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Efficient homogeneous illumination and optical sectioning for quantitative single-molecule localization microscopy

Joran Deschamps, Andreas Rowald, and Jonas Ries

Open Access Open Access

Abstract

Single-molecule localization microscopy (SMLM) relies on the switching of fluorescent molecules between a fluorescent and a dark state to achieve super resolution. This process is inherently dependent on the intensity distribution of the laser light used for both activation from the dark state and excitation of the bright state. Typically, laser light is coupled directly or via a single-mode fiber into the microscope, which leads to a Gaussian intensity profile in total internal reflection (TIR) or epi illumination. As a result, switching dynamics and brightness of the fluorescent molecules vary strongly across the field of view, impacting their localization precision and impeding quantitative analysis. Here we present a simple illumination scheme based on the use of a multimode fiber and a laser speckle-reducer, which results in a flat, homogeneous and speckle-free illumination across the entire field of view. In addition, we combined homogeneous multimode excitation of the sample with single-mode based TIR activation to simultaneously obtain the advantages of both approaches: uniform brightness of single fluorophores and TIR-like optical sectioning.

© 2016 Optical Society of America

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  6. E. M. Puchner, J. M. Walter, R. Kasper, B. Huang, and W. A. Lim, “Counting molecules in single organelles with superresolution microscopy allows tracking of the endosome maturation trajectory,” Proc. Natl. Acad. Sci. U.S.A. 110(40), 16015–16020 (2013).
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2016 (5)

R. Jungmann, M. S. Avendaño, M. Dai, J. B. Woehrstein, S. S. Agasti, Z. Feiger, A. Rodal, and P. Yin, “Quantitative super-resolution imaging with qPAINT,” Nat. Methods 13(5), 439–442 (2016).
[Crossref] [PubMed]

F. Baumgart, A. M. Arnold, K. Leskovar, K. Staszek, M. Fölser, J. Weghuber, H. Stockinger, and G. J. Schütz, “Varying label density allows artifact-free analysis of membrane-protein nanoclusters,” Nat. Methods 13(8), 661–664 (2016).
[Crossref] [PubMed]

K. M. Douglass, C. Sieben, A. Archetti, A. Lambert, and S. Manley, “Super-resolution imaging of multiple cells by optimised flat-field epi-illumination,” Nat. Photonics 10(11), 705–708 (2016).
[Crossref] [PubMed]

P. Georgiades, V. J. Allan, M. Dickinson, and T. A. Waigh, “Reduction of coherent artefacts in super-resolution fluorescence localisation microscopy,” J. Microsc. 00, 1–9 (2016).
[PubMed]

K. Kwakwa, A. Savell, T. Davies, I. Munro, S. Parrinello, M. A. Purbhoo, C. Dunsby, M. A. A. Neil, and P. M. W. French, “easySTORM: a robust, lower-cost approach to localisation and TIRF microscopy,” J. Biophotonics 9(9), 948–957 (2016).
[Crossref] [PubMed]

2015 (6)

P. Almada, S. Culley, and R. Henriques, “PALM and STORM: Into large fields and high-throughput microscopy with sCMOS detectors,” Methods 88, 109–121 (2015).
[Crossref] [PubMed]

W. Q. Ong, Y. R. Citron, J. Schnitzbauer, D. Kamiyama, and B. Huang, “Heavy water: a simple solution to increasing the brightness of fluorescent proteins in super-resolution imaging,” Chem. Commun. (Camb.) 51(70), 13451–13453 (2015).
[Crossref] [PubMed]

R. F. Laine, A. Albecka, S. van de Linde, E. J. Rees, C. M. Crump, and C. F. Kaminski, “Structural analysis of herpes simplex virus by optical super-resolution imaging,” Nat. Commun. 6, 5980 (2015).
[Crossref] [PubMed]

C. Graetzel, M. Suter, and M. Aschwanden, “Reducing laser speckle with electroactive polymer actuators,” Proc. SPIE 9430, 943004 (2015).
[Crossref]

K. Finan, A. Raulf, and M. Heilemann, “A Set of Homo-Oligomeric Standards Allows Accurate Protein Counting,” Angew. Chem. Int. Ed. Engl. 54(41), 12049–12052 (2015).
[Crossref] [PubMed]

R. P. J. Nieuwenhuizen, M. Bates, A. Szymborska, K. A. Lidke, B. Rieger, and S. Stallinga, “Quantitative Localization Microscopy: Effects of Photophysics and Labeling Stoichiometry,” PLoS One 10(5), e0127989 (2015).
[Crossref] [PubMed]

2014 (4)

N. Ehmann, S. van de Linde, A. Alon, D. Ljaschenko, X. Z. Keung, T. Holm, A. Rings, A. DiAntonio, S. Hallermann, U. Ashery, M. Heckmann, M. Sauer, and R. J. Kittel, “Quantitative super-resolution imaging of Bruchpilot distinguishes active zone states,” Nat. Commun. 5, 4650 (2014).
[Crossref] [PubMed]

