Abstract

Localization-based super-resolution microscopy image quality depends on several factors such as dye choice and labeling strategy, microscope quality and user-defined parameters such as frame rate and number as well as the image processing algorithm. Experimental optimization of these parameters can be time-consuming and expensive so we present TestSTORM, a simulator that can be used to optimize these steps. TestSTORM users can select from among four different structures with specific patterns, dye and acquisition parameters. Example results are shown and the results of the vesicle pattern are compared with experimental data. Moreover, image stacks can be generated for further evaluation using localization algorithms, offering a tool for further software developments.

© 2014 Optical Society of America

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2013 (3)

E. J. Rees, M. Erdelyi, G. S. K. Schierle, A. Knight, and C. F. Kaminski, “Elements of image processing in localization microscopy,” J. Opt. 15(9), 094012 (2013).
[Crossref]

D. J. Metcalf, R. Edwards, N. Kumarswami, and A. E. Knight, “Test samples for optimizing STORM super-resolution microscopy,” J. Vis. Exp. 79, 50579 (2013), doi:.
[Crossref] [PubMed]

M. Erdelyi, E. J. Rees, D. Metcalf, G. S. K. Schierle, L. Dudas, J. Sinko, A. E. Knight, and C. F. Kaminski, “Correcting chromatic offset in multicolor super-resolution localization microscopy,” Opt. Express 21(9), 10978–10988 (2013).
[Crossref] [PubMed]

2012 (5)

S. Stallinga and B. Rieger, “Position and orientation estimation of fixed dipole emitters using an effective Hermite point spread function model,” Opt. Express 20(6), 5896–5921 (2012).
[Crossref] [PubMed]

L. Yang, A. R. Dun, K. J. Martin, Z. Qiu, A. Dunn, G. J. Lord, W. Lu, R. R. Duncan, and C. Rickman, “Secretory vesicles are preferentially targeted to areas of low molecular SNARE density,” PLoS ONE 7(11), e49514 (2012), doi:.
[Crossref] [PubMed]

M. P. Backlund, M. D. Lew, A. S. Backer, S. J. Sahl, G. Grover, A. Agrawal, R. Piestun, and W. E. Moerner, “Simultaneous, accurate measurement of the 3D position and orientation of single molecules,” Proc. Natl. Acad. Sci. U.S.A. 109(47), 19087–19092 (2012).
[Crossref] [PubMed]

E. A. Mukamel and M. J. Schnitzer, “Unified resolution bounds for conventional and stochastic localization fluorescence microscopy,” Phys. Rev. Lett. 109(16), 168102 (2012).
[Crossref] [PubMed]

E. J. Rees, M. Erdelyi, D. Pinotsi, A. Knight, D. Metcalf, and C. F. Kaminski, “Blind assessment of localization microscopy image resolution,” Opt. Nanoscopy 1(1), 12 (2012), doi:.
[Crossref]

2011 (8)

G. S. Kaminski Schierle, S. van de Linde, M. Erdelyi, E. K. Esbjörner, T. Klein, E. Rees, C. W. Bertoncini, C. M. Dobson, M. Sauer, and C. F. Kaminski, “In situ measurements of the formation and morphology of intracellular β-amyloid fibrils by super-resolution fluorescence imaging,” J. Am. Chem. Soc. 133(33), 12902–12905 (2011).
[Crossref] [PubMed]

S. van de Linde, I. Krstić, T. Prisner, S. Doose, M. Heilemann, and M. Sauer, “Photoinduced formation of reversible dye radicals and their impact on super-resolution imaging,” Photochem. Photobiol. Sci. 10(4), 499–506 (2011).
[Crossref] [PubMed]

S. Cox, E. Rosten, J. Monypenny, T. Jovanovic-Talisman, D. T. Burnette, J. Lippincott-Schwartz, G. E. Jones, and R. Heintzmann, “Bayesian localization microscopy reveals nanoscale podosome dynamics,” Nat. Methods 9(2), 195–200 (2011).
[Crossref] [PubMed]

G. T. Dempsey, J. C. Vaughan, K. H. Chen, M. Bates, and X. Zhuang, “Evaluation of fluorophores for optimal performance in localization-based super-resolution imaging,” Nat. Methods 8(12), 1027–1036 (2011).
[Crossref] [PubMed]

S. van de Linde, A. Löschberger, T. Klein, M. Heidbreder, S. Wolter, M. Heilemann, and M. Sauer, “Direct stochastic optical reconstruction microscopy with standard fluorescent probes,” Nat. Protoc. 6(7), 991–1009 (2011).
[Crossref] [PubMed]

F. Huang, S. L. Schwartz, J. M. Byars, and K. A. Lidke, “Simultaneous multiple-emitter fitting for single molecule super-resolution imaging,” Biomed. Opt. Express 2(5), 1377–1393 (2011).
[Crossref] [PubMed]

P. Annibale, S. Vanni, M. Scarselli, U. Rothlisberger, and A. Radenovic, “Identification of clustering artifacts in photoactivated localization microscopy,” Nat. Methods 8(7), 527–528 (2011).
[Crossref] [PubMed]

D. Baddeley, D. Crossman, S. Rossberger, J. E. Cheyne, J. M. Montgomery, I. D. Jayasinghe, C. Cremer, M. B. Cannell, and C. Soeller, “4D Super-resolution microscopy with conventional fluorophores and single wavelength excitation in optically thick cells and tissues,” PLoS ONE 6(5), e20645 (2011).
[Crossref] [PubMed]

2010 (4)

S. Stallinga and B. Rieger, “Accuracy of the Gaussian point spread function model in 2D localization microscopy,” Opt. Express 18(24), 24461–24476 (2010).
[Crossref] [PubMed]

S. van de Linde, S. Wolter, M. Heilemann, and M. Sauer, “The effect of photoswitching kinetics and labeling densities on super-resolution fluorescence imaging,” J. Biotechnol. 149(4), 260–266 (2010).
[Crossref] [PubMed]

R. Henriques, M. Lelek, E. F. Fornasiero, F. Valtorta, C. Zimmer, and M. M. Mhlanga, “QuickPALM: 3D real-time photoactivation nanoscopy image processing in ImageJ,” Nat. Methods 7(5), 339–340 (2010).
[Crossref] [PubMed]

