Abstract

In recent years, the diffraction barrier in fluorescence imaging has been broken and optical nanoscopes now routinely image with resolutions of down to 20 nm, an improvement of more than 10 fold. Because this allows imaging much smaller features and because all super-resolution approaches trade off speed for spatial resolution, mechanical instabilities of the microscopes become a limiting factor. Here, we propose a fully data-driven statistical registration method for drift detection and drift correction for single marker switching (SMS) imaging schemes, including a guideline for parameter choice and quality checks of the drift analysis. The necessary assumptions about the drift are minimal, allowing a model-free approach, but more specific models can easily be integrated. We determine the resulting performance on standard SMS measurements and show that the drift determination can be routinely brought to the range of precision achievable by fiducial marker-tracking methods.

© 2012 OSA

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2011 (1)

2010 (3)

U. Endesfelder, S. van de Linde, S. Wolter, M. Sauer, and M. Heilemann, “Subdiffraction-resolution fluorescence microscopy of Myosin-Actin motility,” ChemPhysChem 11(4), 836–840 (2010).
[Crossref] [PubMed]

L. Brown, T. Cai, and H. Zhou, “Nonparamteric regression in exponential families,” Ann. Stat. 38(4), 2005–2046 (2010).
[Crossref]

A. Pertsinidis, Y. X. Zhang, and S. Chu, “Subnanometre single-molecule localization, registration and distance measurements,” Nature 466(7306), 647–651 (2010).
[Crossref] [PubMed]

2009 (5)

S. Ram, P. Prabhat, E. S. Ward, and R. J. Ober, “Improved single particle localization accuracy with dual objective multifocal plane microscopy,” Opt. Express 17(8), 6881–6898 (2009).
[Crossref] [PubMed]

V. N. Belov, M. L. Bossi, J. Fölling, V. P. Boyarskiy, and S. W. Hell, “Rhodamine Spiroamides for Multicolor Single-Molecule Switching Fluorescent Nanoscopy,” Chem.-Eur. J. 15(41), 10762–10776 (2009).
[Crossref] [PubMed]

G. Shtengel, J. A. Galbraith, C. G. Galbraith, J. Lippincott-Schwartz, J. M. Gillette, S. Manley, R. Sougrat, C. M. Waterman, P. Kanchanawong, M. W. Davidson, R. D. Fetter, and H. F. Hess, “Interferometric fluorescent super-resolution microscopy resolves 3D cellular ultrastructure,” Proc. Natl. Acad. Sci. U.S.A. 106(9), 3125–3130 (2009).
[Crossref] [PubMed]

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]

D. Greenfield, A. L. McEvoy, H. Shroff, G. E. Crooks, N. S. Wingreen, E. Betzig, and J. Liphardt, “Self-organization of the escherichia coli chemotaxis network imaged with super-resolution light microscopy,” PLoS Biol. 7(6), e1000137 (2009).
[Crossref] [PubMed]

2008 (6)

M. Kreft, N. Vardjan, M. Stenovec, and R. Zorec, “Lateral drift correction in time-laps images by the particle-tracking algorithm,” Eur. Biophys. J. 37(7), 1119–1125 (2008).
[Crossref] [PubMed]

B. Huang, W. Wang, M. Bates, and X. Zhuang, “Three-Dimensional Super-Resolution Imaging by Stochastic Optical Reconstruction Microscopy,” Science 319(5864), 810–813 (2008).
[Crossref] [PubMed]

M. F. Juette, T. J. Gould, M. D. Lessard, M. J. Mlodzianoski, B. S. Nagpure, B. T. Bennett, S. T. Hess, and J. Bewersdorf, “Three-dimensional sub-100 nm resolution fluorescence microscopy of thick samples,” Nat. Methods 5(6), 527–529 (2008).
[Crossref] [PubMed]

N. Ji, H. Shroff, H. N. Zhong, and E. Betzig, “Advances in the speed and resolution of light microscopy,” Curr. Opin. Neurobiol. 18(6), 605–616 (2008).
[Crossref] [PubMed]

M. Bates, B. Huang, and X. W. Zhuang, “Super-resolution microscopy by nanoscale localization of photo-switchable fluorescent probes,” Curr. Opin. Chem. Biol. 12(5), 505–514 (2008).
[Crossref] [PubMed]