Y. Fujimaki and H. Taniguchi, “Reduction of speckle contrast in multimode fibers using piezoelectric vibrator,” Proc. SPIE 8960, 89601S (2014).
[Crossref]

S. J. Holden, T. Pengo, K. L. Meibom, C. Fernandez Fernandez, J. Collier, and S. Manley, “High throughput 3D super-resolution microscopy reveals Caulobacter crescentus in vivo Z-ring organization,” Proc. Natl. Acad. Sci. U.S.A. 111(12), 4566–4571 (2014).
[Crossref] [PubMed]

J. Deschamps, M. Mund, and J. Ries, “3D superresolution microscopy by supercritical angle detection,” Opt. Express 22(23), 29081–29091 (2014).
[Crossref] [PubMed]

2013 (4)

F. Huang, T. M. P. Hartwich, F. E. Rivera-Molina, Y. Lin, W. C. Duim, J. J. Long, P. D. Uchil, J. R. Myers, M. A. Baird, W. Mothes, M. W. Davidson, D. Toomre, and J. Bewersdorf, “Video-rate nanoscopy using sCMOS camera-specific single-molecule localization algorithms,” Nat. Methods 10(7), 653–658 (2013).
[Crossref] [PubMed]

E. M. Puchner, J. M. Walter, R. Kasper, B. Huang, and W. A. Lim, “Counting molecules in single organelles with superresolution microscopy allows tracking of the endosome maturation trajectory,” Proc. Natl. Acad. Sci. U.S.A. 110(40), 16015–16020 (2013).
[Crossref] [PubMed]

X. Nan, E. A. Collisson, S. Lewis, J. Huang, T. M. Tamgüney, J. T. Liphardt, F. McCormick, J. W. Gray, and S. Chu, “Single-molecule superresolution imaging allows quantitative analysis of RAF multimer formation and signaling,” Proc. Natl. Acad. Sci. U.S.A. 110(46), 18519–18524 (2013).
[Crossref] [PubMed]

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]

2012 (4)

S. L. Veatch, B. B. Machta, S. A. Shelby, E. N. Chiang, D. A. Holowka, and B. A. Baird, “Correlation functions quantify super-resolution images and estimate apparent clustering due to over-counting,” PLoS One 7(2), e31457 (2012).
[Crossref] [PubMed]

S.-H. Lee, J. Y. Shin, A. Lee, and C. Bustamante, “Counting single photoactivatable fluorescent molecules by photoactivated localization microscopy (PALM),” Proc. Natl. Acad. Sci. U.S.A. 109(43), 17436–17441 (2012).
[Crossref] [PubMed]

D. S. Mehta, D. N. Naik, R. K. Singh, and M. Takeda, “Laser speckle reduction by multimode optical fiber bundle with combined temporal, spatial, and angular diversity,” Appl. Opt. 51(12), 1894–1904 (2012).
[Crossref] [PubMed]

I. Izeddin, J. Boulanger, V. Racine, C. G. Specht, A. Kechkar, D. Nair, A. Triller, D. Choquet, M. Dahan, and J. B. Sibarita, “Wavelet analysis for single molecule localization microscopy,” Opt. Express 20(3), 2081–2095 (2012).
[Crossref] [PubMed]

2011 (3)

I. Schoen, J. Ries, E. Klotzsch, H. Ewers, and V. Vogel, “Binding-activated localization microscopy of DNA structures,” Nano Lett. 11(9), 4008–4011 (2011).
[Crossref] [PubMed]

P. Sengupta, T. Jovanovic-Talisman, D. Skoko, M. Renz, S. L. Veatch, and J. Lippincott-Schwartz, “Probing protein heterogeneity in the plasma membrane using PALM and pair correlation analysis,” Nat. Methods 8(11), 969–975 (2011).
[Crossref] [PubMed]

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

2010 (1)

C. S. Smith, N. Joseph, B. Rieger, and K. A. Lidke, “Fast, single-molecule localization that achieves theoretically minimum uncertainty,” Nat. Methods 7(5), 373–375 (2010).
[Crossref] [PubMed]

2009 (1)

2008 (1)

M. Heilemann, S. van de Linde, M. Schüttpelz, R. Kasper, B. Seefeldt, A. Mukherjee, P. Tinnefeld, and M. Sauer, “Subdiffraction-resolution fluorescence imaging with conventional fluorescent probes,” Angew. Chem. Int. Ed. Engl. 47(33), 6172–6176 (2008).
[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]

2001 (2)

D. Axelrod, “Total internal reflection fluorescence microscopy in cell biology,” Traffic 2(11), 764–774 (2001).
[Crossref] [PubMed]

