Abstract

We present a structured illumination microscopy based point localization estimator (SIMPLE) that achieves a 2-fold increase in single molecule localization precision compared to conventional centroid estimation methods. SIMPLE advances the recently introduced MINFLUX concept by using precisely phase-shifted sinusoidal wave patterns as nanometric rulers for simultaneous particle localization based on photon count variation over a 20 μm field of view. We validate SIMPLE in silico and experimentally on a TIRF-SIM setup using a digital micro-mirror device (DMD) as a spatial light modulator.

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

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  1. L. Schermelleh, A. Ferrand, T. Huser, C. Eggeling, M. Sauer, O. Biehlmaier, and G. P. Drummen, “Super-resolution microscopy demystified,” Nat. Cell Biol. 21, 72–84 (2019).
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    [Crossref] [PubMed]
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    [Crossref] [PubMed]
  6. I. Izeddin, M. El Beheiry, J. Andilla, D. Ciepielewski, X. Darzacq, and M. Dahan, “PSF shaping using adaptive optics for three-dimensional single-molecule super-resolution imaging and tracking,” Opt. Express 20, 4957 (2012).
    [Crossref] [PubMed]
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    [Crossref]
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    [Crossref]
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    [Crossref]
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    [Crossref] [PubMed]
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    [Crossref]
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    [Crossref]
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    [Crossref] [PubMed]
  24. S. Wieser, M. Axmann, and G. J. Schütz, “Versatile analysis of single-molecule tracking data by comprehensive testing against Monte Carlo simulations,” Biophys. J. 95, 5988–6001 (2008).
    [Crossref] [PubMed]
  25. R. Jungmann, M. S. Avendaño, J. B. Woehrstein, M. Dai, W. M. Shih, and P. Yin, “Multiplexed 3D cellular super-resolution imaging with DNA-PAINT and Exchange-PAINT,” Nat. Methods 11, 313–318 (2014).
    [Crossref] [PubMed]
  26. S. Wolter, U. Endesfelder, S. van de Linde, M. Heilemann, and M. Sauer, “Measuring localization performance of super-resolution algorithms on very active samples,” Opt. Express 19, 7020 (2011).
    [Crossref] [PubMed]
  27. D. Sage, T. A. Pham, H. Babcock, T. Lukes, T. Pengo, J. Chao, R. Velmurugan, A. Herbert, A. Agrawal, S. Colabrese, A. Wheeler, A. Archetti, B. Rieger, R. Ober, G. M. Hagen, J. B. Sibarita, J. Ries, R. Henriques, M. Unser, and S. Holden, “Super-resolution fight club: assessment of 2D and 3D single-molecule localization microscopy software,” Nat. Methods 16, 387–395 (2019).
    [Crossref] [PubMed]

2019 (2)

L. Schermelleh, A. Ferrand, T. Huser, C. Eggeling, M. Sauer, O. Biehlmaier, and G. P. Drummen, “Super-resolution microscopy demystified,” Nat. Cell Biol. 21, 72–84 (2019).
[Crossref] [PubMed]

D. Sage, T. A. Pham, H. Babcock, T. Lukes, T. Pengo, J. Chao, R. Velmurugan, A. Herbert, A. Agrawal, S. Colabrese, A. Wheeler, A. Archetti, B. Rieger, R. Ober, G. M. Hagen, J. B. Sibarita, J. Ries, R. Henriques, M. Unser, and S. Holden, “Super-resolution fight club: assessment of 2D and 3D single-molecule localization microscopy software,” Nat. Methods 16, 387–395 (2019).
[Crossref] [PubMed]

2018 (1)

Y. Eilers, H. Ta, K. C. Gwosch, F. Balzarotti, and S. W. Hell, “MINFLUX monitors rapid molecular jumps with superior spatiotemporal resolution,” Proc. Natl. Acad. Sci. 115, 6117–6122 (2018).
[Crossref] [PubMed]

2017 (3)

L.-H. Yeh, L. Tian, and L. Waller, “Structured illumination microscopy with unknown patterns and a statistical prior,” Biomed. Opt. Express 8, 695 (2017).
[Crossref] [PubMed]

R. Heintzmann and T. Huser, “Super-Resolution Structured Illumination Microscopy,” Chem. Rev. 117, 13890–13908 (2017).
[Crossref] [PubMed]

F. Balzarotti, Y. Eilers, K. C. Gwosch, A. H. Gynnå, V. Westphal, F. D. Stefani, J. Elf, and S. W. Hell, “Nanometer resolution imaging and tracking of fluorescent molecules with minimal photon fluxes,” Science 355, 606–612 (2017).
[Crossref]

2016 (1)

M. Müller, V. Mönkemöller, S. Hennig, W. Hübner, and T. Huser, “Open-source image reconstruction of super-resolution structured illumination microscopy data in ImageJ,” Nat. Commun. 7, 10980 (2016).
[Crossref] [PubMed]

2015 (2)

D. Li, L. Shao, B.-C. Chen, X. Zhang, M. Zhang, B. Moses, D. E. Milkie, J. R. Beach, J. A. Hammer, M. Pasham, T. Kirchhausen, M. A. Baird, M. W. Davidson, P. Xu, and E. Betzig, “Extended-resolution structured illumination imaging of endocytic and cytoskeletal dynamics,” Science 349, aab3500 (2015).
[Crossref]

N. Chakrova, R. Heintzmann, B. Rieger, and S. Stallinga, “Studying different illumination patterns for resolution improvement in fluorescence microscopy,” Opt. Express 23, 31367 (2015).
[Crossref] [PubMed]

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, 2389–2390 (2014).
[Crossref] [PubMed]

R. Jungmann, M. S. Avendaño, J. B. Woehrstein, M. Dai, W. M. Shih, and P. Yin, “Multiplexed 3D cellular super-resolution imaging with DNA-PAINT and Exchange-PAINT,” Nat. Methods 11, 313–318 (2014).
[Crossref] [PubMed]

2012 (2)

I. Izeddin, M. El Beheiry, J. Andilla, D. Ciepielewski, X. Darzacq, and M. Dahan, “PSF shaping using adaptive optics for three-dimensional single-molecule super-resolution imaging and tracking,” Opt. Express 20, 4957 (2012).
[Crossref] [PubMed]

R. Fiolka, L. Shao, E. H. Rego, M. W. Davidson, and M. G. L. Gustafsson, “Time-lapse two-color 3D imaging of live cells with doubled resolution using structured illumination,” Proc. Natl. Acad. Sci. United States Am. 109, 5311 (2012).
[Crossref]

2011 (1)

2010 (2)

K. I. Mortensen, L. S. Churchman, J. A. Spudich, and H. Flyvbjerg, “Optimized localization analysis for single-molecule tracking and super-resolution microscopy,” Nat. Methods 7, 377–381 (2010).
[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, 373–375 (2010).
[Crossref] [PubMed]

2008 (2)

S. Wieser and G. J. Schütz, “Tracking single molecules in the live cell plasma membrane-Do’s and Don’t’s,” Methods 46, 131–140 (2008).
[Crossref] [PubMed]

S. Wieser, M. Axmann, and G. J. Schütz, “Versatile analysis of single-molecule tracking data by comprehensive testing against Monte Carlo simulations,” Biophys. J. 95, 5988–6001 (2008).
[Crossref] [PubMed]

2007 (1)

S. Wieser, M. Moertelmaier, E. Fuertbauer, H. Stockinger, and G. J. Schütz, “(Un)confined diffusion of CD59 in the plasma membrane determined by high-resolution single molecule microscopy,” Biophys. J. 92, 3719–3728 (2007).
[Crossref] [PubMed]

2006 (3)

S. Ram, E. S. Ward, and R. J. Ober, “Beyond Rayleigh’s criterion: A resolution measure with application to single-molecule microscopy,” Proc. Natl. Acad. Sci. 103, 4457–4462 (2006).
[Crossref]

M. J. Rust, M. Bates, and X. Zhuang, “Sub-diffraction-limit imaging by stochastic optical reconstruction microscopy (STORM),” Nat. Methods 3, 793–795 (2006).
[Crossref] [PubMed]

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

2005 (1)

K. Ritchie, X. Y. Shan, J. Kondo, K. Iwasawa, T. Fujiwara, and A. Kusumi, “Detection of non-Brownian diffusion in the cell membrane in single molecule tracking,” Biophys. J. 88, 2266–2277 (2005).
[Crossref]

2004 (1)

R. J. Ober, S. Ram, and E. S. Ward, “Localization Accuracy in Single-Molecule Microscopy,” Biophys. J. 86, 1185–1200 (2004).
[Crossref] [PubMed]

2002 (1)

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

1999 (1)

M. G. Gustafsson, D. A. Agard, and J. W. Sedat, “I5M: 3D widefield light microscopy with better than 100 nm axial resolution,” J. Microsc. 195, 10–16 (1999).
[Crossref] [PubMed]

Agard, D. A.