I. Testa, A. Schönle, C. von Middendorff, C. Geisler, R. Medda, C. A. Wurm, A. C. Stiel, S. Jakobs, M. Bossi, C. Eggeling, S. W. Hell, and A. Egner, “Nanoscale separation of molecular species based on their rotational mobility,” Opt. Express 16(25), 21093–21104 (2008).
[Crossref] [PubMed]

2007 (6)

A. R. Carter, G. M. King, T. A. Ulrich, W. Halsey, D. Alchenberger, and T. T. Perkins, “Stabilization of an optical microscope to 0.1 nm in three dimensions,” Appl. Opt. 46(3), 421–427 (2007).
[Crossref] [PubMed]

M. Bates, B. Huang, G. T. Dempsey, and X. Zhuang, “Multicolor super-resolution imaging with photo-switchable fluorescent probes,” Science 317(5845), 1749–1753 (2007).
[Crossref] [PubMed]

A. Egner, C. Geisler, C. von Middendorff, H. Bock, D. Wenzel, R. Medda, M. Andresen, A. C. Stiel, S. Jakobs, C. Eggeling, A. Schönle, and S. W. Hell, “Fluorescence nanoscopy in whole cells by asynchronous localization of photoswitching emitters,” Biophys. J. 93(9), 3285–3290 (2007).
[Crossref] [PubMed]

C. Geisler, A. Schönle, C. von Middendorff, H. Bock, C. Eggeling, A. Egner, and S. W. Hell, “Resolution of l/10 in fluorescence microscopy using fast single molecule photo-switching,” Appl. Phys., A Mater. Sci. Process. 88(2), 223–226 (2007).
[Crossref]

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

H. Shroff, C. G. Galbraith, J. A. Galbraith, H. White, J. Gillette, S. Olenych, M. W. Davidson, and E. Betzig, “Dual-color superresolution imaging of genetically expressed probes within individual adhesion complexes,” Proc. Natl. Acad. Sci. U.S.A. 104(51), 20308–20313 (2007).
[Crossref] [PubMed]

2006 (3)

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]

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]

2003 (2)

B. Zitova and J. Flusser, “Image registration methods: a survey,” Image Vis. Comput. 21(11), 977–1000 (2003).
[Crossref]

J. Adler and S. N. Pagakis, “Reducing image distortions due to temperature-related microscope stage drift,” J. Microsc. 210(2), 131–137 (2003).
[Crossref] [PubMed]

2002 (1)

R. E. Thompson, D. R. Larson, and W. W. Webb, “Precise nanometer localization analysis for individual fluorescent probes,” Biophys. J. 82(5), 2775–2783 (2002).
[Crossref] [PubMed]

2001 (1)

D. L. G. Hill, P. G. Batchelor, M. Holden, and D. J. Hawkes, “Medical image registration,” Phys. Med. Biol. 46(3), R1–R45 (2001).
[Crossref] [PubMed]

1999 (1)

1998 (1)

J. B. Maintz and M. A. Viergever, “A survey of medical image registration,” Med. Image Anal. 2(1), 1–36 (1998).
[Crossref] [PubMed]

1994 (1)

1992 (1)

L. G. Brown, “A Survey of Image Registration Techniques,” Computing Surveys 24(4), 325–376 (1992).
[Crossref]

1968 (1)

M. B. Wilk and R. Gnanadesikan, “Probability Plotting Methods for Analysis of Data,” Biometrika 55(1), 1–17 (1968).
[PubMed]

1949 (1)

C. E. Shannon, “Communication in the presence of noise,” Proc. Inst. Radio Eng. 37(1), 10–21 (1949).

Adler, J.

J. Adler and S. N. Pagakis, “Reducing image distortions due to temperature-related microscope stage drift,” J. Microsc. 210(2), 131–137 (2003).
[Crossref] [PubMed]

Alchenberger, D.

Andresen, M.

A. Egner, C. Geisler, C. von Middendorff, H. Bock, D. Wenzel, R. Medda, M. Andresen, A. C. Stiel, S. Jakobs, C. Eggeling, A. Schönle, and S. W. Hell, “Fluorescence nanoscopy in whole cells by asynchronous localization of photoswitching emitters,” Biophys. J. 93(9), 3285–3290 (2007).
[Crossref] [PubMed]

Batchelor, P. G.