S. Inoué, R. A. Knudson, M. Goda, K. Suzuki, C. Nagano, N. Okada, H. Takahashi, K. Ichie, M. Iida, and K. Yamanaka, “Centrifuge polarizing microscope. I. Rationale, design and instrument performance,” J. Microsc. 201(3), 341–356 (2001).
[Crossref] [PubMed]

1984 (1)

D. Axelrod, T. P. Burghardt, and N. L. Thompson, “Total internal reflection fluorescence,” Annu. Rev. Biophys. Bioeng. 13(1), 247–268 (1984).
[Crossref] [PubMed]

1981 (1)

D. Axelrod, “Cell-substrate contacts illuminated by total internal reflection fluorescence,” J. Cell Biol. 89(1), 141–145 (1981).
[Crossref] [PubMed]

Agasti, S. S.

R. Jungmann, M. S. Avendaño, M. Dai, J. B. Woehrstein, S. S. Agasti, Z. Feiger, A. Rodal, and P. Yin, “Quantitative super-resolution imaging with qPAINT,” Nat. Methods 13(5), 439–442 (2016).
[Crossref] [PubMed]

Albecka, A.

R. F. Laine, A. Albecka, S. van de Linde, E. J. Rees, C. M. Crump, and C. F. Kaminski, “Structural analysis of herpes simplex virus by optical super-resolution imaging,” Nat. Commun. 6, 5980 (2015).
[Crossref] [PubMed]

Allan, V. J.

P. Georgiades, V. J. Allan, M. Dickinson, and T. A. Waigh, “Reduction of coherent artefacts in super-resolution fluorescence localisation microscopy,” J. Microsc. 00, 1–9 (2016).
[PubMed]

Almada, P.

P. Almada, S. Culley, and R. Henriques, “PALM and STORM: Into large fields and high-throughput microscopy with sCMOS detectors,” Methods 88, 109–121 (2015).
[Crossref] [PubMed]

Alon, A.

N. Ehmann, S. van de Linde, A. Alon, D. Ljaschenko, X. Z. Keung, T. Holm, A. Rings, A. DiAntonio, S. Hallermann, U. Ashery, M. Heckmann, M. Sauer, and R. J. Kittel, “Quantitative super-resolution imaging of Bruchpilot distinguishes active zone states,” Nat. Commun. 5, 4650 (2014).
[Crossref] [PubMed]

Annibale, P.

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

Archetti, A.

K. M. Douglass, C. Sieben, A. Archetti, A. Lambert, and S. Manley, “Super-resolution imaging of multiple cells by optimised flat-field epi-illumination,” Nat. Photonics 10(11), 705–708 (2016).
[Crossref] [PubMed]

Arnold, A. M.

F. Baumgart, A. M. Arnold, K. Leskovar, K. Staszek, M. Fölser, J. Weghuber, H. Stockinger, and G. J. Schütz, “Varying label density allows artifact-free analysis of membrane-protein nanoclusters,” Nat. Methods 13(8), 661–664 (2016).
[Crossref] [PubMed]

Aschwanden, M.

C. Graetzel, M. Suter, and M. Aschwanden, “Reducing laser speckle with electroactive polymer actuators,” Proc. SPIE 9430, 943004 (2015).
[Crossref]

Ashery, U.

N. Ehmann, S. van de Linde, A. Alon, D. Ljaschenko, X. Z. Keung, T. Holm, A. Rings, A. DiAntonio, S. Hallermann, U. Ashery, M. Heckmann, M. Sauer, and R. J. Kittel, “Quantitative super-resolution imaging of Bruchpilot distinguishes active zone states,” Nat. Commun. 5, 4650 (2014).
[Crossref] [PubMed]

Avendaño, M. S.

R. Jungmann, M. S. Avendaño, M. Dai, J. B. Woehrstein, S. S. Agasti, Z. Feiger, A. Rodal, and P. Yin, “Quantitative super-resolution imaging with qPAINT,” Nat. Methods 13(5), 439–442 (2016).
[Crossref] [PubMed]

Axelrod, D.

D. Axelrod, “Total internal reflection fluorescence microscopy in cell biology,” Traffic 2(11), 764–774 (2001).
[Crossref] [PubMed]

D. Axelrod, T. P. Burghardt, and N. L. Thompson, “Total internal reflection fluorescence,” Annu. Rev. Biophys. Bioeng. 13(1), 247–268 (1984).
[Crossref] [PubMed]

D. Axelrod, “Cell-substrate contacts illuminated by total internal reflection fluorescence,” J. Cell Biol. 89(1), 141–145 (1981).
[Crossref] [PubMed]

Baird, B. A.

S. L. Veatch, B. B. Machta, S. A. Shelby, E. N. Chiang, D. A. Holowka, and B. A. Baird, “Correlation functions quantify super-resolution images and estimate apparent clustering due to over-counting,” PLoS One 7(2), e31457 (2012).
[Crossref] [PubMed]

Baird, M. A.

