Abstract

Single molecule localization microscopy (SMLM) has been established to acquire images with unprecedented resolution down to several nanometers. A typical time scale for image acquisition is several minutes to hours. Yet it is difficult to avoid completely sample drift for long time measurements. To estimate drift, we present a method based on the evaluation of speckle patterns formed by backscattered laser light from the cells using a single molecule localization microscope setup. A z-stack of unique speckle patterns is recorded prior to the measurements as a three-dimensional position reference. During the experiment, images of scattered laser light were acquired, and correlated individually with each of the images of the speckle reference stack to estimate x, y and z drift. Our method shows highly comparable results with a fiducial marker approach, achieving a precision of several nanometers. This method allows for high precision three dimensional drift correction of microscope systems without any additional sample preparation.

© 2019 Optical Society of America under the terms of the OSA Open Access Publishing Agreement

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References

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2019 (1)

A. Balinovic, D. Albrecht, and U. Endesfelder, “Spectrally red-shifted fluorescent fiducial markers for optimal drift correction in localization microscopy,” J. Phys. D: Appl. Phys. 52(20), 204002 (2019).
[Crossref]

2018 (3)

2017 (2)

A. Szczurek, L. Klewes, J. Xing, A. Gourram, U. Birk, H. Knecht, J. W. Dobrucki, S. Mai, and C. Cremer, “Imaging chromatin nanostructure with binding-activated localization microscopy based on DNA structure fluctuations,” Nucleic Acids Res. 45(8), e56 (2017).
[Crossref]

H. Ma, J. Xu, J. Jin, Y. Huang, and Y. Liu, “A simple marker-assisted 3D nanometer drift correction method for superresolution microscopy,” Biophys. J. 112(10), 2196–2208 (2017).
[Crossref]

2015 (2)

R. Han, L. Wang, F. Xu, Y. Zhang, M. Zhang, Z. Liu, F. Ren, and F. Zhang, “Drift correction for single-molecule imaging by molecular constraint field, a distance minimum metric,” BMC Biophys. 8(1), 1–14 (2015).
[Crossref]

T. Cremer, M. Cremer, B. Hübner, H. Strickfaden, D. Smeets, J. Popken, M. Sterr, Y. Markaki, K. Rippe, and C. Cremer, “The 4D nucleome: Evidence for a dynamic nuclear landscape based on co-aligned active and inactive nuclear compartments,” FEBS Lett. 589(20 PartA), 2931–2943 (2015).
[Crossref]

2014 (2)

M. Ovesný, P. Křížek, J. Borkovec, Z. Švindrych, and G. M. Hagen, “ThunderSTORM: a comprehensive ImageJ plug-in for PALM and STORM data analysis and super-resolution imaging,” Bioinformatics 30(16), 2389–2390 (2014).
[Crossref]

Y. Wang, J. Schnitzbauer, Z. Hu, X. Li, Y. Cheng, Z.-L. Huang, and B. Huang, “Localization events-based sample drift correction for localization microscopy with redundant cross-correlation algorithm,” Opt. Express 22(13), 15982–15991 (2014).
[Crossref]

2013 (2)

C. Cremer and B. R. Masters, “Resolution enhancement techniques in microscopy,” Eur. Phys. J. H 38(3), 281–344 (2013).
[Crossref]

R. McGorty, D. Kamiyama, and B. Huang, “Active microscope stabilization in three dimensions using image correlation,” Opt. Nanoscopy 2(1), 3–7 (2013).
[Crossref]

2012 (1)

2011 (2)

2009 (1)

M. Draijer, E. Hondebrink, T. van Leeuwen, and W. Steenbergen, “Review of laser speckle contrast techniques for visualizing tissue perfusion,” Lasers Med. Sci. 24(4), 639–651 (2009).
[Crossref]

2008 (3)

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]

M. Guizar-Sicairos, S. T. Thurman, and J. R. Fienup, “Efficient subpixel image registration algorithms,” Opt. Lett. 33(2), 156–158 (2008).
[Crossref]

P. Lemmer, M. Gunkel, D. Baddeley, R. Kaufmann, A. Urich, Y. Weiland, J. Reymann, P. Müller, M. Hausmann, and C. Cremer, “SPDM: light microscopy with single-molecule resolution at the nanoscale,” Appl. Phys. B: Lasers Opt. 93(1), 1–12 (2008).
[Crossref]

2006 (2)

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]

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]

2001 (1)

T. Cremer and C. Cremer, “Chromosome territories, nuclear architecture and gene regulation in mammalian cells,” Nat. Rev. Genet. 2(4), 292–301 (2001).
[Crossref]

1994 (1)

H. P. Kao and A. S. Verkman, “Tracking of single fluorescent particles in three dimensions: use of cylindrical optics to encode particle position,” Biophys. J. 67(3), 1291–1300 (1994).
[Crossref]

1976 (1)

Albrecht, D.