D. L. G. Hill, P. G. Batchelor, M. Holden, and D. J. Hawkes, “Medical image registration,” Phys. Med. Biol. 46(3), R1–R45 (2001).
[Crossref] [PubMed]

Bates, M.

B. Huang, W. Wang, M. Bates, and X. Zhuang, “Three-Dimensional Super-Resolution Imaging by Stochastic Optical Reconstruction Microscopy,” Science 319(5864), 810–813 (2008).
[Crossref] [PubMed]

M. Bates, B. Huang, and X. W. Zhuang, “Super-resolution microscopy by nanoscale localization of photo-switchable fluorescent probes,” Curr. Opin. Chem. Biol. 12(5), 505–514 (2008).
[Crossref] [PubMed]

M. Bates, B. Huang, G. T. Dempsey, and X. Zhuang, “Multicolor super-resolution imaging with photo-switchable fluorescent probes,” Science 317(5845), 1749–1753 (2007).
[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]

Belov, V. N.

V. N. Belov, M. L. Bossi, J. Fölling, V. P. Boyarskiy, and S. W. Hell, “Rhodamine Spiroamides for Multicolor Single-Molecule Switching Fluorescent Nanoscopy,” Chem.-Eur. J. 15(41), 10762–10776 (2009).
[Crossref] [PubMed]

Bennett, B. T.

M. F. Juette, T. J. Gould, M. D. Lessard, M. J. Mlodzianoski, B. S. Nagpure, B. T. Bennett, S. T. Hess, and J. Bewersdorf, “Three-dimensional sub-100 nm resolution fluorescence microscopy of thick samples,” Nat. Methods 5(6), 527–529 (2008).
[Crossref] [PubMed]

Betzig, E.

D. Greenfield, A. L. McEvoy, H. Shroff, G. E. Crooks, N. S. Wingreen, E. Betzig, and J. Liphardt, “Self-organization of the escherichia coli chemotaxis network imaged with super-resolution light microscopy,” PLoS Biol. 7(6), e1000137 (2009).
[Crossref] [PubMed]

N. Ji, H. Shroff, H. N. Zhong, and E. Betzig, “Advances in the speed and resolution of light microscopy,” Curr. Opin. Neurobiol. 18(6), 605–616 (2008).
[Crossref] [PubMed]

H. Shroff, C. G. Galbraith, J. A. Galbraith, H. White, J. Gillette, S. Olenych, M. W. Davidson, and E. Betzig, “Dual-color superresolution imaging of genetically expressed probes within individual adhesion complexes,” Proc. Natl. Acad. Sci. U.S.A. 104(51), 20308–20313 (2007).
[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]

Bewersdorf, J.

M. J. Mlodzianoski, J. M. Schreiner, S. P. Callahan, K. Smolková, A. Dlasková, J. Santorová, P. Ježek, and J. Bewersdorf, “Sample drift correction in 3D fluorescence photoactivation localization microscopy,” Opt. Express 19(16), 15009–15019 (2011).
[Crossref] [PubMed]

M. F. Juette, T. J. Gould, M. D. Lessard, M. J. Mlodzianoski, B. S. Nagpure, B. T. Bennett, S. T. Hess, and J. Bewersdorf, “Three-dimensional sub-100 nm resolution fluorescence microscopy of thick samples,” Nat. Methods 5(6), 527–529 (2008).
[Crossref] [PubMed]

Bock, H.

A. Egner, C. Geisler, C. von Middendorff, H. Bock, D. Wenzel, R. Medda, M. Andresen, A. C. Stiel, S. Jakobs, C. Eggeling, A. Schönle, and S. W. Hell, “Fluorescence nanoscopy in whole cells by asynchronous localization of photoswitching emitters,” Biophys. J. 93(9), 3285–3290 (2007).
[Crossref] [PubMed]

C. Geisler, A. Schönle, C. von Middendorff, H. Bock, C. Eggeling, A. Egner, and S. W. Hell, “Resolution of l/10 in fluorescence microscopy using fast single molecule photo-switching,” Appl. Phys., A Mater. Sci. Process. 88(2), 223–226 (2007).
[Crossref]

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]

Bossi, M.

Bossi, M. L.

