = {2011},
     21518  title = {{ErbB1} dimerization is promoted by domain
     21519co-confinement and stabilized by ligand binding},
     21520  pages = {1244-1252},
     21521  journal = {Nature Structural \& Molecular Biology},
     21522  volume = {18},
     21523  author = {Low-Nam, S.T. and Lidke, K.A. and Cutler, P.J. and Roovers, R.C. and van Bergen en Henegouwen, P.M.P. and Wilson, B.S. and Lidke, D.S.}
     21524}
     21525@misc{Yoshitoshi1987,
     21526  month = {April},
     21527  year = {1987},
     21528  title = {Focusing detection apparatus },
     21529  howpublished = {US Patent 4,823,331},
     21530  author = {Yoshitoshi, Y. and Matsumoto, Y. and Kume, H.}
     21531}
     21532@article{Bricot1976,
     21533  number = {4},
     21534  year = {1976},
     21535  title = {Optical readout of videodisc},
     21536  pages = {304-308},
     21537  journal = {IEEE Transactions on Consumer Electronics},
     21538  volume = {22},
     21539  author = {Bricot, C. and Lehureau, J.C. and Puech, C.}
     21540}
     21541@article{Meddens2013,
     21542  number = {1},
     21543  year = {2013},
     21544  title = {Automated Podosome Identification and Characterization in Fluorescence Microscopy Images},
     21545  pages = {180-189},
     21546  note = {doi:10.1017/S1431927612014018},
     21547  journal = {Microscopy and Microanalysis},
     21548  volume = {19},
     21549  author = {Meddens, M.B.M. and Rieger, B. and Figdor, C.G. and Cambi, A. and Dries, K. van den}
     21550}
     21551@article{Gopinath2012,
     21552  number = {12},
     21553  year = {2012},
     21554  title = {Shape-Based Regularization of Electron Tomographic Reconstruction},
     21555  pages = {2241-2253},
     21556  journal = {IEEE TRANSACTIONS ON MEDICAL IMAGING},
     21557  volume = {31},
     21558  author = {Gopinath, A. and Xu, G. and Ress, D. and {\"Oktem}, O. and Subramaniam, S. and Baja, C.}
     21559}
     21560@article{Scheres2012,
     21561  number = {9},
     21562  month = {July},
     21563  year = {2012},
     21564  title = {Prevention of overfitting in cryo-EM structure determination},
     21565  pages = {853-854},
     21566  journal = {Nature Methods},
     21567  volume = {9},
     21568  author = {Scheres, S.H.W. and Chen, S.}
     21569}
     21570@article{Liao2010,
     21571  number = {7},
     21572  month = {July},
     21573  year = {2010},
     21574  title = {Definition and Estimation of Resolution
     21575in Single-Particle Reconstructions},
     21576  pages = {768-775},
     21577  journal = {Structure},
     21578  volume = {18},
     21579  author = {Liao, H.Y. and Frank, J.}
     21580}
     21581@article{Dani2010,
     21582  year = {2010},
     21583  title = {Superresolution Imaging of Chemical Synapses in the Brain},
     21584  pages = {843-856},
     21585  journal = {Neuron},
     21586  volume = {68},
     21587  author = {Dani, A. and Huang, B. and Bergan, J. and Dulac, C. and Zhuang, X.}
     21588}
     21589@article{Jones2011,
     21590  number = {6},
     21591  year = {2011},
     21592  title = {Fast, three-dimensional super-resolution imaging
     21593of live cells},
     21594  pages = {499-505},
     21595  journal = {Nature Methods},
     21596  volume = {8},
     21597  author = {Jones, S.A. and Shim, S.-H. and He, J. and Zhuang, X.}
     21598}
     21599@article{Kanchanawong2010,
     21600  year = {2010},
     21601  title = {Nanoscale architecture of integrin-based cell adhesions},
     21602  pages = {580-584},
     21603  journal = {Nature},
     21604  volume = {468},
     21605  author = {Kanchanawong, P. and Shtengel, G. and Pasapera, A.M. and Ramko, E.B. and Davidson, M.W. and Hess, H.F. and Waterman, C.M.}
     21606}
     21607@article{Lando2012,
     21608  year = {2012},
     21609  title = {Quantitative single-molecule microscopy reveals that CENP-ACnp1 deposition occurs during G2 in fission yeast},
     21610  pages = {120078},
     21611  journal = {Open Biology},
     21612  volume = {2},
     21613  author = {Lando, D. and Endesfelder, U. and Berger, H. and Subramanian, L. and Dunne, P.D. and McColl, J. and Klenerman, D. and Carr, A.M. and Sauer, M. and Allshire, R. and Heilemann, M. and Laue, E.D.}
     21614}
     21615@article{Shim2012,
     21616  number = {35},
     21617  year = {2012},
     21618  title = {Super-resolution fluorescence imaging of organelles
     21619in live cells with photoswitchable membrane probes},
     21620  pages = {13978-13983},
     21621  journal = {Proceedings of the National Academy of Sciences USA},
     21622  volume = {109},
     21623  author = {Shim, S.H. and Xia, C. and Zhong, G. and Babcock, G. and Vaughan, J.C. and Huang, B. and Wang, X. and Xu, C. and Bi, G.-Q. and Zhuang, X.}
     21624}
     21625@article{Vogelsang2009,
     21626  number = {20},
     21627  month = {May},
     21628  year = {2009},
     21629  title = {Controlling the fluorescence of ordinary oxazine
     21630dyes for single-molecule switching and superresolution microscopy},
     21631  pages = {8107-8112},
     21632  journal = {Proceedings of the National Academy of Sciences of the USA},
     21633  volume = {106},
     21634  author = {Vogelsang, J. and Cordes, T. and Forthmann, C. and Steinhauer, C. and Tinnefeld, P.}
     21635}
     21636@article{Kirshner2013,
     21637  number = {1},
     21638  year = {2013},
     21639  title = {{3-D PSF} fitting for fluorescence microscopy: implementation and localization application},
     21640  pages = {13-25},
     21641  journal = {Journal of Microscopy},
     21642  volume = {249},
     21643  author = {Kirshner, H. and Aguet, F. and Sage, D. and Unser, M.}
     21644}
     21645@article{Dan2013,
     21646  year = {2013},
     21647  title = {{DMD-based} {LED}-illumination Super-resolution and optical sectioning microscopy},
     21648  pages = {1116},
     21649  journal = {Scientific Reports},
     21650  volume = {3},
     21651  author = {Dan, D. and Lei, M. and Yao, B. and Wang, W. and Winterhalder, M. and Zumbusch, A. and Qi, Y. and Xia, L. and Yan, S. and Yang, Y. and Gao, P. and Ye, T. and Zhao, W.}
     21652}
     21653@article{Treacy2012,
     21654  year = {2012},
     21655  title = {A surprise in the first {Born} approximation for electron scattering},
     21656  pages = {57-62},
     21657  journal = {Ultramicroscopy},
     21658  volume = {119},
     21659  author = {Treacy, M.M.J. and Dyck, D. van}
     21660}
     21661@article{Shang2012,
     21662  year = {2012},
     21663  title = {Hydration-layer models for {cryo-EM} image simulation},
     21664  pages = {10-16},
     21665  journal = {Journal of Structural Biology},
     21666  volume = {180},
     21667  author = {Shang, Z. and Sigworth, F.J.}
     21668}
     21669@article{Blab2004,
     21670  number = {7},
     21671  year = {2004},
     21672  title = {Simultaneous wide-field imaging and spectroscopy
     21673of localized fluorophores},
     21674  pages = {727-729},
     21675  journal = {Optics Letters},
     21676  volume = {29},
     21677  author = {Blab, G.A. and Oellerich, S. and Schumm, R. and Schmidt, T.}
     21678}
     21679@article{Han2008,
     21680  year = {2008},
     21681  title = {Spectral imaging of single molecules by transmission grating-based epi-fluorescence microscopy},
     21682  pages = {209-214},
     21683  journal = {Analytica Chimica Acta},
     21684  volume = {619},
     21685  author = {Han, R. and Zhang, Y. and Dong, X .and Gai, H. and Yeung, E.S.}
     21686}
     21687@article{Heider2010,
     21688  number = {1},
     21689  year = {2010},
     21690  title = {Identification of Single Fluorescent Labels Using
     21691Spectroscopic Microscopy},
     21692  pages = {37-45},
     21693  journal = {Applied Spectroscopy},
     21694  volume = {64},
     21695  author = {Heider, E.C. and Barhoum, M. and Peterson, E.M. and Schaefer, J. and Harris, J.M.}
     21696}
     21697@article{Isailovic2011,