S. Wolter, M. Schüttpelz, M. Tscherepanow, S. Van De Linde, M. Heilemann, and M. Sauer, “Real-time computation of subdiffraction-resolution fluorescence images,” J. Microsc. 237(1), 12–22 (2010).
[Crossref] [PubMed]

2009 (1)

T. J. Gould, V. V. Verkhusha, and S. T. Hess, “Imaging biological structures with fluorescence photoactivation localization microscopy,” Nat. Protoc. 4(3), 291–308 (2009).
[Crossref] [PubMed]

2008 (1)

H. Shroff, C. G. Galbraith, J. A. Galbraith, and E. Betzig, “Live-cell photoactivated localization microscopy of nanoscale adhesion dynamics,” Nat. Methods 5(5), 417–423 (2008).
[Crossref] [PubMed]

2007 (2)

K. I. Willig, B. Harke, R. Medda, and S. W. Hell, “STED microscopy with continuous wave beams,” Nat. Methods 4(11), 915–918 (2007).
[Crossref] [PubMed]

S. W. Hell, “Far-field optical nanoscopy,” Science 316(5828), 1153–1158 (2007).
[Crossref] [PubMed]

2006 (3)

S. T. Hess, T. P. K. Girirajan, and M. D. Mason, “Ultra-high resolution imaging by fluorescence photoactivation localization microscopy,” Biophys. J. 91(11), 4258–4272 (2006).
[Crossref] [PubMed]

E. Betzig, G. H. Patterson, R. Sougrat, O. W. Lindwasser, S. Olenych, J. S. Bonifacino, M. W. Davidson, J. Lippincott-Schwartz, and H. F. Hess, “Imaging intracellular fluorescent proteins at nanometer resolution,” Science 313(5793), 1642–1645 (2006).
[Crossref] [PubMed]

M. J. Rust, M. Bates, and X. Zhuang, “Sub-diffraction-limit imaging by stochastic optical reconstruction microscopy (STORM),” Nat. Methods 3(10), 793–796 (2006).
[Crossref] [PubMed]

2003 (1)

2000 (1)

M. G. L. Gustafsson, “Surpassing the lateral resolution limit by a factor of two using structured illumination microscopy,” J. Microsc. 198(2), 82–87 (2000).
[Crossref] [PubMed]

1994 (1)

1873 (1)

E. Abbe, “Beiträge zur theorie des Mikroskops und der mikro-skopischer Wahrnehmung,” Arch. Mikrosk. Anat. 9(1), 413–418 (1873).
[Crossref]

Abbe, E.

E. Abbe, “Beiträge zur theorie des Mikroskops und der mikro-skopischer Wahrnehmung,” Arch. Mikrosk. Anat. 9(1), 413–418 (1873).
[Crossref]

Agrawal, A.

M. P. Backlund, M. D. Lew, A. S. Backer, S. J. Sahl, G. Grover, A. Agrawal, R. Piestun, and W. E. Moerner, “Simultaneous, accurate measurement of the 3D position and orientation of single molecules,” Proc. Natl. Acad. Sci. U.S.A. 109(47), 19087–19092 (2012).
[Crossref] [PubMed]

Annibale, P.

P. Annibale, S. Vanni, M. Scarselli, U. Rothlisberger, and A. Radenovic, “Identification of clustering artifacts in photoactivated localization microscopy,” Nat. Methods 8(7), 527–528 (2011).
[Crossref] [PubMed]

Backer, A. S.

M. P. Backlund, M. D. Lew, A. S. Backer, S. J. Sahl, G. Grover, A. Agrawal, R. Piestun, and W. E. Moerner, “Simultaneous, accurate measurement of the 3D position and orientation of single molecules,” Proc. Natl. Acad. Sci. U.S.A. 109(47), 19087–19092 (2012).
[Crossref] [PubMed]

Backlund, M. P.

M. P. Backlund, M. D. Lew, A. S. Backer, S. J. Sahl, G. Grover, A. Agrawal, R. Piestun, and W. E. Moerner, “Simultaneous, accurate measurement of the 3D position and orientation of single molecules,” Proc. Natl. Acad. Sci. U.S.A. 109(47), 19087–19092 (2012).
[Crossref] [PubMed]

Baddeley, D.

D. Baddeley, D. Crossman, S. Rossberger, J. E. Cheyne, J. M. Montgomery, I. D. Jayasinghe, C. Cremer, M. B. Cannell, and C. Soeller, “4D Super-resolution microscopy with conventional fluorophores and single wavelength excitation in optically thick cells and tissues,” PLoS ONE 6(5), e20645 (2011).
[Crossref] [PubMed]

Bates, M.

G. T. Dempsey, J. C. Vaughan, K. H. Chen, M. Bates, and X. Zhuang, “Evaluation of fluorophores for optimal performance in localization-based super-resolution imaging,” Nat. Methods 8(12), 1027–1036 (2011).
[Crossref] [PubMed]

M. J. Rust, M. Bates, and X. Zhuang, “Sub-diffraction-limit imaging by stochastic optical reconstruction microscopy (STORM),” Nat. Methods 3(10), 793–796 (2006).
[Crossref] [PubMed]

Bertoncini, C. W.

G. S. Kaminski Schierle, S. van de Linde, M. Erdelyi, E. K. Esbjörner, T. Klein, E. Rees, C. W. Bertoncini, C. M. Dobson, M. Sauer, and C. F. Kaminski, “In situ measurements of the formation and morphology of intracellular β-amyloid fibrils by super-resolution fluorescence imaging,” J. Am. Chem. Soc. 133(33), 12902–12905 (2011).
[Crossref] [PubMed]

Betzig, E.

H. Shroff, C. G. Galbraith, J. A. Galbraith, and E. Betzig, “Live-cell photoactivated localization microscopy of nanoscale adhesion dynamics,” Nat. Methods 5(5), 417–423 (2008).
[Crossref] [PubMed]

E. Betzig, G. H. Patterson, R. Sougrat, O. W. Lindwasser, S. Olenych, J. S. Bonifacino, M. W. Davidson, J. Lippincott-Schwartz, and H. F. Hess, “Imaging intracellular fluorescent proteins at nanometer resolution,” Science 313(5793), 1642–1645 (2006).
[Crossref] [PubMed]

Böhmer, M.

Bonifacino, J. S.

