Abstract

Stochastic optical fluctuation imaging (SOFI) is a super-resolution fluorescence imaging technique that makes use of stochastic fluctuations in the emission of the fluorophores. During a SOFI measurement multiple fluorescence images are acquired from the sample, followed by the calculation of the spatiotemporal cumulants of the intensities observed at each position. Compared to other techniques, SOFI works well under conditions of low signal-to-noise, high background, or high emitter densities. However, it can be difficult to unambiguously determine the reliability of images produced by any superresolution imaging technique. In this work we present a strategy that enables the estimation of the variance or uncertainty associated with each pixel in the SOFI image. In addition to estimating the image quality or reliability, we show that this can be used to optimize the signal-to-noise ratio (SNR) of SOFI images by including multiple pixel combinations in the cumulant calculation. We present an algorithm to perform this optimization, which automatically takes all relevant instrumental, sample, and probe parameters into account. Depending on the optical magnification of the system, this strategy can be used to improve the SNR of a SOFI image by 40% to 90%. This gain in information is entirely free, in the sense that it does not require additional efforts or complications. Alternatively our approach can be applied to reduce the number of fluorescence images to meet a particular quality level by about 30% to 50%, strongly improving the temporal resolution of SOFI imaging.

© 2016 Optical Society of America

Full Article  |  PDF Article
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References

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  1. P. Dedecker, F. C. De Schryver, and J. Hofkens, “Fluorescent proteins: shine on, you crazy diamond,” J. Am. Chem. Soc. 135, 2387–2402 (2013).
    [Crossref] [PubMed]
  2. S. W. Hell and J. Wichmann, “Breaking the diffraction resolution limit by stimulated emission: stimulated-emission-depletion fluorescence microscopy,” Opt. Lett. 19, 780–782 (1994).
    [Crossref] [PubMed]
  3. S. W. Hell, “Toward fluorescence nanoscopy,” Nat. Biotechnol. 21, 1347–1355 (2003).
    [Crossref] [PubMed]
  4. 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]
  5. M. J. Rust, M. Bates, and X. Zhuang, “Sub-diffraction-limit imaging by stochastic optical reconstruction microscopy (STORM),” Nat. Meth. 3, 793–796 (2006).
    [Crossref]
  6. S. T. Hess, T. P. K. Girirajan, and M. D. Mason, “Ultra-high resolution imaging by fluorescence photoactivation localization microscopy,” Biophys. J. 91, 4258–4272 (2006).
    [Crossref] [PubMed]
  7. W. Vandenberg, M. Leutenegger, T. Lasser, J. Hofkens, and P. Dedecker, “Diffraction-unlimited imaging: from pretty pictures to hard numbers,” Cell Tissue Res. 360, 151–178 (2015).
    [Crossref] [PubMed]
  8. T. Dertinger, R. Colyer, G. Iyer, S. Weiss, and J. Enderlein, “Fast, background-free, 3D super-resolution optical fluctuation imaging (SOFI),” Proc. Natl. Acad. Sci. U.S.A. 106, 22287–22292 (2009).
    [Crossref] [PubMed]
  9. T. Dertinger, R. Colyer, R. Vogel, J. Enderlein, and S. Weiss, “Achieving increased resolution and more pixels with superresolution optical fluctuation imaging (SOFI),” Opt. Express 18, 18875–18885 (2010).
    [Crossref] [PubMed]
  10. S. Geissbuehler, C. Dellagiacoma, and T. Lasser, “Comparison between SOFI and STORM,” Biomed. Opt. Express 2, 408–420 (2011).
    [Crossref] [PubMed]
  11. Z. Zeng, X. Chen, H. Wang, N. Huang, C. Shan, H. Zhang, J. Teng, and P. Xi, “Fast super-resolution imaging with ultra-high labeling density achieved by joint tagging super-resolution optical fluctuation imaging,” Sci. Rep. 5, 8359 (2015).
    [Crossref] [PubMed]
  12. T. Dertinger, M. Heilemann, R. Vogel, M. Sauer, and S. Weiss, “Superresolution Optical Fluctuation Imaging with Organic Dyes,” Angew. Chem. Int. Ed. Engl. 49, 9441–9443 (2010).
    [Crossref] [PubMed]
  13. S. Geissbuehler, N. Bocchio, C. Dellagiacoma, C. Berclaz, M. Leutenegger, and T. Lasser, “Mapping molecular statistics with balanced super-resolution optical fluctuation imaging (bSOFI),” Opt. Nanoscopy 1, 4 (2012).
    [Crossref]
  14. P. Dedecker, G. C. H. Mo, T. Dertinger, and J. Zhang, “Widely accessible method for superresolution fluorescence imaging of living systems,” Proc. Natl. Acad. Sci. U.S.A. 109, 10909–10914 (2012).
    [Crossref] [PubMed]
  15. B. Moeyaert, N. NguyenBich, E. De Zitter, S. Rocha, K. Clays, H. Mizuno, L. van Meervelt, J. Hofkens, and P. Dedecker, “Green-to-red photoconvertible dronpa mutant for multimodal super-resolution fluorescence microscopy,” ACS Nano 8, 1664–1673 (2014).
    [Crossref] [PubMed]
  16. S. Geissbuehler, A. Sharipov, A. Godinat, N. L. Bocchio, P. A. Sandoz, A. Huss, N. A. Jensen, S. Jakobs, J. Enderlein, F. Gisou van der Goot, E. A. Dubikovskaya, T. Lasser, and M. Leutenegger, “Live-cell multiplane three-dimensional super-resolution optical fluctuation imaging,” Nat. Commun. 5, 5830 (2014).
    [Crossref] [PubMed]
  17. X. Zhang, X. Chen, Z. Zeng, M. Zhang, Y. Sun, P. Xi, J. Peng, and P. Xu, “Development of a reversibly switchable fluorescent protein for super-resolution optical fluctuation imaging (SOFI),” ACS Nano 9, 2659–2667 (2015).
    [Crossref] [PubMed]
  18. S. Duwe, E. De Zitter, V. Gielen, B. Moeyaert, W. Vandenberg, T. Grotjohann, K. Clays, S. Jakobs, L. Van Meervelt, and P. Dedecker, “Expression-enhanced fluorescent proteins based on enhanced green fluorescent protein for super-resolution microscopy,” ACS Nano (2015).
    [Crossref] [PubMed]
  19. S. Cho, J. Jang, C. Song, H. Lee, P. Ganesan, T.-Y. Yoon, M. W. Kim, M. C. Choi, H. Ihee, W. D. Heo, and Y. Park, “Simple super-resolution live-cell imaging based on diffusion-assisted förster resonance energy transfer,” Sci. Rep. 3, 1208 (2013).
    [Crossref]
  20. Z. Ristanović, M. M. Kerssens, A. V. Kubarev, F. C. Hendriks, P. Dedecker, J. Hofkens, M. B. J. Roeffaers, and B. M. Weckhuysen, “High-resolution single-molecule fluorescence imaging of zeolite aggregates within real-life fluid catalytic cracking particles,” Angew. Chem. Int. Ed. Engl. 54, 1836–1840 (2015).
    [Crossref]
  21. L. Kisley, R. Brunetti, L. J. Tauzin, B. Shuang, X. Yi, A. W. Kirkeminde, D. A. Higgins, S. Weiss, and C. F. Landes, “Characterization of porous materials by fluorescence correlation spectroscopy super-resolution optical fluctuation imaging,” ACS Nano 9, 9158–9166 (2015).
    [Crossref] [PubMed]
  22. A. Stuart and K. Ord, Kendall’s Advanced Theory of Statistics: Volume 1: Distribution Theory, no. v. 1; v. 1994 in Kendall’s Advanced Theory of Statistics (Wiley, 2009).
  23. S. C. Stein, A. Huss, D. Hahnel, I. Gregor, and J. Enderlein, “Fourier interpolation stochastic optical fluctuation imaging,” Opt. Express 23, 16154–16163 (2015).
    [Crossref] [PubMed]
  24. A. J. Stromberg, “Robust covariance estimates based on resampling,” Journal of Statistical Planning and Inference 57, 321–334 (1997). Robust Statistics and Data Analysis, Part {II}.
    [Crossref]
  25. P. Dedecker, S. Duwé, R. K. Neely, and J. Zhang, “Localizer: fast, accurate, open-source, and modular software package for superresolution microscopy,” J. Biomed. Opt. 17, 126008 (2012).
    [Crossref] [PubMed]

2015 (6)

W. Vandenberg, M. Leutenegger, T. Lasser, J. Hofkens, and P. Dedecker, “Diffraction-unlimited imaging: from pretty pictures to hard numbers,” Cell Tissue Res. 360, 151–178 (2015).
[Crossref] [PubMed]