A. Balinovic, D. Albrecht, and U. Endesfelder, “Spectrally red-shifted fluorescent fiducial markers for optimal drift correction in localization microscopy,” J. Phys. D: Appl. Phys. 52(20), 204002 (2019).
[Crossref]

Baday, M.

Baddeley, D.

P. Lemmer, M. Gunkel, D. Baddeley, R. Kaufmann, A. Urich, Y. Weiland, J. Reymann, P. Müller, M. Hausmann, and C. Cremer, “SPDM: light microscopy with single-molecule resolution at the nanoscale,” Appl. Phys. B: Lasers Opt. 93(1), 1–12 (2008).
[Crossref]

Balinovic, A.

A. Balinovic, D. Albrecht, and U. Endesfelder, “Spectrally red-shifted fluorescent fiducial markers for optimal drift correction in localization microscopy,” J. Phys. D: Appl. Phys. 52(20), 204002 (2019).
[Crossref]

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]

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]

Bestvater, F.

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]

Bewersdorf, J.

Birk, U.

A. Szczurek, U. Birk, H. Knecht, J. Dobrucki, S. Mai, and C. Cremer, “Super-resolution binding activated localization microscopy through reversible change of DNA conformation,” Nucleus 9(1), 182–189 (2018).
[Crossref]

A. Szczurek, L. Klewes, J. Xing, A. Gourram, U. Birk, H. Knecht, J. W. Dobrucki, S. Mai, and C. Cremer, “Imaging chromatin nanostructure with binding-activated localization microscopy based on DNA structure fluctuations,” Nucleic Acids Res. 45(8), e56 (2017).
[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]

Borkovec, J.

M. Ovesný, P. Křížek, J. Borkovec, Z. Švindrych, and G. M. Hagen, “ThunderSTORM: a comprehensive ImageJ plug-in for PALM and STORM data analysis and super-resolution imaging,” Bioinformatics 30(16), 2389–2390 (2014).
[Crossref]

Cai, E.

Callahan, S. P.

Chen, S.-Y.

Cheng, Y.

Cremer, C.

S.-Y. Chen, F. Bestvater, W. Schaufler, R. Heintzmann, and C. Cremer, “Patterned illumination single molecule localization microscopy (piSMLM): user defined blinking regions of interest,” Opt. Express 26(23), 30009–30020 (2018).
[Crossref]

A. Szczurek, U. Birk, H. Knecht, J. Dobrucki, S. Mai, and C. Cremer, “Super-resolution binding activated localization microscopy through reversible change of DNA conformation,” Nucleus 9(1), 182–189 (2018).
[Crossref]

A. Szczurek, L. Klewes, J. Xing, A. Gourram, U. Birk, H. Knecht, J. W. Dobrucki, S. Mai, and C. Cremer, “Imaging chromatin nanostructure with binding-activated localization microscopy based on DNA structure fluctuations,” Nucleic Acids Res. 45(8), e56 (2017).
[Crossref]

T. Cremer, M. Cremer, B. Hübner, H. Strickfaden, D. Smeets, J. Popken, M. Sterr, Y. Markaki, K. Rippe, and C. Cremer, “The 4D nucleome: Evidence for a dynamic nuclear landscape based on co-aligned active and inactive nuclear compartments,” FEBS Lett. 589(20 PartA), 2931–2943 (2015).
[Crossref]

C. Cremer and B. R. Masters, “Resolution enhancement techniques in microscopy,” Eur. Phys. J. H 38(3), 281–344 (2013).
[Crossref]

P. Lemmer, M. Gunkel, D. Baddeley, R. Kaufmann, A. Urich, Y. Weiland, J. Reymann, P. Müller, M. Hausmann, and C. Cremer, “SPDM: light microscopy with single-molecule resolution at the nanoscale,” Appl. Phys. B: Lasers Opt. 93(1), 1–12 (2008).
[Crossref]

T. Cremer and C. Cremer, “Chromosome territories, nuclear architecture and gene regulation in mammalian cells,” Nat. Rev. Genet. 2(4), 292–301 (2001).
[Crossref]

Cremer, M.

T. Cremer, M. Cremer, B. Hübner, H. Strickfaden, D. Smeets, J. Popken, M. Sterr, Y. Markaki, K. Rippe, and C. Cremer, “The 4D nucleome: Evidence for a dynamic nuclear landscape based on co-aligned active and inactive nuclear compartments,” FEBS Lett. 589(20 PartA), 2931–2943 (2015).
[Crossref]

Cremer, T.