E. Betzig, G. H. Patterson, R. Sougrat, O. W. Lindwasser, S. Olenych, J. S. Bonifacino, M. W. Davidson, J. Lippincott-Schwartz, and H. F. Hess, “Imaging intracellular fluorescent proteins at nanometer resolution,” Science 313(5793), 1642–1645 (2006).
[Crossref] [PubMed]

Burnette, D. T.

S. Cox, E. Rosten, J. Monypenny, T. Jovanovic-Talisman, D. T. Burnette, J. Lippincott-Schwartz, G. E. Jones, and R. Heintzmann, “Bayesian localization microscopy reveals nanoscale podosome dynamics,” Nat. Methods 9(2), 195–200 (2011).
[Crossref] [PubMed]

Byars, J. M.

Cannell, M. B.

D. Baddeley, D. Crossman, S. Rossberger, J. E. Cheyne, J. M. Montgomery, I. D. Jayasinghe, C. Cremer, M. B. Cannell, and C. Soeller, “4D Super-resolution microscopy with conventional fluorophores and single wavelength excitation in optically thick cells and tissues,” PLoS ONE 6(5), e20645 (2011).
[Crossref] [PubMed]

Chen, K. H.

G. T. Dempsey, J. C. Vaughan, K. H. Chen, M. Bates, and X. Zhuang, “Evaluation of fluorophores for optimal performance in localization-based super-resolution imaging,” Nat. Methods 8(12), 1027–1036 (2011).
[Crossref] [PubMed]

Cheyne, J. E.

D. Baddeley, D. Crossman, S. Rossberger, J. E. Cheyne, J. M. Montgomery, I. D. Jayasinghe, C. Cremer, M. B. Cannell, and C. Soeller, “4D Super-resolution microscopy with conventional fluorophores and single wavelength excitation in optically thick cells and tissues,” PLoS ONE 6(5), e20645 (2011).
[Crossref] [PubMed]

Cox, S.

S. Cox, E. Rosten, J. Monypenny, T. Jovanovic-Talisman, D. T. Burnette, J. Lippincott-Schwartz, G. E. Jones, and R. Heintzmann, “Bayesian localization microscopy reveals nanoscale podosome dynamics,” Nat. Methods 9(2), 195–200 (2011).
[Crossref] [PubMed]

Cremer, C.

D. Baddeley, D. Crossman, S. Rossberger, J. E. Cheyne, J. M. Montgomery, I. D. Jayasinghe, C. Cremer, M. B. Cannell, and C. Soeller, “4D Super-resolution microscopy with conventional fluorophores and single wavelength excitation in optically thick cells and tissues,” PLoS ONE 6(5), e20645 (2011).
[Crossref] [PubMed]

Crossman, D.

D. Baddeley, D. Crossman, S. Rossberger, J. E. Cheyne, J. M. Montgomery, I. D. Jayasinghe, C. Cremer, M. B. Cannell, and C. Soeller, “4D Super-resolution microscopy with conventional fluorophores and single wavelength excitation in optically thick cells and tissues,” PLoS ONE 6(5), e20645 (2011).
[Crossref] [PubMed]

Davidson, M. W.

E. Betzig, G. H. Patterson, R. Sougrat, O. W. Lindwasser, S. Olenych, J. S. Bonifacino, M. W. Davidson, J. Lippincott-Schwartz, and H. F. Hess, “Imaging intracellular fluorescent proteins at nanometer resolution,” Science 313(5793), 1642–1645 (2006).
[Crossref] [PubMed]

Dempsey, G. T.

G. T. Dempsey, J. C. Vaughan, K. H. Chen, M. Bates, and X. Zhuang, “Evaluation of fluorophores for optimal performance in localization-based super-resolution imaging,” Nat. Methods 8(12), 1027–1036 (2011).
[Crossref] [PubMed]

Dobson, C. M.

G. S. Kaminski Schierle, S. van de Linde, M. Erdelyi, E. K. Esbjörner, T. Klein, E. Rees, C. W. Bertoncini, C. M. Dobson, M. Sauer, and C. F. Kaminski, “In situ measurements of the formation and morphology of intracellular β-amyloid fibrils by super-resolution fluorescence imaging,” J. Am. Chem. Soc. 133(33), 12902–12905 (2011).
[Crossref] [PubMed]

Doose, S.

S. van de Linde, I. Krstić, T. Prisner, S. Doose, M. Heilemann, and M. Sauer, “Photoinduced formation of reversible dye radicals and their impact on super-resolution imaging,” Photochem. Photobiol. Sci. 10(4), 499–506 (2011).
[Crossref] [PubMed]

Dudas, L.

Dun, A. R.

L. Yang, A. R. Dun, K. J. Martin, Z. Qiu, A. Dunn, G. J. Lord, W. Lu, R. R. Duncan, and C. Rickman, “Secretory vesicles are preferentially targeted to areas of low molecular SNARE density,” PLoS ONE 7(11), e49514 (2012), doi:.
[Crossref] [PubMed]

Duncan, R. R.

L. Yang, A. R. Dun, K. J. Martin, Z. Qiu, A. Dunn, G. J. Lord, W. Lu, R. R. Duncan, and C. Rickman, “Secretory vesicles are preferentially targeted to areas of low molecular SNARE density,” PLoS ONE 7(11), e49514 (2012), doi:.
[Crossref] [PubMed]

Dunn, A.

L. Yang, A. R. Dun, K. J. Martin, Z. Qiu, A. Dunn, G. J. Lord, W. Lu, R. R. Duncan, and C. Rickman, “Secretory vesicles are preferentially targeted to areas of low molecular SNARE density,” PLoS ONE 7(11), e49514 (2012), doi:.
[Crossref] [PubMed]

Edwards, R.

D. J. Metcalf, R. Edwards, N. Kumarswami, and A. E. Knight, “Test samples for optimizing STORM super-resolution microscopy,” J. Vis. Exp. 79, 50579 (2013), doi:.
[Crossref] [PubMed]

Enderlein, J.

Erdelyi, M.

