Abstract

Highly accurate sample drift correction is essential in super-resolution localization microscopy to guarantee a high spatial resolution, especially when the technique is used to visualize small cell organelle. Here we present a localization events-based drift correction method using a redundant cross-correlation algorithm originally developed to correct beam-induced motion in cryo-electron microscopy. With simulated, synthesized as well as experimental data, we have demonstrated its superior precision compared to previously published localization events-based drift correction methods. The major advantage of this method is the robustness when the number of localization events is low, either because a short correction time step is required or because the imaged structure is small and sparse. This method has allowed us to improve the effective resolution when imaging Golgi apparatus in mammalian cells.

© 2014 Optical Society of America

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References

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2013 (4)

A. Szymborska, A. de Marco, N. Daigle, V. C. Cordes, J. A. G. Briggs, and J. Ellenberg, “Nuclear Pore Scaffold Structure Analyzed by Super-Resolution Microscopy and Particle Averaging,” Science 341(6146), 655–658 (2013).
[Crossref] [PubMed]

R. McGorty, D. Kamiyama, and B. Huang, “Active microscope stabilization in three dimensions using image correlation,” Opt Nanoscopy 2(1), 1–7 (2013).
[Crossref] [PubMed]

X. M. Li, P. Mooney, S. Zheng, C. R. Booth, M. B. Braunfeld, S. Gubbens, D. A. Agard, and Y. F. Cheng, “Electron counting and beam-induced motion correction enable near-atomic-resolution single-particle cryo-EM,” Nat. Methods 10(6), 584–590 (2013).
[Crossref] [PubMed]

R. P. J. Nieuwenhuizen, K. A. Lidke, M. Bates, D. L. Puig, D. Grünwald, S. Stallinga, and B. Rieger, “Measuring image resolution in optical nanoscopy,” Nat. Methods 10(6), 557–562 (2013).
[Crossref] [PubMed]

2012 (4)

J. C. Vaughan, S. Jia, and X. W. Zhuang, “Ultrabright photoactivatable fluorophores created by reductive caging,” Nat. Methods 9(12), 1181–1184 (2012).
[Crossref] [PubMed]

V. Mennella, B. Keszthelyi, K. L. McDonald, B. Chhun, F. Kan, G. C. Rogers, B. Huang, and D. A. Agard, “Subdiffraction-resolution fluorescence microscopy reveals a domain of the centrosome critical for pericentriolar material organization,” Nat. Cell Biol. 14(11), 1159–1168 (2012).
[Crossref] [PubMed]

C. Geisler, T. Hotz, A. Schönle, S. W. Hell, A. Munk, and A. Egner, “Drift estimation for single marker switching based imaging schemes,” Opt. Express 20(7), 7274–7289 (2012).
[Crossref] [PubMed]

S. H. Lee, M. Baday, M. Tjioe, P. D. Simonson, R. B. Zhang, E. Cai, and P. R. Selvin, “Using fixed fiduciary markers for stage drift correction,” Opt. Express 20(11), 12177–12183 (2012).
[Crossref] [PubMed]

2011 (2)

M. D. Lew, S. F. Lee, J. L. Ptacin, M. K. Lee, R. J. Twieg, L. Shapiro, and W. E. Moerner, “Three-dimensional superresolution colocalization of intracellular protein superstructures and the cell surface in live Caulobacter crescentus,” Proc. Natl. Acad. Sci. U.S.A. 108(46), E1102–E1110 (2011).
[Crossref] [PubMed]

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]

2010 (2)

2008 (1)

B. Huang, W. Q. Wang, M. Bates, and X. W. Zhuang, “Three-dimensional super-resolution imaging by stochastic optical reconstruction microscopy,” Science 319(5864), 810–813 (2008).
[Crossref] [PubMed]

2007 (3)

M. Bates, B. Huang, G. T. Dempsey, and X. W. 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]

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]

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]

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]

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

Agard, D. A.

X. M. Li, P. Mooney, S. Zheng, C. R. Booth, M. B. Braunfeld, S. Gubbens, D. A. Agard, and Y. F. Cheng, “Electron counting and beam-induced motion correction enable near-atomic-resolution single-particle cryo-EM,” Nat. Methods 10(6), 584–590 (2013).
[Crossref] [PubMed]

V. Mennella, B. Keszthelyi, K. L. McDonald, B. Chhun, F. Kan, G. C. Rogers, B. Huang, and D. A. Agard, “Subdiffraction-resolution fluorescence microscopy reveals a domain of the centrosome critical for pericentriolar material organization,” Nat. Cell Biol. 14(11), 1159–1168 (2012).
[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]

Baday, M.