M. G. Gustafsson, D. A. Agard, and J. W. Sedat, “I5M: 3D widefield light microscopy with better than 100 nm axial resolution,” J. Microsc. 195, 10–16 (1999).
[Crossref] [PubMed]

Agrawal, A.

D. Sage, T. A. Pham, H. Babcock, T. Lukes, T. Pengo, J. Chao, R. Velmurugan, A. Herbert, A. Agrawal, S. Colabrese, A. Wheeler, A. Archetti, B. Rieger, R. Ober, G. M. Hagen, J. B. Sibarita, J. Ries, R. Henriques, M. Unser, and S. Holden, “Super-resolution fight club: assessment of 2D and 3D single-molecule localization microscopy software,” Nat. Methods 16, 387–395 (2019).
[Crossref] [PubMed]

Andilla, J.

Archetti, A.

D. Sage, T. A. Pham, H. Babcock, T. Lukes, T. Pengo, J. Chao, R. Velmurugan, A. Herbert, A. Agrawal, S. Colabrese, A. Wheeler, A. Archetti, B. Rieger, R. Ober, G. M. Hagen, J. B. Sibarita, J. Ries, R. Henriques, M. Unser, and S. Holden, “Super-resolution fight club: assessment of 2D and 3D single-molecule localization microscopy software,” Nat. Methods 16, 387–395 (2019).
[Crossref] [PubMed]

Avendaño, M. S.

R. Jungmann, M. S. Avendaño, J. B. Woehrstein, M. Dai, W. M. Shih, and P. Yin, “Multiplexed 3D cellular super-resolution imaging with DNA-PAINT and Exchange-PAINT,” Nat. Methods 11, 313–318 (2014).
[Crossref] [PubMed]

Axmann, M.

S. Wieser, M. Axmann, and G. J. Schütz, “Versatile analysis of single-molecule tracking data by comprehensive testing against Monte Carlo simulations,” Biophys. J. 95, 5988–6001 (2008).
[Crossref] [PubMed]

Babcock, H.

D. Sage, T. A. Pham, H. Babcock, T. Lukes, T. Pengo, J. Chao, R. Velmurugan, A. Herbert, A. Agrawal, S. Colabrese, A. Wheeler, A. Archetti, B. Rieger, R. Ober, G. M. Hagen, J. B. Sibarita, J. Ries, R. Henriques, M. Unser, and S. Holden, “Super-resolution fight club: assessment of 2D and 3D single-molecule localization microscopy software,” Nat. Methods 16, 387–395 (2019).
[Crossref] [PubMed]

Baird, M. A.

D. Li, L. Shao, B.-C. Chen, X. Zhang, M. Zhang, B. Moses, D. E. Milkie, J. R. Beach, J. A. Hammer, M. Pasham, T. Kirchhausen, M. A. Baird, M. W. Davidson, P. Xu, and E. Betzig, “Extended-resolution structured illumination imaging of endocytic and cytoskeletal dynamics,” Science 349, aab3500 (2015).
[Crossref]

Balzarotti, F.

Y. Eilers, H. Ta, K. C. Gwosch, F. Balzarotti, and S. W. Hell, “MINFLUX monitors rapid molecular jumps with superior spatiotemporal resolution,” Proc. Natl. Acad. Sci. 115, 6117–6122 (2018).
[Crossref] [PubMed]

F. Balzarotti, Y. Eilers, K. C. Gwosch, A. H. Gynnå, V. Westphal, F. D. Stefani, J. Elf, and S. W. Hell, “Nanometer resolution imaging and tracking of fluorescent molecules with minimal photon fluxes,” Science 355, 606–612 (2017).
[Crossref]

Bates, M.

M. J. Rust, M. Bates, and X. Zhuang, “Sub-diffraction-limit imaging by stochastic optical reconstruction microscopy (STORM),” Nat. Methods 3, 793–795 (2006).
[Crossref] [PubMed]

Beach, J. R.

D. Li, L. Shao, B.-C. Chen, X. Zhang, M. Zhang, B. Moses, D. E. Milkie, J. R. Beach, J. A. Hammer, M. Pasham, T. Kirchhausen, M. A. Baird, M. W. Davidson, P. Xu, and E. Betzig, “Extended-resolution structured illumination imaging of endocytic and cytoskeletal dynamics,” Science 349, aab3500 (2015).
[Crossref]

Betzig, E.

D. Li, L. Shao, B.-C. Chen, X. Zhang, M. Zhang, B. Moses, D. E. Milkie, J. R. Beach, J. A. Hammer, M. Pasham, T. Kirchhausen, M. A. Baird, M. W. Davidson, P. Xu, and E. Betzig, “Extended-resolution structured illumination imaging of endocytic and cytoskeletal dynamics,” Science 349, aab3500 (2015).
[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, 1642–1645 (2006).
[Crossref] [PubMed]

Biehlmaier, O.

L. Schermelleh, A. Ferrand, T. Huser, C. Eggeling, M. Sauer, O. Biehlmaier, and G. P. Drummen, “Super-resolution microscopy demystified,” Nat. Cell Biol. 21, 72–84 (2019).
[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, 1642–1645 (2006).
[Crossref] [PubMed]

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, 2389–2390 (2014).
[Crossref] [PubMed]

Chakrova, N.

Chao, J.

D. Sage, T. A. Pham, H. Babcock, T. Lukes, T. Pengo, J. Chao, R. Velmurugan, A. Herbert, A. Agrawal, S. Colabrese, A. Wheeler, A. Archetti, B. Rieger, R. Ober, G. M. Hagen, J. B. Sibarita, J. Ries, R. Henriques, M. Unser, and S. Holden, “Super-resolution fight club: assessment of 2D and 3D single-molecule localization microscopy software,” Nat. Methods 16, 387–395 (2019).
[Crossref] [PubMed]

Chen, B.-C.

D. Li, L. Shao, B.-C. Chen, X. Zhang, M. Zhang, B. Moses, D. E. Milkie, J. R. Beach, J. A. Hammer, M. Pasham, T. Kirchhausen, M. A. Baird, M. W. Davidson, P. Xu, and E. Betzig, “Extended-resolution structured illumination imaging of endocytic and cytoskeletal dynamics,” Science 349, aab3500 (2015).
[Crossref]

Churchman, L. S.

K. I. Mortensen, L. S. Churchman, J. A. Spudich, and H. Flyvbjerg, “Optimized localization analysis for single-molecule tracking and super-resolution microscopy,” Nat. Methods 7, 377–381 (2010).
[Crossref] [PubMed]

Ciepielewski, D.

Cnossen, J.

J. Cnossen, T. Hinsdale, R. Thorsen, F. Schueder, R. Jungmann, C. S. Smith, B. Rieger, and S. Stallinga, “Localization microscopy at doubled precision with patterned illumination,” bioRxiv p. 554337 (2019).

Colabrese, S.

D. Sage, T. A. Pham, H. Babcock, T. Lukes, T. Pengo, J. Chao, R. Velmurugan, A. Herbert, A. Agrawal, S. Colabrese, A. Wheeler, A. Archetti, B. Rieger, R. Ober, G. M. Hagen, J. B. Sibarita, J. Ries, R. Henriques, M. Unser, and S. Holden, “Super-resolution fight club: assessment of 2D and 3D single-molecule localization microscopy software,” Nat. Methods 16, 387–395 (2019).
[Crossref] [PubMed]

Dahan, M.