T. Cremer, M. Cremer, B. Hübner, H. Strickfaden, D. Smeets, J. Popken, M. Sterr, Y. Markaki, K. Rippe, and C. Cremer, “The 4D nucleome: Evidence for a dynamic nuclear landscape based on co-aligned active and inactive nuclear compartments,” FEBS Lett. 589(20 PartA), 2931–2943 (2015).
[Crossref]

T. Cremer and C. Cremer, “Chromosome territories, nuclear architecture and gene regulation in mammalian cells,” Nat. Rev. Genet. 2(4), 292–301 (2001).
[Crossref]

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]

Dlasková, A.

Dobrucki, J.

A. Szczurek, U. Birk, H. Knecht, J. Dobrucki, S. Mai, and C. Cremer, “Super-resolution binding activated localization microscopy through reversible change of DNA conformation,” Nucleus 9(1), 182–189 (2018).
[Crossref]

Dobrucki, J. W.

A. Szczurek, L. Klewes, J. Xing, A. Gourram, U. Birk, H. Knecht, J. W. Dobrucki, S. Mai, and C. Cremer, “Imaging chromatin nanostructure with binding-activated localization microscopy based on DNA structure fluctuations,” Nucleic Acids Res. 45(8), e56 (2017).
[Crossref]

Draijer, M.

M. Draijer, E. Hondebrink, T. van Leeuwen, and W. Steenbergen, “Review of laser speckle contrast techniques for visualizing tissue perfusion,” Lasers Med. Sci. 24(4), 639–651 (2009).
[Crossref]

Endesfelder, U.

A. Balinovic, D. Albrecht, and U. Endesfelder, “Spectrally red-shifted fluorescent fiducial markers for optimal drift correction in localization microscopy,” J. Phys. D: Appl. Phys. 52(20), 204002 (2019).
[Crossref]

Fienup, J. R.

Goodmann, J. W.

Gourram, A.

A. Szczurek, L. Klewes, J. Xing, A. Gourram, U. Birk, H. Knecht, J. W. Dobrucki, S. Mai, and C. Cremer, “Imaging chromatin nanostructure with binding-activated localization microscopy based on DNA structure fluctuations,” Nucleic Acids Res. 45(8), e56 (2017).
[Crossref]

Guizar-Sicairos, M.

Gunkel, M.

P. Lemmer, M. Gunkel, D. Baddeley, R. Kaufmann, A. Urich, Y. Weiland, J. Reymann, P. Müller, M. Hausmann, and C. Cremer, “SPDM: light microscopy with single-molecule resolution at the nanoscale,” Appl. Phys. B: Lasers Opt. 93(1), 1–12 (2008).
[Crossref]

Hagen, G. M.

M. Ovesný, P. Křížek, J. Borkovec, Z. Švindrych, and G. M. Hagen, “ThunderSTORM: a comprehensive ImageJ plug-in for PALM and STORM data analysis and super-resolution imaging,” Bioinformatics 30(16), 2389–2390 (2014).
[Crossref]

Han, R.

R. Han, L. Wang, F. Xu, Y. Zhang, M. Zhang, Z. Liu, F. Ren, and F. Zhang, “Drift correction for single-molecule imaging by molecular constraint field, a distance minimum metric,” BMC Biophys. 8(1), 1–14 (2015).
[Crossref]

Hausmann, M.

P. Lemmer, M. Gunkel, D. Baddeley, R. Kaufmann, A. Urich, Y. Weiland, J. Reymann, P. Müller, M. Hausmann, and C. Cremer, “SPDM: light microscopy with single-molecule resolution at the nanoscale,” Appl. Phys. B: Lasers Opt. 93(1), 1–12 (2008).
[Crossref]

He, J.

S. A. Jones, S. H. Shim, J. He, and X. Zhuang, “Fast, three-dimensional super-resolution imaging of live cells,” Nat. Methods 8(6), 499–505 (2011).
[Crossref]

Heintzmann, R.

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]

Hondebrink, E.

M. Draijer, E. Hondebrink, T. van Leeuwen, and W. Steenbergen, “Review of laser speckle contrast techniques for visualizing tissue perfusion,” Lasers Med. Sci. 24(4), 639–651 (2009).
[Crossref]

Hu, Z.

Huang, B.

Y. Wang, J. Schnitzbauer, Z. Hu, X. Li, Y. Cheng, Z.-L. Huang, and B. Huang, “Localization events-based sample drift correction for localization microscopy with redundant cross-correlation algorithm,” Opt. Express 22(13), 15982–15991 (2014).
[Crossref]

R. McGorty, D. Kamiyama, and B. Huang, “Active microscope stabilization in three dimensions using image correlation,” Opt. Nanoscopy 2(1), 3–7 (2013).
[Crossref]

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]

Huang, Y.