Z. Zeng, X. Chen, H. Wang, N. Huang, C. Shan, H. Zhang, J. Teng, and P. Xi, “Fast super-resolution imaging with ultra-high labeling density achieved by joint tagging super-resolution optical fluctuation imaging,” Sci. Rep. 5, 8359 (2015).
[Crossref] [PubMed]

X. Zhang, X. Chen, Z. Zeng, M. Zhang, Y. Sun, P. Xi, J. Peng, and P. Xu, “Development of a reversibly switchable fluorescent protein for super-resolution optical fluctuation imaging (SOFI),” ACS Nano 9, 2659–2667 (2015).
[Crossref] [PubMed]

Z. Ristanović, M. M. Kerssens, A. V. Kubarev, F. C. Hendriks, P. Dedecker, J. Hofkens, M. B. J. Roeffaers, and B. M. Weckhuysen, “High-resolution single-molecule fluorescence imaging of zeolite aggregates within real-life fluid catalytic cracking particles,” Angew. Chem. Int. Ed. Engl. 54, 1836–1840 (2015).
[Crossref]

L. Kisley, R. Brunetti, L. J. Tauzin, B. Shuang, X. Yi, A. W. Kirkeminde, D. A. Higgins, S. Weiss, and C. F. Landes, “Characterization of porous materials by fluorescence correlation spectroscopy super-resolution optical fluctuation imaging,” ACS Nano 9, 9158–9166 (2015).
[Crossref] [PubMed]

S. C. Stein, A. Huss, D. Hahnel, I. Gregor, and J. Enderlein, “Fourier interpolation stochastic optical fluctuation imaging,” Opt. Express 23, 16154–16163 (2015).
[Crossref] [PubMed]

2014 (2)

B. Moeyaert, N. NguyenBich, E. De Zitter, S. Rocha, K. Clays, H. Mizuno, L. van Meervelt, J. Hofkens, and P. Dedecker, “Green-to-red photoconvertible dronpa mutant for multimodal super-resolution fluorescence microscopy,” ACS Nano 8, 1664–1673 (2014).
[Crossref] [PubMed]

S. Geissbuehler, A. Sharipov, A. Godinat, N. L. Bocchio, P. A. Sandoz, A. Huss, N. A. Jensen, S. Jakobs, J. Enderlein, F. Gisou van der Goot, E. A. Dubikovskaya, T. Lasser, and M. Leutenegger, “Live-cell multiplane three-dimensional super-resolution optical fluctuation imaging,” Nat. Commun. 5, 5830 (2014).
[Crossref] [PubMed]

2013 (2)

S. Cho, J. Jang, C. Song, H. Lee, P. Ganesan, T.-Y. Yoon, M. W. Kim, M. C. Choi, H. Ihee, W. D. Heo, and Y. Park, “Simple super-resolution live-cell imaging based on diffusion-assisted förster resonance energy transfer,” Sci. Rep. 3, 1208 (2013).
[Crossref]

P. Dedecker, F. C. De Schryver, and J. Hofkens, “Fluorescent proteins: shine on, you crazy diamond,” J. Am. Chem. Soc. 135, 2387–2402 (2013).
[Crossref] [PubMed]

2012 (3)

S. Geissbuehler, N. Bocchio, C. Dellagiacoma, C. Berclaz, M. Leutenegger, and T. Lasser, “Mapping molecular statistics with balanced super-resolution optical fluctuation imaging (bSOFI),” Opt. Nanoscopy 1, 4 (2012).
[Crossref]

P. Dedecker, G. C. H. Mo, T. Dertinger, and J. Zhang, “Widely accessible method for superresolution fluorescence imaging of living systems,” Proc. Natl. Acad. Sci. U.S.A. 109, 10909–10914 (2012).
[Crossref] [PubMed]

P. Dedecker, S. Duwé, R. K. Neely, and J. Zhang, “Localizer: fast, accurate, open-source, and modular software package for superresolution microscopy,” J. Biomed. Opt. 17, 126008 (2012).
[Crossref] [PubMed]

2011 (1)

2010 (2)

T. Dertinger, M. Heilemann, R. Vogel, M. Sauer, and S. Weiss, “Superresolution Optical Fluctuation Imaging with Organic Dyes,” Angew. Chem. Int. Ed. Engl. 49, 9441–9443 (2010).
[Crossref] [PubMed]

T. Dertinger, R. Colyer, R. Vogel, J. Enderlein, and S. Weiss, “Achieving increased resolution and more pixels with superresolution optical fluctuation imaging (SOFI),” Opt. Express 18, 18875–18885 (2010).
[Crossref] [PubMed]

2009 (1)

T. Dertinger, R. Colyer, G. Iyer, S. Weiss, and J. Enderlein, “Fast, background-free, 3D super-resolution optical fluctuation imaging (SOFI),” Proc. Natl. Acad. Sci. U.S.A. 106, 22287–22292 (2009).
[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, 1642–1645 (2006).
[Crossref] [PubMed]

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

S. T. Hess, T. P. K. Girirajan, and M. D. Mason, “Ultra-high resolution imaging by fluorescence photoactivation localization microscopy,” Biophys. J. 91, 4258–4272 (2006).
[Crossref] [PubMed]

2003 (1)

S. W. Hell, “Toward fluorescence nanoscopy,” Nat. Biotechnol. 21, 1347–1355 (2003).
[Crossref] [PubMed]

1997 (1)

A. J. Stromberg, “Robust covariance estimates based on resampling,” Journal of Statistical Planning and Inference 57, 321–334 (1997). Robust Statistics and Data Analysis, Part {II}.
[Crossref]

1994 (1)

Bates, M.

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

Berclaz, C.

S. Geissbuehler, N. Bocchio, C. Dellagiacoma, C. Berclaz, M. Leutenegger, and T. Lasser, “Mapping molecular statistics with balanced super-resolution optical fluctuation imaging (bSOFI),” Opt. Nanoscopy 1, 4 (2012).
[Crossref]

Betzig, E.

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

Bocchio, N.

S. Geissbuehler, N. Bocchio, C. Dellagiacoma, C. Berclaz, M. Leutenegger, and T. Lasser, “Mapping molecular statistics with balanced super-resolution optical fluctuation imaging (bSOFI),” Opt. Nanoscopy 1, 4 (2012).
[Crossref]

Bocchio, N. L.

S. Geissbuehler, A. Sharipov, A. Godinat, N. L. Bocchio, P. A. Sandoz, A. Huss, N. A. Jensen, S. Jakobs, J. Enderlein, F. Gisou van der Goot, E. A. Dubikovskaya, T. Lasser, and M. Leutenegger, “Live-cell multiplane three-dimensional super-resolution optical fluctuation imaging,” Nat. Commun. 5, 5830 (2014).
[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]

Brunetti, R.

L. Kisley, R. Brunetti, L. J. Tauzin, B. Shuang, X. Yi, A. W. Kirkeminde, D. A. Higgins, S. Weiss, and C. F. Landes, “Characterization of porous materials by fluorescence correlation spectroscopy super-resolution optical fluctuation imaging,” ACS Nano 9, 9158–9166 (2015).
[Crossref] [PubMed]

Chen, X.

Z. Zeng, X. Chen, H. Wang, N. Huang, C. Shan, H. Zhang, J. Teng, and P. Xi, “Fast super-resolution imaging with ultra-high labeling density achieved by joint tagging super-resolution optical fluctuation imaging,” Sci. Rep. 5, 8359 (2015).
[Crossref] [PubMed]

X. Zhang, X. Chen, Z. Zeng, M. Zhang, Y. Sun, P. Xi, J. Peng, and P. Xu, “Development of a reversibly switchable fluorescent protein for super-resolution optical fluctuation imaging (SOFI),” ACS Nano 9, 2659–2667 (2015).
[Crossref] [PubMed]

Cho, S.

S. Cho, J. Jang, C. Song, H. Lee, P. Ganesan, T.-Y. Yoon, M. W. Kim, M. C. Choi, H. Ihee, W. D. Heo, and Y. Park, “Simple super-resolution live-cell imaging based on diffusion-assisted förster resonance energy transfer,” Sci. Rep. 3, 1208 (2013).
[Crossref]

Choi, M. C.

S. Cho, J. Jang, C. Song, H. Lee, P. Ganesan, T.-Y. Yoon, M. W. Kim, M. C. Choi, H. Ihee, W. D. Heo, and Y. Park, “Simple super-resolution live-cell imaging based on diffusion-assisted förster resonance energy transfer,” Sci. Rep. 3, 1208 (2013).
[Crossref]

Clays, K.