Bates, M.

R. P. J. Nieuwenhuizen, K. A. Lidke, M. Bates, D. L. Puig, D. Grünwald, S. Stallinga, and B. Rieger, “Measuring image resolution in optical nanoscopy,” Nat. Methods 10(6), 557–562 (2013).
[Crossref] [PubMed]

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

Betzig, E.

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.

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]

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]

Booth, C. R.

X. M. Li, P. Mooney, S. Zheng, C. R. Booth, M. B. Braunfeld, S. Gubbens, D. A. Agard, and Y. F. Cheng, “Electron counting and beam-induced motion correction enable near-atomic-resolution single-particle cryo-EM,” Nat. Methods 10(6), 584–590 (2013).
[Crossref] [PubMed]

Braunfeld, M. B.

X. M. Li, P. Mooney, S. Zheng, C. R. Booth, M. B. Braunfeld, S. Gubbens, D. A. Agard, and Y. F. Cheng, “Electron counting and beam-induced motion correction enable near-atomic-resolution single-particle cryo-EM,” Nat. Methods 10(6), 584–590 (2013).
[Crossref] [PubMed]

Briggs, J. A. G.

A. Szymborska, A. de Marco, N. Daigle, V. C. Cordes, J. A. G. Briggs, and J. Ellenberg, “Nuclear Pore Scaffold Structure Analyzed by Super-Resolution Microscopy and Particle Averaging,” Science 341(6146), 655–658 (2013).
[Crossref] [PubMed]

Cai, E.

Callahan, S. P.

Carter, A. R.

Cheng, Y. F.

X. M. Li, P. Mooney, S. Zheng, C. R. Booth, M. B. Braunfeld, S. Gubbens, D. A. Agard, and Y. F. Cheng, “Electron counting and beam-induced motion correction enable near-atomic-resolution single-particle cryo-EM,” Nat. Methods 10(6), 584–590 (2013).
[Crossref] [PubMed]

Chhun, B.

V. Mennella, B. Keszthelyi, K. L. McDonald, B. Chhun, F. Kan, G. C. Rogers, B. Huang, and D. A. Agard, “Subdiffraction-resolution fluorescence microscopy reveals a domain of the centrosome critical for pericentriolar material organization,” Nat. Cell Biol. 14(11), 1159–1168 (2012).
[Crossref] [PubMed]

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]

Cordes, V. C.

A. Szymborska, A. de Marco, N. Daigle, V. C. Cordes, J. A. G. Briggs, and J. Ellenberg, “Nuclear Pore Scaffold Structure Analyzed by Super-Resolution Microscopy and Particle Averaging,” Science 341(6146), 655–658 (2013).
[Crossref] [PubMed]

Daigle, N.

A. Szymborska, A. de Marco, N. Daigle, V. C. Cordes, J. A. G. Briggs, and J. Ellenberg, “Nuclear Pore Scaffold Structure Analyzed by Super-Resolution Microscopy and Particle Averaging,” Science 341(6146), 655–658 (2013).
[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]

de Marco, A.

A. Szymborska, A. de Marco, N. Daigle, V. C. Cordes, J. A. G. Briggs, and J. Ellenberg, “Nuclear Pore Scaffold Structure Analyzed by Super-Resolution Microscopy and Particle Averaging,” Science 341(6146), 655–658 (2013).
[Crossref] [PubMed]

Dempsey, G. T.

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

Dlasková, A.

Eggeling, C.

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]

Egner, A.

C. Geisler, T. Hotz, A. Schönle, S. W. Hell, A. Munk, and A. Egner, “Drift estimation for single marker switching based imaging schemes,” Opt. Express 20(7), 7274–7289 (2012).
[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]

Ellenberg, J.

A. Szymborska, A. de Marco, N. Daigle, V. C. Cordes, J. A. G. Briggs, and J. Ellenberg, “Nuclear Pore Scaffold Structure Analyzed by Super-Resolution Microscopy and Particle Averaging,” Science 341(6146), 655–658 (2013).
[Crossref] [PubMed]

Geisler, C.

