Abstract

Super-resolution optical fluctuation imaging (SOFI) provides super-resolution (SR) fluorescence imaging by analyzing fluctuations in the fluorophore emission. The technique has been used both to acquire quantitative SR images and to provide SR biosensing by monitoring changes in fluorophore blinking dynamics. Proper analysis of such data relies on a fully quantitative model of the imaging. However, previous SOFI imaging models made several assumptions that can not be realized in practice. In this work we address these limitations by developing and verifying a fully quantitative model that better approximates real-world imaging conditions. Our model shows that (i) SOFI images are free of bias, or can be made so, if the signal is stationary and fluorophores blink independently, (ii) allows a fully quantitative description of the link between SOFI imaging and probe dynamics, and (iii) paves the way for more advanced SOFI image reconstruction by offering a computationally fast way to calculate SOFI images for arbitrary probe, sample and instrumental properties.

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

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  5. W. Vandenberg, M. Leutenegger, T. Lasser, J. Hofkens, and P. Dedecker, “Diffraction-unlimited imaging: from pretty pictures to hard numbers,” Cell Tissue Res. 360(1), 151–178 (2015).
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    [Crossref]
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    [Crossref]
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    [Crossref]
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    [Crossref]
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    [Crossref]
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    [Crossref]
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    [Crossref]
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    [Crossref]
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2019 (1)

A. Purohit, W. Vandenberg, T. Dertinger, P. Dedecker, and J. Enderlein, “Spatio-temporal correlation super-resolution optical fluctuation imaging,” EPL 125(2), 20005 (2019).
[Crossref]

2018 (2)

A. Descloux, K. Grußmayer, E. Bostan, T. Lukeš, A. Bouwens, A. Sharipov, S. Geissbuehler, A. Mahul-Mellier, H. Lashuel, M. Leutenegger, and T. Lasser, “Combined multi-plane phase retrieval and super-resolution optical fluctuation imaging for 4D cell microscopy,” Nat. Photonics 12(3), 165–172 (2018).
[Crossref]

T. Lukeš, J. Pospíšil, K. Fliegel, T. Lasser, and G. Hagen, “Quantitative super-resolution single molecule microscopy dataset of YFP-tagged growth factor receptors,” GigaScience 7(3), giy002 (2018).
[Crossref]

2017 (5)

G. C. Mo, B. Ross, F. Hertel, P. Manna, X. Yang, E. Greenwald, C. Booth, A. M. Plummer, B. Tenner, Z. Chen, Y. Wang, E. J. Kennedy, P. A. Cole, K. G. Fleming, A. Palmer, R. Jimenez, J. Xiao, P. Dedecker, and J. Zhang, “Genetically encoded biosensors for visualizing live-cell biochemical activity at super-resolution,” Nat. Methods 14(4), 427–434 (2017).
[Crossref]

W. Vandenberg and P. Dedecker, “Effect of probe diffusion on the SOFi imaging accuracy,” Sci. Rep. 7(1), 44665 (2017).
[Crossref]

Y. Peeters, W. Vandenberg, S. Duwé, A. Bouwens, T. Lukeš, C. Ruckebusch, T. Lasser, and P. Dedecker, “Correcting for photodestruction in super-resolution optical fluctuation imaging,” Sci. Rep. 7(1), 10470 (2017).
[Crossref]

T. Lukeš, D. Glatzova, Z. Kvicalova, F. Levet, A. Benda, T. Brdicka, T. Lasser, and M. Cebecauer, “Quantifying protein densities on cell membranes using super-resolution optical fluctuation imaging,” Nat. Commun. 8(1), 1731 (2017).
[Crossref]

S. Duwé, W. Vandenberg, and P. Dedecker, “Live-cell monochromatic dual-label sub-diffraction microscopy by mt-pcSOFI,” Chem. Commun. 53(53), 7242–7245 (2017).
[Crossref]

2016 (5)

H. Deschout, T. Lukeš, A. Sharipov, D. Szlag, L. Feletti, W. Vandenberg, P. Dedecker, J. Hofkens, M. Leutenegger, T. Lasser, and A. Radenovic, “Complementarity of PALM and SOFI for super-resolution live-cell imaging of focal adhesions,” Nat. Commun. 7(1), 13693–00 (2016).
[Crossref]

A. Girsault, T. Lukeš, A. Sharipov, S. Geissbuehler, M. Leutenegger, W. Vandenberg, P. Dedecker, J. Hofkens, and T. Lasser, “SOFI simulation tool: a software package for simulating and testing super-resolution optical fluctuation imaging,” PLoS One 11(9), e0161602–0 (2016).
[Crossref]