     21698  number = {6},
     21699  year = {2011},
     21700  title = {Multimodal Spectral Imaging of Cells Using a Transmission Diffraction Grating on a Light Microscope},
     21701  pages = {575-583},
     21702  journal = {Applied Spectroscopy},
     21703  volume = {65},
     21704  author = {Isailovic, D. and Xu, Y. and Copus, T. and Sarawat, S. and Nauli, S.M. }
     21705}
     21706@article{Li2008,
     21707  year = {2008},
     21708  title = {Tracking single quantum dot and its spectrum in free solution with controllable thermal diffusion suppression},
     21709  pages = {176-181},
     21710  journal = {Analytical Biochemistry},
     21711  volume = {277},
     21712  author = {Li, Q. and Han, R. and Meng, X. and Gai, H. and Yeung, E.S. }
     21713}
     21714@article{Ma2000,
     21715  year = {2000},
     21716  title = {High-Throughput Single-Molecule Spectroscopy in
     21717Free Solution},
     21718  pages = {4640-4645},
     21719  journal = {Analytical Chemistry},
     21720  volume = {72},
     21721  author = {Ma, Y. and Shortreed, M.R. and Yeung, E.S.}
     21722}
     21723@article{Shi2012,
     21724  year = {2012},
     21725  title = {Superlocalization Spectral Imaging Microscopy of a Multicolor Quantum Dot Complex},
     21726  pages = {1504-1509},
     21727  journal = {Analytical Chemistry},
     21728  volume = {84},
     21729  author = {Shi, X. and Xie, Z. and Song, Y. and Tan, Y. and Yeung, E.S. and Gia, H.}
     21730}
     21731@article{Lee2012,
     21732  number = {43},
     21733  year = {2012},
     21734  title = {Counting single photoactivatable fluorescent molecules by photoactivated localization microscopy {(PALM)}},
     21735  pages = {17436-17441},
     21736  journal = {Proceedings of the National Academy of Sciences USA},
     21737  volume = {109},
     21738  author = {Lee, S.-H. and Shin, J.Y. and Lee, A. and Bustamante, C.}
     21739}
     21740@article{Coltharp2012,
     21741  number = {12},
     21742  year = {2012},
     21743  title = {Accurate Construction of Photoactivated Localization Microscopy (PALM) Images for Quantitative Measurements},
     21744  pages = {e51725},
     21745  journal = {PLoS ONE},
     21746  volume = {7},
     21747  author = {Coltharp, C. and Kessler, R.P. and Xiao, J.}
     21748}
     21749@article{Annibale2011_PlosONE,
     21750  number = {7},
     21751  year = {2011},
     21752  title = {Quantitative Photo Activated Localization Microscopy: Unraveling the Effects of Photoblinking},
     21753  pages = {e22678},
     21754  journal = {PLoS ONE},
     21755  volume = {6},
     21756  author = {Annibale, P. and Vanni, S. and Scarselli, M. and Rothlisberger, U. and Radenovic, A.}
     21757}
     21758@article{Nieuwenhuizen2013,
     21759  month = {June},
     21760  year = {2013},
     21761  title = {Measuring Image Resolution in Optical Nanoscopy},
     21762  pages = {557-562},
     21763  journal = {Nature Methods},
     21764  volume = {10},
     21765  author = {Nieuwenhuizen, R.P.J. and Lidke, K.A. and Bates, M. and Leyton Puig, D. and {Gr\"unwald}, D. and Stallinga, S. and Rieger, B.}
     21766}
     21767@article{Toplak2012,
     21768  year = {2012},
     21769  title = {{STICCS} Reveals Matrix-Dependent Adhesion Slipping and Gripping in Migrating Cells},
     21770  pages = {1672-1682},
     21771  journal = {Biophysical Journal},
     21772  volume = {103},
     21773  author = {Toplak, T. and Pandzic, E. and Chen, L. and Vicente-Manzanares, M. and Horwitz, A.R. and Wiseman, P.W.}
     21774}
     21775@article{Mudry2012,
     21776  year = {2012},
     21777  title = {Structured illumination microscopy using unknown speckle patterns},
     21778  pages = {312-314},
     21779  journal = {Nature Photonics},
     21780  volume = {6},
     21781  author = {Mudry, E. and Belkebir, K. and Girard, J. and Savatier, J. and Le Moal, E. and Nicoletti, C. and Allain, M. and Sentenac, A.}
     21782}
     21783@article{Kromann2012,
     21784  number = {11},
     21785  year = {2012},
     21786  title = {Quantitative pupil analysis in stimulated emission depletion microscopy using phase retrieval},
     21787  pages = {1805-1807},
     21788  journal = {Optics Letters},
     21789  volume = {37},
     21790  author = {Kromann, B. and Gould, T.J. and Juette, M.F. and Wilhjelm, J.E. and Bewersdorf, J.}
     21791}
     21792@article{Levoy2009,
     21793  number = {2},
     21794  year = {2009},
     21795  title = {Recording and controlling the {4D} light field in a microscope using microlens arrays},
     21796  pages = {144-162},
     21797  journal = {Journal of Microscopy},
     21798  volume = {235},
     21799  author = {Levoy, M. and Zhang, Z. and Mcdowall, I.}
     21800}
     21801@article{Kress2011,
     21802  year = {2011},
     21803  title = {Probing Orientational Behvior of {MHC} Class {I} Protein and Lipid Probes in Cell Membranes by Fluorescence Polarization-Resolved Imaging},
     21804  pages = {468-476},
     21805  journal = {Biophysical Journal},
     21806  volume = {101},
     21807  author = {Kress, A. and Ferrand, P. and Rigneault, H. and Trombik, T. and He, H.-T. and Marguet, D. and Brasselet, S.}
     21808}
     21809@article{Hinde2010,
     21810  number = {38},
     21811  year = {2010},
     21812  title = {In vivo pair correlation analysis of {EGFP} intranuclear diffusion reveals {DNA-dependent} molecular flow},
     21813  pages = {16560-16565},
     21814  journal = {Proceedings of the National Academy of Sciences USA},
     21815  volume = {107},
     21816  author = {Hinde, E. and Cardarelli, F. and Digman, M.A. and Gratton, E.}
     21817}
     21818@article{Grotjohann2012,
     21819  year = {2012},
     21820  title = {{rsEGFP2} enables fast {RESOLFT} nanoscopy of living cells},
     21821  pages = {e00248},
     21822  journal = {eLIFE},
     21823  volume = {1},
     21824  author = {Grotjohann, T. and Testa, I. and Reuss, M. and Brakemann, T. and Eggeling, C. and Hell, S.W. and Jakobs, S.}
     21825}
     21826@article{Grotjohann2011,
     21827  year = {2011},
     21828  title = {Diffraction-unlimited all-optical imaging and writing with a photochromic {GFP}},
     21829  pages = {204-208},
     21830  journal = {Nature},
     21831  volume = {478},
     21832  author = {Grotjohann, T. and Testa, T. and Leutenegger, M. and Bock, H. and Urban, N.T. and Lavoie-Cardinal, F. and Willig, K.I. and Eggeling, C. and Hell, S.W.}
     21833}
     21834@article{Gould2012,
     21835  number = {19},
     21836  year = {2012},
     21837  title = {Adaptive optics enables {3D STED} microscopy in aberrating specimens},
     21838  pages = {20998-21009},
     21839  journal = {Optics Express},
     21840  volume = {20},
     21841  author = {Gould, T.J. and Burke, D. and Bewersdorf, J. and Booth, M.J.}
     21842}
     21843@article{Geissbuehler2012,
     21844  number = {4},
     21845  year = {2012},
     21846  title = {Mapping molecular statistics with balanced
     21847super-resolution optical fluctuation
     21848imaging {(bSOFI)}},
     21849  journal = {Optical Nanoscopy},
     21850  volume = {1},
     21851  author = {Geissbuehler, S. and Bocchio, N.L. and Dellagiacoma, C. and Berclaz, C. and Letenegger, M. and Lasser, T.}
     21852}
     21853@article{Dries2013,
     21854  year = {2013},
     21855  title = {Interplay between myosin {IIA}-mediated contractility and actin network integrity orchestrates podosome composition and oscillations},
     21856  pages = {1412},
     21857  journal = {Nature Communications},
     21858  volume = {4},
     21859  author = {Dries, K. van den and Meddens, M.B.M. and Keijzer, S de and Shekhar, S. and Subramaniam, V. and Figdor, C.G. and Cambi,A.}
     21860}
     21861@article{Digman2009,
     21862  year = {2009},
     21863  title = {Detecting Protein Complexes in Living Cells from Laser Scanning Confocal Image Sequences by the Cross Correlation Raster Image Spectroscopy Method},
     21864  pages = {707-716},