B. Moeyaert, N. NguyenBich, E. De Zitter, S. Rocha, K. Clays, H. Mizuno, L. van Meervelt, J. Hofkens, and P. Dedecker, “Green-to-red photoconvertible dronpa mutant for multimodal super-resolution fluorescence microscopy,” ACS Nano 8, 1664–1673 (2014).
[Crossref] [PubMed]

S. Duwe, E. De Zitter, V. Gielen, B. Moeyaert, W. Vandenberg, T. Grotjohann, K. Clays, S. Jakobs, L. Van Meervelt, and P. Dedecker, “Expression-enhanced fluorescent proteins based on enhanced green fluorescent protein for super-resolution microscopy,” ACS Nano (2015).
[Crossref] [PubMed]

Colyer, R.

T. Dertinger, R. Colyer, R. Vogel, J. Enderlein, and S. Weiss, “Achieving increased resolution and more pixels with superresolution optical fluctuation imaging (SOFI),” Opt. Express 18, 18875–18885 (2010).
[Crossref] [PubMed]

T. Dertinger, R. Colyer, G. Iyer, S. Weiss, and J. Enderlein, “Fast, background-free, 3D super-resolution optical fluctuation imaging (SOFI),” Proc. Natl. Acad. Sci. U.S.A. 106, 22287–22292 (2009).
[Crossref] [PubMed]

Davidson, M. W.

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

De Schryver, F. C.

P. Dedecker, F. C. De Schryver, and J. Hofkens, “Fluorescent proteins: shine on, you crazy diamond,” J. Am. Chem. Soc. 135, 2387–2402 (2013).
[Crossref] [PubMed]

De Zitter, E.

B. Moeyaert, N. NguyenBich, E. De Zitter, S. Rocha, K. Clays, H. Mizuno, L. van Meervelt, J. Hofkens, and P. Dedecker, “Green-to-red photoconvertible dronpa mutant for multimodal super-resolution fluorescence microscopy,” ACS Nano 8, 1664–1673 (2014).
[Crossref] [PubMed]

S. Duwe, E. De Zitter, V. Gielen, B. Moeyaert, W. Vandenberg, T. Grotjohann, K. Clays, S. Jakobs, L. Van Meervelt, and P. Dedecker, “Expression-enhanced fluorescent proteins based on enhanced green fluorescent protein for super-resolution microscopy,” ACS Nano (2015).
[Crossref] [PubMed]

Dedecker, P.

Z. Ristanović, M. M. Kerssens, A. V. Kubarev, F. C. Hendriks, P. Dedecker, J. Hofkens, M. B. J. Roeffaers, and B. M. Weckhuysen, “High-resolution single-molecule fluorescence imaging of zeolite aggregates within real-life fluid catalytic cracking particles,” Angew. Chem. Int. Ed. Engl. 54, 1836–1840 (2015).
[Crossref]

W. Vandenberg, M. Leutenegger, T. Lasser, J. Hofkens, and P. Dedecker, “Diffraction-unlimited imaging: from pretty pictures to hard numbers,” Cell Tissue Res. 360, 151–178 (2015).
[Crossref] [PubMed]

B. Moeyaert, N. NguyenBich, E. De Zitter, S. Rocha, K. Clays, H. Mizuno, L. van Meervelt, J. Hofkens, and P. Dedecker, “Green-to-red photoconvertible dronpa mutant for multimodal super-resolution fluorescence microscopy,” ACS Nano 8, 1664–1673 (2014).
[Crossref] [PubMed]

P. Dedecker, F. C. De Schryver, and J. Hofkens, “Fluorescent proteins: shine on, you crazy diamond,” J. Am. Chem. Soc. 135, 2387–2402 (2013).
[Crossref] [PubMed]

P. Dedecker, S. Duwé, R. K. Neely, and J. Zhang, “Localizer: fast, accurate, open-source, and modular software package for superresolution microscopy,” J. Biomed. Opt. 17, 126008 (2012).
[Crossref] [PubMed]

P. Dedecker, G. C. H. Mo, T. Dertinger, and J. Zhang, “Widely accessible method for superresolution fluorescence imaging of living systems,” Proc. Natl. Acad. Sci. U.S.A. 109, 10909–10914 (2012).
[Crossref] [PubMed]

S. Duwe, E. De Zitter, V. Gielen, B. Moeyaert, W. Vandenberg, T. Grotjohann, K. Clays, S. Jakobs, L. Van Meervelt, and P. Dedecker, “Expression-enhanced fluorescent proteins based on enhanced green fluorescent protein for super-resolution microscopy,” ACS Nano (2015).
[Crossref] [PubMed]

Dellagiacoma, C.

S. Geissbuehler, N. Bocchio, C. Dellagiacoma, C. Berclaz, M. Leutenegger, and T. Lasser, “Mapping molecular statistics with balanced super-resolution optical fluctuation imaging (bSOFI),” Opt. Nanoscopy 1, 4 (2012).
[Crossref]

S. Geissbuehler, C. Dellagiacoma, and T. Lasser, “Comparison between SOFI and STORM,” Biomed. Opt. Express 2, 408–420 (2011).
[Crossref] [PubMed]

Dertinger, T.

P. Dedecker, G. C. H. Mo, T. Dertinger, and J. Zhang, “Widely accessible method for superresolution fluorescence imaging of living systems,” Proc. Natl. Acad. Sci. U.S.A. 109, 10909–10914 (2012).
[Crossref] [PubMed]

T. Dertinger, R. Colyer, R. Vogel, J. Enderlein, and S. Weiss, “Achieving increased resolution and more pixels with superresolution optical fluctuation imaging (SOFI),” Opt. Express 18, 18875–18885 (2010).
[Crossref] [PubMed]

T. Dertinger, M. Heilemann, R. Vogel, M. Sauer, and S. Weiss, “Superresolution Optical Fluctuation Imaging with Organic Dyes,” Angew. Chem. Int. Ed. Engl. 49, 9441–9443 (2010).
[Crossref] [PubMed]

T. Dertinger, R. Colyer, G. Iyer, S. Weiss, and J. Enderlein, “Fast, background-free, 3D super-resolution optical fluctuation imaging (SOFI),” Proc. Natl. Acad. Sci. U.S.A. 106, 22287–22292 (2009).
[Crossref] [PubMed]

Dubikovskaya, E. A.

S. Geissbuehler, A. Sharipov, A. Godinat, N. L. Bocchio, P. A. Sandoz, A. Huss, N. A. Jensen, S. Jakobs, J. Enderlein, F. Gisou van der Goot, E. A. Dubikovskaya, T. Lasser, and M. Leutenegger, “Live-cell multiplane three-dimensional super-resolution optical fluctuation imaging,” Nat. Commun. 5, 5830 (2014).
[Crossref] [PubMed]

Duwe, S.

S. Duwe, E. De Zitter, V. Gielen, B. Moeyaert, W. Vandenberg, T. Grotjohann, K. Clays, S. Jakobs, L. Van Meervelt, and P. Dedecker, “Expression-enhanced fluorescent proteins based on enhanced green fluorescent protein for super-resolution microscopy,” ACS Nano (2015).
[Crossref] [PubMed]

Duwé, S.

P. Dedecker, S. Duwé, R. K. Neely, and J. Zhang, “Localizer: fast, accurate, open-source, and modular software package for superresolution microscopy,” J. Biomed. Opt. 17, 126008 (2012).
[Crossref] [PubMed]

Enderlein, J.

S. C. Stein, A. Huss, D. Hahnel, I. Gregor, and J. Enderlein, “Fourier interpolation stochastic optical fluctuation imaging,” Opt. Express 23, 16154–16163 (2015).
[Crossref] [PubMed]

S. Geissbuehler, A. Sharipov, A. Godinat, N. L. Bocchio, P. A. Sandoz, A. Huss, N. A. Jensen, S. Jakobs, J. Enderlein, F. Gisou van der Goot, E. A. Dubikovskaya, T. Lasser, and M. Leutenegger, “Live-cell multiplane three-dimensional super-resolution optical fluctuation imaging,” Nat. Commun. 5, 5830 (2014).
[Crossref] [PubMed]

T. Dertinger, R. Colyer, R. Vogel, J. Enderlein, and S. Weiss, “Achieving increased resolution and more pixels with superresolution optical fluctuation imaging (SOFI),” Opt. Express 18, 18875–18885 (2010).
[Crossref] [PubMed]

T. Dertinger, R. Colyer, G. Iyer, S. Weiss, and J. Enderlein, “Fast, background-free, 3D super-resolution optical fluctuation imaging (SOFI),” Proc. Natl. Acad. Sci. U.S.A. 106, 22287–22292 (2009).
[Crossref] [PubMed]

Ganesan, P.