F. Hertel, G. C. Mo, S. Duwé, P. Dedecker, and J. Zhang, “RefSOFI for mapping nanoscale organization of protein-protein interactions in living cells,” Cell Rep. 14(2), 390–400 (2016).
[Crossref]

A. M. Chizhik, S. Stein, M. O. Dekaliuk, C. Battle, W. Li, A. Huss, M. Platen, I. A. Schaap, I. Gregor, A. P. Demchenko, C. F. Schmidt, J. Enderlein, and A. I. Chizhik, “Super-resolution optical fluctuation bio-imaging with dual-color carbon nanodots,” Nano Lett. 16(1), 237–242 (2016).
[Crossref]

W. Vandenberg, S. Duwé, M. Leutenegger, B. Moeyaert, B. Krajnik, T. Lasser, and P. Dedecker, “Model-free uncertainty estimation in stochastical optical fluctuation imaging (SOFI) leads to a doubled temporal resolution,” Biomed. Opt. Express 7(2), 467–480 (2016).
[Crossref]

2015 (4)

S. Duwé, 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 9(10), 9528–9541 (2015).
[Crossref]

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(3), 2659–2667 (2015).
[Crossref]

S. C. Stein, A. Huss, D. Hahnel, I. Gregor, and J. Enderlein, “Fourier interpolation stochastic optical fluctuation imaging,” Opt. Express 23(12), 16154–16163 (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(1), 151–178 (2015).
[Crossref]

2014 (2)

B. Moeyaert, N. Nguyen Bich, 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(2), 1664–1673 (2014).
[Crossref]

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(1), 5830 (2014).
[Crossref]

2013 (1)

M. Hirsch, R. J. Wareham, M. L. Martin-Fernandez, M. P. Hobson, and D. J. Rolfe, “A stochastic model for electron multiplication charge-coupled devices–from theory to practice,” PLoS One 8(1), e53671 (2013).
[Crossref]

2012 (3)

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(12), 126008 (2012).
[Crossref]

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

P. Dedecker, G. C. Mo, T. Dertinger, and J. Zhang, “Widely accessible method for superresolution fluorescence imaging of living systems,” Proc. Natl. Acad. Sci. U. S. A. 109(27), 10909–10914 (2012).
[Crossref]

2011 (1)

2010 (3)

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(18), 18875–18885 (2010).
[Crossref]

T. Dertinger, M. Heilemann, R. Vogel, M. Sauer, and S. Weiss, “Superresolution optical fluctuation imaging with organic dyes,” Angew. Chem., Int. Ed. 49(49), 9441–9443 (2010).
[Crossref]

J. Widengren, “Fluorescence-based transient state monitoring for biomolecular spectroscopy and imaging,” J. R. Soc., Interface 7(49), 1135–1144 (2010).
[Crossref]

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. 106(52), 22287–22292 (2009).
[Crossref]

Battle, C.

A. M. Chizhik, S. Stein, M. O. Dekaliuk, C. Battle, W. Li, A. Huss, M. Platen, I. A. Schaap, I. Gregor, A. P. Demchenko, C. F. Schmidt, J. Enderlein, and A. I. Chizhik, “Super-resolution optical fluctuation bio-imaging with dual-color carbon nanodots,” Nano Lett. 16(1), 237–242 (2016).
[Crossref]

Benda, A.

T. Lukeš, D. Glatzova, Z. Kvicalova, F. Levet, A. Benda, T. Brdicka, T. Lasser, and M. Cebecauer, “Quantifying protein densities on cell membranes using super-resolution optical fluctuation imaging,” Nat. Commun. 8(1), 1731 (2017).
[Crossref]

Berclaz, C.

S. Geissbuehler, N. L. Bocchio, C. Dellagiacoma, C. Berclaz, M. Leutenegger, and T. Lasser, “Mapping molecular statistics with balanced super-resolution optical fluctuation imaging (bSOFI)),” Biomed. Opt. Phase Microsc. Nanosc. 1(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(1), 5830 (2014).
[Crossref]

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

Booth, C.

G. C. Mo, B. Ross, F. Hertel, P. Manna, X. Yang, E. Greenwald, C. Booth, A. M. Plummer, B. Tenner, Z. Chen, Y. Wang, E. J. Kennedy, P. A. Cole, K. G. Fleming, A. Palmer, R. Jimenez, J. Xiao, P. Dedecker, and J. Zhang, “Genetically encoded biosensors for visualizing live-cell biochemical activity at super-resolution,” Nat. Methods 14(4), 427–434 (2017).
[Crossref]

Bostan, E.