     21865  journal = {Biophysical Journal},
     21866  volume = {96},
     21867  author = {Digman, M.A. and Wiseman, P.W. and Horwitz, A.R. and Gratton, E.}
     21868}
     21869@article{Chao2013,
     21870  year = {2013},
     21871  title = {Ultrahigh accuracy imaging modality for super-localization microscopy},
     21872  pages = {335-338},
     21873  journal = {Nature Methods},
     21874  volume = {10},
     21875  author = {Chao, J. and Ram, S. and Ward, E.S. and Ober, R.J.}
     21876}
     21877@article{Bishop2012,
     21878  number = {5},
     21879  year = {2012},
     21880  title = {The Light Field Camera: Extended Depth of Field, Aliasing, and Superresolution},
     21881  pages = {972-986},
     21882  journal = {IEEE Transactions on Pattern Analysis and Machine Intelligence},
     21883  volume = {34},
     21884  author = {Bishop, T.E. and Favaro, P.}
     21885}
     21886@article{Brede2012,
     21887  year = {2012},
     21888  title = {{GraspJ:} an open source, real-time analysis
     21889package for super-resolution imaging},
     21890  pages = {11},
     21891  journal = {Optical Nanoscopy},
     21892  volume = {1},
     21893  author = {Brede, N. and Lakadamyali, M.}
     21894}
     21895@article{Dyck2011,
     21896  year = {2011},
     21897  title = {Persistent misconceptions about incoherence in electron microscopy},
     21898  pages = {894-900},
     21899  journal = {Ultramicroscopy},
     21900  volume = {111},
     21901  author = {Dyck, D. van}
     21902}
     21903@article{Fanelli2008,
     21904  year = {2008},
     21905  title = {Electron tomography: a short overview with an
     21906emphasis on the absorption potential model for the
     21907forward problem},
     21908  pages = {013001},
     21909  journal = {Inverse Problems},
     21910  volume = {24},
     21911  author = {Fanelli, D. and {\"Oktem}, O.}
     21912}
     21913@article{Boothroyd2013,
     21914  year = {2013},
     21915  title = {Comparison of approaches and artefacts in the measurement of detector modulation transfer functions},
     21916  pages = {18-29},
     21917  journal = {Ultramicroscopy},
     21918  volume = {129},
     21919  author = {Boothroyd, C.B. and Kasama, T. and Dunin-Borkowski, R.E.}
     21920}
     21921@article{Adams2013,
     21922  number = {6},
     21923  year = {2013},
     21924  title = {Uncovering Nuclear Pore Complexity with Innovation},
     21925  pages = {1218-1221},
     21926  journal = {Cell},
     21927  volume = {152},
     21928  author = {Adams, R.L. and Wente, S.R.}
     21929}
     21930@article{Vulovic2013,
     21931  number = {1},
     21932  year = {2013},
     21933  title = {Image Formation Modeling in Cryo Electron Microscopy},
     21934  pages = {19-32},
     21935  journal = {Journal of Structural Biology},
     21936  volume = {183},
     21937  author = {Vulovic, M. and Ravelli, R.B.G. and Vliet, L.J. van and Koster, A.J. and Lazic, I. and {L\"ucken}, U. and {Rullg{\aa}rgd}, H. and {\"Oktem}, O. and Rieger, B.}
     21938}
     21939@article{Briege2013,
     21940  year = {2013},
     21941  title = {The challenge of determining handedness in electron tomography and the use of DNA origami gold nanoparticle helices as molecular standards},
     21942  journal = {Journal of Structural Biology},
     21943  author = {Briegel, A. and Pilhofer, M. and Mastronade, D.N. and Jensen, G.J.}
     21944}
     21945@article{Briegel2012,
     21946  year = {2012},
     21947  title = {Bacterial chemoreceptor arrays are hexagonally
     21948packed trimers of receptor dimers networked
     21949by rings of kinase and coupling proteins},
     21950  note = {doi/10.1073/pnas.1115719109},
     21951  journal = {Proceedings of the National Academy of Sciences USA},
     21952  author = {Briegel, A. and Li, X. and Bilwes, A.M. and Hughes, K.T. and Jensen, G.J. and Crane, B.R.}
     21953}
     21954@article{Schlimpert2012,
     21955  year = {2012},
     21956  title = {General protein diffusion barries create compartments within barcterial cells},
     21957  pages = {1270-1282},
     21958  journal = {Cell},
     21959  volume = {151},
     21960  author = {Schimpfert, S. and Klein, E.A. and Briegel, A. and Hughes, V. and Kahnt, J. and Bolte, K. and Maier, U.G. and Brun, Y.V. and Jensen, G.J. and Gitai, Z. and Thanbichler, M.}
     21961}
     21962@article{Briegel2010,
     21963  year = {2010},
     21964  title = {Correlated light and electron cryo-micrscopy},
     21965  pages = {317-342},
     21966  journal = {Methods in  Enzymology},
     21967  volume = {481},
     21968  author = {Briegel, A. and Chen, S. and Koster, A.J. and Plitzko, J.M. and Schwartz, C.L. Jensen, G.J.}
     21969}
     21970@article{Jensen2007,
     21971  year = {2007},
     21972  title = {How electron cryotomography is opening a new window
     21973onto prokaryotic ultrastructure},
     21974  pages = {260-267},
     21975  journal = {Current Opinion in Structural Biology},
     21976  volume = {17},
     21977  author = {Jensen, G.J. and Briegel, A.}
     21978}
     21979@article{Cowley1962,
     21980  number = {supp B-II},
     21981  year = {1962},
     21982  title = {The scattering of electrons by thin crystals},
     21983  pages = {86-91},
     21984  journal = {Journal of the Physical Society of Japan},
     21985  volume = {17},
     21986  author = {Cowely, J.M. and Moodie, A.F. }
     21987}
     21988@article{Dempsey2009,
     21989  number = {51},
     21990  year = {2009},
     21991  title = {Photoswitching Mechanism of Cyanine Dyes},
     21992  pages = {18192-18193},
     21993  journal = {Journal of the American Chemical Society},
     21994  volume = {131},
     21995  author = {Dempsey, G.T. and Bates, M. and Kowtoniuk, W.E. and Liu, D.R. and Tsien, R.Y. and Zhuang, X.}
     21996}
     21997@article{Betzig1995,
     21998  number = {3},
     21999  year = {1995},
     22000  title = {Proposed method for molecular optical imaging},
     22001  pages = {237-239},
     22002  journal = {Optics Letters},
     22003  volume = {20},
     22004  author = {Betzig, E.}
     22005}
     22006@article{Vaughan2012,
     22007  number = {12},
     22008  year = {2012},
     22009  title = {Ultrabright photoactivatable fluorophores created by reductive caging},
     22010  pages = {1181-1184},
     22011  journal = {Nature Methods},
     22012  volume = {9},
     22013  author = {Vaughan, J.C. and Jia, S. and Zhuang, X.}
     22014}
     22015@article{Xu2013,
     22016  year = {2013},
     22017  title = {Actin, Spectrin, and Associated Proteins Form a Periodic Cytoskeletal Structure in Axons},
     22018  pages = {452-456},
     22019  journal = {Science},
     22020  volume = {339},
     22021  author = {Xu, K. and Zhong, G. and Zhuang, X.}
     22022}
     22023@article{Rees2012,
     22024  year = {2012},
     22025  title = {Blind assessment of localisation microscope
     22026image resolution},
     22027  pages = {12},
     22028  journal = {Optical Nanoscopy},
     22029  volume = {1},
     22030  author = {Rees, E.J. and Erdelyi, M. and Pinotsi, D. and Knight, A. and Metcalf, D. and Kaminski, C.F.}
     22031}
     22032@article{Huang2013,
     22033  number = {7},
     22034  year = {2013},
     22035  title = {Video-rate nanoscopy using {sCMOS} camera-specific
     22036single-molecule localization algorithms},
     22037  pages = {653-658},
     22038  journal = {Nature Methods},
     22039  volume = {10},
     22040  author = {Huang, F. and Hartwich, T.M.P. and Rivera-Molina, F.E. and Lin, Y. and Whitney, C. and Long, J.J. and Uchil, P.D. and Myers, J.R. and Baird, M.A. and Mothes, W. and Davidson, M.W. and Toomre, D. and Bewersdorf, J.}
     22041}
     22042@article{Li2013,
     22043  number = {6},
     22044  year = {2013},
     22045  title = {Electron counting and beam-induced motion correction enable near-atomic-resolution single-particle {cryo-EM}},
     22046  pages = {584-590},