C. Geisler, T. Hotz, A. Schönle, S. W. Hell, A. Munk, and A. Egner, “Drift estimation for single marker switching based imaging schemes,” Opt. Express 20(7), 7274–7289 (2012).
[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]

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]

Grünwald, D.

R. P. J. Nieuwenhuizen, K. A. Lidke, M. Bates, D. L. Puig, D. Grünwald, S. Stallinga, and B. Rieger, “Measuring image resolution in optical nanoscopy,” Nat. Methods 10(6), 557–562 (2013).
[Crossref] [PubMed]

Gubbens, S.

X. M. Li, P. Mooney, S. Zheng, C. R. Booth, M. B. Braunfeld, S. Gubbens, D. A. Agard, and Y. F. Cheng, “Electron counting and beam-induced motion correction enable near-atomic-resolution single-particle cryo-EM,” Nat. Methods 10(6), 584–590 (2013).
[Crossref] [PubMed]

Halsey, W.

Hedde, P. N.

Hell, S. W.

C. Geisler, T. Hotz, A. Schönle, S. W. Hell, A. Munk, and A. Egner, “Drift estimation for single marker switching based imaging schemes,” Opt. Express 20(7), 7274–7289 (2012).
[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]

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.

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]

Hotz, T.

Huang, B.

R. McGorty, D. Kamiyama, and B. Huang, “Active microscope stabilization in three dimensions using image correlation,” Opt Nanoscopy 2(1), 1–7 (2013).
[Crossref] [PubMed]

V. Mennella, B. Keszthelyi, K. L. McDonald, B. Chhun, F. Kan, G. C. Rogers, B. Huang, and D. A. Agard, “Subdiffraction-resolution fluorescence microscopy reveals a domain of the centrosome critical for pericentriolar material organization,” Nat. Cell Biol. 14(11), 1159–1168 (2012).
[Crossref] [PubMed]

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

Huang, Z. L.

Jakobs, S.

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]

Ježek, P.

Jia, S.

J. C. Vaughan, S. Jia, and X. W. Zhuang, “Ultrabright photoactivatable fluorophores created by reductive caging,” Nat. Methods 9(12), 1181–1184 (2012).
[Crossref] [PubMed]

Kamiyama, D.

R. McGorty, D. Kamiyama, and B. Huang, “Active microscope stabilization in three dimensions using image correlation,” Opt Nanoscopy 2(1), 1–7 (2013).
[Crossref] [PubMed]

Kan, F.

V. Mennella, B. Keszthelyi, K. L. McDonald, B. Chhun, F. Kan, G. C. Rogers, B. Huang, and D. A. Agard, “Subdiffraction-resolution fluorescence microscopy reveals a domain of the centrosome critical for pericentriolar material organization,” Nat. Cell Biol. 14(11), 1159–1168 (2012).
[Crossref] [PubMed]

Keszthelyi, B.

V. Mennella, B. Keszthelyi, K. L. McDonald, B. Chhun, F. Kan, G. C. Rogers, B. Huang, and D. A. Agard, “Subdiffraction-resolution fluorescence microscopy reveals a domain of the centrosome critical for pericentriolar material organization,” Nat. Cell Biol. 14(11), 1159–1168 (2012).
[Crossref] [PubMed]

King, G. M.

Lee, M. K.

M. D. Lew, S. F. Lee, J. L. Ptacin, M. K. Lee, R. J. Twieg, L. Shapiro, and W. E. Moerner, “Three-dimensional superresolution colocalization of intracellular protein superstructures and the cell surface in live Caulobacter crescentus,” Proc. Natl. Acad. Sci. U.S.A. 108(46), E1102–E1110 (2011).
[Crossref] [PubMed]

Lee, S. F.

M. D. Lew, S. F. Lee, J. L. Ptacin, M. K. Lee, R. J. Twieg, L. Shapiro, and W. E. Moerner, “Three-dimensional superresolution colocalization of intracellular protein superstructures and the cell surface in live Caulobacter crescentus,” Proc. Natl. Acad. Sci. U.S.A. 108(46), E1102–E1110 (2011).
[Crossref] [PubMed]

Lee, S. H.

Lew, M. D.

M. D. Lew, S. F. Lee, J. L. Ptacin, M. K. Lee, R. J. Twieg, L. Shapiro, and W. E. Moerner, “Three-dimensional superresolution colocalization of intracellular protein superstructures and the cell surface in live Caulobacter crescentus,” Proc. Natl. Acad. Sci. U.S.A. 108(46), E1102–E1110 (2011).
[Crossref] [PubMed]

Li, P. C.