A. Descloux, K. Grußmayer, E. Bostan, T. Lukeš, A. Bouwens, A. Sharipov, S. Geissbuehler, A. Mahul-Mellier, H. Lashuel, M. Leutenegger, and T. Lasser, “Combined multi-plane phase retrieval and super-resolution optical fluctuation imaging for 4D cell microscopy,” Nat. Photonics 12(3), 165–172 (2018).
[Crossref]

Bouwens, A.

A. Descloux, K. Grußmayer, E. Bostan, T. Lukeš, A. Bouwens, A. Sharipov, S. Geissbuehler, A. Mahul-Mellier, H. Lashuel, M. Leutenegger, and T. Lasser, “Combined multi-plane phase retrieval and super-resolution optical fluctuation imaging for 4D cell microscopy,” Nat. Photonics 12(3), 165–172 (2018).
[Crossref]

Y. Peeters, W. Vandenberg, S. Duwé, A. Bouwens, T. Lukeš, C. Ruckebusch, T. Lasser, and P. Dedecker, “Correcting for photodestruction in super-resolution optical fluctuation imaging,” Sci. Rep. 7(1), 10470 (2017).
[Crossref]

Brdicka, T.

T. Lukeš, D. Glatzova, Z. Kvicalova, F. Levet, A. Benda, T. Brdicka, T. Lasser, and M. Cebecauer, “Quantifying protein densities on cell membranes using super-resolution optical fluctuation imaging,” Nat. Commun. 8(1), 1731 (2017).
[Crossref]

Cebecauer, M.

T. Lukeš, D. Glatzova, Z. Kvicalova, F. Levet, A. Benda, T. Brdicka, T. Lasser, and M. Cebecauer, “Quantifying protein densities on cell membranes using super-resolution optical fluctuation imaging,” Nat. Commun. 8(1), 1731 (2017).
[Crossref]

Chen, 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(3), 2659–2667 (2015).
[Crossref]

Chen, Z.

G. C. Mo, B. Ross, F. Hertel, P. Manna, X. Yang, E. Greenwald, C. Booth, A. M. Plummer, B. Tenner, Z. Chen, Y. Wang, E. J. Kennedy, P. A. Cole, K. G. Fleming, A. Palmer, R. Jimenez, J. Xiao, P. Dedecker, and J. Zhang, “Genetically encoded biosensors for visualizing live-cell biochemical activity at super-resolution,” Nat. Methods 14(4), 427–434 (2017).
[Crossref]

Chizhik, A. I.

A. M. Chizhik, S. Stein, M. O. Dekaliuk, C. Battle, W. Li, A. Huss, M. Platen, I. A. Schaap, I. Gregor, A. P. Demchenko, C. F. Schmidt, J. Enderlein, and A. I. Chizhik, “Super-resolution optical fluctuation bio-imaging with dual-color carbon nanodots,” Nano Lett. 16(1), 237–242 (2016).
[Crossref]

Chizhik, A. M.

A. M. Chizhik, S. Stein, M. O. Dekaliuk, C. Battle, W. Li, A. Huss, M. Platen, I. A. Schaap, I. Gregor, A. P. Demchenko, C. F. Schmidt, J. Enderlein, and A. I. Chizhik, “Super-resolution optical fluctuation bio-imaging with dual-color carbon nanodots,” Nano Lett. 16(1), 237–242 (2016).
[Crossref]

Clays, K.

S. Duwé, 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 9(10), 9528–9541 (2015).
[Crossref]

B. Moeyaert, N. Nguyen Bich, 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(2), 1664–1673 (2014).
[Crossref]

Cole, P. A.

G. C. Mo, B. Ross, F. Hertel, P. Manna, X. Yang, E. Greenwald, C. Booth, A. M. Plummer, B. Tenner, Z. Chen, Y. Wang, E. J. Kennedy, P. A. Cole, K. G. Fleming, A. Palmer, R. Jimenez, J. Xiao, P. Dedecker, and J. Zhang, “Genetically encoded biosensors for visualizing live-cell biochemical activity at super-resolution,” Nat. Methods 14(4), 427–434 (2017).
[Crossref]

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(18), 18875–18885 (2010).
[Crossref]

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. 106(52), 22287–22292 (2009).
[Crossref]

De Zitter, E.