     22047  journal = {Nature Methods},
     22048  volume = {10},
     22049  author = {Li, X. and Mooney, P. and Zheng, S.and Booth, C.R. and Braunfeld, M.B. and Gubbens, S. and Agard, D.A. and Yifan, C.}
     22050}
     22051@article{Nellist2008,
     22052  year = {2008},
     22053  title = {Imaging Modes for Scanning Confocal Electron Microscopy in a Double Aberration-Corrected Transmission Electron Microscope},
     22054  pages = {82-88},
     22055  journal = {Microscopy and Microanalysis},
     22056  volume = {14},
     22057  author = {Nellist, P.D. and Cosgriff, E.C. and Behan, G. and Kirkland, A.I.}
     22058}
     22059@article{Cosgriff2008,
     22060  year = {2008},
     22061  title = {Three-dimensional imaging in double aberration-corrected scanning confocal electron microscopy, Part {I}: Elastic scattering},
     22062  journal = {Ultramicroscopy},
     22063  author = {Cosgriff, E.C .and D'Alfonso, A.J. and Alleen, L.J. and Findlay, S.D. and Kirkland, A.I. and Nellist, P.D.}
     22064}
     22065@article{Dalfonso2008,
     22066  year = {2008},
     22067  title = {Three-dimensional imaging in double aberration-corrected scanning confocal electron microscopy, Part {II}: Inelastic scattering},
     22068  pages = {1567-1578},
     22069  journal = {Ultramicroscopy},
     22070  volume = {108},
     22071  author = {D'Alfonso, A.J. and Cosgriff, E.C. and Behan, G. and Kirkland, A.I. and Nellist, P.D.}
     22072}
     22073@article{Wang2008b,
     22074  year = {2008},
     22075  title = {Nanoscale Energy-Filtered Scanning Confocal Electron Microscopy Using a Double-Aberration-Corrected Transmission Electron Microscope},
     22076  pages = {200801},
     22077  journal = {Physical Review Letters},
     22078  volume = {104},
     22079  author = {Wang, P. and Behan, G. and Takeguchi, M. and Hasimoto, A. and Mituishi, K. and Shimojo, M. and Kirkland, A.I. and Nellist, P.D.}
     22080}
     22081@article{Erdelyi2013,
     22082  number = {9},
     22083  month = {May},
     22084  year = {2013},
     22085  title = {Correcting chromatic offset in multicolor superresolution localization microscopy},
     22086  pages = {10978-10988},
     22087  journal = {Optics Express},
     22088  volume = {21},
     22089  author = {Erdelyi, M. and Rees, E. and Metcalf, D. and Kaminski Schierle, G.S. and Dudas, L. and Sinko, J. and Knight, J. and Kaminski, C.F.}
     22090}
     22091@article{Endesfelder2013,
     22092  year = {2013},
     22093  title = {Multiscale Spatial Organization of {RNA} Polymerase in {Escherichia} coli},
     22094  note = {doi.org/10.1016/j.bpj.2013.05.048},
     22095  journal = {Biophysical Journal},
     22096  volume = {105},
     22097  author = {Endesfelder, U. and Finan, K. and Holden, S.J. and Cook, P.R. and Kapanidis, A.N. and Heilemann, M.}
     22098}
     22099@article{Bertolotti2012,
     22100  year = {2012},
     22101  title = {Non-invasive imaging through opaque scattering
     22102layers},
     22103  pages = {232-234},
     22104  journal = {Nature},
     22105  volume = {491},
     22106  author = {Bertolotti, J. and Putten, E.G. van and Blum, C. and Lagendijk, A. and Vos, W.L. and Mosk, A.P.}
     22107}
     22108@article{Kohler2011,
     22109  year = {2011},
     22110  title = {Structure formation in active networks},
     22111  pages = {462-468},
     22112  journal = {Nature Materials},
     22113  volume = {10},
     22114  author = {{K\"ohler}, S. and Schaller, V. and Bausch, A.R.}
     22115}
     22116@article{Matov2010,
     22117  number = {9},
     22118  year = {2010},
     22119  title = {Analysis of microtubule dynamic instability using
     22120a plus-end growth marker},
     22121  pages = {761-768},
     22122  journal = {Nature Methods},
     22123  volume = {7},
     22124  author = {Matov, A. and Applegate, K. and Kumar, P. and Thoma, C. and Krek, W. and Danuser, G. and Wittmann, T.}
     22125}
     22126@article{Smith2010b,
     22127  year = {2010},
     22128  title = {Segmentation and Tracking of Cytoskeletal Filaments
     22129Using Open Active Contours},
     22130  pages = {693-705},
     22131  journal = {Cytoskeleton},
     22132  volume = {67},
     22133  author = {Smith, M.B. and Li, H. and Shen, T. and Huang, X. and Yusuf, E. and Vavylonis, D.}
     22134}
     22135@phdthesis{Vulovic2013a,
     22136  month = {13 June},
     22137  year = {2013},
     22138  title = {Modeling of Image Formation in Cryo Electron Microscopy},
     22139  school = {Delft University of Technology},
     22140  author = {Vulovic, M.}
     22141}
     22142@phdthesis{Karreman2013,
     22143  month = {March},
     22144  year = {2013},
     22145  title = {Light will guide you},
     22146  school = {Utrecht University},
     22147  author = {Karreman, M.A.}
     22148}
     22149@article{Szymborska2013,
     22150  year = {2013},
     22151  title = {Nuclear Pore Scaffold Structure Analyzed by Super-Resolution Microscopy and Particle Averaging},
     22152  pages = {10.1126},
     22153  journal = {Science Express},
     22154  author = {Szymborska, A. and Marco, A de. Daigle, N. and Cordes, V.C. and Briggs, J.A.G. and Elllenberg, J.}
     22155}
     22156@article{Cutler2013,
     22157  number = {5},
     22158  year = {2013},
     22159  title = {Multi-Color Quantum Dot Tracking Using a High-Speed
     22160Hyperspectral Line-Scanning Microscope},
     22161  pages = {e64320},
     22162  journal = {PLOS One},
     22163  volume = {8},
     22164  author = {Culter, P.J. and Malik, M.D. and Sheng, L. and Byars, J.M. and Lidke, D.S. and Lidke, K.A.}
     22165}
     22166@article{Shigematsu2013,
     22167  year = {2013},
     22168  title = {Noise models and cryo-EM drift correction with a direct-electron detector},
     22169  pages = {61-69},
     22170  journal = {Ultramicroscopy},
     22171  volume = {131},
     22172  author = {Shigematsu, H. and Sigworth, F.J.}
     22173}
     22174@article{Genc2013,
     22175  year = {2013},
     22176  title = {XEDS STEM tomography for 3D chemical characterization of nano scale particles},
     22177  pages = {24-32},
     22178  journal = {Ultramicroscopy},
     22179  volume = {131},
     22180  author = {Genc, A. and Kovarik, L. and Gu, M. and Cheng, H. and Plachinda, P. and Pullan, L. and Freitag, B. and Wang, C.}
     22181}
     22182@article{Kechkar2013,
     22183  number = {4},
     22184  month = {04},
     22185  year = {2013},
     22186  title = {Real-Time Analysis and Visualization for Single-Molecule Based Super-Resolution Microscopy},
     22187  pages = {e62918},
     22188  journal = {PLoS ONE},
     22189  volume = {8},
     22190  author = {Kechkar, A. AND Nair, D. AND Heilemann, M. AND Choquet, Da. AND Sibarita, J.-B.}
     22191}
     22192@article{Banterle2013,
     22193  year = {2013},
     22194  title = {Fourier ring correlation as a resolution criterion for super-resolution microscopy},
     22195  journal = {Journal of Structural Biology},
     22196  author = {Banterle, N. and Bui, K.H. and Lemke, E.A. and Beck, M.}
     22197}
     22198@article{Quirin2013,
     22199  number = {13},
     22200  year = {2013},
     22201  title = {Instantaneous three-dimensional sensing using spatial light modulator illumination with extended depth of field imaging},
     22202  pages = {16007-16021},
     22203  journal = {Optics Express},
     22204  volume = {21},
     22205  author = {Quirin, S. and  Peterka, D.S. and Yuste, R.}
     22206}
     22207@article{Chmyrov2013,
     22208  number = {8},
     22209  year = {2013},
     22210  title = {Nanoscopy with more than 100,000 'doughnuts'},
     22211  pages = {737-740},
     22212  journal = {Nature Methods},
     22213  volume = {10},
     22214  author = {Chmyrov, A. and Keller, J. and Grotjohann, T. and Ratz, M. and d'Este, E. and Jakobs, S. and Eggeling, C. and Hell, S.W.}
     22215}
     22216@article{Krizek2013,
     22217  number = {22},
     22218  year = {2013},