Dai, M.

R. Jungmann, M. S. Avendaño, J. B. Woehrstein, M. Dai, W. M. Shih, and P. Yin, “Multiplexed 3D cellular super-resolution imaging with DNA-PAINT and Exchange-PAINT,” Nat. Methods 11, 313–318 (2014).
[Crossref] [PubMed]

Darzacq, X.

Davidson, M. W.

D. Li, L. Shao, B.-C. Chen, X. Zhang, M. Zhang, B. Moses, D. E. Milkie, J. R. Beach, J. A. Hammer, M. Pasham, T. Kirchhausen, M. A. Baird, M. W. Davidson, P. Xu, and E. Betzig, “Extended-resolution structured illumination imaging of endocytic and cytoskeletal dynamics,” Science 349, aab3500 (2015).
[Crossref]

R. Fiolka, L. Shao, E. H. Rego, M. W. Davidson, and M. G. L. Gustafsson, “Time-lapse two-color 3D imaging of live cells with doubled resolution using structured illumination,” Proc. Natl. Acad. Sci. United States Am. 109, 5311 (2012).
[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, 1642–1645 (2006).
[Crossref] [PubMed]

Drummen, G. P.

L. Schermelleh, A. Ferrand, T. Huser, C. Eggeling, M. Sauer, O. Biehlmaier, and G. P. Drummen, “Super-resolution microscopy demystified,” Nat. Cell Biol. 21, 72–84 (2019).
[Crossref] [PubMed]

Eggeling, C.

L. Schermelleh, A. Ferrand, T. Huser, C. Eggeling, M. Sauer, O. Biehlmaier, and G. P. Drummen, “Super-resolution microscopy demystified,” Nat. Cell Biol. 21, 72–84 (2019).
[Crossref] [PubMed]

Eilers, Y.

Y. Eilers, H. Ta, K. C. Gwosch, F. Balzarotti, and S. W. Hell, “MINFLUX monitors rapid molecular jumps with superior spatiotemporal resolution,” Proc. Natl. Acad. Sci. 115, 6117–6122 (2018).
[Crossref] [PubMed]

F. Balzarotti, Y. Eilers, K. C. Gwosch, A. H. Gynnå, V. Westphal, F. D. Stefani, J. Elf, and S. W. Hell, “Nanometer resolution imaging and tracking of fluorescent molecules with minimal photon fluxes,” Science 355, 606–612 (2017).
[Crossref]

El Beheiry, M.

Elf, J.

F. Balzarotti, Y. Eilers, K. C. Gwosch, A. H. Gynnå, V. Westphal, F. D. Stefani, J. Elf, and S. W. Hell, “Nanometer resolution imaging and tracking of fluorescent molecules with minimal photon fluxes,” Science 355, 606–612 (2017).
[Crossref]

Endesfelder, U.

Ferrand, A.

L. Schermelleh, A. Ferrand, T. Huser, C. Eggeling, M. Sauer, O. Biehlmaier, and G. P. Drummen, “Super-resolution microscopy demystified,” Nat. Cell Biol. 21, 72–84 (2019).
[Crossref] [PubMed]

Fiolka, R.

R. Fiolka, L. Shao, E. H. Rego, M. W. Davidson, and M. G. L. Gustafsson, “Time-lapse two-color 3D imaging of live cells with doubled resolution using structured illumination,” Proc. Natl. Acad. Sci. United States Am. 109, 5311 (2012).
[Crossref]

Flyvbjerg, H.

K. I. Mortensen, L. S. Churchman, J. A. Spudich, and H. Flyvbjerg, “Optimized localization analysis for single-molecule tracking and super-resolution microscopy,” Nat. Methods 7, 377–381 (2010).
[Crossref] [PubMed]

Fuertbauer, E.

S. Wieser, M. Moertelmaier, E. Fuertbauer, H. Stockinger, and G. J. Schütz, “(Un)confined diffusion of CD59 in the plasma membrane determined by high-resolution single molecule microscopy,” Biophys. J. 92, 3719–3728 (2007).
[Crossref] [PubMed]

Fujiwara, T.

K. Ritchie, X. Y. Shan, J. Kondo, K. Iwasawa, T. Fujiwara, and A. Kusumi, “Detection of non-Brownian diffusion in the cell membrane in single molecule tracking,” Biophys. J. 88, 2266–2277 (2005).
[Crossref]

Gustafsson, M. G.

M. G. Gustafsson, D. A. Agard, and J. W. Sedat, “I5M: 3D widefield light microscopy with better than 100 nm axial resolution,” J. Microsc. 195, 10–16 (1999).
[Crossref] [PubMed]

Gustafsson, M. G. L.

R. Fiolka, L. Shao, E. H. Rego, M. W. Davidson, and M. G. L. Gustafsson, “Time-lapse two-color 3D imaging of live cells with doubled resolution using structured illumination,” Proc. Natl. Acad. Sci. United States Am. 109, 5311 (2012).
[Crossref]

Gwosch, K. C.

Y. Eilers, H. Ta, K. C. Gwosch, F. Balzarotti, and S. W. Hell, “MINFLUX monitors rapid molecular jumps with superior spatiotemporal resolution,” Proc. Natl. Acad. Sci. 115, 6117–6122 (2018).
[Crossref] [PubMed]

F. Balzarotti, Y. Eilers, K. C. Gwosch, A. H. Gynnå, V. Westphal, F. D. Stefani, J. Elf, and S. W. Hell, “Nanometer resolution imaging and tracking of fluorescent molecules with minimal photon fluxes,” Science 355, 606–612 (2017).
[Crossref]

Gynnå, A. H.

F. Balzarotti, Y. Eilers, K. C. Gwosch, A. H. Gynnå, V. Westphal, F. D. Stefani, J. Elf, and S. W. Hell, “Nanometer resolution imaging and tracking of fluorescent molecules with minimal photon fluxes,” Science 355, 606–612 (2017).
[Crossref]

Hagen, G. M.

D. Sage, T. A. Pham, H. Babcock, T. Lukes, T. Pengo, J. Chao, R. Velmurugan, A. Herbert, A. Agrawal, S. Colabrese, A. Wheeler, A. Archetti, B. Rieger, R. Ober, G. M. Hagen, J. B. Sibarita, J. Ries, R. Henriques, M. Unser, and S. Holden, “Super-resolution fight club: assessment of 2D and 3D single-molecule localization microscopy software,” Nat. Methods 16, 387–395 (2019).
[Crossref] [PubMed]

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, 2389–2390 (2014).
[Crossref] [PubMed]

Hammer, J. A.

D. Li, L. Shao, B.-C. Chen, X. Zhang, M. Zhang, B. Moses, D. E. Milkie, J. R. Beach, J. A. Hammer, M. Pasham, T. Kirchhausen, M. A. Baird, M. W. Davidson, P. Xu, and E. Betzig, “Extended-resolution structured illumination imaging of endocytic and cytoskeletal dynamics,” Science 349, aab3500 (2015).
[Crossref]

Heilemann, M.

Heintzmann, R.

Hell, S. W.

Y. Eilers, H. Ta, K. C. Gwosch, F. Balzarotti, and S. W. Hell, “MINFLUX monitors rapid molecular jumps with superior spatiotemporal resolution,” Proc. Natl. Acad. Sci. 115, 6117–6122 (2018).
[Crossref] [PubMed]

F. Balzarotti, Y. Eilers, K. C. Gwosch, A. H. Gynnå, V. Westphal, F. D. Stefani, J. Elf, and S. W. Hell, “Nanometer resolution imaging and tracking of fluorescent molecules with minimal photon fluxes,” Science 355, 606–612 (2017).
[Crossref]

Hennig, S.

M. Müller, V. Mönkemöller, S. Hennig, W. Hübner, and T. Huser, “Open-source image reconstruction of super-resolution structured illumination microscopy data in ImageJ,” Nat. Commun. 7, 10980 (2016).
[Crossref] [PubMed]

Henriques, R.