M. Erdelyi, E. J. Rees, D. Metcalf, G. S. K. Schierle, L. Dudas, J. Sinko, A. E. Knight, and C. F. Kaminski, “Correcting chromatic offset in multicolor super-resolution localization microscopy,” Opt. Express 21(9), 10978–10988 (2013).
[Crossref] [PubMed]

E. J. Rees, M. Erdelyi, G. S. K. Schierle, A. Knight, and C. F. Kaminski, “Elements of image processing in localization microscopy,” J. Opt. 15(9), 094012 (2013).
[Crossref]

E. J. Rees, M. Erdelyi, D. Pinotsi, A. Knight, D. Metcalf, and C. F. Kaminski, “Blind assessment of localization microscopy image resolution,” Opt. Nanoscopy 1(1), 12 (2012), doi:.
[Crossref]

G. S. Kaminski Schierle, S. van de Linde, M. Erdelyi, E. K. Esbjörner, T. Klein, E. Rees, C. W. Bertoncini, C. M. Dobson, M. Sauer, and C. F. Kaminski, “In situ measurements of the formation and morphology of intracellular β-amyloid fibrils by super-resolution fluorescence imaging,” J. Am. Chem. Soc. 133(33), 12902–12905 (2011).
[Crossref] [PubMed]

Esbjörner, E. K.

G. S. Kaminski Schierle, S. van de Linde, M. Erdelyi, E. K. Esbjörner, T. Klein, E. Rees, C. W. Bertoncini, C. M. Dobson, M. Sauer, and C. F. Kaminski, “In situ measurements of the formation and morphology of intracellular β-amyloid fibrils by super-resolution fluorescence imaging,” J. Am. Chem. Soc. 133(33), 12902–12905 (2011).
[Crossref] [PubMed]

Fornasiero, E. F.

R. Henriques, M. Lelek, E. F. Fornasiero, F. Valtorta, C. Zimmer, and M. M. Mhlanga, “QuickPALM: 3D real-time photoactivation nanoscopy image processing in ImageJ,” Nat. Methods 7(5), 339–340 (2010).
[Crossref] [PubMed]

Galbraith, C. G.

H. Shroff, C. G. Galbraith, J. A. Galbraith, and E. Betzig, “Live-cell photoactivated localization microscopy of nanoscale adhesion dynamics,” Nat. Methods 5(5), 417–423 (2008).
[Crossref] [PubMed]

Galbraith, J. A.

H. Shroff, C. G. Galbraith, J. A. Galbraith, and E. Betzig, “Live-cell photoactivated localization microscopy of nanoscale adhesion dynamics,” Nat. Methods 5(5), 417–423 (2008).
[Crossref] [PubMed]

Girirajan, T. P. K.

S. T. Hess, T. P. K. Girirajan, and M. D. Mason, “Ultra-high resolution imaging by fluorescence photoactivation localization microscopy,” Biophys. J. 91(11), 4258–4272 (2006).
[Crossref] [PubMed]

Gould, T. J.

T. J. Gould, V. V. Verkhusha, and S. T. Hess, “Imaging biological structures with fluorescence photoactivation localization microscopy,” Nat. Protoc. 4(3), 291–308 (2009).
[Crossref] [PubMed]

Grover, G.

M. P. Backlund, M. D. Lew, A. S. Backer, S. J. Sahl, G. Grover, A. Agrawal, R. Piestun, and W. E. Moerner, “Simultaneous, accurate measurement of the 3D position and orientation of single molecules,” Proc. Natl. Acad. Sci. U.S.A. 109(47), 19087–19092 (2012).
[Crossref] [PubMed]

Gustafsson, M. G. L.

M. G. L. Gustafsson, “Surpassing the lateral resolution limit by a factor of two using structured illumination microscopy,” J. Microsc. 198(2), 82–87 (2000).
[Crossref] [PubMed]

Harke, B.

K. I. Willig, B. Harke, R. Medda, and S. W. Hell, “STED microscopy with continuous wave beams,” Nat. Methods 4(11), 915–918 (2007).
[Crossref] [PubMed]

Heidbreder, M.

S. van de Linde, A. Löschberger, T. Klein, M. Heidbreder, S. Wolter, M. Heilemann, and M. Sauer, “Direct stochastic optical reconstruction microscopy with standard fluorescent probes,” Nat. Protoc. 6(7), 991–1009 (2011).
[Crossref] [PubMed]

Heilemann, M.

S. van de Linde, A. Löschberger, T. Klein, M. Heidbreder, S. Wolter, M. Heilemann, and M. Sauer, “Direct stochastic optical reconstruction microscopy with standard fluorescent probes,” Nat. Protoc. 6(7), 991–1009 (2011).
[Crossref] [PubMed]

S. van de Linde, I. Krstić, T. Prisner, S. Doose, M. Heilemann, and M. Sauer, “Photoinduced formation of reversible dye radicals and their impact on super-resolution imaging,” Photochem. Photobiol. Sci. 10(4), 499–506 (2011).
[Crossref] [PubMed]

S. Wolter, M. Schüttpelz, M. Tscherepanow, S. Van De Linde, M. Heilemann, and M. Sauer, “Real-time computation of subdiffraction-resolution fluorescence images,” J. Microsc. 237(1), 12–22 (2010).
[Crossref] [PubMed]

S. van de Linde, S. Wolter, M. Heilemann, and M. Sauer, “The effect of photoswitching kinetics and labeling densities on super-resolution fluorescence imaging,” J. Biotechnol. 149(4), 260–266 (2010).
[Crossref] [PubMed]

Heintzmann, R.

S. Cox, E. Rosten, J. Monypenny, T. Jovanovic-Talisman, D. T. Burnette, J. Lippincott-Schwartz, G. E. Jones, and R. Heintzmann, “Bayesian localization microscopy reveals nanoscale podosome dynamics,” Nat. Methods 9(2), 195–200 (2011).
[Crossref] [PubMed]

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S. W. Hell, “Far-field optical nanoscopy,” Science 316(5828), 1153–1158 (2007).
[Crossref] [PubMed]

K. I. Willig, B. Harke, R. Medda, and S. W. Hell, “STED microscopy with continuous wave beams,” Nat. Methods 4(11), 915–918 (2007).
[Crossref] [PubMed]

S. W. Hell and J. Wichmann, “Breaking the diffraction resolution limit by stimulated emission: stimulated-emission-depletion fluorescence microscopy,” Opt. Lett. 19(11), 780–782 (1994).
[Crossref] [PubMed]

Henriques, R.