     22219  title = {Flexible structured illumination microscope with a programmable illumination array},
     22220  pages = {24585-24589},
     22221  journal = {Optics Express},
     22222  volume = {20},
     22223  author = {Krizek, P. and Raska, I. and Hagen, G.M.}
     22224}
     22225@article{Hoebe2007,
     22226  number = {2},
     22227  year = {2007},
     22228  title = {Controlled light-exposure microscopy reduces photobleaching and phototoxicity in fluorescence live-cell imaging},
     22229  pages = {249-253},
     22230  journal = {Nature Biotechnology},
     22231  volume = {25},
     22232  author = {Hoebe, R.A. and Oven, C.H. van and Gadella, T.W. jr and Dhonukshe, P.B. and Noorden, C.J. van and Manders, E.M.M.}
     22233}
     22234@article{Backer2013,
     22235  year = {2013},
     22236  title = {Single-molecule orientation measurements with a quadrated pupil},
     22237  pages = {1521-1523},
     22238  journal = {Optics Letters},
     22239  volume = {38},
     22240  author = {Backer, A.S. and Backlund, M.P. and Lew, M.D. and Moerner, W.E. }
     22241}
     22242@article{Lampe2012,
     22243  year = {2012},
     22244  title = {Multi-colour direct {STORM} with red emitting carbocyanines},
     22245  pages = {1-9},
     22246  journal = {Biology of the Cell},
     22247  volume = {104},
     22248  author = {Lampe, A. and Haucke, V. and Sigrist, S.J. and Heilemann, M. and Schmoranzer, J.}
     22249}
     22250@article{Burnette2011,
     22251  number = {52},
     22252  year = {2011},
     22253  title = {Bleaching/blinking assisted localization microscopy for superresolution imaging using standard fluorescent molecules},
     22254  pages = {21081-6},
     22255  journal = {Proceedings of the National Academy of Sciences USA},
     22256  volume = {108},
     22257  author = {Burnette, D.T. and Sengupta, P. and Dai, Y. and Lippincott-Schwartz, J. and Kachar, B.}
     22258}
     22259@article{Barsic2013,
     22260  year = {2013},
     22261  title = {Super-resolution of dense nanoscale emitters beyond the diffraction limit using spatial and temporal information},
     22262  pages = {231103},
     22263  journal = {Applied Physics Letters},
     22264  volume = {102},
     22265  author = {Barsic, A. and Piestun, R.}
     22266}
     22267@article{Broek2013,
     22268  year = {2013},
     22269  title = {General framework for quantitative three-dimensional reconstruction from arbitrary detection geometries in {TEM}},
     22270  pages = {184108},
     22271  journal = {Physical Review B},
     22272  volume = {87},
     22273  author = {Broek, W. van den and Koch, C.T.}
     22274}
     22275@incollection{Lindeberg2013,
     22276  series = {Volume 178},
     22277  year = {2013},
     22278  title = {Generalized Axiomatic Scale-Space Theory},
     22279  booktitle = {Advances in Imaging and Electron Physics},
     22280  pages = {1-96},
     22281  author = {Lindeberg, T.}
     22282}
     22283@article{Huang2012,
     22284  year = {2012},
     22285  title = {Far-field photostable optical nanoscopy ({PHOTON}) for real-time superresolution single-molecular imaging of signaling pathways of single live cells},
     22286  pages = {2797},
     22287  journal = {Nanoscale},
     22288  volume = {4},
     22289  author = {Huang, T. and Browning, L.M. and Nancy Xu, X.-H.}
     22290}
     22291@article{Vulovic2014,
     22292  year = {2014},
     22293  title = {When to use the projection assumption and the weak-phase object approximation in phase contrast {cryo-EM}},
     22294  pages = {61-66},
     22295  journal = {Ultramircoscopy},
     22296  volume = {136},
     22297  author = {Vulovic, M. and Voortman, L.M. and Vliet, L.J. van and Rieger, B.}
     22298}
     22299@article{Lepiany2013,
     22300  year = {2013},
     22301  title = {Chemical 3D tomography of 28 nm high K metal gate transistor: {STEM XEDS}
     22302experimental method and results},
     22303  pages = {43-49},
     22304  journal = {Micron},
     22305  volume = {47},
     22306  author = {Lepinay, K. and Lorut, F. and Pantel, R. and Epicier, T.}
     22307}
     22308@article{Gittes1993,
     22309  number = {4},
     22310  month = {November},
     22311  year = {1993},
     22312  title = {Flexural rigidity of microtubules and actin filaments measured from thermal fluctuations in shape.},
     22313  pages = {923-934},
     22314  journal = {Journal of Cell Biology},
     22315  volume = {120},
     22316  author = {Gittes, F. and Mickey, B. Nettleton, J. and Howard, J.}
     22317}
     22318@misc{Pengo2013,
     22319  year = {2013},
     22320  title = {{PALM-siever}: {V}isualization and analysis platform for single-molecule localization microscopy},
     22321  note = {[Online; accessed 12-September-2013]},
     22322  url = {http://code.google.com/p/palm-siever/},
     22323  author = {Pengo, T.}
     22324}
     22325@inproceedings{Nieuwenhuizen2013b,
     22326  series = {SPIE Conference vol. 8815},
     22327  month = {Augustus 26-30},
     22328  year = {2013},
     22329  title = {Image resolution in optical nanoscopy },
     22330  booktitle = {Nanoimaging and Nanospectroscopy},
     22331  pages = {881508},
     22332  note = {doi: 10.1117/12.2025352},
     22333  editor = {Verma, P. and Egner, A.},
     22334  address = {San Diego, USA},
     22335  author = {Nieuwenhuizen, R.P.J. and Stallinga, S. and Rieger, B.}
     22336}
     22337@inbook{Nieuwenhuizen2014,
     22338  year = {2014},
     22339  title = {Cell Membrane Nanodomains: from Biochemistry to Nanoscopy},
     22340  editor = {Lidke, D.S. and Cambi, A.},
     22341  chapter = {Visualization and Resolution in Localization Microscopy},
     22342  publisher = {Taylor and Francis},
     22343  author = {Nieuwenhuizen, R.P.J.  and Stallinga, S. and Rieger, B.}
     22344}
     22345@article{Angelo2008,
     22346  number = {10},
     22347  year = {2008},
     22348  title = {Structure, dynamics and function of nuclear pore complexes},
     22349  pages = {456-466},
     22350  journal = {Trends in Cell Biology},
     22351  volume = {18},
     22352  author = {D'Angelo, M.A. and Hetzer, M.W.}
     22353}
     22354@article{Griffis_MolBiolCell_2003,
     22355  year = {2003},
     22356  title = {Nup98 Localizes to Both Nuclear and Cytoplasmic
     22357Sides of the Nuclear Pore and Binds to Two Distinct
     22358Nucleoporin Subcomplexes},
     22359  pages = {600-610},
     22360  journal = {Molecular Biology of the Cell},
     22361  volume = {14},
     22362  author = {Griffs, E.R. and Xu, S. and Powers, M.A.}
     22363}
     22364@article{York2013,
     22365  year = {2013},
     22366  title = {Instant super-resolution imaging in live cells and embryos via analog image processing},
     22367  note = {doi:10.1038/nmeth.2687},
     22368  journal = {Nature Methods},
     22369  author = {York, A.G. and Chandris, P. and Dalle Nogare, D. and Head, J. and Wawrzusin, P. and Fischer, R.S. and Chitnis, A. and Shroff, H. }
     22370}
     22371@inproceedings{Weisenburg2013,
     22372  series = {Proc. of SPIE Vol. 8815},
     22373  month = {22-29 Augustus},
     22374  year = {2013},
     22375  title = {Cryogenic localization of single molecules with Angstrom precision},
     22376  booktitle = {Nanoimaging and Nanospectroscopy},
     22377  pages = {88450D},
     22378  editor = {Prama, V. and Egner, A.},
     22379  address = {San Diego, USA},
     22380  author = {Weisenburger, S. and Jing, B. and Renn, A. and Sandoghdar, V.}
     22381}
     22382@article{Jinschek2012,
     22383  year = {2012},
     22384  title = {Image resolution and sensitivity in an environmental transmission electron microscope},
     22385  pages = {1156-1168},
     22386  journal = {Micron},
     22387  volume = {43},
     22388  author = {Jinscheck, J.R. and Helveg, S.}
     22389}
     22390@article{Faas2013,
     22391  year = {2013},