H. Ma, J. Xu, J. Jin, Y. Huang, and Y. Liu, “A simple marker-assisted 3D nanometer drift correction method for superresolution microscopy,” Biophys. J. 112(10), 2196–2208 (2017).
[Crossref]

Huang, Z.-L.

Hübner, B.

T. Cremer, M. Cremer, B. Hübner, H. Strickfaden, D. Smeets, J. Popken, M. Sterr, Y. Markaki, K. Rippe, and C. Cremer, “The 4D nucleome: Evidence for a dynamic nuclear landscape based on co-aligned active and inactive nuclear compartments,” FEBS Lett. 589(20 PartA), 2931–2943 (2015).
[Crossref]

Ishitsuka, Y.

Ježek, P.

Jin, C.

Jin, J.

H. Ma, J. Xu, J. Jin, Y. Huang, and Y. Liu, “A simple marker-assisted 3D nanometer drift correction method for superresolution microscopy,” Biophys. J. 112(10), 2196–2208 (2017).
[Crossref]

Jones, S. A.

S. A. Jones, S. H. Shim, J. He, and X. Zhuang, “Fast, three-dimensional super-resolution imaging of live cells,” Nat. Methods 8(6), 499–505 (2011).
[Crossref]

Kamiyama, D.

R. McGorty, D. Kamiyama, and B. Huang, “Active microscope stabilization in three dimensions using image correlation,” Opt. Nanoscopy 2(1), 3–7 (2013).
[Crossref]

Kao, H. P.

H. P. Kao and A. S. Verkman, “Tracking of single fluorescent particles in three dimensions: use of cylindrical optics to encode particle position,” Biophys. J. 67(3), 1291–1300 (1994).
[Crossref]

Kaufmann, R.

P. Lemmer, M. Gunkel, D. Baddeley, R. Kaufmann, A. Urich, Y. Weiland, J. Reymann, P. Müller, M. Hausmann, and C. Cremer, “SPDM: light microscopy with single-molecule resolution at the nanoscale,” Appl. Phys. B: Lasers Opt. 93(1), 1–12 (2008).
[Crossref]

Klewes, L.

A. Szczurek, L. Klewes, J. Xing, A. Gourram, U. Birk, H. Knecht, J. W. Dobrucki, S. Mai, and C. Cremer, “Imaging chromatin nanostructure with binding-activated localization microscopy based on DNA structure fluctuations,” Nucleic Acids Res. 45(8), e56 (2017).
[Crossref]

Knecht, H.

A. Szczurek, U. Birk, H. Knecht, J. Dobrucki, S. Mai, and C. Cremer, “Super-resolution binding activated localization microscopy through reversible change of DNA conformation,” Nucleus 9(1), 182–189 (2018).
[Crossref]

A. Szczurek, L. Klewes, J. Xing, A. Gourram, U. Birk, H. Knecht, J. W. Dobrucki, S. Mai, and C. Cremer, “Imaging chromatin nanostructure with binding-activated localization microscopy based on DNA structure fluctuations,” Nucleic Acids Res. 45(8), e56 (2017).
[Crossref]

Krížek, P.

M. Ovesný, P. Křížek, J. Borkovec, Z. Švindrych, and G. M. Hagen, “ThunderSTORM: a comprehensive ImageJ plug-in for PALM and STORM data analysis and super-resolution imaging,” Bioinformatics 30(16), 2389–2390 (2014).
[Crossref]

Lee, S. H.

Lemmer, P.

P. Lemmer, M. Gunkel, D. Baddeley, R. Kaufmann, A. Urich, Y. Weiland, J. Reymann, P. Müller, M. Hausmann, and C. Cremer, “SPDM: light microscopy with single-molecule resolution at the nanoscale,” Appl. Phys. B: Lasers Opt. 93(1), 1–12 (2008).
[Crossref]

Li, X.

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]

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]

Liu, Y.

H. Ma, J. Xu, J. Jin, Y. Huang, and Y. Liu, “A simple marker-assisted 3D nanometer drift correction method for superresolution microscopy,” Biophys. J. 112(10), 2196–2208 (2017).
[Crossref]

Liu, Z.

R. Han, L. Wang, F. Xu, Y. Zhang, M. Zhang, Z. Liu, F. Ren, and F. Zhang, “Drift correction for single-molecule imaging by molecular constraint field, a distance minimum metric,” BMC Biophys. 8(1), 1–14 (2015).
[Crossref]

Ma, H.