R. Henriques, M. Lelek, E. F. Fornasiero, F. Valtorta, C. Zimmer, and M. M. Mhlanga, “QuickPALM: 3D real-time photoactivation nanoscopy image processing in ImageJ,” Nat. Methods 7(5), 339–340 (2010).
[Crossref] [PubMed]

Hess, H. F.

E. Betzig, G. H. Patterson, R. Sougrat, O. W. Lindwasser, S. Olenych, J. S. Bonifacino, M. W. Davidson, J. Lippincott-Schwartz, and H. F. Hess, “Imaging intracellular fluorescent proteins at nanometer resolution,” Science 313(5793), 1642–1645 (2006).
[Crossref] [PubMed]

Hess, S. T.

T. J. Gould, V. V. Verkhusha, and S. T. Hess, “Imaging biological structures with fluorescence photoactivation localization microscopy,” Nat. Protoc. 4(3), 291–308 (2009).
[Crossref] [PubMed]

S. T. Hess, T. P. K. Girirajan, and M. D. Mason, “Ultra-high resolution imaging by fluorescence photoactivation localization microscopy,” Biophys. J. 91(11), 4258–4272 (2006).
[Crossref] [PubMed]

Huang, F.

Jayasinghe, I. D.

D. Baddeley, D. Crossman, S. Rossberger, J. E. Cheyne, J. M. Montgomery, I. D. Jayasinghe, C. Cremer, M. B. Cannell, and C. Soeller, “4D Super-resolution microscopy with conventional fluorophores and single wavelength excitation in optically thick cells and tissues,” PLoS ONE 6(5), e20645 (2011).
[Crossref] [PubMed]

Jones, G. E.

S. Cox, E. Rosten, J. Monypenny, T. Jovanovic-Talisman, D. T. Burnette, J. Lippincott-Schwartz, G. E. Jones, and R. Heintzmann, “Bayesian localization microscopy reveals nanoscale podosome dynamics,” Nat. Methods 9(2), 195–200 (2011).
[Crossref] [PubMed]

Jovanovic-Talisman, T.

S. Cox, E. Rosten, J. Monypenny, T. Jovanovic-Talisman, D. T. Burnette, J. Lippincott-Schwartz, G. E. Jones, and R. Heintzmann, “Bayesian localization microscopy reveals nanoscale podosome dynamics,” Nat. Methods 9(2), 195–200 (2011).
[Crossref] [PubMed]

Kaminski, C. F.

E. J. Rees, M. Erdelyi, G. S. K. Schierle, A. Knight, and C. F. Kaminski, “Elements of image processing in localization microscopy,” J. Opt. 15(9), 094012 (2013).
[Crossref]

M. Erdelyi, E. J. Rees, D. Metcalf, G. S. K. Schierle, L. Dudas, J. Sinko, A. E. Knight, and C. F. Kaminski, “Correcting chromatic offset in multicolor super-resolution localization microscopy,” Opt. Express 21(9), 10978–10988 (2013).
[Crossref] [PubMed]

E. J. Rees, M. Erdelyi, D. Pinotsi, A. Knight, D. Metcalf, and C. F. Kaminski, “Blind assessment of localization microscopy image resolution,” Opt. Nanoscopy 1(1), 12 (2012), doi:.
[Crossref]

G. S. Kaminski Schierle, S. van de Linde, M. Erdelyi, E. K. Esbjörner, T. Klein, E. Rees, C. W. Bertoncini, C. M. Dobson, M. Sauer, and C. F. Kaminski, “In situ measurements of the formation and morphology of intracellular β-amyloid fibrils by super-resolution fluorescence imaging,” J. Am. Chem. Soc. 133(33), 12902–12905 (2011).
[Crossref] [PubMed]

Kaminski Schierle, G. S.

G. S. Kaminski Schierle, S. van de Linde, M. Erdelyi, E. K. Esbjörner, T. Klein, E. Rees, C. W. Bertoncini, C. M. Dobson, M. Sauer, and C. F. Kaminski, “In situ measurements of the formation and morphology of intracellular β-amyloid fibrils by super-resolution fluorescence imaging,” J. Am. Chem. Soc. 133(33), 12902–12905 (2011).
[Crossref] [PubMed]

Klein, T.

G. S. Kaminski Schierle, S. van de Linde, M. Erdelyi, E. K. Esbjörner, T. Klein, E. Rees, C. W. Bertoncini, C. M. Dobson, M. Sauer, and C. F. Kaminski, “In situ measurements of the formation and morphology of intracellular β-amyloid fibrils by super-resolution fluorescence imaging,” J. Am. Chem. Soc. 133(33), 12902–12905 (2011).
[Crossref] [PubMed]

S. van de Linde, A. Löschberger, T. Klein, M. Heidbreder, S. Wolter, M. Heilemann, and M. Sauer, “Direct stochastic optical reconstruction microscopy with standard fluorescent probes,” Nat. Protoc. 6(7), 991–1009 (2011).
[Crossref] [PubMed]

Knight, A.

E. J. Rees, M. Erdelyi, G. S. K. Schierle, A. Knight, and C. F. Kaminski, “Elements of image processing in localization microscopy,” J. Opt. 15(9), 094012 (2013).
[Crossref]

E. J. Rees, M. Erdelyi, D. Pinotsi, A. Knight, D. Metcalf, and C. F. Kaminski, “Blind assessment of localization microscopy image resolution,” Opt. Nanoscopy 1(1), 12 (2012), doi:.
[Crossref]

Knight, A. E.

Krstic, I.

S. van de Linde, I. Krstić, T. Prisner, S. Doose, M. Heilemann, and M. Sauer, “Photoinduced formation of reversible dye radicals and their impact on super-resolution imaging,” Photochem. Photobiol. Sci. 10(4), 499–506 (2011).
[Crossref] [PubMed]

Kumarswami, N.

D. J. Metcalf, R. Edwards, N. Kumarswami, and A. E. Knight, “Test samples for optimizing STORM super-resolution microscopy,” J. Vis. Exp. 79, 50579 (2013), doi:.
[Crossref] [PubMed]

Lelek, M.

R. Henriques, M. Lelek, E. F. Fornasiero, F. Valtorta, C. Zimmer, and M. M. Mhlanga, “QuickPALM: 3D real-time photoactivation nanoscopy image processing in ImageJ,” Nat. Methods 7(5), 339–340 (2010).
[Crossref] [PubMed]

Lew, M. D.