F. Huang, T. M. P. Hartwich, F. E. Rivera-Molina, Y. Lin, W. C. Duim, J. J. Long, P. D. Uchil, J. R. Myers, M. A. Baird, W. Mothes, M. W. Davidson, D. Toomre, and J. Bewersdorf, “Video-rate nanoscopy using sCMOS camera-specific single-molecule localization algorithms,” Nat. Methods 10(7), 653–658 (2013).
[Crossref] [PubMed]

Bates, M.

R. P. J. Nieuwenhuizen, M. Bates, A. Szymborska, K. A. Lidke, B. Rieger, and S. Stallinga, “Quantitative Localization Microscopy: Effects of Photophysics and Labeling Stoichiometry,” PLoS One 10(5), e0127989 (2015).
[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]

Baumgart, F.

F. Baumgart, A. M. Arnold, K. Leskovar, K. Staszek, M. Fölser, J. Weghuber, H. Stockinger, and G. J. Schütz, “Varying label density allows artifact-free analysis of membrane-protein nanoclusters,” Nat. Methods 13(8), 661–664 (2016).
[Crossref] [PubMed]

Betzig, E.

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S. L. Veatch, B. B. Machta, S. A. Shelby, E. N. Chiang, D. A. Holowka, and B. A. Baird, “Correlation functions quantify super-resolution images and estimate apparent clustering due to over-counting,” PLoS One 7(2), e31457 (2012).
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W. Q. Ong, Y. R. Citron, J. Schnitzbauer, D. Kamiyama, and B. Huang, “Heavy water: a simple solution to increasing the brightness of fluorescent proteins in super-resolution imaging,” Chem. Commun. (Camb.) 51(70), 13451–13453 (2015).
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X. Nan, E. A. Collisson, S. Lewis, J. Huang, T. M. Tamgüney, J. T. Liphardt, F. McCormick, J. W. Gray, and S. Chu, “Single-molecule superresolution imaging allows quantitative analysis of RAF multimer formation and signaling,” Proc. Natl. Acad. Sci. U.S.A. 110(46), 18519–18524 (2013).
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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).
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R. F. Laine, A. Albecka, S. van de Linde, E. J. Rees, C. M. Crump, and C. F. Kaminski, “Structural analysis of herpes simplex virus by optical super-resolution imaging,” Nat. Commun. 6, 5980 (2015).
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K. M. Douglass, C. Sieben, A. Archetti, A. Lambert, and S. Manley, “Super-resolution imaging of multiple cells by optimised flat-field epi-illumination,” Nat. Photonics 10(11), 705–708 (2016).
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F. Huang, T. M. P. Hartwich, F. E. Rivera-Molina, Y. Lin, W. C. Duim, J. J. Long, P. D. Uchil, J. R. Myers, M. A. Baird, W. Mothes, M. W. Davidson, D. Toomre, and J. Bewersdorf, “Video-rate nanoscopy using sCMOS camera-specific single-molecule localization algorithms,” Nat. Methods 10(7), 653–658 (2013).
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K. Kwakwa, A. Savell, T. Davies, I. Munro, S. Parrinello, M. A. Purbhoo, C. Dunsby, M. A. A. Neil, and P. M. W. French, “easySTORM: a robust, lower-cost approach to localisation and TIRF microscopy,” J. Biophotonics 9(9), 948–957 (2016).
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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).
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I. Schoen, J. Ries, E. Klotzsch, H. Ewers, and V. Vogel, “Binding-activated localization microscopy of DNA structures,” Nano Lett. 11(9), 4008–4011 (2011).
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S. J. Holden, T. Pengo, K. L. Meibom, C. Fernandez Fernandez, J. Collier, and S. Manley, “High throughput 3D super-resolution microscopy reveals Caulobacter crescentus in vivo Z-ring organization,” Proc. Natl. Acad. Sci. U.S.A. 111(12), 4566–4571 (2014).
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K. Kwakwa, A. Savell, T. Davies, I. Munro, S. Parrinello, M. A. Purbhoo, C. Dunsby, M. A. A. Neil, and P. M. W. French, “easySTORM: a robust, lower-cost approach to localisation and TIRF microscopy,” J. Biophotonics 9(9), 948–957 (2016).
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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).
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Ha, W.

Hallermann, S.