Li, X. M.

X. M. Li, P. Mooney, S. Zheng, C. R. Booth, M. B. Braunfeld, S. Gubbens, D. A. Agard, and Y. F. Cheng, “Electron counting and beam-induced motion correction enable near-atomic-resolution single-particle cryo-EM,” Nat. Methods 10(6), 584–590 (2013).
[Crossref] [PubMed]

Lidke, K. A.

R. P. J. Nieuwenhuizen, K. A. Lidke, M. Bates, D. L. Puig, D. Grünwald, S. Stallinga, and B. Rieger, “Measuring image resolution in optical nanoscopy,” Nat. Methods 10(6), 557–562 (2013).
[Crossref] [PubMed]

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.

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]

Long, F.

Luo, Q. M.

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]

McDonald, K. L.

V. Mennella, B. Keszthelyi, K. L. McDonald, B. Chhun, F. Kan, G. C. Rogers, B. Huang, and D. A. Agard, “Subdiffraction-resolution fluorescence microscopy reveals a domain of the centrosome critical for pericentriolar material organization,” Nat. Cell Biol. 14(11), 1159–1168 (2012).
[Crossref] [PubMed]

McGorty, R.

R. McGorty, D. Kamiyama, and B. Huang, “Active microscope stabilization in three dimensions using image correlation,” Opt Nanoscopy 2(1), 1–7 (2013).
[Crossref] [PubMed]

Medda, R.

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]

Mennella, V.

V. Mennella, B. Keszthelyi, K. L. McDonald, B. Chhun, F. Kan, G. C. Rogers, B. Huang, and D. A. Agard, “Subdiffraction-resolution fluorescence microscopy reveals a domain of the centrosome critical for pericentriolar material organization,” Nat. Cell Biol. 14(11), 1159–1168 (2012).
[Crossref] [PubMed]

Mlodzianoski, M. J.

Moerner, W. E.

M. D. Lew, S. F. Lee, J. L. Ptacin, M. K. Lee, R. J. Twieg, L. Shapiro, and W. E. Moerner, “Three-dimensional superresolution colocalization of intracellular protein superstructures and the cell surface in live Caulobacter crescentus,” Proc. Natl. Acad. Sci. U.S.A. 108(46), E1102–E1110 (2011).
[Crossref] [PubMed]

Mooney, P.

X. M. Li, P. Mooney, S. Zheng, C. R. Booth, M. B. Braunfeld, S. Gubbens, D. A. Agard, and Y. F. Cheng, “Electron counting and beam-induced motion correction enable near-atomic-resolution single-particle cryo-EM,” Nat. Methods 10(6), 584–590 (2013).
[Crossref] [PubMed]

Munk, A.

Nienhaus, G. U.

Nieuwenhuizen, R. P. J.

R. P. J. Nieuwenhuizen, K. A. Lidke, M. Bates, D. L. Puig, D. Grünwald, S. Stallinga, and B. Rieger, “Measuring image resolution in optical nanoscopy,” Nat. Methods 10(6), 557–562 (2013).
[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]

Perkins, T. T.

Pertsinidis, A.

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

Ptacin, J. L.

M. D. Lew, S. F. Lee, J. L. Ptacin, M. K. Lee, R. J. Twieg, L. Shapiro, and W. E. Moerner, “Three-dimensional superresolution colocalization of intracellular protein superstructures and the cell surface in live Caulobacter crescentus,” Proc. Natl. Acad. Sci. U.S.A. 108(46), E1102–E1110 (2011).
[Crossref] [PubMed]

Puig, D. L.

R. P. J. Nieuwenhuizen, K. A. Lidke, M. Bates, D. L. Puig, D. Grünwald, S. Stallinga, and B. Rieger, “Measuring image resolution in optical nanoscopy,” Nat. Methods 10(6), 557–562 (2013).
[Crossref] [PubMed]

Quan, T. W.

Rieger, B.

R. P. J. Nieuwenhuizen, K. A. Lidke, M. Bates, D. L. Puig, D. Grünwald, S. Stallinga, and B. Rieger, “Measuring image resolution in optical nanoscopy,” Nat. Methods 10(6), 557–562 (2013).
[Crossref] [PubMed]

Rogers, G. C.