H. Ma, J. Xu, J. Jin, Y. Huang, and Y. Liu, “A simple marker-assisted 3D nanometer drift correction method for superresolution microscopy,” Biophys. J. 112(10), 2196–2208 (2017).
[Crossref]

Mai, S.

A. Szczurek, U. Birk, H. Knecht, J. Dobrucki, S. Mai, and C. Cremer, “Super-resolution binding activated localization microscopy through reversible change of DNA conformation,” Nucleus 9(1), 182–189 (2018).
[Crossref]

A. Szczurek, L. Klewes, J. Xing, A. Gourram, U. Birk, H. Knecht, J. W. Dobrucki, S. Mai, and C. Cremer, “Imaging chromatin nanostructure with binding-activated localization microscopy based on DNA structure fluctuations,” Nucleic Acids Res. 45(8), e56 (2017).
[Crossref]

Markaki, Y.

T. Cremer, M. Cremer, B. Hübner, H. Strickfaden, D. Smeets, J. Popken, M. Sterr, Y. Markaki, K. Rippe, and C. Cremer, “The 4D nucleome: Evidence for a dynamic nuclear landscape based on co-aligned active and inactive nuclear compartments,” FEBS Lett. 589(20 PartA), 2931–2943 (2015).
[Crossref]

Masters, B. R.

C. Cremer and B. R. Masters, “Resolution enhancement techniques in microscopy,” Eur. Phys. J. H 38(3), 281–344 (2013).
[Crossref]

McGorty, R.

R. McGorty, D. Kamiyama, and B. Huang, “Active microscope stabilization in three dimensions using image correlation,” Opt. Nanoscopy 2(1), 3–7 (2013).
[Crossref]

Mlodzianoski, M. J.

Müller, P.

P. Lemmer, M. Gunkel, D. Baddeley, R. Kaufmann, A. Urich, Y. Weiland, J. Reymann, P. Müller, M. Hausmann, and C. Cremer, “SPDM: light microscopy with single-molecule resolution at the nanoscale,” Appl. Phys. B: Lasers Opt. 93(1), 1–12 (2008).
[Crossref]

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]

Ovesný, M.

M. Ovesný, P. Křížek, J. Borkovec, Z. Švindrych, and G. M. Hagen, “ThunderSTORM: a comprehensive ImageJ plug-in for PALM and STORM data analysis and super-resolution imaging,” Bioinformatics 30(16), 2389–2390 (2014).
[Crossref]

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]

Pawley, J. B.

J. B. Pawley, Handbook of Biological Confocal Microscopy (Springer, 2006), Chap. 9.

Popken, J.

T. Cremer, M. Cremer, B. Hübner, H. Strickfaden, D. Smeets, J. Popken, M. Sterr, Y. Markaki, K. Rippe, and C. Cremer, “The 4D nucleome: Evidence for a dynamic nuclear landscape based on co-aligned active and inactive nuclear compartments,” FEBS Lett. 589(20 PartA), 2931–2943 (2015).
[Crossref]

Ren, F.

R. Han, L. Wang, F. Xu, Y. Zhang, M. Zhang, Z. Liu, F. Ren, and F. Zhang, “Drift correction for single-molecule imaging by molecular constraint field, a distance minimum metric,” BMC Biophys. 8(1), 1–14 (2015).
[Crossref]

Reymann, J.

P. Lemmer, M. Gunkel, D. Baddeley, R. Kaufmann, A. Urich, Y. Weiland, J. Reymann, P. Müller, M. Hausmann, and C. Cremer, “SPDM: light microscopy with single-molecule resolution at the nanoscale,” Appl. Phys. B: Lasers Opt. 93(1), 1–12 (2008).
[Crossref]

Rippe, K.

T. Cremer, M. Cremer, B. Hübner, H. Strickfaden, D. Smeets, J. Popken, M. Sterr, Y. Markaki, K. Rippe, and C. Cremer, “The 4D nucleome: Evidence for a dynamic nuclear landscape based on co-aligned active and inactive nuclear compartments,” FEBS Lett. 589(20 PartA), 2931–2943 (2015).
[Crossref]

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]

Šantorová, J.

Schaufler, W.

Schnitzbauer, J.

Schreiner, J. M.

Selvin, P. R.

Shim, S. H.

S. A. Jones, S. H. Shim, J. He, and X. Zhuang, “Fast, three-dimensional super-resolution imaging of live cells,” Nat. Methods 8(6), 499–505 (2011).
[Crossref]

Simonson, P. D.

Smeets, D.