V. N. Belov, M. L. Bossi, J. Fölling, V. P. Boyarskiy, and S. W. Hell, “Rhodamine Spiroamides for Multicolor Single-Molecule Switching Fluorescent Nanoscopy,” Chem.-Eur. J. 15(41), 10762–10776 (2009).
[Crossref] [PubMed]

Boyarskiy, V. P.

V. N. Belov, M. L. Bossi, J. Fölling, V. P. Boyarskiy, and S. W. Hell, “Rhodamine Spiroamides for Multicolor Single-Molecule Switching Fluorescent Nanoscopy,” Chem.-Eur. J. 15(41), 10762–10776 (2009).
[Crossref] [PubMed]

Brakenhoff, G. J.

Brown, L.

L. Brown, T. Cai, and H. Zhou, “Nonparamteric regression in exponential families,” Ann. Stat. 38(4), 2005–2046 (2010).
[Crossref]

Brown, L. G.

L. G. Brown, “A Survey of Image Registration Techniques,” Computing Surveys 24(4), 325–376 (1992).
[Crossref]

Cai, T.

L. Brown, T. Cai, and H. Zhou, “Nonparamteric regression in exponential families,” Ann. Stat. 38(4), 2005–2046 (2010).
[Crossref]

Callahan, S. P.

Carter, A. R.

Chu, S.

A. Pertsinidis, Y. X. Zhang, and S. Chu, “Subnanometre single-molecule localization, registration and distance measurements,” Nature 466(7306), 647–651 (2010).
[Crossref] [PubMed]

Crooks, G. E.

D. Greenfield, A. L. McEvoy, H. Shroff, G. E. Crooks, N. S. Wingreen, E. Betzig, and J. Liphardt, “Self-organization of the escherichia coli chemotaxis network imaged with super-resolution light microscopy,” PLoS Biol. 7(6), e1000137 (2009).
[Crossref] [PubMed]

Davidson, M. W.

G. Shtengel, J. A. Galbraith, C. G. Galbraith, J. Lippincott-Schwartz, J. M. Gillette, S. Manley, R. Sougrat, C. M. Waterman, P. Kanchanawong, M. W. Davidson, R. D. Fetter, and H. F. Hess, “Interferometric fluorescent super-resolution microscopy resolves 3D cellular ultrastructure,” Proc. Natl. Acad. Sci. U.S.A. 106(9), 3125–3130 (2009).
[Crossref] [PubMed]

H. Shroff, C. G. Galbraith, J. A. Galbraith, H. White, J. Gillette, S. Olenych, M. W. Davidson, and E. Betzig, “Dual-color superresolution imaging of genetically expressed probes within individual adhesion complexes,” Proc. Natl. Acad. Sci. U.S.A. 104(51), 20308–20313 (2007).
[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]

Dempsey, G. T.

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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]

Stenovec, M.

M. Kreft, N. Vardjan, M. Stenovec, and R. Zorec, “Lateral drift correction in time-laps images by the particle-tracking algorithm,” Eur. Biophys. J. 37(7), 1119–1125 (2008).
[Crossref] [PubMed]

Stiel, A. C.

I. Testa, A. Schönle, C. von Middendorff, C. Geisler, R. Medda, C. A. Wurm, A. C. Stiel, S. Jakobs, M. Bossi, C. Eggeling, S. W. Hell, and A. Egner, “Nanoscale separation of molecular species based on their rotational mobility,” Opt. Express 16(25), 21093–21104 (2008).
[Crossref] [PubMed]

A. Egner, C. Geisler, C. von Middendorff, H. Bock, D. Wenzel, R. Medda, M. Andresen, A. C. Stiel, S. Jakobs, C. Eggeling, A. Schönle, and S. W. Hell, “Fluorescence nanoscopy in whole cells by asynchronous localization of photoswitching emitters,” Biophys. J. 93(9), 3285–3290 (2007).
[Crossref] [PubMed]

Testa, I.

Thompson, R. E.

R. E. Thompson, D. R. Larson, and W. W. Webb, “Precise nanometer localization analysis for individual fluorescent probes,” Biophys. J. 82(5), 2775–2783 (2002).
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Ulrich, T. A.

van de Linde, S.

U. Endesfelder, S. van de Linde, S. Wolter, M. Sauer, and M. Heilemann, “Subdiffraction-resolution fluorescence microscopy of Myosin-Actin motility,” ChemPhysChem 11(4), 836–840 (2010).
[Crossref] [PubMed]

van Oijen, A. M.