S. Cho, J. Jang, C. Song, H. Lee, P. Ganesan, T.-Y. Yoon, M. W. Kim, M. C. Choi, H. Ihee, W. D. Heo, and Y. Park, “Simple super-resolution live-cell imaging based on diffusion-assisted förster resonance energy transfer,” Sci. Rep. 3, 1208 (2013).
[Crossref]

Geissbuehler, S.

S. Geissbuehler, A. Sharipov, A. Godinat, N. L. Bocchio, P. A. Sandoz, A. Huss, N. A. Jensen, S. Jakobs, J. Enderlein, F. Gisou van der Goot, E. A. Dubikovskaya, T. Lasser, and M. Leutenegger, “Live-cell multiplane three-dimensional super-resolution optical fluctuation imaging,” Nat. Commun. 5, 5830 (2014).
[Crossref] [PubMed]

S. Geissbuehler, N. Bocchio, C. Dellagiacoma, C. Berclaz, M. Leutenegger, and T. Lasser, “Mapping molecular statistics with balanced super-resolution optical fluctuation imaging (bSOFI),” Opt. Nanoscopy 1, 4 (2012).
[Crossref]

S. Geissbuehler, C. Dellagiacoma, and T. Lasser, “Comparison between SOFI and STORM,” Biomed. Opt. Express 2, 408–420 (2011).
[Crossref] [PubMed]

Gielen, V.

S. Duwe, E. De Zitter, V. Gielen, B. Moeyaert, W. Vandenberg, T. Grotjohann, K. Clays, S. Jakobs, L. Van Meervelt, and P. Dedecker, “Expression-enhanced fluorescent proteins based on enhanced green fluorescent protein for super-resolution microscopy,” ACS Nano (2015).
[Crossref] [PubMed]

Girirajan, T. P. K.

S. T. Hess, T. P. K. Girirajan, and M. D. Mason, “Ultra-high resolution imaging by fluorescence photoactivation localization microscopy,” Biophys. J. 91, 4258–4272 (2006).
[Crossref] [PubMed]

Gisou van der Goot, F.

S. Geissbuehler, A. Sharipov, A. Godinat, N. L. Bocchio, P. A. Sandoz, A. Huss, N. A. Jensen, S. Jakobs, J. Enderlein, F. Gisou van der Goot, E. A. Dubikovskaya, T. Lasser, and M. Leutenegger, “Live-cell multiplane three-dimensional super-resolution optical fluctuation imaging,” Nat. Commun. 5, 5830 (2014).
[Crossref] [PubMed]

Godinat, A.

S. Geissbuehler, A. Sharipov, A. Godinat, N. L. Bocchio, P. A. Sandoz, A. Huss, N. A. Jensen, S. Jakobs, J. Enderlein, F. Gisou van der Goot, E. A. Dubikovskaya, T. Lasser, and M. Leutenegger, “Live-cell multiplane three-dimensional super-resolution optical fluctuation imaging,” Nat. Commun. 5, 5830 (2014).
[Crossref] [PubMed]

Gregor, I.

Grotjohann, T.

S. Duwe, E. De Zitter, V. Gielen, B. Moeyaert, W. Vandenberg, T. Grotjohann, K. Clays, S. Jakobs, L. Van Meervelt, and P. Dedecker, “Expression-enhanced fluorescent proteins based on enhanced green fluorescent protein for super-resolution microscopy,” ACS Nano (2015).
[Crossref] [PubMed]

Hahnel, D.

Heilemann, M.

T. Dertinger, M. Heilemann, R. Vogel, M. Sauer, and S. Weiss, “Superresolution Optical Fluctuation Imaging with Organic Dyes,” Angew. Chem. Int. Ed. Engl. 49, 9441–9443 (2010).
[Crossref] [PubMed]

Hell, S. W.

Hendriks, F. C.

Z. Ristanović, M. M. Kerssens, A. V. Kubarev, F. C. Hendriks, P. Dedecker, J. Hofkens, M. B. J. Roeffaers, and B. M. Weckhuysen, “High-resolution single-molecule fluorescence imaging of zeolite aggregates within real-life fluid catalytic cracking particles,” Angew. Chem. Int. Ed. Engl. 54, 1836–1840 (2015).
[Crossref]

Heo, W. D.

S. Cho, J. Jang, C. Song, H. Lee, P. Ganesan, T.-Y. Yoon, M. W. Kim, M. C. Choi, H. Ihee, W. D. Heo, and Y. Park, “Simple super-resolution live-cell imaging based on diffusion-assisted förster resonance energy transfer,” Sci. Rep. 3, 1208 (2013).
[Crossref]

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]

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, 4258–4272 (2006).
[Crossref] [PubMed]

Higgins, D. A.

L. Kisley, R. Brunetti, L. J. Tauzin, B. Shuang, X. Yi, A. W. Kirkeminde, D. A. Higgins, S. Weiss, and C. F. Landes, “Characterization of porous materials by fluorescence correlation spectroscopy super-resolution optical fluctuation imaging,” ACS Nano 9, 9158–9166 (2015).
[Crossref] [PubMed]

Hofkens, J.

W. Vandenberg, M. Leutenegger, T. Lasser, J. Hofkens, and P. Dedecker, “Diffraction-unlimited imaging: from pretty pictures to hard numbers,” Cell Tissue Res. 360, 151–178 (2015).
[Crossref] [PubMed]

Z. Ristanović, M. M. Kerssens, A. V. Kubarev, F. C. Hendriks, P. Dedecker, J. Hofkens, M. B. J. Roeffaers, and B. M. Weckhuysen, “High-resolution single-molecule fluorescence imaging of zeolite aggregates within real-life fluid catalytic cracking particles,” Angew. Chem. Int. Ed. Engl. 54, 1836–1840 (2015).
[Crossref]

B. Moeyaert, N. NguyenBich, E. De Zitter, S. Rocha, K. Clays, H. Mizuno, L. van Meervelt, J. Hofkens, and P. Dedecker, “Green-to-red photoconvertible dronpa mutant for multimodal super-resolution fluorescence microscopy,” ACS Nano 8, 1664–1673 (2014).
[Crossref] [PubMed]

P. Dedecker, F. C. De Schryver, and J. Hofkens, “Fluorescent proteins: shine on, you crazy diamond,” J. Am. Chem. Soc. 135, 2387–2402 (2013).
[Crossref] [PubMed]

Huang, N.

Z. Zeng, X. Chen, H. Wang, N. Huang, C. Shan, H. Zhang, J. Teng, and P. Xi, “Fast super-resolution imaging with ultra-high labeling density achieved by joint tagging super-resolution optical fluctuation imaging,” Sci. Rep. 5, 8359 (2015).
[Crossref] [PubMed]

Huss, A.

S. C. Stein, A. Huss, D. Hahnel, I. Gregor, and J. Enderlein, “Fourier interpolation stochastic optical fluctuation imaging,” Opt. Express 23, 16154–16163 (2015).
[Crossref] [PubMed]

S. Geissbuehler, A. Sharipov, A. Godinat, N. L. Bocchio, P. A. Sandoz, A. Huss, N. A. Jensen, S. Jakobs, J. Enderlein, F. Gisou van der Goot, E. A. Dubikovskaya, T. Lasser, and M. Leutenegger, “Live-cell multiplane three-dimensional super-resolution optical fluctuation imaging,” Nat. Commun. 5, 5830 (2014).
[Crossref] [PubMed]

Ihee, H.

S. Cho, J. Jang, C. Song, H. Lee, P. Ganesan, T.-Y. Yoon, M. W. Kim, M. C. Choi, H. Ihee, W. D. Heo, and Y. Park, “Simple super-resolution live-cell imaging based on diffusion-assisted förster resonance energy transfer,” Sci. Rep. 3, 1208 (2013).
[Crossref]

Iyer, G.

T. Dertinger, R. Colyer, G. Iyer, S. Weiss, and J. Enderlein, “Fast, background-free, 3D super-resolution optical fluctuation imaging (SOFI),” Proc. Natl. Acad. Sci. U.S.A. 106, 22287–22292 (2009).
[Crossref] [PubMed]

Jakobs, S.