T. Cremer, M. Cremer, B. Hübner, H. Strickfaden, D. Smeets, J. Popken, M. Sterr, Y. Markaki, K. Rippe, and C. Cremer, “The 4D nucleome: Evidence for a dynamic nuclear landscape based on co-aligned active and inactive nuclear compartments,” FEBS Lett. 589(20 PartA), 2931–2943 (2015).
[Crossref]

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]

Steenbergen, W.

M. Draijer, E. Hondebrink, T. van Leeuwen, and W. Steenbergen, “Review of laser speckle contrast techniques for visualizing tissue perfusion,” Lasers Med. Sci. 24(4), 639–651 (2009).
[Crossref]

Sterr, M.

T. Cremer, M. Cremer, B. Hübner, H. Strickfaden, D. Smeets, J. Popken, M. Sterr, Y. Markaki, K. Rippe, and C. Cremer, “The 4D nucleome: Evidence for a dynamic nuclear landscape based on co-aligned active and inactive nuclear compartments,” FEBS Lett. 589(20 PartA), 2931–2943 (2015).
[Crossref]

Strickfaden, H.

T. Cremer, M. Cremer, B. Hübner, H. Strickfaden, D. Smeets, J. Popken, M. Sterr, Y. Markaki, K. Rippe, and C. Cremer, “The 4D nucleome: Evidence for a dynamic nuclear landscape based on co-aligned active and inactive nuclear compartments,” FEBS Lett. 589(20 PartA), 2931–2943 (2015).
[Crossref]

Švindrych, Z.

M. Ovesný, P. Křížek, J. Borkovec, Z. Švindrych, and G. M. Hagen, “ThunderSTORM: a comprehensive ImageJ plug-in for PALM and STORM data analysis and super-resolution imaging,” Bioinformatics 30(16), 2389–2390 (2014).
[Crossref]

Szczurek, A.

A. Szczurek, U. Birk, H. Knecht, J. Dobrucki, S. Mai, and C. Cremer, “Super-resolution binding activated localization microscopy through reversible change of DNA conformation,” Nucleus 9(1), 182–189 (2018).
[Crossref]

A. Szczurek, L. Klewes, J. Xing, A. Gourram, U. Birk, H. Knecht, J. W. Dobrucki, S. Mai, and C. Cremer, “Imaging chromatin nanostructure with binding-activated localization microscopy based on DNA structure fluctuations,” Nucleic Acids Res. 45(8), e56 (2017).
[Crossref]

Thurman, S. T.

Tjioe, M.

Urich, A.

P. Lemmer, M. Gunkel, D. Baddeley, R. Kaufmann, A. Urich, Y. Weiland, J. Reymann, P. Müller, M. Hausmann, and C. Cremer, “SPDM: light microscopy with single-molecule resolution at the nanoscale,” Appl. Phys. B: Lasers Opt. 93(1), 1–12 (2008).
[Crossref]

van Leeuwen, T.

M. Draijer, E. Hondebrink, T. van Leeuwen, and W. Steenbergen, “Review of laser speckle contrast techniques for visualizing tissue perfusion,” Lasers Med. Sci. 24(4), 639–651 (2009).
[Crossref]

Verkman, A. S.

H. P. Kao and A. S. Verkman, “Tracking of single fluorescent particles in three dimensions: use of cylindrical optics to encode particle position,” Biophys. J. 67(3), 1291–1300 (1994).
[Crossref]

Wang, L.

R. Han, L. Wang, F. Xu, Y. Zhang, M. Zhang, Z. Liu, F. Ren, and F. Zhang, “Drift correction for single-molecule imaging by molecular constraint field, a distance minimum metric,” BMC Biophys. 8(1), 1–14 (2015).
[Crossref]

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]

Wang, Y.

Weiland, Y.

P. Lemmer, M. Gunkel, D. Baddeley, R. Kaufmann, A. Urich, Y. Weiland, J. Reymann, P. Müller, M. Hausmann, and C. Cremer, “SPDM: light microscopy with single-molecule resolution at the nanoscale,” Appl. Phys. B: Lasers Opt. 93(1), 1–12 (2008).
[Crossref]

Xing, J.

A. Szczurek, L. Klewes, J. Xing, A. Gourram, U. Birk, H. Knecht, J. W. Dobrucki, S. Mai, and C. Cremer, “Imaging chromatin nanostructure with binding-activated localization microscopy based on DNA structure fluctuations,” Nucleic Acids Res. 45(8), e56 (2017).
[Crossref]

Xu, F.

R. Han, L. Wang, F. Xu, Y. Zhang, M. Zhang, Z. Liu, F. Ren, and F. Zhang, “Drift correction for single-molecule imaging by molecular constraint field, a distance minimum metric,” BMC Biophys. 8(1), 1–14 (2015).
[Crossref]

Xu, J.