N. Ehmann, S. van de Linde, A. Alon, D. Ljaschenko, X. Z. Keung, T. Holm, A. Rings, A. DiAntonio, S. Hallermann, U. Ashery, M. Heckmann, M. Sauer, and R. J. Kittel, “Quantitative super-resolution imaging of Bruchpilot distinguishes active zone states,” Nat. Commun. 5, 4650 (2014).
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F. Huang, T. M. P. Hartwich, F. E. Rivera-Molina, Y. Lin, W. C. Duim, J. J. Long, P. D. Uchil, J. R. Myers, M. A. Baird, W. Mothes, M. W. Davidson, D. Toomre, and J. Bewersdorf, “Video-rate nanoscopy using sCMOS camera-specific single-molecule localization algorithms,” Nat. Methods 10(7), 653–658 (2013).
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N. Ehmann, S. van de Linde, A. Alon, D. Ljaschenko, X. Z. Keung, T. Holm, A. Rings, A. DiAntonio, S. Hallermann, U. Ashery, M. Heckmann, M. Sauer, and R. J. Kittel, “Quantitative super-resolution imaging of Bruchpilot distinguishes active zone states,” Nat. Commun. 5, 4650 (2014).
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K. Finan, A. Raulf, and M. Heilemann, “A Set of Homo-Oligomeric Standards Allows Accurate Protein Counting,” Angew. Chem. Int. Ed. Engl. 54(41), 12049–12052 (2015).
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M. Heilemann, S. van de Linde, M. Schüttpelz, R. Kasper, B. Seefeldt, A. Mukherjee, P. Tinnefeld, and M. Sauer, “Subdiffraction-resolution fluorescence imaging with conventional fluorescent probes,” Angew. Chem. Int. Ed. Engl. 47(33), 6172–6176 (2008).
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P. Almada, S. Culley, and R. Henriques, “PALM and STORM: Into large fields and high-throughput microscopy with sCMOS detectors,” Methods 88, 109–121 (2015).
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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).
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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).
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S. J. Holden, T. Pengo, K. L. Meibom, C. Fernandez Fernandez, J. Collier, and S. Manley, “High throughput 3D super-resolution microscopy reveals Caulobacter crescentus in vivo Z-ring organization,” Proc. Natl. Acad. Sci. U.S.A. 111(12), 4566–4571 (2014).
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N. Ehmann, S. van de Linde, A. Alon, D. Ljaschenko, X. Z. Keung, T. Holm, A. Rings, A. DiAntonio, S. Hallermann, U. Ashery, M. Heckmann, M. Sauer, and R. J. Kittel, “Quantitative super-resolution imaging of Bruchpilot distinguishes active zone states,” Nat. Commun. 5, 4650 (2014).
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S. L. Veatch, B. B. Machta, S. A. Shelby, E. N. Chiang, D. A. Holowka, and B. A. Baird, “Correlation functions quantify super-resolution images and estimate apparent clustering due to over-counting,” PLoS One 7(2), e31457 (2012).
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W. Q. Ong, Y. R. Citron, J. Schnitzbauer, D. Kamiyama, and B. Huang, “Heavy water: a simple solution to increasing the brightness of fluorescent proteins in super-resolution imaging,” Chem. Commun. (Camb.) 51(70), 13451–13453 (2015).
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E. M. Puchner, J. M. Walter, R. Kasper, B. Huang, and W. A. Lim, “Counting molecules in single organelles with superresolution microscopy allows tracking of the endosome maturation trajectory,” Proc. Natl. Acad. Sci. U.S.A. 110(40), 16015–16020 (2013).
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Huang, F.

F. Huang, T. M. P. Hartwich, F. E. Rivera-Molina, Y. Lin, W. C. Duim, J. J. Long, P. D. Uchil, J. R. Myers, M. A. Baird, W. Mothes, M. W. Davidson, D. Toomre, and J. Bewersdorf, “Video-rate nanoscopy using sCMOS camera-specific single-molecule localization algorithms,” Nat. Methods 10(7), 653–658 (2013).
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Huang, J.

X. Nan, E. A. Collisson, S. Lewis, J. Huang, T. M. Tamgüney, J. T. Liphardt, F. McCormick, J. W. Gray, and S. Chu, “Single-molecule superresolution imaging allows quantitative analysis of RAF multimer formation and signaling,” Proc. Natl. Acad. Sci. U.S.A. 110(46), 18519–18524 (2013).
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Ichie, K.

S. Inoué, R. A. Knudson, M. Goda, K. Suzuki, C. Nagano, N. Okada, H. Takahashi, K. Ichie, M. Iida, and K. Yamanaka, “Centrifuge polarizing microscope. I. Rationale, design and instrument performance,” J. Microsc. 201(3), 341–356 (2001).
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Iida, M.

S. Inoué, R. A. Knudson, M. Goda, K. Suzuki, C. Nagano, N. Okada, H. Takahashi, K. Ichie, M. Iida, and K. Yamanaka, “Centrifuge polarizing microscope. I. Rationale, design and instrument performance,” J. Microsc. 201(3), 341–356 (2001).
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S. Inoué, R. A. Knudson, M. Goda, K. Suzuki, C. Nagano, N. Okada, H. Takahashi, K. Ichie, M. Iida, and K. Yamanaka, “Centrifuge polarizing microscope. I. Rationale, design and instrument performance,” J. Microsc. 201(3), 341–356 (2001).
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Izeddin, I.