     22392  title = {Localization of fluorescently labeled structures in frozen-hydrated samples using integrated light electron microscopy},
     22393  pages = {283-290},
     22394  journal = {Journal of Structural Biology},
     22395  volume = {181},
     22396  author = {Faas, F.G.A. and Barcena, M. and Agronskaia, A.V. and Gerritsen, H.C. and Moscicika, K.B. and Diebolder, C.A. and Driel, L.F. van and Limpens, R.W.A.L. and Bos, E. and Ravelli, R.B.G. and Koning, R.I. and Koster, A.J.}
     22397}
     22398@article{Roth2013,
     22399  year = {2013},
     22400  title = {Optical photon reassignment microscopy {(OPRA)}},
     22401  pages = {5},
     22402  note = {doi:10.1186/2192-2853-2-5},
     22403  journal = {Optical nanoscopy},
     22404  volume = {2},
     22405  author = {Roth, S. and Sheppard, C.J.R. and Wicker, K. and Heintzmann, R.}
     22406}
     22407@article{Luca2013,
     22408  number = {11},
     22409  year = {2013},
     22410  title = {Re-scan confocal microscopy: scanning twice for better resolution },
     22411  pages = {2644-2656},
     22412  journal = {Biomedical Optical Express},
     22413  volume = {4},
     22414  author = {Luca, G.M.R. De and Breedijk, R.M.P. and Brandt, R.A.J. and Zeelenberg, C.H.C. and Jong, B.E. de and Timmermanns, W. and Azar, L.N. and Hoebe, R.A. and Stallinga, S. and Manders, E.M.M. }
     22415}
     22416@article{Ruskin2013,
     22417  year = {2013},
     22418  title = {Quantitative characterization of electron detectors for transmission electron microscopy},
     22419  note = {http://dx.doi.org/10.1016/j.jsb.2013.10.016},
     22420  journal = {Journal of Structural Biology},
     22421  author = {Ruskin, R.S. and Yu, Z. and Grigorieff, N.}
     22422}
     22423@article{Righolt2013,
     22424  number = {21},
     22425  year = {2013},
     22426  title = {Image filtering in structured illumination microscopy using the {Lukosz} bound},
     22427  pages = {24431-24451},
     22428  journal = {Optics Express},
     22429  volume = {21},
     22430  author = {Righolt, C.H. and Slotman, J.A. and Young, I.T. and Mai, S. and Vliet, L.J. van and Stallinga, S.}
     22431}
     22432@article{Abrahamsson2013,
     22433  number = {1},
     22434  year = {2013},
     22435  title = {Fast multicolor 3D imaging using aberration corrected multifocus microscopy},
     22436  pages = {60-65},
     22437  journal = {Nature Methods},
     22438  volume = {10},
     22439  author = {Abrahamsson, S. and Chen, J. and Hajj, B. and Stallinga, S. and Katsov, A.Y. and Wisnieski, J. and Mizuguchi, G. and Soule, P. and Mueller, F. and Daugast Darzacq, C. and Darzacq, X. and Wu, C. and Bargmann, C.I. and Agard, D.A. and Dahan, M. and Gustafsson, M.G.L.}
     22440}
     22441@article{Heidari2013,
     22442  year = {2013},
     22443  title = {Quantitative electron tomography: The effect of the three-dimensional point spread function},
     22444  pages = {1-5},
     22445  journal = {Ultramicroscopy},
     22446  volume = {135},
     22447  author = {Heidari, H. and Broek, W. van den and Bals, S.}
     22448}
     22449@article{Fuerstenberg2013,
     22450  number = {36},
     22451  year = {2013},
     22452  title = {Single-molecule localization microscopy -
     22453near-molecular spatial resolution in light
     22454microscopy with photoswitchable fluorophores},
     22455  pages = {14919-14930},
     22456  journal = {Physical Chemistry Chemical Physics},
     22457  volume = {15},
     22458  author = {Fuerstenberg, A. and Heilemann, M.}
     22459}
     22460@article{Sengupta2012,
     22461  number = {6},
     22462  month = {December},
     22463  year = {2012},
     22464  title = {Visualizing Cell Structure and Function
     22465with Point-Localization Superresolution Imaging},
     22466  pages = {1092-1102},
     22467  journal = {Developmental Cell},
     22468  volume = {23},
     22469  author = {Sengupta, P. and Engelenburg, S. van and Lippincott-Schwartz, J.}
     22470}
     22471@article{Kamiyama2012,
     22472  number = {6},
     22473  month = {December},
     22474  year = {2012},
     22475  title = {Development in the STORM},
     22476  pages = {1103-1110},
     22477  journal = {Developmental Cell},
     22478  volume = {23},
     22479  author = {Kamiyama, D. and Huang, B.}
     22480}
     22481@article{Liu2013,
     22482  number = {24},
     22483  year = {2013},
     22484  title = {Three dimensional single molecule localization using a phase retrieved pupil function},
     22485  pages = {29462-29487},
     22486  journal = {Optics Express},
     22487  volume = {21},
     22488  author = {Liu, S. and Kromann, E.B. and Krueger, W.D. and Bewersdorf, J. and Lidke, K.A.}
     22489}
     22490@article{Diebold2013,
     22491  year = {2013},
     22492  title = {Digitally synthesized beat frequency multiplexing
     22493for sub-millisecond fluorescence microscopy},
     22494  pages = {806-810},
     22495  journal = {Nature Photonics},
     22496  volume = {7},
     22497  author = {Diebold, E.D. and Buckley, B.W. and Gossett, D.R. and Jalali, B.}
     22498}
     22499@article{Stennett2014,
     22500  year = {2014},
     22501  title = {Photophysical processes in single molecule organic fluorescent probes},
     22502  note = {DOI: 10.1039/c3cs60211g},
     22503  journal = {Chem Soc Rev},
     22504  author = {Stennett, E.M.S. and Ciuba, M.A. and Levitus, M.}
     22505}
     22506@article{Levitus2011,
     22507  number = {1},
     22508  year = {2011},
     22509  title = {Cyanine dyes inbiophysical research: the
     22510photophysics of polymethine fluorescentdyes
     22511inbiomolecular environments},
     22512  pages = {123-151},
     22513  journal = {Quarterly Reviews of Biophysics},
     22514  volume = {44},
     22515  author = {Levitus, M. and Ranjit, S.}
     22516}
     22517@article{Glaeser2014,
     22518  year = {2014},
     22519  title = {GENERALIZATION OF THE MATSUMOTO-TONOMURA APPROXIMATION FOR THE PHASE SHIFT WITHIN AN OPEN APERTURE},
     22520  note = {http://dx.doi.org/10.1016/j.ultramic.2013.11.009},
     22521  journal = {Ultramicroscopy},
     22522  author = {Glaeser, R.M. and {M\"uller}, H.}
     22523}
     22524@article{Rieger2014,
     22525  number = {4},
     22526  year = {2014},
     22527  title = {The Lateral and Axial Localization Uncertainty in Super-Resolution Light Microscopy},
     22528  pages = {664-670},
     22529  journal = {ChemPhysChem},
     22530  volume = {15},
     22531  author = {Rieger, B. and Stallinga, S.}
     22532}
     22533@article{Shivanandan2013,
     22534  year = {2013},
     22535  title = {MosaicIA: an ImageJ/Fiji plugin for spatial pattern and interaction analysis},
     22536  pages = {349},
     22537  journal = {BMC Bioinformatics},
     22538  volume = {14},
     22539  author = {Shivanandan, A. and Radenovic, A. and Sbalzarini, I.F.}
     22540}
     22541@article{Cardone2013,
     22542  number = {2},
     22543  year = {2013},
     22544  title = {One number does not fit all: Mapping local variations in resolution in cryo-EM reconstructions},
     22545  pages = {226-236},
     22546  journal = {Journal of Structural Biology},
     22547  volume = {184},
     22548  author = {Cardone, G. and Heymann, J.B. and Steven, A.C.}
     22549}
     22550@article{Kucukelbir2013_NatMeth,
     22551  number = {XX},
     22552  year = {2013},
     22553  title = {Quantifying the local resolution of cryo-EM density maps},
     22554  journal = {Nature Methods},
     22555  volume = {XX},
     22556  author = {Kucukelbir, A. and Sigworth, F.J. and Tagare, H.D.}
     22557}
     22558@article{Kudrayashev2013,
     22559  number = {2},
     22560  year = {2012},
     22561  title = {Limiting factors in single particle cryo electron tomography},
     22562  pages = {e201207002},
     22563  journal = {Computational and Structural Biotechnology Journal},
     22564  volume = {1},
     22565  author = {Kudrayashev, M. and Castano-Diez, D. and Stahlberg, H.}
     22566}
     22567@article{Owen2010,