S. Geissbuehler, A. Sharipov, A. Godinat, N. L. Bocchio, P. A. Sandoz, A. Huss, N. A. Jensen, S. Jakobs, J. Enderlein, F. Gisou van der Goot, E. A. Dubikovskaya, T. Lasser, and M. Leutenegger, “Live-cell multiplane three-dimensional super-resolution optical fluctuation imaging,” Nat. Commun. 5, 5830 (2014).
[Crossref] [PubMed]

S. Duwe, E. De Zitter, V. Gielen, B. Moeyaert, W. Vandenberg, T. Grotjohann, K. Clays, S. Jakobs, L. Van Meervelt, and P. Dedecker, “Expression-enhanced fluorescent proteins based on enhanced green fluorescent protein for super-resolution microscopy,” ACS Nano (2015).
[Crossref] [PubMed]

Jang, J.

S. Cho, J. Jang, C. Song, H. Lee, P. Ganesan, T.-Y. Yoon, M. W. Kim, M. C. Choi, H. Ihee, W. D. Heo, and Y. Park, “Simple super-resolution live-cell imaging based on diffusion-assisted förster resonance energy transfer,” Sci. Rep. 3, 1208 (2013).
[Crossref]

Jensen, N. A.

S. Geissbuehler, A. Sharipov, A. Godinat, N. L. Bocchio, P. A. Sandoz, A. Huss, N. A. Jensen, S. Jakobs, J. Enderlein, F. Gisou van der Goot, E. A. Dubikovskaya, T. Lasser, and M. Leutenegger, “Live-cell multiplane three-dimensional super-resolution optical fluctuation imaging,” Nat. Commun. 5, 5830 (2014).
[Crossref] [PubMed]

Kerssens, M. M.

Z. Ristanović, M. M. Kerssens, A. V. Kubarev, F. C. Hendriks, P. Dedecker, J. Hofkens, M. B. J. Roeffaers, and B. M. Weckhuysen, “High-resolution single-molecule fluorescence imaging of zeolite aggregates within real-life fluid catalytic cracking particles,” Angew. Chem. Int. Ed. Engl. 54, 1836–1840 (2015).
[Crossref]

Kim, M. W.

S. Cho, J. Jang, C. Song, H. Lee, P. Ganesan, T.-Y. Yoon, M. W. Kim, M. C. Choi, H. Ihee, W. D. Heo, and Y. Park, “Simple super-resolution live-cell imaging based on diffusion-assisted förster resonance energy transfer,” Sci. Rep. 3, 1208 (2013).
[Crossref]

Kirkeminde, A. W.

L. Kisley, R. Brunetti, L. J. Tauzin, B. Shuang, X. Yi, A. W. Kirkeminde, D. A. Higgins, S. Weiss, and C. F. Landes, “Characterization of porous materials by fluorescence correlation spectroscopy super-resolution optical fluctuation imaging,” ACS Nano 9, 9158–9166 (2015).
[Crossref] [PubMed]

Kisley, L.

L. Kisley, R. Brunetti, L. J. Tauzin, B. Shuang, X. Yi, A. W. Kirkeminde, D. A. Higgins, S. Weiss, and C. F. Landes, “Characterization of porous materials by fluorescence correlation spectroscopy super-resolution optical fluctuation imaging,” ACS Nano 9, 9158–9166 (2015).
[Crossref] [PubMed]

Kubarev, A. V.

Z. Ristanović, M. M. Kerssens, A. V. Kubarev, F. C. Hendriks, P. Dedecker, J. Hofkens, M. B. J. Roeffaers, and B. M. Weckhuysen, “High-resolution single-molecule fluorescence imaging of zeolite aggregates within real-life fluid catalytic cracking particles,” Angew. Chem. Int. Ed. Engl. 54, 1836–1840 (2015).
[Crossref]

Landes, C. F.

L. Kisley, R. Brunetti, L. J. Tauzin, B. Shuang, X. Yi, A. W. Kirkeminde, D. A. Higgins, S. Weiss, and C. F. Landes, “Characterization of porous materials by fluorescence correlation spectroscopy super-resolution optical fluctuation imaging,” ACS Nano 9, 9158–9166 (2015).
[Crossref] [PubMed]

Lasser, T.

W. Vandenberg, M. Leutenegger, T. Lasser, J. Hofkens, and P. Dedecker, “Diffraction-unlimited imaging: from pretty pictures to hard numbers,” Cell Tissue Res. 360, 151–178 (2015).
[Crossref] [PubMed]

S. Geissbuehler, A. Sharipov, A. Godinat, N. L. Bocchio, P. A. Sandoz, A. Huss, N. A. Jensen, S. Jakobs, J. Enderlein, F. Gisou van der Goot, E. A. Dubikovskaya, T. Lasser, and M. Leutenegger, “Live-cell multiplane three-dimensional super-resolution optical fluctuation imaging,” Nat. Commun. 5, 5830 (2014).
[Crossref] [PubMed]

S. Geissbuehler, N. Bocchio, C. Dellagiacoma, C. Berclaz, M. Leutenegger, and T. Lasser, “Mapping molecular statistics with balanced super-resolution optical fluctuation imaging (bSOFI),” Opt. Nanoscopy 1, 4 (2012).
[Crossref]

S. Geissbuehler, C. Dellagiacoma, and T. Lasser, “Comparison between SOFI and STORM,” Biomed. Opt. Express 2, 408–420 (2011).
[Crossref] [PubMed]

Lee, H.

S. Cho, J. Jang, C. Song, H. Lee, P. Ganesan, T.-Y. Yoon, M. W. Kim, M. C. Choi, H. Ihee, W. D. Heo, and Y. Park, “Simple super-resolution live-cell imaging based on diffusion-assisted förster resonance energy transfer,” Sci. Rep. 3, 1208 (2013).
[Crossref]

Leutenegger, M.

W. Vandenberg, M. Leutenegger, T. Lasser, J. Hofkens, and P. Dedecker, “Diffraction-unlimited imaging: from pretty pictures to hard numbers,” Cell Tissue Res. 360, 151–178 (2015).
[Crossref] [PubMed]

S. Geissbuehler, A. Sharipov, A. Godinat, N. L. Bocchio, P. A. Sandoz, A. Huss, N. A. Jensen, S. Jakobs, J. Enderlein, F. Gisou van der Goot, E. A. Dubikovskaya, T. Lasser, and M. Leutenegger, “Live-cell multiplane three-dimensional super-resolution optical fluctuation imaging,” Nat. Commun. 5, 5830 (2014).
[Crossref] [PubMed]

S. Geissbuehler, N. Bocchio, C. Dellagiacoma, C. Berclaz, M. Leutenegger, and T. Lasser, “Mapping molecular statistics with balanced super-resolution optical fluctuation imaging (bSOFI),” Opt. Nanoscopy 1, 4 (2012).
[Crossref]

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]

Mason, M. D.

S. T. Hess, T. P. K. Girirajan, and M. D. Mason, “Ultra-high resolution imaging by fluorescence photoactivation localization microscopy,” Biophys. J. 91, 4258–4272 (2006).
[Crossref] [PubMed]

Mizuno, H.

B. Moeyaert, N. NguyenBich, E. De Zitter, S. Rocha, K. Clays, H. Mizuno, L. van Meervelt, J. Hofkens, and P. Dedecker, “Green-to-red photoconvertible dronpa mutant for multimodal super-resolution fluorescence microscopy,” ACS Nano 8, 1664–1673 (2014).
[Crossref] [PubMed]

Mo, G. C. H.

P. Dedecker, G. C. H. Mo, T. Dertinger, and J. Zhang, “Widely accessible method for superresolution fluorescence imaging of living systems,” Proc. Natl. Acad. Sci. U.S.A. 109, 10909–10914 (2012).
[Crossref] [PubMed]

Moeyaert, B.

B. Moeyaert, N. NguyenBich, E. De Zitter, S. Rocha, K. Clays, H. Mizuno, L. van Meervelt, J. Hofkens, and P. Dedecker, “Green-to-red photoconvertible dronpa mutant for multimodal super-resolution fluorescence microscopy,” ACS Nano 8, 1664–1673 (2014).
[Crossref] [PubMed]

S. Duwe, E. De Zitter, V. Gielen, B. Moeyaert, W. Vandenberg, T. Grotjohann, K. Clays, S. Jakobs, L. Van Meervelt, and P. Dedecker, “Expression-enhanced fluorescent proteins based on enhanced green fluorescent protein for super-resolution microscopy,” ACS Nano (2015).
[Crossref] [PubMed]

Neely, R. K.

P. Dedecker, S. Duwé, R. K. Neely, and J. Zhang, “Localizer: fast, accurate, open-source, and modular software package for superresolution microscopy,” J. Biomed. Opt. 17, 126008 (2012).
[Crossref] [PubMed]

NguyenBich, N.

B. Moeyaert, N. NguyenBich, E. De Zitter, S. Rocha, K. Clays, H. Mizuno, L. van Meervelt, J. Hofkens, and P. Dedecker, “Green-to-red photoconvertible dronpa mutant for multimodal super-resolution fluorescence microscopy,” ACS Nano 8, 1664–1673 (2014).
[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]

Ord, K.