V. Mennella, B. Keszthelyi, K. L. McDonald, B. Chhun, F. Kan, G. C. Rogers, B. Huang, and D. A. Agard, “Subdiffraction-resolution fluorescence microscopy reveals a domain of the centrosome critical for pericentriolar material organization,” Nat. Cell Biol. 14(11), 1159–1168 (2012).
[Crossref] [PubMed]

Rust, M. J.

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

Santorová, J.

Schönle, A.

C. Geisler, T. Hotz, A. Schönle, S. W. Hell, A. Munk, and A. Egner, “Drift estimation for single marker switching based imaging schemes,” Opt. Express 20(7), 7274–7289 (2012).
[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]

Schreiner, J. M.

Selvin, P. R.

Shapiro, L.

M. D. Lew, S. F. Lee, J. L. Ptacin, M. K. Lee, R. J. Twieg, L. Shapiro, and W. E. Moerner, “Three-dimensional superresolution colocalization of intracellular protein superstructures and the cell surface in live Caulobacter crescentus,” Proc. Natl. Acad. Sci. U.S.A. 108(46), E1102–E1110 (2011).
[Crossref] [PubMed]

Simonson, P. D.

Smolková, K.

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.

R. P. J. Nieuwenhuizen, K. A. Lidke, M. Bates, D. L. Puig, D. Grünwald, S. Stallinga, and B. Rieger, “Measuring image resolution in optical nanoscopy,” Nat. Methods 10(6), 557–562 (2013).
[Crossref] [PubMed]

Stiel, A. C.

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]

Szymborska, A.

A. Szymborska, A. de Marco, N. Daigle, V. C. Cordes, J. A. G. Briggs, and J. Ellenberg, “Nuclear Pore Scaffold Structure Analyzed by Super-Resolution Microscopy and Particle Averaging,” Science 341(6146), 655–658 (2013).
[Crossref] [PubMed]

Tjioe, M.

Twieg, R. J.

M. D. Lew, S. F. Lee, J. L. Ptacin, M. K. Lee, R. J. Twieg, L. Shapiro, and W. E. Moerner, “Three-dimensional superresolution colocalization of intracellular protein superstructures and the cell surface in live Caulobacter crescentus,” Proc. Natl. Acad. Sci. U.S.A. 108(46), E1102–E1110 (2011).
[Crossref] [PubMed]

Ulrich, T. A.

Vaughan, J. C.

J. C. Vaughan, S. Jia, and X. W. Zhuang, “Ultrabright photoactivatable fluorophores created by reductive caging,” Nat. Methods 9(12), 1181–1184 (2012).
[Crossref] [PubMed]

von Middendorff, C.

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. Q.

B. Huang, W. Q. Wang, M. Bates, and X. W. Zhuang, “Three-dimensional super-resolution imaging by stochastic optical reconstruction microscopy,” Science 319(5864), 810–813 (2008).
[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]

Zeng, S. Q.

Zhang, R. B.

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]

Zheng, S.

X. M. Li, P. Mooney, S. Zheng, C. R. Booth, M. B. Braunfeld, S. Gubbens, D. A. Agard, and Y. F. Cheng, “Electron counting and beam-induced motion correction enable near-atomic-resolution single-particle cryo-EM,” Nat. Methods 10(6), 584–590 (2013).
[Crossref] [PubMed]

Zhuang, X. W.

J. C. Vaughan, S. Jia, and X. W. Zhuang, “Ultrabright photoactivatable fluorophores created by reductive caging,” Nat. Methods 9(12), 1181–1184 (2012).
[Crossref] [PubMed]

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

Appl. Opt. (1)

Biophys. J. (2)

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]

Nat. Cell Biol. (1)

V. Mennella, B. Keszthelyi, K. L. McDonald, B. Chhun, F. Kan, G. C. Rogers, B. Huang, and D. A. Agard, “Subdiffraction-resolution fluorescence microscopy reveals a domain of the centrosome critical for pericentriolar material organization,” Nat. Cell Biol. 14(11), 1159–1168 (2012).
[Crossref] [PubMed]

Nat. Methods (4)

X. M. Li, P. Mooney, S. Zheng, C. R. Booth, M. B. Braunfeld, S. Gubbens, D. A. Agard, and Y. F. Cheng, “Electron counting and beam-induced motion correction enable near-atomic-resolution single-particle cryo-EM,” Nat. Methods 10(6), 584–590 (2013).
[Crossref] [PubMed]