     22568  number = {7},
     22569  year = {2010},
     22570  title = {{PALM} imaging and cluster analysis of protein heterogeneity at the cell surface},
     22571  journal = {Journal of Biophotonics},
     22572  volume = {3},
     22573  author = {Owen, D.M. and Rentero, C. and Rossy, J. and Magenau, A. and Williamson, D. and Rodriguez, M. and Gaus, K.}
     22574}
     22575@article{Sang2014,
     22576  year = {2014},
     22577  title = {Revolving scanning transmission electron microscopy: Correcting sample drift distortion without prior knowledge},
     22578  journal = {Ultramicroscopy},
     22579  author = {Sang, X. and LeBeau, J.M.}
     22580}
     22581@article{Ayuk2013,
     22582  number = {22},
     22583  year = {2013},
     22584  title = {Structured illumination fluorescence microscopy
     22585with distorted excitations using a filtered blind-{SIM} algorithm},
     22586  pages = {4723-4726},
     22587  journal = {Optics Letters},
     22588  volume = {38},
     22589  author = {Ayuk, R. and Giovannini, H. and Jost, A. and Mudry, E. and Girard, J. and Mangeat, T. and Sandeau, N. and Heintzmann, R. and Wicker, K. and Belkebir, K. and Sentenac, A.}
     22590}
     22591@article{Cohen2013,
     22592  number = {24},
     22593  year = {2013},
     22594  title = {Analysis of Point Based Image Registration Errors
     22595With Applications in Single Molecule Microscopy},
     22596  pages = {6291-6306},
     22597  journal = {IEEE Transactions on Signal Processing},
     22598  volume = {61},
     22599  author = {Cohen, E.A.K. and Ober, R.J.}
     22600}
     22601@article{Chizhik2014,
     22602  year = {2014},
     22603  title = {Metal-induced energy transfer for live cell nanoscopy},
     22604  note = {DOI: 10.1038/NPHOTON.2013.345},
     22605  journal = {Nature Photonics},
     22606  author = {Chizhik, A.I. and Rother, J. and Gregor, I. and Janshoff, A. and Enderlein, J.}
     22607}
     22608@article{Schulz2013,
     22609  year = {2013},
     22610  title = {Resolution doubling in fluorescence microscopy with
     22611confocal spinning-disk image scanning microscopy},
     22612  note = {doi/10.1073/pnas.1315858110},
     22613  journal = {Proceedings of the National Academy of Sciences USA},
     22614  author = {Schulz, O. and Pieper, C. and Clever, M. and Pfaff, J. and Ruhlandt, A. and Kehlenbach, R.H. and Wouters, F.S. and Groshans, J. and Bunt, G. and Enderlein, J.}
     22615}
     22616@article{Min2013,
     22617  year = {2013},
     22618  title = {Fluorescent microscopy beyond diffraction limits using speckle illumination and joint support recovery},
     22619  pages = {2075},
     22620  journal = {Scientific Reports},
     22621  volume = {3},
     22622  author = {Min, J. and Jang, J. and Keum, D. and Ryu, S.-W. and Choi, C. and Jeong, K.-H. and Ye, J.-C.}
     22623}
     22624@article{Legros2009,
     22625  number = {1},
     22626  year = {2009},
     22627  title = {High-aperture cryogenic light microscopy},
     22628  pages = {1-8},
     22629  journal = {Journal of Microscopy},
     22630  volume = {235},
     22631  author = {Le Gros, M.A. and McDermott, G. and Uchida, M. and  Knoechel, C.G. and Larabell, C.A.}
     22632}
     22633@article{Kucukelbir2014,
     22634  number = {1},
     22635  year = {2014},
     22636  title = {Quantifying the local resolution of cryo-{EM} density maps},
     22637  pages = {63-65},
     22638  journal = {Nature Methods},
     22639  volume = {11},
     22640  author = {Kucukelbir, A. and Sigworth, F.J. and Tagare, H.D.}
     22641}
     22642@article{McGorty2013,
     22643  year = {2013},
     22644  title = {Active microscope stabilization in three
     22645dimensions using image correlation},
     22646  pages = {3},
     22647  journal = {Optical Nanoscopy},
     22648  volume = {2},
     22649  author = {McGorty, R .and Kamiyama, D. and Huang, B.}
     22650}
     22651@article{Klein2014,
     22652  year = {2014},
     22653  title = {Eight years of single-molecule localization microscopy},
     22654  note = {DOI 10.1007/s00418-014-1184-3},
     22655  journal = {Histochem Cell Biology},
     22656  author = {Klein, T. and Proppert, S. and Sauer, M.}
     22657}
     22658@article{VanDeLinde2011,
     22659  year = {2011},
     22660  title = {Photoinduced formation of reversible dye radicals and their impact on super-resolution imaging},
     22661  pages = {499-506},
     22662  journal = {Photochemical \& Photobiological Sciences},
     22663  volume = {10},
     22664  author = {Linde, S. van de and Krstic, I. and Psisner, T. and Doose, S. and Heilemann, M. and Sauer, M.}
     22665}
     22666@article{Faro2011,
     22667  year = {2011},
     22668  title = {Low-Temperature Chromophore Isomerization Reveals the Photoswitching Mechanism of the Fluorescent Protein Padron},
     22669  pages = {16362-16365},
     22670  journal = {Journal of the American Chemical Society},
     22671  volume = {133},
     22672  author = {Faro, A.R. and Carpentier, P. and Jonasson, G. and Pompidor, G. and Arcizet, D. and Demachy, I. and Bourgeois, D.}
     22673}
     22674@mastersthesis{Pfaff2013,
     22675  year = {2013},
     22676  title = {Cryo Fluorescence Single Molecule Microscopy},
     22677  address = {{W\"urzburg}, Germany},
     22678  school = {Julius-Maximilians-{Universit\"at} {W\"urzburg}},
     22679  author = {Pfaff, D.}
     22680}
     22681@article{Jungmann2014,
     22682  year = {2014},
     22683  title = {Multiplexed {3D} cellular super-resolution imaging with {DNA-PAINT} and Exchange-{PAINT}},
     22684  note = {doi:10.1038/nmeth.2835},
     22685  journal = {Nature Methods},
     22686  author = {Jungmann, R. and Avendano, M. and Woehrstein, J.B. and Dai, M. and Shih, W.M. and Yin, P.}
     22687}
     22688@article{Zhao2011,
     22689  year = {2011},
     22690  title = {Photon budget analysis for fluorescence lifetime imaging microscop},
     22691  pages = {086007},
     22692  journal = {Journal of Biomedical Optics},
     22693  volume = {16},
     22694  author = {Zhao, Q. and Young, I.T. and Sander de Jong, D.G.}
     22695}
     22696@article{Dai2005,
     22697  number = {23},
     22698  year = {2005},
     22699  title = {Measuring large numerical apertures by imaging
     22700the angular distribution of radiation of fluorescing molecules},
     22701  pages = {9409-9414},
     22702  journal = {Optics Express},
     22703  volume = {13},
     22704  author = {Dia, L. and Gergor, I. and Hocht, I. von der, Ruckstuhl, T. and Enderlein, J.}
     22705}
     22706@article{Endesfelder2014,
     22707  month = {February},
     22708  year = {2014},
     22709  title = {A simple method to estimate the average localization precision of a single-molecule localization microscopy experiment},
     22710  journal = {Histochemistry and Cell Biology},
     22711  author = {Endesfelder, U. and Malkusch, S. and Fricke, F. and Heilemann, M.}
     22712}
     22713@article{Duan2014,
     22714  year = {2014},
     22715  title = {Some fast projection methods based on Chan-Vese model for image segmentation},
     22716  pages = {1-6},
     22717  journal = {{EURASIP} Journal on Image and Video Processing},
     22718  volume = {7},
     22719  author = {Duan, J. and Pan, Z. and Yin, X. and Wang, G.}
     22720}
     22721@article{Li2013b,
     22722  number = {6},
     22723  year = {2013},
     22724  title = {Fast and Efficient Molecule
     22725Detection in Localization-Based
     22726Super-Resolution Microscopy by Parallel
     22727Adaptive Histogram Equalization},
     22728  pages = {5207-5214},
     22729  journal = {ACS Nano},
     22730  volume = {7},
     22731  author = {Li, Y. and Ishitsuka, Y. and Hedde, P.E. and Nienhaus, G.U.}
     22732}
     22733@article{Hoogendoorn2014,
     22734  year = {2014},
     22735  title = {The fidelity of stochastic single-molecule
     22736super-resolution reconstructions critically