D. Sage, T. A. Pham, H. Babcock, T. Lukes, T. Pengo, J. Chao, R. Velmurugan, A. Herbert, A. Agrawal, S. Colabrese, A. Wheeler, A. Archetti, B. Rieger, R. Ober, G. M. Hagen, J. B. Sibarita, J. Ries, R. Henriques, M. Unser, and S. Holden, “Super-resolution fight club: assessment of 2D and 3D single-molecule localization microscopy software,” Nat. Methods 16, 387–395 (2019).
[Crossref] [PubMed]

Herbert, A.

D. Sage, T. A. Pham, H. Babcock, T. Lukes, T. Pengo, J. Chao, R. Velmurugan, A. Herbert, A. Agrawal, S. Colabrese, A. Wheeler, A. Archetti, B. Rieger, R. Ober, G. M. Hagen, J. B. Sibarita, J. Ries, R. Henriques, M. Unser, and S. Holden, “Super-resolution fight club: assessment of 2D and 3D single-molecule localization microscopy software,” Nat. Methods 16, 387–395 (2019).
[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, 1642–1645 (2006).
[Crossref] [PubMed]

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J. Cnossen, T. Hinsdale, R. Thorsen, F. Schueder, R. Jungmann, C. S. Smith, B. Rieger, and S. Stallinga, “Localization microscopy at doubled precision with patterned illumination,” bioRxiv p. 554337 (2019).

Holden, S.

D. Sage, T. A. Pham, H. Babcock, T. Lukes, T. Pengo, J. Chao, R. Velmurugan, A. Herbert, A. Agrawal, S. Colabrese, A. Wheeler, A. Archetti, B. Rieger, R. Ober, G. M. Hagen, J. B. Sibarita, J. Ries, R. Henriques, M. Unser, and S. Holden, “Super-resolution fight club: assessment of 2D and 3D single-molecule localization microscopy software,” Nat. Methods 16, 387–395 (2019).
[Crossref] [PubMed]

Hübner, W.

M. Müller, V. Mönkemöller, S. Hennig, W. Hübner, and T. Huser, “Open-source image reconstruction of super-resolution structured illumination microscopy data in ImageJ,” Nat. Commun. 7, 10980 (2016).
[Crossref] [PubMed]

Huser, T.

L. Schermelleh, A. Ferrand, T. Huser, C. Eggeling, M. Sauer, O. Biehlmaier, and G. P. Drummen, “Super-resolution microscopy demystified,” Nat. Cell Biol. 21, 72–84 (2019).
[Crossref] [PubMed]

R. Heintzmann and T. Huser, “Super-Resolution Structured Illumination Microscopy,” Chem. Rev. 117, 13890–13908 (2017).
[Crossref] [PubMed]

M. Müller, V. Mönkemöller, S. Hennig, W. Hübner, and T. Huser, “Open-source image reconstruction of super-resolution structured illumination microscopy data in ImageJ,” Nat. Commun. 7, 10980 (2016).
[Crossref] [PubMed]

Iwasawa, K.

K. Ritchie, X. Y. Shan, J. Kondo, K. Iwasawa, T. Fujiwara, and A. Kusumi, “Detection of non-Brownian diffusion in the cell membrane in single molecule tracking,” Biophys. J. 88, 2266–2277 (2005).
[Crossref]

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, 373–375 (2010).
[Crossref] [PubMed]

Jungmann, R.

R. Jungmann, M. S. Avendaño, J. B. Woehrstein, M. Dai, W. M. Shih, and P. Yin, “Multiplexed 3D cellular super-resolution imaging with DNA-PAINT and Exchange-PAINT,” Nat. Methods 11, 313–318 (2014).
[Crossref] [PubMed]

J. Cnossen, T. Hinsdale, R. Thorsen, F. Schueder, R. Jungmann, C. S. Smith, B. Rieger, and S. Stallinga, “Localization microscopy at doubled precision with patterned illumination,” bioRxiv p. 554337 (2019).

Kirchhausen, T.

D. Li, L. Shao, B.-C. Chen, X. Zhang, M. Zhang, B. Moses, D. E. Milkie, J. R. Beach, J. A. Hammer, M. Pasham, T. Kirchhausen, M. A. Baird, M. W. Davidson, P. Xu, and E. Betzig, “Extended-resolution structured illumination imaging of endocytic and cytoskeletal dynamics,” Science 349, aab3500 (2015).
[Crossref]

Kondo, J.

K. Ritchie, X. Y. Shan, J. Kondo, K. Iwasawa, T. Fujiwara, and A. Kusumi, “Detection of non-Brownian diffusion in the cell membrane in single molecule tracking,” Biophys. J. 88, 2266–2277 (2005).
[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, 2389–2390 (2014).
[Crossref] [PubMed]

Kusumi, A.

K. Ritchie, X. Y. Shan, J. Kondo, K. Iwasawa, T. Fujiwara, and A. Kusumi, “Detection of non-Brownian diffusion in the cell membrane in single molecule tracking,” Biophys. J. 88, 2266–2277 (2005).
[Crossref]

Larson, D. R.

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

D. Li, L. Shao, B.-C. Chen, X. Zhang, M. Zhang, B. Moses, D. E. Milkie, J. R. Beach, J. A. Hammer, M. Pasham, T. Kirchhausen, M. A. Baird, M. W. Davidson, P. Xu, and E. Betzig, “Extended-resolution structured illumination imaging of endocytic and cytoskeletal dynamics,” Science 349, aab3500 (2015).
[Crossref]

Lidke, K. A.

C. S. Smith, N. Joseph, B. Rieger, and K. A. Lidke, “Fast, single-molecule localization that achieves theoretically minimum uncertainty,” Nat. Methods 7, 373–375 (2010).
[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, 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, 1642–1645 (2006).
[Crossref] [PubMed]

Lukes, T.

D. Sage, T. A. Pham, H. Babcock, T. Lukes, T. Pengo, J. Chao, R. Velmurugan, A. Herbert, A. Agrawal, S. Colabrese, A. Wheeler, A. Archetti, B. Rieger, R. Ober, G. M. Hagen, J. B. Sibarita, J. Ries, R. Henriques, M. Unser, and S. Holden, “Super-resolution fight club: assessment of 2D and 3D single-molecule localization microscopy software,” Nat. Methods 16, 387–395 (2019).
[Crossref] [PubMed]

Milkie, D. E.

D. Li, L. Shao, B.-C. Chen, X. Zhang, M. Zhang, B. Moses, D. E. Milkie, J. R. Beach, J. A. Hammer, M. Pasham, T. Kirchhausen, M. A. Baird, M. W. Davidson, P. Xu, and E. Betzig, “Extended-resolution structured illumination imaging of endocytic and cytoskeletal dynamics,” Science 349, aab3500 (2015).
[Crossref]

Moertelmaier, M.

S. Wieser, M. Moertelmaier, E. Fuertbauer, H. Stockinger, and G. J. Schütz, “(Un)confined diffusion of CD59 in the plasma membrane determined by high-resolution single molecule microscopy,” Biophys. J. 92, 3719–3728 (2007).
[Crossref] [PubMed]

Mönkemöller, V.

M. Müller, V. Mönkemöller, S. Hennig, W. Hübner, and T. Huser, “Open-source image reconstruction of super-resolution structured illumination microscopy data in ImageJ,” Nat. Commun. 7, 10980 (2016).
[Crossref] [PubMed]

Mortensen, K. I.

K. I. Mortensen, L. S. Churchman, J. A. Spudich, and H. Flyvbjerg, “Optimized localization analysis for single-molecule tracking and super-resolution microscopy,” Nat. Methods 7, 377–381 (2010).
[Crossref] [PubMed]

Moses, B.

D. Li, L. Shao, B.-C. Chen, X. Zhang, M. Zhang, B. Moses, D. E. Milkie, J. R. Beach, J. A. Hammer, M. Pasham, T. Kirchhausen, M. A. Baird, M. W. Davidson, P. Xu, and E. Betzig, “Extended-resolution structured illumination imaging of endocytic and cytoskeletal dynamics,” Science 349, aab3500 (2015).
[Crossref]

Müller, M.

M. Müller, V. Mönkemöller, S. Hennig, W. Hübner, and T. Huser, “Open-source image reconstruction of super-resolution structured illumination microscopy data in ImageJ,” Nat. Commun. 7, 10980 (2016).
[Crossref] [PubMed]

Ober, R.