Vardjan, N.

M. Kreft, N. Vardjan, M. Stenovec, and R. Zorec, “Lateral drift correction in time-laps images by the particle-tracking algorithm,” Eur. Biophys. J. 37(7), 1119–1125 (2008).
[Crossref] [PubMed]

Verkhusha, V. V.

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]

Viergever, M. A.

J. B. Maintz and M. A. Viergever, “A survey of medical image registration,” Med. Image Anal. 2(1), 1–36 (1998).
[Crossref] [PubMed]

von Middendorff, C.

I. Testa, A. Schönle, C. von Middendorff, C. Geisler, R. Medda, C. A. Wurm, A. C. Stiel, S. Jakobs, M. Bossi, C. Eggeling, S. W. Hell, and A. Egner, “Nanoscale separation of molecular species based on their rotational mobility,” Opt. Express 16(25), 21093–21104 (2008).
[Crossref] [PubMed]

C. Geisler, A. Schönle, C. von Middendorff, H. Bock, C. Eggeling, A. Egner, and S. W. Hell, “Resolution of l/10 in fluorescence microscopy using fast single molecule photo-switching,” Appl. Phys., A Mater. Sci. Process. 88(2), 223–226 (2007).
[Crossref]

A. Egner, C. Geisler, C. von Middendorff, H. Bock, D. Wenzel, R. Medda, M. Andresen, A. C. Stiel, S. Jakobs, C. Eggeling, A. Schönle, and S. W. Hell, “Fluorescence nanoscopy in whole cells by asynchronous localization of photoswitching emitters,” Biophys. J. 93(9), 3285–3290 (2007).
[Crossref] [PubMed]

Wang, W.

B. Huang, W. Wang, M. Bates, and X. Zhuang, “Three-Dimensional Super-Resolution Imaging by Stochastic Optical Reconstruction Microscopy,” Science 319(5864), 810–813 (2008).
[Crossref] [PubMed]

Ward, E. S.

Waterman, C. M.

G. Shtengel, J. A. Galbraith, C. G. Galbraith, J. Lippincott-Schwartz, J. M. Gillette, S. Manley, R. Sougrat, C. M. Waterman, P. Kanchanawong, M. W. Davidson, R. D. Fetter, and H. F. Hess, “Interferometric fluorescent super-resolution microscopy resolves 3D cellular ultrastructure,” Proc. Natl. Acad. Sci. U.S.A. 106(9), 3125–3130 (2009).
[Crossref] [PubMed]

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R. E. Thompson, D. R. Larson, and W. W. Webb, “Precise nanometer localization analysis for individual fluorescent probes,” Biophys. J. 82(5), 2775–2783 (2002).
[Crossref] [PubMed]

Wenzel, D.

A. Egner, C. Geisler, C. von Middendorff, H. Bock, D. Wenzel, R. Medda, M. Andresen, A. C. Stiel, S. Jakobs, C. Eggeling, A. Schönle, and S. W. Hell, “Fluorescence nanoscopy in whole cells by asynchronous localization of photoswitching emitters,” Biophys. J. 93(9), 3285–3290 (2007).
[Crossref] [PubMed]

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H. Shroff, C. G. Galbraith, J. A. Galbraith, H. White, J. Gillette, S. Olenych, M. W. Davidson, and E. Betzig, “Dual-color superresolution imaging of genetically expressed probes within individual adhesion complexes,” Proc. Natl. Acad. Sci. U.S.A. 104(51), 20308–20313 (2007).
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M. B. Wilk and R. Gnanadesikan, “Probability Plotting Methods for Analysis of Data,” Biometrika 55(1), 1–17 (1968).
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D. Greenfield, A. L. McEvoy, H. Shroff, G. E. Crooks, N. S. Wingreen, E. Betzig, and J. Liphardt, “Self-organization of the escherichia coli chemotaxis network imaged with super-resolution light microscopy,” PLoS Biol. 7(6), e1000137 (2009).
[Crossref] [PubMed]

Wolter, S.

U. Endesfelder, S. van de Linde, S. Wolter, M. Sauer, and M. Heilemann, “Subdiffraction-resolution fluorescence microscopy of Myosin-Actin motility,” ChemPhysChem 11(4), 836–840 (2010).
[Crossref] [PubMed]

Wurm, C. A.