     22737depends upon robust background
     22738estimation},
     22739  pages = {3854},
     22740  note = {doi:10.1038/srep03854},
     22741  journal = {Scientific Reports},
     22742  volume = {4},
     22743  author = {Hoogendoorn, E. and Crosby, K.C. and Leyton-Puig, D. and Breedijk, R.M.P. and Jalink, K. and Gadella, T.W.J. and Postma, M.}
     22744}
     22745@article{Juette2008,
     22746  number = {6},
     22747  year = {2008},
     22748  title = {Three-dimensional sub 100 nm resolution fluorescence microscopy of thick samples},
     22749  pages = {527-529},
     22750  journal = {Nature Methods},
     22751  volume = {5},
     22752  author = {Juette, M.F. and Gould, T.J. and Lessard, M.D. and Mlodzianoski, M.J. and Nagpure, B.S. and Bennett, B.T. and Hess, S.T. and Bewersdorf, J.}
     22753}
     22754@article{Weisenburger2014,
     22755  year = {2014},
     22756  title = {Cryogenic Colocalization Microscopy for Nanometer-Distance Measurements},
     22757  pages = {763-770},
     22758  journal = {ChemPhysChem},
     22759  volume = {15},
     22760  author = {Wiesenburger, S. and Jing, B. and {H\"anni}, D. and Reymond, L. and Schuler, B. and Renn, A. and Sandoghdar, V.}
     22761}
     22762@article{Blythe2014,
     22763  year = {2014},
     22764  title = {Triplet-State-Mediated Super-Resolution Imaging of Fluorophore-Labeled Gold Nanorods},
     22765  pages = {784-793},
     22766  journal = {ChemPhysChem},
     22767  volume = {15},
     22768  author = {Blythe, K.L. and Titus, E.J. and Willets, K.A.}
     22769}
     22770@article{Grussmayer2014,
     22771  number = {734-742},
     22772  year = {2014},
     22773  title = {Single-Molecule Studies on the Label Number Distribution of Fluorescent Markers},
     22774  journal = {ChemPhysChem},
     22775  volume = {15},
     22776  author = {Grussmayer, K.S. and Kurz, A. and Herten, D.-P.}
     22777}
     22778@article{Hafi2014,
     22779  year = {2014},
     22780  title = {Fluorescence nanoscopy by polarization modulation and polarization angle narrowing},
     22781  note = {doi:10.1038/nmeth.2919},
     22782  journal = {Nature Methods},
     22783  author = {Hafi, N. and Grunwald, M. and Heuvel, L.S. van den and Aspelmeier, T. and Chen, J.-H. and Zagrebelsky, M. and {Sch\"utte}, O.M. and Steinem, C. and Korte, M. and Munk, A. and Walla, P.J.}
     22784}
     22785@article{Richards2010,
     22786  number = {1},
     22787  year = {2010},
     22788  title = {Synchronously Amplified Fluorescence Image Recovery {(SAFIRe)}},
     22789  pages = {660-665},
     22790  journal = {Journal of Physical Chemistry B},
     22791  volume = {114},
     22792  author = {Richards, C.I. and Hsiang, J.-C. and Dickson, R.M.}
     22793}
     22794@article{Marriott2008,
     22795  number = {46},
     22796  year = {2008},
     22797  title = {Optical lock-in detection imaging microscopy
     22798for contrast-enhanced imaging in living cells},
     22799  pages = {17789-17794},
     22800  journal = {Proceedings of the National Academy of Sciences USA },
     22801  volume = {105},
     22802  author = {Mariott, G. and Mao, S. and Skata, T. and Ran, J. and Jacksson, D.K. and Petchprayoon, C. and Gomez, T.J. and Warp, E. and Tulyathan, P. and Aaron, H.L. and Isacoff, E.Y. and Yan, Y.}
     22803}
     22804@article{Vicidomini2011,
     22805  number = {7},
     22806  year = {2011},
     22807  title = {Sharper low-power {STED} nanoscopy by time gating},
     22808  pages = {571-573},
     22809  journal = {Nature Methods},
     22810  volume = {8},
     22811  author = {Vicidomini, G. and Moneron, G. and Han, K.Y. and Westphal, V. and Ta, H. and Reuss, M. and Engelhardt, J. and Eggeling, C. and Hell, S.W.}
     22812}
     22813@article{Hettich2002,
     22814  year = {2002},
     22815  title = {Nanometer Resolution and Coherent Optical Dipole Coupling of Two Individual Molecules},
     22816  pages = {385-388},
     22817  journal = {Science},
     22818  volume = {298},
     22819  author = {Hettich, C. and Schmitt, C. and Zitzmann, J. and {K\"uhn}, S. and Gerhardt, I. and Sandoghdar, V.}
     22820}
     22821@article{SChur2013,
     22822  number = {3},
     22823  year = {2013},
     22824  title = {Determination of protein structure at 8.5 {\AA} resolution using cryo-electron tomography and sub-tomogram averaging},
     22825  pages = {394-400},
     22826  journal = {Journal of Structural Biology},
     22827  volume = {184},
     22828  author = {Schur, F.K.M. and  Hagen, W.J.H. and  Marco, A. de and Briggs, J.A.G.}
     22829}
     22830@article{Vogelsang2008,
     22831  number = {29},
     22832  year = {2008},
     22833  title = {A Reducing and Oxidizing System Minimizes Photobleaching and Blinking of Fluorescent Dyes},
     22834  pages = {5465-5469},
     22835  journal = {Angewandte Chemie International Edition},
     22836  volume = {47},
     22837  author = {Vogelsang, J. and Kasper, R. and Steinhauer, C. and Person, B. and Heilemann, M. and Sauer, M. and Tinnefeld, P.}
     22838}
     22839@article{Proppert2014,
     22840  number = {9},
     22841  year = {2014},
     22842  title = {Cubic B-spline calibration for 3D super-resolution measurements using astigmatic imaging},
     22843  pages = {10304-10316},
     22844  journal = {Optics Express},
     22845  volume = {22},
     22846  author = {Proppert, S. and Wolter, S. and Holm, T. and Klein, T. and Linde, S. van de and Sauer, M.}
     22847}
     22848@article{Broeken2014,
     22849  year = {2014},
     22850  title = {Simultaneous measurement of position and color of single fluorescent emitters using diffractive optics},
     22851  journal = {Optics Letters},
     22852  author = {Broeken, J. and Rieger, B. and Stallinga, S.}
     22853}
     22854@phdthesis{Giske2007,
     22855  month = {November},
     22856  year = {2007},
     22857  title = {CryoSTED microscopy: A new spectroscopic approach for improving the resolution of {STED} microscopy using low temperature},
     22858  school = {University of Heidelberg},
     22859  author = {Giske, A.}
     22860}
     22861@article{Gros2009,
     22862  number = {1},
     22863  year = {2009},
     22864  title = {High-aperture cryogenic light microscopy},
     22865  pages = {1-8},
     22866  journal = {Journal of Microscopy},
     22867  volume = {235},
     22868  author = {Gros, M.A. le and McDermott, G. and Uchida, M. and Knoechel, C.G. and Larabell, C.A.}
     22869}
     22870@article{Moerner1999,
     22871  year = {1999},
     22872  title = {Illuminating single molecules in condensed matter},
     22873  pages = {1670-1676},
     22874  journal = {Science},
     22875  volume = {283},
     22876  author = {Moerner, W.E. and Orrit, M.}
     22877}
     22878@article{Ha1996,
     22879  number = {19},
     22880  year = {1996},
     22881  title = {Single Molecule Dynamics studied by Polarization Modulation},
     22882  pages = {3979-3982},
     22883  journal = {Physical Review Letters},
     22884  volume = {77},
     22885  author = {Ha, T. and Enderle, Th. and Cehmla, D.S. and Selvin, P.R. and Weiss, S.}
     22886}
     22887@inproceedings{Kuffner2004,
     22888  month = {April },
     22889  year = {2004},
     22890  title = {Effective Sampling and Distance Metrics for 3D Rigid Body Path Planning},
     22891  booktitle = {IEEE International Conference on Robotics and Automation},
     22892  pages = {3993-3998},
     22893  address = {New Orleans, USA},
     22894  author = {Kuffner, J.J.}
     22895}
     22896@article{Geisler2012,
     22897  number = {7},
     22898  year = {2012},
     22899  title = {Drift estimation for single marker switching
     22900based imaging schemes},
     22901  pages = {7274-7289},
     22902  journal = {Optics Express},
     22903  volume = {20},
     22904  author = {Geisler, C. and Hotz, T. and {Sch\"onle}, A. and Hell, S.W. and Munk, A. and Egner, A.}
     22905}
Note: See TracChangeset for help on using the changeset viewer.