A. Stuart and K. Ord, Kendall’s Advanced Theory of Statistics: Volume 1: Distribution Theory, no. v. 1; v. 1994 in Kendall’s Advanced Theory of Statistics (Wiley, 2009).

Park, Y.

S. Cho, J. Jang, C. Song, H. Lee, P. Ganesan, T.-Y. Yoon, M. W. Kim, M. C. Choi, H. Ihee, W. D. Heo, and Y. Park, “Simple super-resolution live-cell imaging based on diffusion-assisted förster resonance energy transfer,” Sci. Rep. 3, 1208 (2013).
[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]

Peng, J.

X. Zhang, X. Chen, Z. Zeng, M. Zhang, Y. Sun, P. Xi, J. Peng, and P. Xu, “Development of a reversibly switchable fluorescent protein for super-resolution optical fluctuation imaging (SOFI),” ACS Nano 9, 2659–2667 (2015).
[Crossref] [PubMed]

Ristanovic, Z.

Z. Ristanović, M. M. Kerssens, A. V. Kubarev, F. C. Hendriks, P. Dedecker, J. Hofkens, M. B. J. Roeffaers, and B. M. Weckhuysen, “High-resolution single-molecule fluorescence imaging of zeolite aggregates within real-life fluid catalytic cracking particles,” Angew. Chem. Int. Ed. Engl. 54, 1836–1840 (2015).
[Crossref]

Rocha, S.

B. Moeyaert, N. NguyenBich, E. De Zitter, S. Rocha, K. Clays, H. Mizuno, L. van Meervelt, J. Hofkens, and P. Dedecker, “Green-to-red photoconvertible dronpa mutant for multimodal super-resolution fluorescence microscopy,” ACS Nano 8, 1664–1673 (2014).
[Crossref] [PubMed]

Roeffaers, M. B. J.

Z. Ristanović, M. M. Kerssens, A. V. Kubarev, F. C. Hendriks, P. Dedecker, J. Hofkens, M. B. J. Roeffaers, and B. M. Weckhuysen, “High-resolution single-molecule fluorescence imaging of zeolite aggregates within real-life fluid catalytic cracking particles,” Angew. Chem. Int. Ed. Engl. 54, 1836–1840 (2015).
[Crossref]

Rust, M. J.

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

Sandoz, P. A.

S. Geissbuehler, A. Sharipov, A. Godinat, N. L. Bocchio, P. A. Sandoz, A. Huss, N. A. Jensen, S. Jakobs, J. Enderlein, F. Gisou van der Goot, E. A. Dubikovskaya, T. Lasser, and M. Leutenegger, “Live-cell multiplane three-dimensional super-resolution optical fluctuation imaging,” Nat. Commun. 5, 5830 (2014).
[Crossref] [PubMed]

Sauer, M.

T. Dertinger, M. Heilemann, R. Vogel, M. Sauer, and S. Weiss, “Superresolution Optical Fluctuation Imaging with Organic Dyes,” Angew. Chem. Int. Ed. Engl. 49, 9441–9443 (2010).
[Crossref] [PubMed]

Shan, C.

Z. Zeng, X. Chen, H. Wang, N. Huang, C. Shan, H. Zhang, J. Teng, and P. Xi, “Fast super-resolution imaging with ultra-high labeling density achieved by joint tagging super-resolution optical fluctuation imaging,” Sci. Rep. 5, 8359 (2015).
[Crossref] [PubMed]

Sharipov, A.

S. Geissbuehler, A. Sharipov, A. Godinat, N. L. Bocchio, P. A. Sandoz, A. Huss, N. A. Jensen, S. Jakobs, J. Enderlein, F. Gisou van der Goot, E. A. Dubikovskaya, T. Lasser, and M. Leutenegger, “Live-cell multiplane three-dimensional super-resolution optical fluctuation imaging,” Nat. Commun. 5, 5830 (2014).
[Crossref] [PubMed]

Shuang, B.

L. Kisley, R. Brunetti, L. J. Tauzin, B. Shuang, X. Yi, A. W. Kirkeminde, D. A. Higgins, S. Weiss, and C. F. Landes, “Characterization of porous materials by fluorescence correlation spectroscopy super-resolution optical fluctuation imaging,” ACS Nano 9, 9158–9166 (2015).
[Crossref] [PubMed]

Song, C.

S. Cho, J. Jang, C. Song, H. Lee, P. Ganesan, T.-Y. Yoon, M. W. Kim, M. C. Choi, H. Ihee, W. D. Heo, and Y. Park, “Simple super-resolution live-cell imaging based on diffusion-assisted förster resonance energy transfer,” Sci. Rep. 3, 1208 (2013).
[Crossref]

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]

Stein, S. C.

Stromberg, A. J.

A. J. Stromberg, “Robust covariance estimates based on resampling,” Journal of Statistical Planning and Inference 57, 321–334 (1997). Robust Statistics and Data Analysis, Part {II}.
[Crossref]

Stuart, A.

A. Stuart and K. Ord, Kendall’s Advanced Theory of Statistics: Volume 1: Distribution Theory, no. v. 1; v. 1994 in Kendall’s Advanced Theory of Statistics (Wiley, 2009).

Sun, Y.

X. Zhang, X. Chen, Z. Zeng, M. Zhang, Y. Sun, P. Xi, J. Peng, and P. Xu, “Development of a reversibly switchable fluorescent protein for super-resolution optical fluctuation imaging (SOFI),” ACS Nano 9, 2659–2667 (2015).
[Crossref] [PubMed]

Tauzin, L. J.

L. Kisley, R. Brunetti, L. J. Tauzin, B. Shuang, X. Yi, A. W. Kirkeminde, D. A. Higgins, S. Weiss, and C. F. Landes, “Characterization of porous materials by fluorescence correlation spectroscopy super-resolution optical fluctuation imaging,” ACS Nano 9, 9158–9166 (2015).
[Crossref] [PubMed]

Teng, J.

Z. Zeng, X. Chen, H. Wang, N. Huang, C. Shan, H. Zhang, J. Teng, and P. Xi, “Fast super-resolution imaging with ultra-high labeling density achieved by joint tagging super-resolution optical fluctuation imaging,” Sci. Rep. 5, 8359 (2015).
[Crossref] [PubMed]

van Meervelt, L.

B. Moeyaert, N. NguyenBich, E. De Zitter, S. Rocha, K. Clays, H. Mizuno, L. van Meervelt, J. Hofkens, and P. Dedecker, “Green-to-red photoconvertible dronpa mutant for multimodal super-resolution fluorescence microscopy,” ACS Nano 8, 1664–1673 (2014).
[Crossref] [PubMed]

S. Duwe, E. De Zitter, V. Gielen, B. Moeyaert, W. Vandenberg, T. Grotjohann, K. Clays, S. Jakobs, L. Van Meervelt, and P. Dedecker, “Expression-enhanced fluorescent proteins based on enhanced green fluorescent protein for super-resolution microscopy,” ACS Nano (2015).
[Crossref] [PubMed]

Vandenberg, W.

W. Vandenberg, M. Leutenegger, T. Lasser, J. Hofkens, and P. Dedecker, “Diffraction-unlimited imaging: from pretty pictures to hard numbers,” Cell Tissue Res. 360, 151–178 (2015).
[Crossref] [PubMed]

S. Duwe, E. De Zitter, V. Gielen, B. Moeyaert, W. Vandenberg, T. Grotjohann, K. Clays, S. Jakobs, L. Van Meervelt, and P. Dedecker, “Expression-enhanced fluorescent proteins based on enhanced green fluorescent protein for super-resolution microscopy,” ACS Nano (2015).
[Crossref] [PubMed]

Vogel, R.

T. Dertinger, R. Colyer, R. Vogel, J. Enderlein, and S. Weiss, “Achieving increased resolution and more pixels with superresolution optical fluctuation imaging (SOFI),” Opt. Express 18, 18875–18885 (2010).
[Crossref] [PubMed]

T. Dertinger, M. Heilemann, R. Vogel, M. Sauer, and S. Weiss, “Superresolution Optical Fluctuation Imaging with Organic Dyes,” Angew. Chem. Int. Ed. Engl. 49, 9441–9443 (2010).
[Crossref] [PubMed]

Wang, H.

Z. Zeng, X. Chen, H. Wang, N. Huang, C. Shan, H. Zhang, J. Teng, and P. Xi, “Fast super-resolution imaging with ultra-high labeling density achieved by joint tagging super-resolution optical fluctuation imaging,” Sci. Rep. 5, 8359 (2015).
[Crossref] [PubMed]

Weckhuysen, B. M.