Zhang, Y. X.

A. Pertsinidis, Y. X. Zhang, and S. Chu, “Subnanometre single-molecule localization, registration and distance measurements,” Nature 466(7306), 647–651 (2010).
[Crossref] [PubMed]

Zhong, H. N.

N. Ji, H. Shroff, H. N. Zhong, and E. Betzig, “Advances in the speed and resolution of light microscopy,” Curr. Opin. Neurobiol. 18(6), 605–616 (2008).
[Crossref] [PubMed]

Zhou, H.

L. Brown, T. Cai, and H. Zhou, “Nonparamteric regression in exponential families,” Ann. Stat. 38(4), 2005–2046 (2010).
[Crossref]

Zhuang, X.

B. Huang, W. Wang, M. Bates, and X. Zhuang, “Three-Dimensional Super-Resolution Imaging by Stochastic Optical Reconstruction Microscopy,” Science 319(5864), 810–813 (2008).
[Crossref] [PubMed]

M. Bates, B. Huang, G. T. Dempsey, and X. Zhuang, “Multicolor super-resolution imaging with photo-switchable fluorescent probes,” Science 317(5845), 1749–1753 (2007).
[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]

Zhuang, X. W.

M. Bates, B. Huang, and X. W. Zhuang, “Super-resolution microscopy by nanoscale localization of photo-switchable fluorescent probes,” Curr. Opin. Chem. Biol. 12(5), 505–514 (2008).
[Crossref] [PubMed]

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B. Zitova and J. Flusser, “Image registration methods: a survey,” Image Vis. Comput. 21(11), 977–1000 (2003).
[Crossref]

Zorec, R.

M. Kreft, N. Vardjan, M. Stenovec, and R. Zorec, “Lateral drift correction in time-laps images by the particle-tracking algorithm,” Eur. Biophys. J. 37(7), 1119–1125 (2008).
[Crossref] [PubMed]

Ann. Stat. (1)

L. Brown, T. Cai, and H. Zhou, “Nonparamteric regression in exponential families,” Ann. Stat. 38(4), 2005–2046 (2010).
[Crossref]

Appl. Opt. (1)

Appl. Phys., A Mater. Sci. Process. (1)

C. Geisler, A. Schönle, C. von Middendorff, H. Bock, C. Eggeling, A. Egner, and S. W. Hell, “Resolution of l/10 in fluorescence microscopy using fast single molecule photo-switching,” Appl. Phys., A Mater. Sci. Process. 88(2), 223–226 (2007).
[Crossref]

Biometrika (1)

M. B. Wilk and R. Gnanadesikan, “Probability Plotting Methods for Analysis of Data,” Biometrika 55(1), 1–17 (1968).
[PubMed]

Biophys. J. (3)

R. E. Thompson, D. R. Larson, and W. W. Webb, “Precise nanometer localization analysis for individual fluorescent probes,” Biophys. J. 82(5), 2775–2783 (2002).
[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]

A. Egner, C. Geisler, C. von Middendorff, H. Bock, D. Wenzel, R. Medda, M. Andresen, A. C. Stiel, S. Jakobs, C. Eggeling, A. Schönle, and S. W. Hell, “Fluorescence nanoscopy in whole cells by asynchronous localization of photoswitching emitters,” Biophys. J. 93(9), 3285–3290 (2007).
[Crossref] [PubMed]

Chem.-Eur. J. (1)

V. N. Belov, M. L. Bossi, J. Fölling, V. P. Boyarskiy, and S. W. Hell, “Rhodamine Spiroamides for Multicolor Single-Molecule Switching Fluorescent Nanoscopy,” Chem.-Eur. J. 15(41), 10762–10776 (2009).
[Crossref] [PubMed]

ChemPhysChem (1)

U. Endesfelder, S. van de Linde, S. Wolter, M. Sauer, and M. Heilemann, “Subdiffraction-resolution fluorescence microscopy of Myosin-Actin motility,” ChemPhysChem 11(4), 836–840 (2010).
[Crossref] [PubMed]

Computing Surveys (1)

L. G. Brown, “A Survey of Image Registration Techniques,” Computing Surveys 24(4), 325–376 (1992).
[Crossref]

Curr. Opin. Chem. Biol. (1)