D. Sage, T. A. Pham, H. Babcock, T. Lukes, T. Pengo, J. Chao, R. Velmurugan, A. Herbert, A. Agrawal, S. Colabrese, A. Wheeler, A. Archetti, B. Rieger, R. Ober, G. M. Hagen, J. B. Sibarita, J. Ries, R. Henriques, M. Unser, and S. Holden, “Super-resolution fight club: assessment of 2D and 3D single-molecule localization microscopy software,” Nat. Methods 16, 387–395 (2019).
[Crossref] [PubMed]

Ober, R. J.

S. Ram, E. S. Ward, and R. J. Ober, “Beyond Rayleigh’s criterion: A resolution measure with application to single-molecule microscopy,” Proc. Natl. Acad. Sci. 103, 4457–4462 (2006).
[Crossref]

R. J. Ober, S. Ram, and E. S. Ward, “Localization Accuracy in Single-Molecule Microscopy,” Biophys. J. 86, 1185–1200 (2004).
[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, 1642–1645 (2006).
[Crossref] [PubMed]

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, 2389–2390 (2014).
[Crossref] [PubMed]

Pasham, M.

D. Li, L. Shao, B.-C. Chen, X. Zhang, M. Zhang, B. Moses, D. E. Milkie, J. R. Beach, J. A. Hammer, M. Pasham, T. Kirchhausen, M. A. Baird, M. W. Davidson, P. Xu, and E. Betzig, “Extended-resolution structured illumination imaging of endocytic and cytoskeletal dynamics,” Science 349, aab3500 (2015).
[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, 1642–1645 (2006).
[Crossref] [PubMed]

Pengo, T.

D. Sage, T. A. Pham, H. Babcock, T. Lukes, T. Pengo, J. Chao, R. Velmurugan, A. Herbert, A. Agrawal, S. Colabrese, A. Wheeler, A. Archetti, B. Rieger, R. Ober, G. M. Hagen, J. B. Sibarita, J. Ries, R. Henriques, M. Unser, and S. Holden, “Super-resolution fight club: assessment of 2D and 3D single-molecule localization microscopy software,” Nat. Methods 16, 387–395 (2019).
[Crossref] [PubMed]

Pham, T. A.

D. Sage, T. A. Pham, H. Babcock, T. Lukes, T. Pengo, J. Chao, R. Velmurugan, A. Herbert, A. Agrawal, S. Colabrese, A. Wheeler, A. Archetti, B. Rieger, R. Ober, G. M. Hagen, J. B. Sibarita, J. Ries, R. Henriques, M. Unser, and S. Holden, “Super-resolution fight club: assessment of 2D and 3D single-molecule localization microscopy software,” Nat. Methods 16, 387–395 (2019).
[Crossref] [PubMed]

Ram, S.

S. Ram, E. S. Ward, and R. J. Ober, “Beyond Rayleigh’s criterion: A resolution measure with application to single-molecule microscopy,” Proc. Natl. Acad. Sci. 103, 4457–4462 (2006).
[Crossref]

R. J. Ober, S. Ram, and E. S. Ward, “Localization Accuracy in Single-Molecule Microscopy,” Biophys. J. 86, 1185–1200 (2004).
[Crossref] [PubMed]

Rego, E. H.

R. Fiolka, L. Shao, E. H. Rego, M. W. Davidson, and M. G. L. Gustafsson, “Time-lapse two-color 3D imaging of live cells with doubled resolution using structured illumination,” Proc. Natl. Acad. Sci. United States Am. 109, 5311 (2012).
[Crossref]

Rieger, B.

D. Sage, T. A. Pham, H. Babcock, T. Lukes, T. Pengo, J. Chao, R. Velmurugan, A. Herbert, A. Agrawal, S. Colabrese, A. Wheeler, A. Archetti, B. Rieger, R. Ober, G. M. Hagen, J. B. Sibarita, J. Ries, R. Henriques, M. Unser, and S. Holden, “Super-resolution fight club: assessment of 2D and 3D single-molecule localization microscopy software,” Nat. Methods 16, 387–395 (2019).
[Crossref] [PubMed]

N. Chakrova, R. Heintzmann, B. Rieger, and S. Stallinga, “Studying different illumination patterns for resolution improvement in fluorescence microscopy,” Opt. Express 23, 31367 (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, 373–375 (2010).
[Crossref] [PubMed]

J. Cnossen, T. Hinsdale, R. Thorsen, F. Schueder, R. Jungmann, C. S. Smith, B. Rieger, and S. Stallinga, “Localization microscopy at doubled precision with patterned illumination,” bioRxiv p. 554337 (2019).

Ries, J.

D. Sage, T. A. Pham, H. Babcock, T. Lukes, T. Pengo, J. Chao, R. Velmurugan, A. Herbert, A. Agrawal, S. Colabrese, A. Wheeler, A. Archetti, B. Rieger, R. Ober, G. M. Hagen, J. B. Sibarita, J. Ries, R. Henriques, M. Unser, and S. Holden, “Super-resolution fight club: assessment of 2D and 3D single-molecule localization microscopy software,” Nat. Methods 16, 387–395 (2019).
[Crossref] [PubMed]

Ritchie, K.

K. Ritchie, X. Y. Shan, J. Kondo, K. Iwasawa, T. Fujiwara, and A. Kusumi, “Detection of non-Brownian diffusion in the cell membrane in single molecule tracking,” Biophys. J. 88, 2266–2277 (2005).
[Crossref]

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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, 793–795 (2006).
[Crossref] [PubMed]

Sage, D.

D. Sage, T. A. Pham, H. Babcock, T. Lukes, T. Pengo, J. Chao, R. Velmurugan, A. Herbert, A. Agrawal, S. Colabrese, A. Wheeler, A. Archetti, B. Rieger, R. Ober, G. M. Hagen, J. B. Sibarita, J. Ries, R. Henriques, M. Unser, and S. Holden, “Super-resolution fight club: assessment of 2D and 3D single-molecule localization microscopy software,” Nat. Methods 16, 387–395 (2019).
[Crossref] [PubMed]

Sauer, M.

L. Schermelleh, A. Ferrand, T. Huser, C. Eggeling, M. Sauer, O. Biehlmaier, and G. P. Drummen, “Super-resolution microscopy demystified,” Nat. Cell Biol. 21, 72–84 (2019).
[Crossref] [PubMed]

S. Wolter, U. Endesfelder, S. van de Linde, M. Heilemann, and M. Sauer, “Measuring localization performance of super-resolution algorithms on very active samples,” Opt. Express 19, 7020 (2011).
[Crossref] [PubMed]

Schermelleh, L.

L. Schermelleh, A. Ferrand, T. Huser, C. Eggeling, M. Sauer, O. Biehlmaier, and G. P. Drummen, “Super-resolution microscopy demystified,” Nat. Cell Biol. 21, 72–84 (2019).
[Crossref] [PubMed]

Schueder, F.

J. Cnossen, T. Hinsdale, R. Thorsen, F. Schueder, R. Jungmann, C. S. Smith, B. Rieger, and S. Stallinga, “Localization microscopy at doubled precision with patterned illumination,” bioRxiv p. 554337 (2019).

Schütz, G. J.

S. Wieser, M. Axmann, and G. J. Schütz, “Versatile analysis of single-molecule tracking data by comprehensive testing against Monte Carlo simulations,” Biophys. J. 95, 5988–6001 (2008).
[Crossref] [PubMed]

S. Wieser and G. J. Schütz, “Tracking single molecules in the live cell plasma membrane-Do’s and Don’t’s,” Methods 46, 131–140 (2008).
[Crossref] [PubMed]

S. Wieser, M. Moertelmaier, E. Fuertbauer, H. Stockinger, and G. J. Schütz, “(Un)confined diffusion of CD59 in the plasma membrane determined by high-resolution single molecule microscopy,” Biophys. J. 92, 3719–3728 (2007).
[Crossref] [PubMed]

Sedat, J. W.