R. P. J. Nieuwenhuizen, K. A. Lidke, M. Bates, D. L. Puig, D. Grünwald, S. Stallinga, and B. Rieger, “Measuring image resolution in optical nanoscopy,” Nat. Methods 10(6), 557–562 (2013).
[Crossref] [PubMed]

J. C. Vaughan, S. Jia, and X. W. Zhuang, “Ultrabright photoactivatable fluorophores created by reductive caging,” Nat. Methods 9(12), 1181–1184 (2012).
[Crossref] [PubMed]

M. J. Rust, M. Bates, and X. W. Zhuang, “Sub-diffraction-limit imaging by stochastic optical reconstruction microscopy (STORM),” Nat. Methods 3(10), 793–796 (2006).
[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 Nanoscopy (1)

R. McGorty, D. Kamiyama, and B. Huang, “Active microscope stabilization in three dimensions using image correlation,” Opt Nanoscopy 2(1), 1–7 (2013).
[Crossref] [PubMed]

Opt. Express (4)

Proc. Natl. Acad. Sci. U.S.A. (1)

M. D. Lew, S. F. Lee, J. L. Ptacin, M. K. Lee, R. J. Twieg, L. Shapiro, and W. E. Moerner, “Three-dimensional superresolution colocalization of intracellular protein superstructures and the cell surface in live Caulobacter crescentus,” Proc. Natl. Acad. Sci. U.S.A. 108(46), E1102–E1110 (2011).
[Crossref] [PubMed]

Science (4)

A. Szymborska, A. de Marco, N. Daigle, V. C. Cordes, J. A. G. Briggs, and J. Ellenberg, “Nuclear Pore Scaffold Structure Analyzed by Super-Resolution Microscopy and Particle Averaging,” Science 341(6146), 655–658 (2013).
[Crossref] [PubMed]

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

B. Huang, W. Q. Wang, M. Bates, and X. W. Zhuang, “Three-dimensional super-resolution imaging by stochastic optical reconstruction microscopy,” Science 319(5864), 810–813 (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]

Other (1)

http://bigwww.epfl.ch/smlm/datasets/index.html .

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Figures (4)

Fig. 1
Fig. 1

The effect of correlation time-step size, f, on the cross-correlation map. (a) A super-resolution image of microtubules that contains severe sample drift. The image is spatially binned into a 2D histogram with a bin size of 30 nm. Scale bar: 1 μm. (b) One time segment with f = 1000 frames. (c) The cross-correlation function between the first and the last segments with f = 1000 frames. The white cross shows the auto-correlation peak of the first image. The arrow points out the direction and the amount of the drift between these two intervals. (d) The cross-correlation function between the first and the last segments with f = 100 frames. Note that the SNR in the map is greatly decreased.

Fig. 2
Fig. 2

The drift estimation precision of the direct, mean and redundant cross-correlation methods in analysing simulated super-resolution images. (a) Simulated perfect super-resolution image. Scale bar: 5 μm. (b) The influence of correlation time step size on drift measurement precision. The inset shows the amount of drift adding to the data sets. Each date point was averaged from five independent measurements. The error bars indicate standard deviations.

Fig. 3
Fig. 3

Drift correction performance of the direct, mean and redundant cross-correlation methods in analysing synthesized experimental images. (a) “Ground truth” Golgi super-resolution image. Scale bar: 1 μm. (b) The dependence of the drift measurement precision on correlation time step sizes. (c) The measured and real drift trajectory with the time step size, f = 1000 frames. (d) The dependence FRC resolution after drift correction on the correlation time step size. The black dashed line indicates the resolution of the “ground truth” image in (a).

Fig. 4
Fig. 4

The drift correction performance of the three methods in analysing experimental images containing microtubule (a-c) and Golgi (d-f) structures, showing the original, motion-blurred super-resolution images (a, d) and those corrected for sample drift by RCC (b, e). The independence of the FRC resolution (after drift correction) on the time step size is shown in (c) for the microtubule data set and (f) for the Golgi data set, respectively. The black dashed lines indicate the FRC resolution before drift correction. Scale bars: 1 μm (a,b) and 2 μm (d, e).

Equations (9)

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

D ij = r ij , where r ij maximizes C ij ( r )
D j = r 1j .
r ij = D ij + ε ij .
r ij = D j D i + ε ij .
D j = ( Σ i r ij ) /N.
r ij = D j D i .
r=AD
D= ( A T A ) 1 A T r.
Δr= | | ADr | |.

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