Joseph, N.

C. S. Smith, N. Joseph, B. Rieger, and K. A. Lidke, “Fast, single-molecule localization that achieves theoretically minimum uncertainty,” Nat. Methods 7(5), 373–375 (2010).
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Jovanovic-Talisman, T.

P. Sengupta, T. Jovanovic-Talisman, D. Skoko, M. Renz, S. L. Veatch, and J. Lippincott-Schwartz, “Probing protein heterogeneity in the plasma membrane using PALM and pair correlation analysis,” Nat. Methods 8(11), 969–975 (2011).
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Jung, Y.

Jungmann, R.

R. Jungmann, M. S. Avendaño, M. Dai, J. B. Woehrstein, S. S. Agasti, Z. Feiger, A. Rodal, and P. Yin, “Quantitative super-resolution imaging with qPAINT,” Nat. Methods 13(5), 439–442 (2016).
[Crossref] [PubMed]

Kaminski, C. F.

R. F. Laine, A. Albecka, S. van de Linde, E. J. Rees, C. M. Crump, and C. F. Kaminski, “Structural analysis of herpes simplex virus by optical super-resolution imaging,” Nat. Commun. 6, 5980 (2015).
[Crossref] [PubMed]

Kamiyama, D.

W. Q. Ong, Y. R. Citron, J. Schnitzbauer, D. Kamiyama, and B. Huang, “Heavy water: a simple solution to increasing the brightness of fluorescent proteins in super-resolution imaging,” Chem. Commun. (Camb.) 51(70), 13451–13453 (2015).
[Crossref] [PubMed]

Kasper, R.

E. M. Puchner, J. M. Walter, R. Kasper, B. Huang, and W. A. Lim, “Counting molecules in single organelles with superresolution microscopy allows tracking of the endosome maturation trajectory,” Proc. Natl. Acad. Sci. U.S.A. 110(40), 16015–16020 (2013).
[Crossref] [PubMed]

M. Heilemann, S. van de Linde, M. Schüttpelz, R. Kasper, B. Seefeldt, A. Mukherjee, P. Tinnefeld, and M. Sauer, “Subdiffraction-resolution fluorescence imaging with conventional fluorescent probes,” Angew. Chem. Int. Ed. Engl. 47(33), 6172–6176 (2008).
[Crossref] [PubMed]

Kechkar, A.

Keung, X. Z.

N. Ehmann, S. van de Linde, A. Alon, D. Ljaschenko, X. Z. Keung, T. Holm, A. Rings, A. DiAntonio, S. Hallermann, U. Ashery, M. Heckmann, M. Sauer, and R. J. Kittel, “Quantitative super-resolution imaging of Bruchpilot distinguishes active zone states,” Nat. Commun. 5, 4650 (2014).
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Kim, J.-K.

Kittel, R. J.

N. Ehmann, S. van de Linde, A. Alon, D. Ljaschenko, X. Z. Keung, T. Holm, A. Rings, A. DiAntonio, S. Hallermann, U. Ashery, M. Heckmann, M. Sauer, and R. J. Kittel, “Quantitative super-resolution imaging of Bruchpilot distinguishes active zone states,” Nat. Commun. 5, 4650 (2014).
[Crossref] [PubMed]

Klotzsch, E.

I. Schoen, J. Ries, E. Klotzsch, H. Ewers, and V. Vogel, “Binding-activated localization microscopy of DNA structures,” Nano Lett. 11(9), 4008–4011 (2011).
[Crossref] [PubMed]

Knudson, R. A.

S. Inoué, R. A. Knudson, M. Goda, K. Suzuki, C. Nagano, N. Okada, H. Takahashi, K. Ichie, M. Iida, and K. Yamanaka, “Centrifuge polarizing microscope. I. Rationale, design and instrument performance,” J. Microsc. 201(3), 341–356 (2001).
[Crossref] [PubMed]

Kwakwa, K.

K. Kwakwa, A. Savell, T. Davies, I. Munro, S. Parrinello, M. A. Purbhoo, C. Dunsby, M. A. A. Neil, and P. M. W. French, “easySTORM: a robust, lower-cost approach to localisation and TIRF microscopy,” J. Biophotonics 9(9), 948–957 (2016).
[Crossref] [PubMed]

Laine, R. F.

R. F. Laine, A. Albecka, S. van de Linde, E. J. Rees, C. M. Crump, and C. F. Kaminski, “Structural analysis of herpes simplex virus by optical super-resolution imaging,” Nat. Commun. 6, 5980 (2015).
[Crossref] [PubMed]

Lambert, A.

K. M. Douglass, C. Sieben, A. Archetti, A. Lambert, and S. Manley, “Super-resolution imaging of multiple cells by optimised flat-field epi-illumination,” Nat. Photonics 10(11), 705–708 (2016).
[Crossref] [PubMed]

Lee, A.