M. G. Gustafsson, D. A. Agard, and J. W. Sedat, “I5M: 3D widefield light microscopy with better than 100 nm axial resolution,” J. Microsc. 195, 10–16 (1999).
[Crossref] [PubMed]

Shan, X. Y.

K. Ritchie, X. Y. Shan, J. Kondo, K. Iwasawa, T. Fujiwara, and A. Kusumi, “Detection of non-Brownian diffusion in the cell membrane in single molecule tracking,” Biophys. J. 88, 2266–2277 (2005).
[Crossref]

Shao, L.

D. Li, L. Shao, B.-C. Chen, X. Zhang, M. Zhang, B. Moses, D. E. Milkie, J. R. Beach, J. A. Hammer, M. Pasham, T. Kirchhausen, M. A. Baird, M. W. Davidson, P. Xu, and E. Betzig, “Extended-resolution structured illumination imaging of endocytic and cytoskeletal dynamics,” Science 349, aab3500 (2015).
[Crossref]

R. Fiolka, L. Shao, E. H. Rego, M. W. Davidson, and M. G. L. Gustafsson, “Time-lapse two-color 3D imaging of live cells with doubled resolution using structured illumination,” Proc. Natl. Acad. Sci. United States Am. 109, 5311 (2012).
[Crossref]

Shih, W. M.

R. Jungmann, M. S. Avendaño, J. B. Woehrstein, M. Dai, W. M. Shih, and P. Yin, “Multiplexed 3D cellular super-resolution imaging with DNA-PAINT and Exchange-PAINT,” Nat. Methods 11, 313–318 (2014).
[Crossref] [PubMed]

Sibarita, J. B.

D. Sage, T. A. Pham, H. Babcock, T. Lukes, T. Pengo, J. Chao, R. Velmurugan, A. Herbert, A. Agrawal, S. Colabrese, A. Wheeler, A. Archetti, B. Rieger, R. Ober, G. M. Hagen, J. B. Sibarita, J. Ries, R. Henriques, M. Unser, and S. Holden, “Super-resolution fight club: assessment of 2D and 3D single-molecule localization microscopy software,” Nat. Methods 16, 387–395 (2019).
[Crossref] [PubMed]

Smith, C. S.

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

J. Cnossen, T. Hinsdale, R. Thorsen, F. Schueder, R. Jungmann, C. S. Smith, B. Rieger, and S. Stallinga, “Localization microscopy at doubled precision with patterned illumination,” bioRxiv p. 554337 (2019).

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, 1642–1645 (2006).
[Crossref] [PubMed]

Spudich, J. A.

K. I. Mortensen, L. S. Churchman, J. A. Spudich, and H. Flyvbjerg, “Optimized localization analysis for single-molecule tracking and super-resolution microscopy,” Nat. Methods 7, 377–381 (2010).
[Crossref] [PubMed]

Stallinga, S.

N. Chakrova, R. Heintzmann, B. Rieger, and S. Stallinga, “Studying different illumination patterns for resolution improvement in fluorescence microscopy,” Opt. Express 23, 31367 (2015).
[Crossref] [PubMed]

J. Cnossen, T. Hinsdale, R. Thorsen, F. Schueder, R. Jungmann, C. S. Smith, B. Rieger, and S. Stallinga, “Localization microscopy at doubled precision with patterned illumination,” bioRxiv p. 554337 (2019).

Stefani, F. D.

F. Balzarotti, Y. Eilers, K. C. Gwosch, A. H. Gynnå, V. Westphal, F. D. Stefani, J. Elf, and S. W. Hell, “Nanometer resolution imaging and tracking of fluorescent molecules with minimal photon fluxes,” Science 355, 606–612 (2017).
[Crossref]

Stockinger, H.

S. Wieser, M. Moertelmaier, E. Fuertbauer, H. Stockinger, and G. J. Schütz, “(Un)confined diffusion of CD59 in the plasma membrane determined by high-resolution single molecule microscopy,” Biophys. J. 92, 3719–3728 (2007).
[Crossref] [PubMed]

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, 2389–2390 (2014).
[Crossref] [PubMed]

Ta, H.

Y. Eilers, H. Ta, K. C. Gwosch, F. Balzarotti, and S. W. Hell, “MINFLUX monitors rapid molecular jumps with superior spatiotemporal resolution,” Proc. Natl. Acad. Sci. 115, 6117–6122 (2018).
[Crossref] [PubMed]

Thompson, R. E.

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

Thorsen, R.

J. Cnossen, T. Hinsdale, R. Thorsen, F. Schueder, R. Jungmann, C. S. Smith, B. Rieger, and S. Stallinga, “Localization microscopy at doubled precision with patterned illumination,” bioRxiv p. 554337 (2019).

Tian, L.

Unser, M.

D. Sage, T. A. Pham, H. Babcock, T. Lukes, T. Pengo, J. Chao, R. Velmurugan, A. Herbert, A. Agrawal, S. Colabrese, A. Wheeler, A. Archetti, B. Rieger, R. Ober, G. M. Hagen, J. B. Sibarita, J. Ries, R. Henriques, M. Unser, and S. Holden, “Super-resolution fight club: assessment of 2D and 3D single-molecule localization microscopy software,” Nat. Methods 16, 387–395 (2019).
[Crossref] [PubMed]

van de Linde, S.

Velmurugan, R.

D. Sage, T. A. Pham, H. Babcock, T. Lukes, T. Pengo, J. Chao, R. Velmurugan, A. Herbert, A. Agrawal, S. Colabrese, A. Wheeler, A. Archetti, B. Rieger, R. Ober, G. M. Hagen, J. B. Sibarita, J. Ries, R. Henriques, M. Unser, and S. Holden, “Super-resolution fight club: assessment of 2D and 3D single-molecule localization microscopy software,” Nat. Methods 16, 387–395 (2019).
[Crossref] [PubMed]

Waller, L.

Ward, E. S.

S. Ram, E. S. Ward, and R. J. Ober, “Beyond Rayleigh’s criterion: A resolution measure with application to single-molecule microscopy,” Proc. Natl. Acad. Sci. 103, 4457–4462 (2006).
[Crossref]

R. J. Ober, S. Ram, and E. S. Ward, “Localization Accuracy in Single-Molecule Microscopy,” Biophys. J. 86, 1185–1200 (2004).
[Crossref] [PubMed]

Webb, W. W.

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

Westphal, V.

F. Balzarotti, Y. Eilers, K. C. Gwosch, A. H. Gynnå, V. Westphal, F. D. Stefani, J. Elf, and S. W. Hell, “Nanometer resolution imaging and tracking of fluorescent molecules with minimal photon fluxes,” Science 355, 606–612 (2017).
[Crossref]

Wheeler, A.

D. Sage, T. A. Pham, H. Babcock, T. Lukes, T. Pengo, J. Chao, R. Velmurugan, A. Herbert, A. Agrawal, S. Colabrese, A. Wheeler, A. Archetti, B. Rieger, R. Ober, G. M. Hagen, J. B. Sibarita, J. Ries, R. Henriques, M. Unser, and S. Holden, “Super-resolution fight club: assessment of 2D and 3D single-molecule localization microscopy software,” Nat. Methods 16, 387–395 (2019).
[Crossref] [PubMed]

Wieser, S.

S. Wieser, M. Axmann, and G. J. Schütz, “Versatile analysis of single-molecule tracking data by comprehensive testing against Monte Carlo simulations,” Biophys. J. 95, 5988–6001 (2008).
[Crossref] [PubMed]

S. Wieser and G. J. Schütz, “Tracking single molecules in the live cell plasma membrane-Do’s and Don’t’s,” Methods 46, 131–140 (2008).
[Crossref] [PubMed]

S. Wieser, M. Moertelmaier, E. Fuertbauer, H. Stockinger, and G. J. Schütz, “(Un)confined diffusion of CD59 in the plasma membrane determined by high-resolution single molecule microscopy,” Biophys. J. 92, 3719–3728 (2007).
[Crossref] [PubMed]

Woehrstein, J. B.

R. Jungmann, M. S. Avendaño, J. B. Woehrstein, M. Dai, W. M. Shih, and P. Yin, “Multiplexed 3D cellular super-resolution imaging with DNA-PAINT and Exchange-PAINT,” Nat. Methods 11, 313–318 (2014).
[Crossref] [PubMed]

Wolter, S.