M. P. Backlund, M. D. Lew, A. S. Backer, S. J. Sahl, G. Grover, A. Agrawal, R. Piestun, and W. E. Moerner, “Simultaneous, accurate measurement of the 3D position and orientation of single molecules,” Proc. Natl. Acad. Sci. U.S.A. 109(47), 19087–19092 (2012).
[Crossref] [PubMed]

Lidke, K. A.

Lindwasser, O. W.

E. Betzig, G. H. Patterson, R. Sougrat, O. W. Lindwasser, S. Olenych, J. S. Bonifacino, M. W. Davidson, J. Lippincott-Schwartz, and H. F. Hess, “Imaging intracellular fluorescent proteins at nanometer resolution,” Science 313(5793), 1642–1645 (2006).
[Crossref] [PubMed]

Lippincott-Schwartz, J.

S. Cox, E. Rosten, J. Monypenny, T. Jovanovic-Talisman, D. T. Burnette, J. Lippincott-Schwartz, G. E. Jones, and R. Heintzmann, “Bayesian localization microscopy reveals nanoscale podosome dynamics,” Nat. Methods 9(2), 195–200 (2011).
[Crossref] [PubMed]

E. Betzig, G. H. Patterson, R. Sougrat, O. W. Lindwasser, S. Olenych, J. S. Bonifacino, M. W. Davidson, J. Lippincott-Schwartz, and H. F. Hess, “Imaging intracellular fluorescent proteins at nanometer resolution,” Science 313(5793), 1642–1645 (2006).
[Crossref] [PubMed]

Lord, G. J.

L. Yang, A. R. Dun, K. J. Martin, Z. Qiu, A. Dunn, G. J. Lord, W. Lu, R. R. Duncan, and C. Rickman, “Secretory vesicles are preferentially targeted to areas of low molecular SNARE density,” PLoS ONE 7(11), e49514 (2012), doi:.
[Crossref] [PubMed]

Löschberger, A.

S. van de Linde, A. Löschberger, T. Klein, M. Heidbreder, S. Wolter, M. Heilemann, and M. Sauer, “Direct stochastic optical reconstruction microscopy with standard fluorescent probes,” Nat. Protoc. 6(7), 991–1009 (2011).
[Crossref] [PubMed]

Lu, W.

L. Yang, A. R. Dun, K. J. Martin, Z. Qiu, A. Dunn, G. J. Lord, W. Lu, R. R. Duncan, and C. Rickman, “Secretory vesicles are preferentially targeted to areas of low molecular SNARE density,” PLoS ONE 7(11), e49514 (2012), doi:.
[Crossref] [PubMed]

Martin, K. J.

L. Yang, A. R. Dun, K. J. Martin, Z. Qiu, A. Dunn, G. J. Lord, W. Lu, R. R. Duncan, and C. Rickman, “Secretory vesicles are preferentially targeted to areas of low molecular SNARE density,” PLoS ONE 7(11), e49514 (2012), doi:.
[Crossref] [PubMed]

Mason, M. D.

S. T. Hess, T. P. K. Girirajan, and M. D. Mason, “Ultra-high resolution imaging by fluorescence photoactivation localization microscopy,” Biophys. J. 91(11), 4258–4272 (2006).
[Crossref] [PubMed]

Medda, R.

K. I. Willig, B. Harke, R. Medda, and S. W. Hell, “STED microscopy with continuous wave beams,” Nat. Methods 4(11), 915–918 (2007).
[Crossref] [PubMed]

Metcalf, D.

M. Erdelyi, E. J. Rees, D. Metcalf, G. S. K. Schierle, L. Dudas, J. Sinko, A. E. Knight, and C. F. Kaminski, “Correcting chromatic offset in multicolor super-resolution localization microscopy,” Opt. Express 21(9), 10978–10988 (2013).
[Crossref] [PubMed]

E. J. Rees, M. Erdelyi, D. Pinotsi, A. Knight, D. Metcalf, and C. F. Kaminski, “Blind assessment of localization microscopy image resolution,” Opt. Nanoscopy 1(1), 12 (2012), doi:.
[Crossref]

Metcalf, D. J.

D. J. Metcalf, R. Edwards, N. Kumarswami, and A. E. Knight, “Test samples for optimizing STORM super-resolution microscopy,” J. Vis. Exp. 79, 50579 (2013), doi:.
[Crossref] [PubMed]

Mhlanga, M. M.

R. Henriques, M. Lelek, E. F. Fornasiero, F. Valtorta, C. Zimmer, and M. M. Mhlanga, “QuickPALM: 3D real-time photoactivation nanoscopy image processing in ImageJ,” Nat. Methods 7(5), 339–340 (2010).
[Crossref] [PubMed]

Moerner, W. E.

M. P. Backlund, M. D. Lew, A. S. Backer, S. J. Sahl, G. Grover, A. Agrawal, R. Piestun, and W. E. Moerner, “Simultaneous, accurate measurement of the 3D position and orientation of single molecules,” Proc. Natl. Acad. Sci. U.S.A. 109(47), 19087–19092 (2012).
[Crossref] [PubMed]

Montgomery, J. M.

D. Baddeley, D. Crossman, S. Rossberger, J. E. Cheyne, J. M. Montgomery, I. D. Jayasinghe, C. Cremer, M. B. Cannell, and C. Soeller, “4D Super-resolution microscopy with conventional fluorophores and single wavelength excitation in optically thick cells and tissues,” PLoS ONE 6(5), e20645 (2011).
[Crossref] [PubMed]

Monypenny, J.

S. Cox, E. Rosten, J. Monypenny, T. Jovanovic-Talisman, D. T. Burnette, J. Lippincott-Schwartz, G. E. Jones, and R. Heintzmann, “Bayesian localization microscopy reveals nanoscale podosome dynamics,” Nat. Methods 9(2), 195–200 (2011).
[Crossref] [PubMed]

Mukamel, E. A.

E. A. Mukamel and M. J. Schnitzer, “Unified resolution bounds for conventional and stochastic localization fluorescence microscopy,” Phys. Rev. Lett. 109(16), 168102 (2012).
[Crossref] [PubMed]

Olenych, S.