S.-H. Lee, J. Y. Shin, A. Lee, and C. Bustamante, “Counting single photoactivatable fluorescent molecules by photoactivated localization microscopy (PALM),” Proc. Natl. Acad. Sci. U.S.A. 109(43), 17436–17441 (2012).
[Crossref] [PubMed]

Lee, S.

Lee, S.-H.

S.-H. Lee, J. Y. Shin, A. Lee, and C. Bustamante, “Counting single photoactivatable fluorescent molecules by photoactivated localization microscopy (PALM),” Proc. Natl. Acad. Sci. U.S.A. 109(43), 17436–17441 (2012).
[Crossref] [PubMed]

Leskovar, K.

F. Baumgart, A. M. Arnold, K. Leskovar, K. Staszek, M. Fölser, J. Weghuber, H. Stockinger, and G. J. Schütz, “Varying label density allows artifact-free analysis of membrane-protein nanoclusters,” Nat. Methods 13(8), 661–664 (2016).
[Crossref] [PubMed]

Lewis, S.

X. Nan, E. A. Collisson, S. Lewis, J. Huang, T. M. Tamgüney, J. T. Liphardt, F. McCormick, J. W. Gray, and S. Chu, “Single-molecule superresolution imaging allows quantitative analysis of RAF multimer formation and signaling,” Proc. Natl. Acad. Sci. U.S.A. 110(46), 18519–18524 (2013).
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Lidke, K. A.

R. P. J. Nieuwenhuizen, M. Bates, A. Szymborska, K. A. Lidke, B. Rieger, and S. Stallinga, “Quantitative Localization Microscopy: Effects of Photophysics and Labeling Stoichiometry,” PLoS One 10(5), e0127989 (2015).
[Crossref] [PubMed]

C. S. Smith, N. Joseph, B. Rieger, and K. A. Lidke, “Fast, single-molecule localization that achieves theoretically minimum uncertainty,” Nat. Methods 7(5), 373–375 (2010).
[Crossref] [PubMed]

Lim, W. A.

E. M. Puchner, J. M. Walter, R. Kasper, B. Huang, and W. A. Lim, “Counting molecules in single organelles with superresolution microscopy allows tracking of the endosome maturation trajectory,” Proc. Natl. Acad. Sci. U.S.A. 110(40), 16015–16020 (2013).
[Crossref] [PubMed]

Lin, Y.

F. Huang, T. M. P. Hartwich, F. E. Rivera-Molina, Y. Lin, W. C. Duim, J. J. Long, P. D. Uchil, J. R. Myers, M. A. Baird, W. Mothes, M. W. Davidson, D. Toomre, and J. Bewersdorf, “Video-rate nanoscopy using sCMOS camera-specific single-molecule localization algorithms,” Nat. Methods 10(7), 653–658 (2013).
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E. M. Puchner, J. M. Walter, R. Kasper, B. Huang, and W. A. Lim, “Counting molecules in single organelles with superresolution microscopy allows tracking of the endosome maturation trajectory,” Proc. Natl. Acad. Sci. U.S.A. 110(40), 16015–16020 (2013).
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F. Baumgart, A. M. Arnold, K. Leskovar, K. Staszek, M. Fölser, J. Weghuber, H. Stockinger, and G. J. Schütz, “Varying label density allows artifact-free analysis of membrane-protein nanoclusters,” Nat. Methods 13(8), 661–664 (2016).
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R. Jungmann, M. S. Avendaño, M. Dai, J. B. Woehrstein, S. S. Agasti, Z. Feiger, A. Rodal, and P. Yin, “Quantitative super-resolution imaging with qPAINT,” Nat. Methods 13(5), 439–442 (2016).
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Yamanaka, K.

S. Inoué, R. A. Knudson, M. Goda, K. Suzuki, C. Nagano, N. Okada, H. Takahashi, K. Ichie, M. Iida, and K. Yamanaka, “Centrifuge polarizing microscope. I. Rationale, design and instrument performance,” J. Microsc. 201(3), 341–356 (2001).
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Yin, P.