Xu, P.

D. Li, L. Shao, B.-C. Chen, X. Zhang, M. Zhang, B. Moses, D. E. Milkie, J. R. Beach, J. A. Hammer, M. Pasham, T. Kirchhausen, M. A. Baird, M. W. Davidson, P. Xu, and E. Betzig, “Extended-resolution structured illumination imaging of endocytic and cytoskeletal dynamics,” Science 349, aab3500 (2015).
[Crossref]

Yeh, L.-H.

Yin, P.

R. Jungmann, M. S. Avendaño, J. B. Woehrstein, M. Dai, W. M. Shih, and P. Yin, “Multiplexed 3D cellular super-resolution imaging with DNA-PAINT and Exchange-PAINT,” Nat. Methods 11, 313–318 (2014).
[Crossref] [PubMed]

Zhang, M.

D. Li, L. Shao, B.-C. Chen, X. Zhang, M. Zhang, B. Moses, D. E. Milkie, J. R. Beach, J. A. Hammer, M. Pasham, T. Kirchhausen, M. A. Baird, M. W. Davidson, P. Xu, and E. Betzig, “Extended-resolution structured illumination imaging of endocytic and cytoskeletal dynamics,” Science 349, aab3500 (2015).
[Crossref]

Zhang, X.

D. Li, L. Shao, B.-C. Chen, X. Zhang, M. Zhang, B. Moses, D. E. Milkie, J. R. Beach, J. A. Hammer, M. Pasham, T. Kirchhausen, M. A. Baird, M. W. Davidson, P. Xu, and E. Betzig, “Extended-resolution structured illumination imaging of endocytic and cytoskeletal dynamics,” Science 349, aab3500 (2015).
[Crossref]

Zhuang, X.

M. J. Rust, M. Bates, and X. Zhuang, “Sub-diffraction-limit imaging by stochastic optical reconstruction microscopy (STORM),” Nat. Methods 3, 793–795 (2006).
[Crossref] [PubMed]

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, 2389–2390 (2014).
[Crossref] [PubMed]

Biomed. Opt. Express (1)

Biophys. J. (5)

R. J. Ober, S. Ram, and E. S. Ward, “Localization Accuracy in Single-Molecule Microscopy,” Biophys. J. 86, 1185–1200 (2004).
[Crossref] [PubMed]

K. Ritchie, X. Y. Shan, J. Kondo, K. Iwasawa, T. Fujiwara, and A. Kusumi, “Detection of non-Brownian diffusion in the cell membrane in single molecule tracking,” Biophys. J. 88, 2266–2277 (2005).
[Crossref]

S. Wieser, M. Moertelmaier, E. Fuertbauer, H. Stockinger, and G. J. Schütz, “(Un)confined diffusion of CD59 in the plasma membrane determined by high-resolution single molecule microscopy,” Biophys. J. 92, 3719–3728 (2007).
[Crossref] [PubMed]

S. Wieser, M. Axmann, and G. J. Schütz, “Versatile analysis of single-molecule tracking data by comprehensive testing against Monte Carlo simulations,” Biophys. J. 95, 5988–6001 (2008).
[Crossref] [PubMed]

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

Chem. Rev. (1)

R. Heintzmann and T. Huser, “Super-Resolution Structured Illumination Microscopy,” Chem. Rev. 117, 13890–13908 (2017).
[Crossref] [PubMed]

J. Microsc. (1)

M. G. Gustafsson, D. A. Agard, and J. W. Sedat, “I5M: 3D widefield light microscopy with better than 100 nm axial resolution,” J. Microsc. 195, 10–16 (1999).
[Crossref] [PubMed]

Methods (1)

S. Wieser and G. J. Schütz, “Tracking single molecules in the live cell plasma membrane-Do’s and Don’t’s,” Methods 46, 131–140 (2008).
[Crossref] [PubMed]

Nat. Cell Biol. (1)

L. Schermelleh, A. Ferrand, T. Huser, C. Eggeling, M. Sauer, O. Biehlmaier, and G. P. Drummen, “Super-resolution microscopy demystified,” Nat. Cell Biol. 21, 72–84 (2019).
[Crossref] [PubMed]

Nat. Commun. (1)

M. Müller, V. Mönkemöller, S. Hennig, W. Hübner, and T. Huser, “Open-source image reconstruction of super-resolution structured illumination microscopy data in ImageJ,” Nat. Commun. 7, 10980 (2016).
[Crossref] [PubMed]

Nat. Methods (5)

D. Sage, T. A. Pham, H. Babcock, T. Lukes, T. Pengo, J. Chao, R. Velmurugan, A. Herbert, A. Agrawal, S. Colabrese, A. Wheeler, A. Archetti, B. Rieger, R. Ober, G. M. Hagen, J. B. Sibarita, J. Ries, R. Henriques, M. Unser, and S. Holden, “Super-resolution fight club: assessment of 2D and 3D single-molecule localization microscopy software,” Nat. Methods 16, 387–395 (2019).
[Crossref] [PubMed]

M. J. Rust, M. Bates, and X. Zhuang, “Sub-diffraction-limit imaging by stochastic optical reconstruction microscopy (STORM),” Nat. Methods 3, 793–795 (2006).
[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, 373–375 (2010).
[Crossref] [PubMed]

R. Jungmann, M. S. Avendaño, J. B. Woehrstein, M. Dai, W. M. Shih, and P. Yin, “Multiplexed 3D cellular super-resolution imaging with DNA-PAINT and Exchange-PAINT,” Nat. Methods 11, 313–318 (2014).
[Crossref] [PubMed]

K. I. Mortensen, L. S. Churchman, J. A. Spudich, and H. Flyvbjerg, “Optimized localization analysis for single-molecule tracking and super-resolution microscopy,” Nat. Methods 7, 377–381 (2010).
[Crossref] [PubMed]

Opt. Express (3)

Proc. Natl. Acad. Sci. (2)

S. Ram, E. S. Ward, and R. J. Ober, “Beyond Rayleigh’s criterion: A resolution measure with application to single-molecule microscopy,” Proc. Natl. Acad. Sci. 103, 4457–4462 (2006).
[Crossref]

Y. Eilers, H. Ta, K. C. Gwosch, F. Balzarotti, and S. W. Hell, “MINFLUX monitors rapid molecular jumps with superior spatiotemporal resolution,” Proc. Natl. Acad. Sci. 115, 6117–6122 (2018).
[Crossref] [PubMed]

Proc. Natl. Acad. Sci. United States Am. (1)

R. Fiolka, L. Shao, E. H. Rego, M. W. Davidson, and M. G. L. Gustafsson, “Time-lapse two-color 3D imaging of live cells with doubled resolution using structured illumination,” Proc. Natl. Acad. Sci. United States Am. 109, 5311 (2012).
[Crossref]

Science (3)

D. Li, L. Shao, B.-C. Chen, X. Zhang, M. Zhang, B. Moses, D. E. Milkie, J. R. Beach, J. A. Hammer, M. Pasham, T. Kirchhausen, M. A. Baird, M. W. Davidson, P. Xu, and E. Betzig, “Extended-resolution structured illumination imaging of endocytic and cytoskeletal dynamics,” Science 349, aab3500 (2015).
[Crossref]

F. Balzarotti, Y. Eilers, K. C. Gwosch, A. H. Gynnå, V. Westphal, F. D. Stefani, J. Elf, and S. W. Hell, “Nanometer resolution imaging and tracking of fluorescent molecules with minimal photon fluxes,” Science 355, 606–612 (2017).
[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, 1642–1645 (2006).
[Crossref] [PubMed]

Other (1)

J. Cnossen, T. Hinsdale, R. Thorsen, F. Schueder, R. Jungmann, C. S. Smith, B. Rieger, and S. Stallinga, “Localization microscopy at doubled precision with patterned illumination,” bioRxiv p. 554337 (2019).