M. Bates, B. Huang, and X. W. Zhuang, “Super-resolution microscopy by nanoscale localization of photo-switchable fluorescent probes,” Curr. Opin. Chem. Biol. 12(5), 505–514 (2008).
[Crossref] [PubMed]

Curr. Opin. Neurobiol. (1)

N. Ji, H. Shroff, H. N. Zhong, and E. Betzig, “Advances in the speed and resolution of light microscopy,” Curr. Opin. Neurobiol. 18(6), 605–616 (2008).
[Crossref] [PubMed]

Eur. Biophys. J. (1)

M. Kreft, N. Vardjan, M. Stenovec, and R. Zorec, “Lateral drift correction in time-laps images by the particle-tracking algorithm,” Eur. Biophys. J. 37(7), 1119–1125 (2008).
[Crossref] [PubMed]

Image Vis. Comput. (1)

B. Zitova and J. Flusser, “Image registration methods: a survey,” Image Vis. Comput. 21(11), 977–1000 (2003).
[Crossref]

J. Microsc. (1)

J. Adler and S. N. Pagakis, “Reducing image distortions due to temperature-related microscope stage drift,” J. Microsc. 210(2), 131–137 (2003).
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J. Opt. Soc. Am. A (1)

Med. Image Anal. (1)

J. B. Maintz and M. A. Viergever, “A survey of medical image registration,” Med. Image Anal. 2(1), 1–36 (1998).
[Crossref] [PubMed]

Nat. Methods (2)

M. F. Juette, T. J. Gould, M. D. Lessard, M. J. Mlodzianoski, B. S. Nagpure, B. T. Bennett, S. T. Hess, and J. Bewersdorf, “Three-dimensional sub-100 nm resolution fluorescence microscopy of thick samples,” Nat. Methods 5(6), 527–529 (2008).
[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]

Nat. Protoc. (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]

Nature (1)

A. Pertsinidis, Y. X. Zhang, and S. Chu, “Subnanometre single-molecule localization, registration and distance measurements,” Nature 466(7306), 647–651 (2010).
[Crossref] [PubMed]

Opt. Express (3)

Opt. Lett. (1)

Phys. Med. Biol. (1)

D. L. G. Hill, P. G. Batchelor, M. Holden, and D. J. Hawkes, “Medical image registration,” Phys. Med. Biol. 46(3), R1–R45 (2001).
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PLoS Biol. (1)

D. Greenfield, A. L. McEvoy, H. Shroff, G. E. Crooks, N. S. Wingreen, E. Betzig, and J. Liphardt, “Self-organization of the escherichia coli chemotaxis network imaged with super-resolution light microscopy,” PLoS Biol. 7(6), e1000137 (2009).
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Proc. Inst. Radio Eng. (1)

C. E. Shannon, “Communication in the presence of noise,” Proc. Inst. Radio Eng. 37(1), 10–21 (1949).

Proc. Natl. Acad. Sci. U.S.A. (2)

H. Shroff, C. G. Galbraith, J. A. Galbraith, H. White, J. Gillette, S. Olenych, M. W. Davidson, and E. Betzig, “Dual-color superresolution imaging of genetically expressed probes within individual adhesion complexes,” Proc. Natl. Acad. Sci. U.S.A. 104(51), 20308–20313 (2007).
[Crossref] [PubMed]

G. Shtengel, J. A. Galbraith, C. G. Galbraith, J. Lippincott-Schwartz, J. M. Gillette, S. Manley, R. Sougrat, C. M. Waterman, P. Kanchanawong, M. W. Davidson, R. D. Fetter, and H. F. Hess, “Interferometric fluorescent super-resolution microscopy resolves 3D cellular ultrastructure,” Proc. Natl. Acad. Sci. U.S.A. 106(9), 3125–3130 (2009).
[Crossref] [PubMed]

Science (4)

M. Bates, B. Huang, G. T. Dempsey, and X. Zhuang, “Multicolor super-resolution imaging with photo-switchable fluorescent probes,” Science 317(5845), 1749–1753 (2007).
[Crossref] [PubMed]

B. Huang, W. Wang, M. Bates, and X. Zhuang, “Three-Dimensional Super-Resolution Imaging by Stochastic Optical Reconstruction Microscopy,” Science 319(5864), 810–813 (2008).
[Crossref] [PubMed]