E. Betzig, G. H. Patterson, R. Sougrat, O. W. Lindwasser, S. Olenych, J. S. Bonifacino, M. W. Davidson, J. Lippincott-Schwartz, and H. F. Hess, “Imaging intracellular fluorescent proteins at nanometer resolution,” Science 313(5793), 1642–1645 (2006).
[Crossref] [PubMed]

Patterson, G. H.

E. Betzig, G. H. Patterson, R. Sougrat, O. W. Lindwasser, S. Olenych, J. S. Bonifacino, M. W. Davidson, J. Lippincott-Schwartz, and H. F. Hess, “Imaging intracellular fluorescent proteins at nanometer resolution,” Science 313(5793), 1642–1645 (2006).
[Crossref] [PubMed]

Piestun, R.

M. P. Backlund, M. D. Lew, A. S. Backer, S. J. Sahl, G. Grover, A. Agrawal, R. Piestun, and W. E. Moerner, “Simultaneous, accurate measurement of the 3D position and orientation of single molecules,” Proc. Natl. Acad. Sci. U.S.A. 109(47), 19087–19092 (2012).
[Crossref] [PubMed]

Pinotsi, D.

E. J. Rees, M. Erdelyi, D. Pinotsi, A. Knight, D. Metcalf, and C. F. Kaminski, “Blind assessment of localization microscopy image resolution,” Opt. Nanoscopy 1(1), 12 (2012), doi:.
[Crossref]

Prisner, T.

S. van de Linde, I. Krstić, T. Prisner, S. Doose, M. Heilemann, and M. Sauer, “Photoinduced formation of reversible dye radicals and their impact on super-resolution imaging,” Photochem. Photobiol. Sci. 10(4), 499–506 (2011).
[Crossref] [PubMed]

Qiu, Z.

L. Yang, A. R. Dun, K. J. Martin, Z. Qiu, A. Dunn, G. J. Lord, W. Lu, R. R. Duncan, and C. Rickman, “Secretory vesicles are preferentially targeted to areas of low molecular SNARE density,” PLoS ONE 7(11), e49514 (2012), doi:.
[Crossref] [PubMed]

Radenovic, A.

P. Annibale, S. Vanni, M. Scarselli, U. Rothlisberger, and A. Radenovic, “Identification of clustering artifacts in photoactivated localization microscopy,” Nat. Methods 8(7), 527–528 (2011).
[Crossref] [PubMed]

Rees, E.

G. S. Kaminski Schierle, S. van de Linde, M. Erdelyi, E. K. Esbjörner, T. Klein, E. Rees, C. W. Bertoncini, C. M. Dobson, M. Sauer, and C. F. Kaminski, “In situ measurements of the formation and morphology of intracellular β-amyloid fibrils by super-resolution fluorescence imaging,” J. Am. Chem. Soc. 133(33), 12902–12905 (2011).
[Crossref] [PubMed]

Rees, E. J.

E. J. Rees, M. Erdelyi, G. S. K. Schierle, A. Knight, and C. F. Kaminski, “Elements of image processing in localization microscopy,” J. Opt. 15(9), 094012 (2013).
[Crossref]

M. Erdelyi, E. J. Rees, D. Metcalf, G. S. K. Schierle, L. Dudas, J. Sinko, A. E. Knight, and C. F. Kaminski, “Correcting chromatic offset in multicolor super-resolution localization microscopy,” Opt. Express 21(9), 10978–10988 (2013).
[Crossref] [PubMed]

E. J. Rees, M. Erdelyi, D. Pinotsi, A. Knight, D. Metcalf, and C. F. Kaminski, “Blind assessment of localization microscopy image resolution,” Opt. Nanoscopy 1(1), 12 (2012), doi:.
[Crossref]

Rickman, C.

L. Yang, A. R. Dun, K. J. Martin, Z. Qiu, A. Dunn, G. J. Lord, W. Lu, R. R. Duncan, and C. Rickman, “Secretory vesicles are preferentially targeted to areas of low molecular SNARE density,” PLoS ONE 7(11), e49514 (2012), doi:.
[Crossref] [PubMed]

Rieger, B.

Rossberger, S.

D. Baddeley, D. Crossman, S. Rossberger, J. E. Cheyne, J. M. Montgomery, I. D. Jayasinghe, C. Cremer, M. B. Cannell, and C. Soeller, “4D Super-resolution microscopy with conventional fluorophores and single wavelength excitation in optically thick cells and tissues,” PLoS ONE 6(5), e20645 (2011).
[Crossref] [PubMed]

Rosten, E.

S. Cox, E. Rosten, J. Monypenny, T. Jovanovic-Talisman, D. T. Burnette, J. Lippincott-Schwartz, G. E. Jones, and R. Heintzmann, “Bayesian localization microscopy reveals nanoscale podosome dynamics,” Nat. Methods 9(2), 195–200 (2011).
[Crossref] [PubMed]

Rothlisberger, U.

P. Annibale, S. Vanni, M. Scarselli, U. Rothlisberger, and A. Radenovic, “Identification of clustering artifacts in photoactivated localization microscopy,” Nat. Methods 8(7), 527–528 (2011).
[Crossref] [PubMed]

Rust, M. J.

M. J. Rust, M. Bates, and X. Zhuang, “Sub-diffraction-limit imaging by stochastic optical reconstruction microscopy (STORM),” Nat. Methods 3(10), 793–796 (2006).
[Crossref] [PubMed]

Sahl, S. J.

M. P. Backlund, M. D. Lew, A. S. Backer, S. J. Sahl, G. Grover, A. Agrawal, R. Piestun, and W. E. Moerner, “Simultaneous, accurate measurement of the 3D position and orientation of single molecules,” Proc. Natl. Acad. Sci. U.S.A. 109(47), 19087–19092 (2012).
[Crossref] [PubMed]

Sauer, M.