H. Ma, J. Xu, J. Jin, Y. Huang, and Y. Liu, “A simple marker-assisted 3D nanometer drift correction method for superresolution microscopy,” Biophys. J. 112(10), 2196–2208 (2017).
[Crossref]

Youn, Y.

Zhang, F.

R. Han, L. Wang, F. Xu, Y. Zhang, M. Zhang, Z. Liu, F. Ren, and F. Zhang, “Drift correction for single-molecule imaging by molecular constraint field, a distance minimum metric,” BMC Biophys. 8(1), 1–14 (2015).
[Crossref]

Zhang, M.

R. Han, L. Wang, F. Xu, Y. Zhang, M. Zhang, Z. Liu, F. Ren, and F. Zhang, “Drift correction for single-molecule imaging by molecular constraint field, a distance minimum metric,” BMC Biophys. 8(1), 1–14 (2015).
[Crossref]

Zhang, R.

Zhang, Y.

R. Han, L. Wang, F. Xu, Y. Zhang, M. Zhang, Z. Liu, F. Ren, and F. Zhang, “Drift correction for single-molecule imaging by molecular constraint field, a distance minimum metric,” BMC Biophys. 8(1), 1–14 (2015).
[Crossref]

Zhuang, X.

S. A. Jones, S. H. Shim, J. He, and X. Zhuang, “Fast, three-dimensional super-resolution imaging of live cells,” Nat. Methods 8(6), 499–505 (2011).
[Crossref]

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]

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]

Appl. Phys. B: Lasers Opt. (1)

P. Lemmer, M. Gunkel, D. Baddeley, R. Kaufmann, A. Urich, Y. Weiland, J. Reymann, P. Müller, M. Hausmann, and C. Cremer, “SPDM: light microscopy with single-molecule resolution at the nanoscale,” Appl. Phys. B: Lasers Opt. 93(1), 1–12 (2008).
[Crossref]

Bioinformatics (1)

M. Ovesný, P. Křížek, J. Borkovec, Z. Švindrych, and G. M. Hagen, “ThunderSTORM: a comprehensive ImageJ plug-in for PALM and STORM data analysis and super-resolution imaging,” Bioinformatics 30(16), 2389–2390 (2014).
[Crossref]

Biophys. J. (2)

H. P. Kao and A. S. Verkman, “Tracking of single fluorescent particles in three dimensions: use of cylindrical optics to encode particle position,” Biophys. J. 67(3), 1291–1300 (1994).
[Crossref]

H. Ma, J. Xu, J. Jin, Y. Huang, and Y. Liu, “A simple marker-assisted 3D nanometer drift correction method for superresolution microscopy,” Biophys. J. 112(10), 2196–2208 (2017).
[Crossref]

BMC Biophys. (1)

R. Han, L. Wang, F. Xu, Y. Zhang, M. Zhang, Z. Liu, F. Ren, and F. Zhang, “Drift correction for single-molecule imaging by molecular constraint field, a distance minimum metric,” BMC Biophys. 8(1), 1–14 (2015).
[Crossref]

Eur. Phys. J. H (1)

C. Cremer and B. R. Masters, “Resolution enhancement techniques in microscopy,” Eur. Phys. J. H 38(3), 281–344 (2013).
[Crossref]

FEBS Lett. (1)

T. Cremer, M. Cremer, B. Hübner, H. Strickfaden, D. Smeets, J. Popken, M. Sterr, Y. Markaki, K. Rippe, and C. Cremer, “The 4D nucleome: Evidence for a dynamic nuclear landscape based on co-aligned active and inactive nuclear compartments,” FEBS Lett. 589(20 PartA), 2931–2943 (2015).
[Crossref]

J. Opt. Soc. Am. (1)

J. Phys. D: Appl. Phys. (1)

A. Balinovic, D. Albrecht, and U. Endesfelder, “Spectrally red-shifted fluorescent fiducial markers for optimal drift correction in localization microscopy,” J. Phys. D: Appl. Phys. 52(20), 204002 (2019).
[Crossref]

Lasers Med. Sci. (1)

M. Draijer, E. Hondebrink, T. van Leeuwen, and W. Steenbergen, “Review of laser speckle contrast techniques for visualizing tissue perfusion,” Lasers Med. Sci. 24(4), 639–651 (2009).
[Crossref]

Nat. Methods (2)

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]

S. A. Jones, S. H. Shim, J. He, and X. Zhuang, “Fast, three-dimensional super-resolution imaging of live cells,” Nat. Methods 8(6), 499–505 (2011).
[Crossref]

Nat. Rev. Genet. (1)