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

Other (5)

M. Born and E. Wolf, Principles of Optics (Cambridge University Press, 2002).

S. Weisberg, Applied Linear Regression (John Wiley & Sons, Hoboken, NJ, 2005).

A. W. d. Vaart, Asymptotic Statistics (Cambridge University Press, USA, 1998).

J. Pinheiro and D. Bates, Mixed Effects Models in S and S-Plus (Springer, New York, NY, 2000).

W. Härdle, M. Müller, S. Sperlich, and A. Werwatz, Nonparametric and Semiparametric Models (Springer, Berlin, 2004).

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Figures (5)

Fig. 1
Fig. 1

Simulated image subjected to drift and drift estimation. (a) One-dimensional image comprised of three shifted Gaussians on a small constant background (lines) and sampled “images” (scatters) at three consecutive time points (black, red, green). (b) Drift δ (black) over 15 time points and its estimates δ ^ based on the methods “pre” (blue), “first” (cyan), “model-free” (red), “spline” (green) obtained from one corresponding data set of 15 images. The table reports the rMISE based on 10,000 simulations without and with application of the Anscombe-like transform, which typically halves the rMISE.

Fig. 2
Fig. 2

Drift estimation methods reconstruct a considerably blurred measurement of RhS-labeled β-tubulin network in a fixed PtK2-cell. (a) Histogram of the raw SMS-data. (b) Histogram of the model-free corrected SMS-data. (c) Histogram of the bead tracking corrected SMS-data. The gray rectangle marks the region where the localized events close to the bead were cut out. (d-f) Close ups of the regions marked by the white rectangles. (g) Profiles in x-direction integrated over y within the areas marked in (d-f). (h) Close up of (g), showing data points (markers) and Gaussian fits (lines) for model-free, bead tracking and for the set of curves “first”, “second”, …, “last”.

Fig. 3
Fig. 3

Effects of different temporal and spatial binning on the drift estimates of real data. (a) Comparison of drift estimates δ ^ for the y-direction (for the data shown in section 3.2.4) derived from the model-free approach. (black) time bin = 1000 frames, space bin = 30 nm; (red) time bin = 250 frames, space bin = 20 nm. (b) quantile plot for the data in (a). The inset shows the whole data range. Note that the right y-axis covers a range from −7000 to + 7000 nm.

Fig. 4
Fig. 4

Comparison of drift estimates based on bead-tracking (black, dark yellow), the model-free approach (red) and the linear mixed effects model (green). (a) Continuous experimental drift in y-direction, set of curves “first”, “second”, …, ”last”. The table shows the rISE of the pair of drift estimates indicated by the respective row and column. Here, the Euclidean norm was used in Eq. (10). (b) Discontinuous artificial drift in x-direction. Bin sizes: 1000 frames and 30 nm.

Fig. 5
Fig. 5

Drift compensation is essential for quantitative analysis. (a) Position histograms generated from the raw SMS data (top), drift-corrected by the model-free approach (middle) and by bead-tracking (bottom). The gray rectangle marks the region where the localized events close to the bead were cut out. (b) Close-ups and corresponding profiles of the region marked by the small white rectangle in (a). (c) Close-ups and corresponding profiles of the region marked by the large white rectangle in (a). The positions of the localized events shown in (b) and (c) were rotated by 40° before plotting the histograms.

Equations (14)

Equations on this page are rendered with MathJax. Learn more.

Z i j = # { k : t k = t i and ( x k , y k ) in pixel j } ,
μ i j = < Z i j > = < K i > f ( u j δ x , i , v j δ y , i ) ,
Δ i l = D i l + ε i l
D i l = δ l δ i ,
Δ i l = δ l δ i + ε i l .
δ = X β
D i l = d l d i
d = δ + η = X β + η ,
Δ i l = δ l δ i + η l η i + ε i l = ( X β ) l ( X β ) i + η l η i + ε i l .
min ω 1 n i = 1 n | δ ^ i δ i ω | 2 .
i , l ( Δ i l δ l + δ i ) 2 ,
i , l ( Δ i l δ l + δ i ) 2 + 2 ( i δ i ) 2 .
2 l ( Δ i l Δ l i 2 δ l + 2 δ i ) + 4 l δ l = 4 n δ i 4 l Δ l i ,
δ i = 1 n l Δ l i ,

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