S. van de Linde, A. Löschberger, T. Klein, M. Heidbreder, S. Wolter, M. Heilemann, and M. Sauer, “Direct stochastic optical reconstruction microscopy with standard fluorescent probes,” Nat. Protoc. 6(7), 991–1009 (2011).
[Crossref] [PubMed]

S. van de Linde, I. Krstić, T. Prisner, S. Doose, M. Heilemann, and M. Sauer, “Photoinduced formation of reversible dye radicals and their impact on super-resolution imaging,” Photochem. Photobiol. Sci. 10(4), 499–506 (2011).
[Crossref] [PubMed]

G. S. Kaminski Schierle, S. van de Linde, M. Erdelyi, E. K. Esbjörner, T. Klein, E. Rees, C. W. Bertoncini, C. M. Dobson, M. Sauer, and C. F. Kaminski, “In situ measurements of the formation and morphology of intracellular β-amyloid fibrils by super-resolution fluorescence imaging,” J. Am. Chem. Soc. 133(33), 12902–12905 (2011).
[Crossref] [PubMed]

S. Wolter, M. Schüttpelz, M. Tscherepanow, S. Van De Linde, M. Heilemann, and M. Sauer, “Real-time computation of subdiffraction-resolution fluorescence images,” J. Microsc. 237(1), 12–22 (2010).
[Crossref] [PubMed]

S. van de Linde, S. Wolter, M. Heilemann, and M. Sauer, “The effect of photoswitching kinetics and labeling densities on super-resolution fluorescence imaging,” J. Biotechnol. 149(4), 260–266 (2010).
[Crossref] [PubMed]

Scarselli, M.

P. Annibale, S. Vanni, M. Scarselli, U. Rothlisberger, and A. Radenovic, “Identification of clustering artifacts in photoactivated localization microscopy,” Nat. Methods 8(7), 527–528 (2011).
[Crossref] [PubMed]

Schierle, G. S. K.

Schnitzer, M. J.

E. A. Mukamel and M. J. Schnitzer, “Unified resolution bounds for conventional and stochastic localization fluorescence microscopy,” Phys. Rev. Lett. 109(16), 168102 (2012).
[Crossref] [PubMed]

Schüttpelz, M.

S. Wolter, M. Schüttpelz, M. Tscherepanow, S. Van De Linde, M. Heilemann, and M. Sauer, “Real-time computation of subdiffraction-resolution fluorescence images,” J. Microsc. 237(1), 12–22 (2010).
[Crossref] [PubMed]

Schwartz, S. L.

Shroff, H.

H. Shroff, C. G. Galbraith, J. A. Galbraith, and E. Betzig, “Live-cell photoactivated localization microscopy of nanoscale adhesion dynamics,” Nat. Methods 5(5), 417–423 (2008).
[Crossref] [PubMed]

Sinko, J.

Soeller, C.

D. Baddeley, D. Crossman, S. Rossberger, J. E. Cheyne, J. M. Montgomery, I. D. Jayasinghe, C. Cremer, M. B. Cannell, and C. Soeller, “4D Super-resolution microscopy with conventional fluorophores and single wavelength excitation in optically thick cells and tissues,” PLoS ONE 6(5), e20645 (2011).
[Crossref] [PubMed]

Sougrat, R.

E. Betzig, G. H. Patterson, R. Sougrat, O. W. Lindwasser, S. Olenych, J. S. Bonifacino, M. W. Davidson, J. Lippincott-Schwartz, and H. F. Hess, “Imaging intracellular fluorescent proteins at nanometer resolution,” Science 313(5793), 1642–1645 (2006).
[Crossref] [PubMed]

Stallinga, S.

Tscherepanow, M.

S. Wolter, M. Schüttpelz, M. Tscherepanow, S. Van De Linde, M. Heilemann, and M. Sauer, “Real-time computation of subdiffraction-resolution fluorescence images,” J. Microsc. 237(1), 12–22 (2010).
[Crossref] [PubMed]

Valtorta, F.

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S. van de Linde, I. Krstić, T. Prisner, S. Doose, M. Heilemann, and M. Sauer, “Photoinduced formation of reversible dye radicals and their impact on super-resolution imaging,” Photochem. Photobiol. Sci. 10(4), 499–506 (2011).
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S. van de Linde, A. Löschberger, T. Klein, M. Heidbreder, S. Wolter, M. Heilemann, and M. Sauer, “Direct stochastic optical reconstruction microscopy with standard fluorescent probes,” Nat. Protoc. 6(7), 991–1009 (2011).
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S. van de Linde, A. Löschberger, T. Klein, M. Heidbreder, S. Wolter, M. Heilemann, and M. Sauer, “Direct stochastic optical reconstruction microscopy with standard fluorescent probes,” Nat. Protoc. 6(7), 991–1009 (2011).
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G. T. Dempsey, J. C. Vaughan, K. H. Chen, M. Bates, and X. Zhuang, “Evaluation of fluorophores for optimal performance in localization-based super-resolution imaging,” Nat. Methods 8(12), 1027–1036 (2011).
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[Crossref] [PubMed]

M. J. Rust, M. Bates, and X. Zhuang, “Sub-diffraction-limit imaging by stochastic optical reconstruction microscopy (STORM),” Nat. Methods 3(10), 793–796 (2006).
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Figures (8)

Fig. 1
Fig. 1

The structure of the “star” (a), “array” (b), “vesicles” (c) and “lines” (d) samples

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Fig. 2
Fig. 2

(a) The schematic view of the three state model of fluorescent dye in a switching buffer, (b) Two examples for randomly generated trajectories for fluorescent molecules, (c) Image acquisition model in time with the example-trajectories

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Fig. 3
Fig. 3

The graphical user interface (GUI) of TestSTORM

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Fig. 4
Fig. 4

The reconstructed star pattern at different z planes (0 nm is the focal plane, the contrast is the same in all figures, scale bar: 1µm)

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Fig. 5
Fig. 5

Auto-scaled reconstructed images of array patterns with different numbers of molecules linked to the points of the array (linker length 75 nm, distance between the array points: 400 nm, scale bar: 500 nm). The insets depict the cross sections going through the centers of 5 array points.

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Fig. 6
Fig. 6

The reconstructed line patterns with different numbers of linked molecules/µm (length of the line: 2200 nm, scale bar: 1µm)

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Fig. 7
Fig. 7

Reconstructed image of labeled vesicles of clathrin mediated endocytosis with bridge formation between the vesicles, scale bar: 5 µm

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Fig. 8
Fig. 8

Simulated samples with four vesicles captured with different frame rates and the number of molecules linked to the vesicles was varied, 1 pixel: 160 nm, in the insets: 1 pixel: 16 nm

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Tables (2)

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Table 1 Dye and acquisition parameters used for simulation

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Table 2 Possible artifacts in cases of different sample structures

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Equations (1)

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C=( M ves − M bridge )/ M ves ,

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