Z. Ristanović, M. M. Kerssens, A. V. Kubarev, F. C. Hendriks, P. Dedecker, J. Hofkens, M. B. J. Roeffaers, and B. M. Weckhuysen, “High-resolution single-molecule fluorescence imaging of zeolite aggregates within real-life fluid catalytic cracking particles,” Angew. Chem. Int. Ed. Engl. 54, 1836–1840 (2015).
[Crossref]

Weiss, S.

L. Kisley, R. Brunetti, L. J. Tauzin, B. Shuang, X. Yi, A. W. Kirkeminde, D. A. Higgins, S. Weiss, and C. F. Landes, “Characterization of porous materials by fluorescence correlation spectroscopy super-resolution optical fluctuation imaging,” ACS Nano 9, 9158–9166 (2015).
[Crossref] [PubMed]

T. Dertinger, M. Heilemann, R. Vogel, M. Sauer, and S. Weiss, “Superresolution Optical Fluctuation Imaging with Organic Dyes,” Angew. Chem. Int. Ed. Engl. 49, 9441–9443 (2010).
[Crossref] [PubMed]

T. Dertinger, R. Colyer, R. Vogel, J. Enderlein, and S. Weiss, “Achieving increased resolution and more pixels with superresolution optical fluctuation imaging (SOFI),” Opt. Express 18, 18875–18885 (2010).
[Crossref] [PubMed]

T. Dertinger, R. Colyer, G. Iyer, S. Weiss, and J. Enderlein, “Fast, background-free, 3D super-resolution optical fluctuation imaging (SOFI),” Proc. Natl. Acad. Sci. U.S.A. 106, 22287–22292 (2009).
[Crossref] [PubMed]

Wichmann, J.

Xi, P.

X. Zhang, X. Chen, Z. Zeng, M. Zhang, Y. Sun, P. Xi, J. Peng, and P. Xu, “Development of a reversibly switchable fluorescent protein for super-resolution optical fluctuation imaging (SOFI),” ACS Nano 9, 2659–2667 (2015).
[Crossref] [PubMed]

Z. Zeng, X. Chen, H. Wang, N. Huang, C. Shan, H. Zhang, J. Teng, and P. Xi, “Fast super-resolution imaging with ultra-high labeling density achieved by joint tagging super-resolution optical fluctuation imaging,” Sci. Rep. 5, 8359 (2015).
[Crossref] [PubMed]

Xu, P.

X. Zhang, X. Chen, Z. Zeng, M. Zhang, Y. Sun, P. Xi, J. Peng, and P. Xu, “Development of a reversibly switchable fluorescent protein for super-resolution optical fluctuation imaging (SOFI),” ACS Nano 9, 2659–2667 (2015).
[Crossref] [PubMed]

Yi, X.

L. Kisley, R. Brunetti, L. J. Tauzin, B. Shuang, X. Yi, A. W. Kirkeminde, D. A. Higgins, S. Weiss, and C. F. Landes, “Characterization of porous materials by fluorescence correlation spectroscopy super-resolution optical fluctuation imaging,” ACS Nano 9, 9158–9166 (2015).
[Crossref] [PubMed]

Yoon, T.-Y.

S. Cho, J. Jang, C. Song, H. Lee, P. Ganesan, T.-Y. Yoon, M. W. Kim, M. C. Choi, H. Ihee, W. D. Heo, and Y. Park, “Simple super-resolution live-cell imaging based on diffusion-assisted förster resonance energy transfer,” Sci. Rep. 3, 1208 (2013).
[Crossref]

Zeng, Z.

Z. Zeng, X. Chen, H. Wang, N. Huang, C. Shan, H. Zhang, J. Teng, and P. Xi, “Fast super-resolution imaging with ultra-high labeling density achieved by joint tagging super-resolution optical fluctuation imaging,” Sci. Rep. 5, 8359 (2015).
[Crossref] [PubMed]

X. Zhang, X. Chen, Z. Zeng, M. Zhang, Y. Sun, P. Xi, J. Peng, and P. Xu, “Development of a reversibly switchable fluorescent protein for super-resolution optical fluctuation imaging (SOFI),” ACS Nano 9, 2659–2667 (2015).
[Crossref] [PubMed]

Zhang, H.

Z. Zeng, X. Chen, H. Wang, N. Huang, C. Shan, H. Zhang, J. Teng, and P. Xi, “Fast super-resolution imaging with ultra-high labeling density achieved by joint tagging super-resolution optical fluctuation imaging,” Sci. Rep. 5, 8359 (2015).
[Crossref] [PubMed]

Zhang, J.

P. Dedecker, S. Duwé, R. K. Neely, and J. Zhang, “Localizer: fast, accurate, open-source, and modular software package for superresolution microscopy,” J. Biomed. Opt. 17, 126008 (2012).
[Crossref] [PubMed]

P. Dedecker, G. C. H. Mo, T. Dertinger, and J. Zhang, “Widely accessible method for superresolution fluorescence imaging of living systems,” Proc. Natl. Acad. Sci. U.S.A. 109, 10909–10914 (2012).
[Crossref] [PubMed]

Zhang, M.

X. Zhang, X. Chen, Z. Zeng, M. Zhang, Y. Sun, P. Xi, J. Peng, and P. Xu, “Development of a reversibly switchable fluorescent protein for super-resolution optical fluctuation imaging (SOFI),” ACS Nano 9, 2659–2667 (2015).
[Crossref] [PubMed]

Zhang, X.

X. Zhang, X. Chen, Z. Zeng, M. Zhang, Y. Sun, P. Xi, J. Peng, and P. Xu, “Development of a reversibly switchable fluorescent protein for super-resolution optical fluctuation imaging (SOFI),” ACS Nano 9, 2659–2667 (2015).
[Crossref] [PubMed]

Zhuang, X.

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

ACS Nano (3)

B. Moeyaert, N. NguyenBich, E. De Zitter, S. Rocha, K. Clays, H. Mizuno, L. van Meervelt, J. Hofkens, and P. Dedecker, “Green-to-red photoconvertible dronpa mutant for multimodal super-resolution fluorescence microscopy,” ACS Nano 8, 1664–1673 (2014).
[Crossref] [PubMed]

X. Zhang, X. Chen, Z. Zeng, M. Zhang, Y. Sun, P. Xi, J. Peng, and P. Xu, “Development of a reversibly switchable fluorescent protein for super-resolution optical fluctuation imaging (SOFI),” ACS Nano 9, 2659–2667 (2015).
[Crossref] [PubMed]

L. Kisley, R. Brunetti, L. J. Tauzin, B. Shuang, X. Yi, A. W. Kirkeminde, D. A. Higgins, S. Weiss, and C. F. Landes, “Characterization of porous materials by fluorescence correlation spectroscopy super-resolution optical fluctuation imaging,” ACS Nano 9, 9158–9166 (2015).
[Crossref] [PubMed]

Angew. Chem. Int. Ed. Engl. (2)

T. Dertinger, M. Heilemann, R. Vogel, M. Sauer, and S. Weiss, “Superresolution Optical Fluctuation Imaging with Organic Dyes,” Angew. Chem. Int. Ed. Engl. 49, 9441–9443 (2010).
[Crossref] [PubMed]

Z. Ristanović, M. M. Kerssens, A. V. Kubarev, F. C. Hendriks, P. Dedecker, J. Hofkens, M. B. J. Roeffaers, and B. M. Weckhuysen, “High-resolution single-molecule fluorescence imaging of zeolite aggregates within real-life fluid catalytic cracking particles,” Angew. Chem. Int. Ed. Engl. 54, 1836–1840 (2015).
[Crossref]

Biomed. Opt. Express (1)

Biophys. J. (1)

S. T. Hess, T. P. K. Girirajan, and M. D. Mason, “Ultra-high resolution imaging by fluorescence photoactivation localization microscopy,” Biophys. J. 91, 4258–4272 (2006).
[Crossref] [PubMed]

Cell Tissue Res. (1)

W. Vandenberg, M. Leutenegger, T. Lasser, J. Hofkens, and P. Dedecker, “Diffraction-unlimited imaging: from pretty pictures to hard numbers,” Cell Tissue Res. 360, 151–178 (2015).
[Crossref] [PubMed]

J. Am. Chem. Soc. (1)

P. Dedecker, F. C. De Schryver, and J. Hofkens, “Fluorescent proteins: shine on, you crazy diamond,” J. Am. Chem. Soc. 135, 2387–2402 (2013).
[Crossref] [PubMed]