T. Cremer and C. Cremer, “Chromosome territories, nuclear architecture and gene regulation in mammalian cells,” Nat. Rev. Genet. 2(4), 292–301 (2001).
[Crossref]

Nucleic Acids Res. (1)

A. Szczurek, L. Klewes, J. Xing, A. Gourram, U. Birk, H. Knecht, J. W. Dobrucki, S. Mai, and C. Cremer, “Imaging chromatin nanostructure with binding-activated localization microscopy based on DNA structure fluctuations,” Nucleic Acids Res. 45(8), e56 (2017).
[Crossref]

Nucleus (1)

A. Szczurek, U. Birk, H. Knecht, J. Dobrucki, S. Mai, and C. Cremer, “Super-resolution binding activated localization microscopy through reversible change of DNA conformation,” Nucleus 9(1), 182–189 (2018).
[Crossref]

Opt. Express (5)

Opt. Lett. (1)

Opt. Nanoscopy (1)

R. McGorty, D. Kamiyama, and B. Huang, “Active microscope stabilization in three dimensions using image correlation,” Opt. Nanoscopy 2(1), 3–7 (2013).
[Crossref]

Science (2)

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]

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]

Other (1)

J. B. Pawley, Handbook of Biological Confocal Microscopy (Springer, 2006), Chap. 9.

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Figures (11)

Fig. 1.
Fig. 1. Demonstration of imaging speckle patterns using a standard SMLM setup. (Obj: objective lens, DM: dichroic mirror, EF: emission filter for fluorescent beads measurement and for 3D SMLM, M: mirror, TL: tube lens, CL: cylindrical lens, L: lens)
Fig. 2.
Fig. 2. Speckle pattern of a cell sample. The insets show the ROI at four axial positions (z = - 2 µm, −1 µm, 0 µm and 1 µm). A speckle feature is highlighted by a red circle.
Fig. 3.
Fig. 3. Scheme for drift estimation. A z-stack of speckle patterns f as a position reference of the cell is acquired. Single drift estimation frames g are captured at regular time intervals during the experiment. By finding the maximum correlation in the speckle reference stack f with g, the drift in x, y and z is estimated.
Fig. 4.
Fig. 4. Flow chart of 3D SMLM experiment with speckle- and beads-based drift estimation methods. The dashed boxes are optional and are only used for comparison measurements.
Fig. 5.
Fig. 5. Correlation (normalized to a maximum of one) between the drift estimation frame gexp1(z = 0) and each image of the speckle reference z-stack f obtained from measured data.
Fig. 6.
Fig. 6. Speckle based z-position estimation by a defined z-position with a range of 7 µm and a 250 nm step size. (a) Measured z-position. (b) Residuals of the linear regression.
Fig. 7.
Fig. 7. The repeatability of the speckle-based drift estimation method for 10 seconds in (a) optical axis (z) and (b) lateral axes (x,y).
Fig. 8.
Fig. 8. An experimental result of the sample drift measurement. A pair of image with (a) a speckle pattern and (b) fluorescent beads.
Fig. 9.
Fig. 9. Time dependent measurement for comparing the drift estimation between fluorescent beads and our speckle-based method. The sample was illuminated by the laser with a wavelength of 488 nm. (a,c) Axial and lateral drift measurements. The shaded areas are given by the averaged standard deviation of all bead localizations. (b,d) Difference between beads- and speckle-based drift estimation in axial and in lateral direction. The dashed lines indicate the standard deviation.
Fig. 10.
Fig. 10. Time dependent measurement for comparing the drift estimation between fluorescent beads and our speckle-based method in a 3D SMLM experiment. For the speckle-based method, the laser with a wavelength of 488 nm was used to illuminate the sample; and the laser with a wavelength of 647 nm was used to excite the fluorescence beads. (a) Axial and (b) lateral drift measurements for x and y separately. The shaded areas are given by the averaged standard deviation of all bead localizations.
Fig. 11.
Fig. 11. The intensity sum projection of the drift corrected 3D SMLM image of a nucleus labeled with the DNA dye SytoxOrange [23], excited by the laser with a wavelength of 561 nm. Inset: color-coded maximum intensity projection before and after correction. The color scale indicates the z position.

Equations (5)

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

d = 2.44 λ f # M
C C x y = DFT x y 1 ( DF T x y ( f ( z ) ) DFT x y ( g ) ) ,
D ( z ) = argma x x y | C C x y | .
D F T E R R O R = 1 m a x x y | C C x y | 2 | D F T x y ( f ( z ) ) | 2 | D F T x y ( g ) | 2 .
R D F T ( z ) = 1 D F T E R R O R ( f ( z ) , g ) .