R. Jungmann, M. S. Avendaño, M. Dai, J. B. Woehrstein, S. S. Agasti, Z. Feiger, A. Rodal, and P. Yin, “Quantitative super-resolution imaging with qPAINT,” Nat. Methods 13(5), 439–442 (2016).
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M. J. Rust, M. Bates, and X. Zhuang, “Sub-diffraction-limit imaging by stochastic optical reconstruction microscopy (STORM),” Nat. Methods 3(10), 793–796 (2006).
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K. Finan, A. Raulf, and M. Heilemann, “A Set of Homo-Oligomeric Standards Allows Accurate Protein Counting,” Angew. Chem. Int. Ed. Engl. 54(41), 12049–12052 (2015).
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W. Q. Ong, Y. R. Citron, J. Schnitzbauer, D. Kamiyama, and B. Huang, “Heavy water: a simple solution to increasing the brightness of fluorescent proteins in super-resolution imaging,” Chem. Commun. (Camb.) 51(70), 13451–13453 (2015).
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K. Kwakwa, A. Savell, T. Davies, I. Munro, S. Parrinello, M. A. Purbhoo, C. Dunsby, M. A. A. Neil, and P. M. W. French, “easySTORM: a robust, lower-cost approach to localisation and TIRF microscopy,” J. Biophotonics 9(9), 948–957 (2016).
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S. Inoué, R. A. Knudson, M. Goda, K. Suzuki, C. Nagano, N. Okada, H. Takahashi, K. Ichie, M. Iida, and K. Yamanaka, “Centrifuge polarizing microscope. I. Rationale, design and instrument performance,” J. Microsc. 201(3), 341–356 (2001).
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P. Georgiades, V. J. Allan, M. Dickinson, and T. A. Waigh, “Reduction of coherent artefacts in super-resolution fluorescence localisation microscopy,” J. Microsc. 00, 1–9 (2016).
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P. Almada, S. Culley, and R. Henriques, “PALM and STORM: Into large fields and high-throughput microscopy with sCMOS detectors,” Methods 88, 109–121 (2015).
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Nano Lett. (1)

I. Schoen, J. Ries, E. Klotzsch, H. Ewers, and V. Vogel, “Binding-activated localization microscopy of DNA structures,” Nano Lett. 11(9), 4008–4011 (2011).
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N. Ehmann, S. van de Linde, A. Alon, D. Ljaschenko, X. Z. Keung, T. Holm, A. Rings, A. DiAntonio, S. Hallermann, U. Ashery, M. Heckmann, M. Sauer, and R. J. Kittel, “Quantitative super-resolution imaging of Bruchpilot distinguishes active zone states,” Nat. Commun. 5, 4650 (2014).
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R. F. Laine, A. Albecka, S. van de Linde, E. J. Rees, C. M. Crump, and C. F. Kaminski, “Structural analysis of herpes simplex virus by optical super-resolution imaging,” Nat. Commun. 6, 5980 (2015).
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Nat. Methods (7)

R. Jungmann, M. S. Avendaño, M. Dai, J. B. Woehrstein, S. S. Agasti, Z. Feiger, A. Rodal, and P. Yin, “Quantitative super-resolution imaging with qPAINT,” Nat. Methods 13(5), 439–442 (2016).
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P. Sengupta, T. Jovanovic-Talisman, D. Skoko, M. Renz, S. L. Veatch, and J. Lippincott-Schwartz, “Probing protein heterogeneity in the plasma membrane using PALM and pair correlation analysis,” Nat. Methods 8(11), 969–975 (2011).
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F. Baumgart, A. M. Arnold, K. Leskovar, K. Staszek, M. Fölser, J. Weghuber, H. Stockinger, and G. J. Schütz, “Varying label density allows artifact-free analysis of membrane-protein nanoclusters,” Nat. Methods 13(8), 661–664 (2016).
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Nat. Photonics (1)

K. M. Douglass, C. Sieben, A. Archetti, A. Lambert, and S. Manley, “Super-resolution imaging of multiple cells by optimised flat-field epi-illumination,” Nat. Photonics 10(11), 705–708 (2016).
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Proc. Natl. Acad. Sci. U.S.A. (4)

S.-H. Lee, J. Y. Shin, A. Lee, and C. Bustamante, “Counting single photoactivatable fluorescent molecules by photoactivated localization microscopy (PALM),” Proc. Natl. Acad. Sci. U.S.A. 109(43), 17436–17441 (2012).
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E. M. Puchner, J. M. Walter, R. Kasper, B. Huang, and W. A. Lim, “Counting molecules in single organelles with superresolution microscopy allows tracking of the endosome maturation trajectory,” Proc. Natl. Acad. Sci. U.S.A. 110(40), 16015–16020 (2013).
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X. Nan, E. A. Collisson, S. Lewis, J. Huang, T. M. Tamgüney, J. T. Liphardt, F. McCormick, J. W. Gray, and S. Chu, “Single-molecule superresolution imaging allows quantitative analysis of RAF multimer formation and signaling,” Proc. Natl. Acad. Sci. U.S.A. 110(46), 18519–18524 (2013).
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S. J. Holden, T. Pengo, K. L. Meibom, C. Fernandez Fernandez, J. Collier, and S. Manley, “High throughput 3D super-resolution microscopy reveals Caulobacter crescentus in vivo Z-ring organization,” Proc. Natl. Acad. Sci. U.S.A. 111(12), 4566–4571 (2014).
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Science (2)

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).
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J. W. Goodman, Speckle Phenomena in Optics (Roberts & Company, 2007).

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