J. Biomed. Opt. (1)

P. Dedecker, S. Duwé, R. K. Neely, and J. Zhang, “Localizer: fast, accurate, open-source, and modular software package for superresolution microscopy,” J. Biomed. Opt. 17, 126008 (2012).
[Crossref] [PubMed]

Journal of Statistical Planning and Inference (1)

A. J. Stromberg, “Robust covariance estimates based on resampling,” Journal of Statistical Planning and Inference 57, 321–334 (1997). Robust Statistics and Data Analysis, Part {II}.
[Crossref]

Nat. Biotechnol. (1)

S. W. Hell, “Toward fluorescence nanoscopy,” Nat. Biotechnol. 21, 1347–1355 (2003).
[Crossref] [PubMed]

Nat. Commun. (1)

S. Geissbuehler, A. Sharipov, A. Godinat, N. L. Bocchio, P. A. Sandoz, A. Huss, N. A. Jensen, S. Jakobs, J. Enderlein, F. Gisou van der Goot, E. A. Dubikovskaya, T. Lasser, and M. Leutenegger, “Live-cell multiplane three-dimensional super-resolution optical fluctuation imaging,” Nat. Commun. 5, 5830 (2014).
[Crossref] [PubMed]

Nat. Meth. (1)

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

Opt. Express (2)

Opt. Lett. (1)

Opt. Nanoscopy (1)

S. Geissbuehler, N. Bocchio, C. Dellagiacoma, C. Berclaz, M. Leutenegger, and T. Lasser, “Mapping molecular statistics with balanced super-resolution optical fluctuation imaging (bSOFI),” Opt. Nanoscopy 1, 4 (2012).
[Crossref]

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

P. Dedecker, G. C. H. Mo, T. Dertinger, and J. Zhang, “Widely accessible method for superresolution fluorescence imaging of living systems,” Proc. Natl. Acad. Sci. U.S.A. 109, 10909–10914 (2012).
[Crossref] [PubMed]

T. Dertinger, R. Colyer, G. Iyer, S. Weiss, and J. Enderlein, “Fast, background-free, 3D super-resolution optical fluctuation imaging (SOFI),” Proc. Natl. Acad. Sci. U.S.A. 106, 22287–22292 (2009).
[Crossref] [PubMed]

Sci. Rep. (2)

Z. Zeng, X. Chen, H. Wang, N. Huang, C. Shan, H. Zhang, J. Teng, and P. Xi, “Fast super-resolution imaging with ultra-high labeling density achieved by joint tagging super-resolution optical fluctuation imaging,” Sci. Rep. 5, 8359 (2015).
[Crossref] [PubMed]

S. Cho, J. Jang, C. Song, H. Lee, P. Ganesan, T.-Y. Yoon, M. W. Kim, M. C. Choi, H. Ihee, W. D. Heo, and Y. Park, “Simple super-resolution live-cell imaging based on diffusion-assisted förster resonance energy transfer,” Sci. Rep. 3, 1208 (2013).
[Crossref]

Science (1)

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 (2)

A. Stuart and K. Ord, Kendall’s Advanced Theory of Statistics: Volume 1: Distribution Theory, no. v. 1; v. 1994 in Kendall’s Advanced Theory of Statistics (Wiley, 2009).

S. Duwe, E. De Zitter, V. Gielen, B. Moeyaert, W. Vandenberg, T. Grotjohann, K. Clays, S. Jakobs, L. Van Meervelt, and P. Dedecker, “Expression-enhanced fluorescent proteins based on enhanced green fluorescent protein for super-resolution microscopy,” ACS Nano (2015).
[Crossref] [PubMed]

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Figures (8)

Fig. 1
Fig. 1 a: The same virtual pixel (black box) can be generated using different combinations of detector pixels (green boxes). In general the combination(s) in which the detector pixels are closest together will contain the most signal (red arrow), but there are many more less-favorable combinations (black arrows). b: For three-dimensional SOFI the amount of combinations which exist for the same virtual pixel (black box) is even larger.
Fig. 2
Fig. 2 a: Uncertainty estimation using resampling: from a single SOFI dataset containing N fluorescence images, N derived datasets are created by sequentially discarding a single fluorescence image. This results in N SOFI images that can be compared to obtain the variance associated with each SOFI (virtual) pixel. b: A plot of the standard deviations of each pixel as determined by repeating a computer simulation 100 times versus the standard deviation obtained by resampling analysis on one of the simulated datasets. The black line corresponds to the function y = x.
Fig. 3
Fig. 3 Three images showing the SNRs of the same virtual SOFI pixel, but constructed using different pixel combinations (the insets indicate the detector pixels that were combined). As expected the SNR of the image becomes progressively lower as the distance between the pixel detectors increases.
Fig. 4
Fig. 4 Example results obtained using the procedure outlined in this manuscript. In each case 100 fluorescence images of live HeLa cells expressing Lyn-Dronpa measured at different optical magnifications were analyzed. Shown are a conventional second-order SOFI analysis (where only the closest pixel combination(s) are used) and an analysis where all combinations within a 5 by 5 grid surrounding the virtual pixel are used with optimal weights as determined by the resampling methodology.
Fig. 5
Fig. 5 A plot of the optimal weights for pixel combinations leading to different virtual SOFI pixels, as determined using our algorithm, against the average signal of those pixel combinations. Data is shown for for 2nd(left) and 3rd(right) order SOFI, with different colors representing different virtual pixel types. The lines show a least-squares linear fit with intercept fixed to zero.
Fig. 6
Fig. 6 Comparison of the conventional SOFI imaging, imaging using our optimized algorithm, and using weights derived from a linear approximation.
Fig. 7
Fig. 7 Plot of the weights versus SOFI signal as determined by resampling for a simulation. The only difference between the two simulations is that in the left graph the probe has a brightness of 30,000 detected photons per second in the on-state, in the right graph the brightness is 1,000 detected photons per second.
Fig. 8
Fig. 8 A comparison between the conventional approach and the approach described in this paper a:example histograms of SOFI images calculated for different numbers of fluorescence images using the 48 nm optical pixel size. Data calculated using the conventional method is shown as a continuous line, the equivalent histogram using the method of optimal weights as a dashed line. The optimal weights-based approach reaches a similar histogram width (and quality) using fewer images. b:example SNR histograms of a SOFI image calculated from 100 fluorescence images and using the 107 nm optical pixel size. The SNR of the non-background peak is clearly higher for the optimal weights calculation.

Tables (1)

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Algorithm 1 Algorithm for the calculation of the optimal weights.

Equations (20)

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F ( r , t ) = j = 1 N U ( r r j ) ε j s j ( t )
SOFI 2 ( r , τ ) = C 2 [ F ( r , t ) , F ( r , t + τ ) ]
SOFI n ( r , τ ) = C n [ F ( r , t ) , F ( r , t + τ 1 ) , , F ( r , t + τ n 1 ) ]
C 2 [ F ( r , t ) , F ( r , t + τ ) ] = δ F ( r , t ) δ F ( r , t + τ )
= j = 1 N k = 1 N U ( r r j ) U ( r r k ) ε j ε k Δ s j ( t ) Δ s k ( t + τ )
= j N U 2 ( r r j ) ε j 2 c 2 ( τ )
C 2 [ F ( r , t ) , F ( r + ξ , t + τ ) ] = U ( ξ 2 ) j N U 2 ( r + ξ 2 r j ) ε j 2 c 2 ( τ )
S = w 1 κ 1 + w 2 κ 2 +
SNR = S Var ( S )
κ i ( jack ) = f = 1 N κ i f N
Covar ( κ i , κ j ) = f = 1 N ( κ i f κ i ( jack ) ) ( κ j f κ j ( jack ) ) N 1
A c × c = ( Var ( κ 1 ) Covar ( κ 1 , κ 2 ) Covar ( κ 1 , κ c ) Covar ( κ 2 , κ 1 ) Var ( κ 2 ) Covar ( κ 2 , κ c ) Covar ( κ c , κ 1 ) Covar ( κ c , κ 2 ) Var ( κ c ) )
Var ( S ) = i = 1 c j = 1 c w i w j A i j
SNR = S Var ( S ) = i = 1 c w i κ i i = 1 c j = 1 c w i w j A i j
SNR w m = 0
κ m Var ( S ) S j = 1 c w j A m j Var ( S ) Var ( S ) = 0
j = 1 c w j A m j κ m = Var ( S ) S
j = 1 c w j ( A m j κ m A 1 j κ 1 ) = 0
j 1 c w j w 1 ( A m j κ m A 1 j κ 1 ) = A 11 κ 1 A m 1 κ m
Var ( r S ) r S = r r Var ( S ) S = Var ( S ) S

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