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Figures (8)

Fig. 1
Fig. 1 The SIMPLE concept. (a) Three precisely phase-shifted sinusoidal patterns are used for illuminating a single point emitter. The sinusoidal wave serves as a nanoruler to position a single molecule emitter from which phase-dependent photon counts (n1 = 119 (Φ1), n2 = 73 (Φ2), n3 = 410 (Φ1)) are obtained depending on its relative position (I–III) within the sinusoidal wave. Photon counts ni (red) are fitted with a sine function with three fit parameters (amplitude A, phase ϕ, offset b) to reveal the actual position ϕ within the wave that is mapped to the pixel image coordinate system. (b) In the case of three equally spaced phases (δΦ = 1/3) we find a 2-fold gain in localization precision compared to SMLM (2× smaller standard deviation σ of normally distributed localization points).
Fig. 2
Fig. 2 Simulation and data analysis pipeline. Synthetic data are generated using random positions of single molecule emitters in k = 3 phase shifted illumination patterns with modulation depth m. The photon emission process is modeled as a linear response to the actual illumination intensity with Poissonian distributed photon counts. Photon positions are further normally distributed around the initial single emitter position with a standard deviation based on a defined PSF of the imaging system on a pixelized camera system. Subsequently a white noise contribution is superimposed on the image to account for read-out noise and autofluorescence in fluorescence imaging. For data acquisition, k = 3 phase shifted images are recorded for each direction. Data analysis first predefines pixels with high modulation contrast. In the next step, a mask (see Fig. 4) around the predefined pixel reads the number of photons. The number of photons at the three phase positions are fitted with a sine function to extract the actual position of the particle.
Fig. 3
Fig. 3 Comparison of localization precision between SIMPLE and SMLM (a) Illustration of equidistant phase shifting for increasing number of phase shifts (b) Localization gain of SIMPLE versus SMLM for N = 500 photons for increasing number of phase shifts and various background noise b = 0, 2 and 4 counts/pixel. More phase shifts Φ i result in a larger number of fitting points at the expense of fewer photons per phase shift. In all cases the sum ( n i ) over all phases is kept constant. (c) The localization gain for equally distributed phase shifts with δΦ = 1/3 slightly depends on the actual position within the period (red) reaching localization improvements of about 1.8 to 3.1-fold. For three smaller phase shifts with δΦ = 1/7 (blue) we find a pronounced improvement if the particle is located near the excitation minimum. Green lines indicate theoretical limits of particle localization precision in the minimum (light green) and at the peak (dark green). (d–g) Comparison between SIMPLE and SMLM in the presence of background noise b = 0, 2, 4 and 6 counts/pixel. The theoretical limit of classical SMLM localization precision derived by Mortensen et al. [19] is shown in black (d), highlighting the localization precision improvement of SIMPLE over SMLM.
Fig. 4
Fig. 4 Pixel selection and relation to PSF size for various background levels. (a–c) Change in the localization gain for various mask types, PSF to pixel size ratios (σ) and background noises. The mask size is increased from 4 to 29 pixels (g). By changing the mask size, a larger fraction of the emitters’ signal will be accounted for (d–f), but more read-out noise is accumulated. (g) Corresponding series of figures chosen as the appropriate mask given the experimental parameters (noise, pixel size and PSF).
Fig. 5
Fig. 5 Schematic of the SIMPLE setup and calibration. (a) Excitation laser 473 nm, 500 mW; 10× telescope for beam expansion; half wave plate (HWP); digital micro-mirror device (DMD) as spatial light modulator; quarter wave plate (QWP); neutral density (ND) filter; spatial mask for selection of diffraction orders; segmented “pizza” polarizer (SP) for polarization control; relay lenses; identical dichroic mirrors (DM) for azimuthal polarization conservation; NA 1.49 objective lens; sample on xy piezo stage; sCMOS camera with emission filters in the detection path. (b) Representative image sets of three phases used for period estimation, showing single Alexa Fluor488 molecules bound to functionalized glass. (c) Same image as in (b) with highlighted quadrants and enlarged region of interest (ROI). (d) Power-spectrum visualization of the cross-correlation in the Fourier domain returned by fairSIM. Red circle marks the maximum of correlation. FairSIM performs a fit with sub-pixel resolution and estimates the pattern period. (e) Illustration of the illumination pattern overlaid on an enlarged ROI (c) of recorded signals after each phase-shift representing the camera-based coordinate system and the sinusoidal wave-based coordinate system. (f, g) Period histograms for each quadrant and the full field of view. The precision of the spatial period in the whole FOV can be estimated to (169.1 ± 0.1) nm, and in the individual quadrants (Quadrant1: (168.7 ± 0.2) nm; Quadrant2: (168.8 ± 0.2) nm; Quadrant3: (169.4 ± 0.2) nm; Quadrant4: (169.3 ± 0.2) nm).
Fig. 6
Fig. 6 Exemplary data and processing routine for SIMPLE. (a) Time series of a single Alexa Fluor488 molecule emitting upon repeated excitation (exposure time 50 ms) with three equidistant phases of a sinusoidal pattern. (b) Sketch of the phase steps Φ i = 0, 1/3, 2/3. (c) Intensity time trace of the emitter in (a) reflecting phase-dependent intensity modulation at 300 time points using a centered 3 × 3 mask for photon count calculation. (d) Extraction of the position for each intensity triple via a least-squares fitting routine reflecting the variability due to single emitter shot noise and background noise. We did not notice any sample drift during the acquisition time. (e) Statistics of the fitted positions in (d) for the amplitude (left), background (middle) and normalized phase (right). (f) Comparison of the localization precision for the same particle via multiple positioning using Thunderstorm [18] (green) and SIMPLE (pink) with a localization gain of 2.0-fold.
Fig. 7
Fig. 7 Experimental validation of the SIMPLE method on a 15 μm FOV. (a) FOV showing the sample with sparse single Alexa Fluor488 dyes. (b) Exemplary fitting procedure on ∼ 200 triple images for two isolated emitters in (b) (orange and yellow squares). (c) Histogram of x (upper panel) and y (middle panel) localizations of a single emitter are compared to SMLM centroid fitting using Thunderstorm with a localization gain of SIMPLE versus SMLM of 2.0-fold (x-direction) and 2.4-fold (y-direction). Histogram of x localizations of 40 single molecules in the FOV with an average gain of 2.1-fold (lower panel).
Fig. 8
Fig. 8 Experimental validation of the SIMPLE method using piezo-stage driven 20 nm lateral movements (ground truth) of isolated Alexa Fluor488 emitters. (a) Sketch of piezo-nanopositioning of single molecule emitters. (b) Localization histogram of single emitters at three different positions for d = 20 nm distance and (c) Distance histogram of single emitters using SIMPLE (red) and Thunderstorm (grey) highlighting the power of the method.

Tables (1)

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Table 1 Estimation of the equivalent noise for a reduced modulation depth m.

Equations (9)

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A = 2 2 3 ( n 1 n 2 ) 2 + ( n 1 n 3 ) 2 + ( n 2 n 3 ) 2
ϕ = 1 π arctan ( 2 n 1 + n 2 + n 3 + 2 ( n 1 n 2 ) 2 + ( n 1 n 3 ) 2 + ( n 2 n 3 ) 2 3 ( n 2 n 3 ) )
b = 1 3 ( n 1 + n 2 + n 3 2 ( n 1 n 2 ) 2 + ( n 1 n 3 ) 2 + ( n 2 n 3 ) 2 )
Δ φ = i ( ϕ n i Δ n i ) 2
ϕ n 1 = 3 ( n 2 n 3 ) 2 π ( ( n 1 n 2 ) 2 + ( n 1 n 3 ) 2 + ( n 2 n 3 ) 2 )
ϕ n 2 = 3 ( n 3 n 1 ) 2 π ( ( n 1 n 2 ) 2 + ( n 1 n 3 ) 2 + ( n 2 n 3 ) 2 )
ϕ n 3 = 3 ( n 1 n 2 ) 2 π ( ( n 1 n 2 ) 2 + ( n 1 n 3 ) 2 + ( n 2 n 3 ) 2 )
Δ ϕ = N 3 2 π ( 2 σ + N ) , and for σ = 0 , Δ ϕ = N 3 2 π
Δ ϕ = N 1 2 π ( 6 σ + N ) , and for σ = 0 , Δ ϕ = N 1 2 π

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