S. Duwé, 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 9(10), 9528–9541 (2015).
[Crossref]

B. Moeyaert, N. Nguyen Bich, 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(2), 1664–1673 (2014).
[Crossref]

Dedecker, P.

A. Purohit, W. Vandenberg, T. Dertinger, P. Dedecker, and J. Enderlein, “Spatio-temporal correlation super-resolution optical fluctuation imaging,” EPL 125(2), 20005 (2019).
[Crossref]

G. C. Mo, B. Ross, F. Hertel, P. Manna, X. Yang, E. Greenwald, C. Booth, A. M. Plummer, B. Tenner, Z. Chen, Y. Wang, E. J. Kennedy, P. A. Cole, K. G. Fleming, A. Palmer, R. Jimenez, J. Xiao, P. Dedecker, and J. Zhang, “Genetically encoded biosensors for visualizing live-cell biochemical activity at super-resolution,” Nat. Methods 14(4), 427–434 (2017).
[Crossref]

S. Duwé, W. Vandenberg, and P. Dedecker, “Live-cell monochromatic dual-label sub-diffraction microscopy by mt-pcSOFI,” Chem. Commun. 53(53), 7242–7245 (2017).
[Crossref]

Y. Peeters, W. Vandenberg, S. Duwé, A. Bouwens, T. Lukeš, C. Ruckebusch, T. Lasser, and P. Dedecker, “Correcting for photodestruction in super-resolution optical fluctuation imaging,” Sci. Rep. 7(1), 10470 (2017).
[Crossref]

W. Vandenberg and P. Dedecker, “Effect of probe diffusion on the SOFi imaging accuracy,” Sci. Rep. 7(1), 44665 (2017).
[Crossref]

W. Vandenberg, S. Duwé, M. Leutenegger, B. Moeyaert, B. Krajnik, T. Lasser, and P. Dedecker, “Model-free uncertainty estimation in stochastical optical fluctuation imaging (SOFI) leads to a doubled temporal resolution,” Biomed. Opt. Express 7(2), 467–480 (2016).
[Crossref]

H. Deschout, T. Lukeš, A. Sharipov, D. Szlag, L. Feletti, W. Vandenberg, P. Dedecker, J. Hofkens, M. Leutenegger, T. Lasser, and A. Radenovic, “Complementarity of PALM and SOFI for super-resolution live-cell imaging of focal adhesions,” Nat. Commun. 7(1), 13693–00 (2016).
[Crossref]

A. Girsault, T. Lukeš, A. Sharipov, S. Geissbuehler, M. Leutenegger, W. Vandenberg, P. Dedecker, J. Hofkens, and T. Lasser, “SOFI simulation tool: a software package for simulating and testing super-resolution optical fluctuation imaging,” PLoS One 11(9), e0161602–0 (2016).
[Crossref]

F. Hertel, G. C. Mo, S. Duwé, P. Dedecker, and J. Zhang, “RefSOFI for mapping nanoscale organization of protein-protein interactions in living cells,” Cell Rep. 14(2), 390–400 (2016).
[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(1), 151–178 (2015).
[Crossref]

S. Duwé, 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 9(10), 9528–9541 (2015).
[Crossref]

B. Moeyaert, N. Nguyen Bich, 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(2), 1664–1673 (2014).
[Crossref]

P. Dedecker, G. C. Mo, T. Dertinger, and J. Zhang, “Widely accessible method for superresolution fluorescence imaging of living systems,” Proc. Natl. Acad. Sci. U. S. A. 109(27), 10909–10914 (2012).
[Crossref]

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(12), 126008 (2012).
[Crossref]

Dekaliuk, M. O.

A. M. Chizhik, S. Stein, M. O. Dekaliuk, C. Battle, W. Li, A. Huss, M. Platen, I. A. Schaap, I. Gregor, A. P. Demchenko, C. F. Schmidt, J. Enderlein, and A. I. Chizhik, “Super-resolution optical fluctuation bio-imaging with dual-color carbon nanodots,” Nano Lett. 16(1), 237–242 (2016).
[Crossref]

Dellagiacoma, C.

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

S. Geissbuehler, C. Dellagiacoma, and T. Lasser, “Comparison between SOFI and STORM,” Biomed. Opt. Express 2(3), 408–420 (2011).
[Crossref]

Demchenko, A. P.

A. M. Chizhik, S. Stein, M. O. Dekaliuk, C. Battle, W. Li, A. Huss, M. Platen, I. A. Schaap, I. Gregor, A. P. Demchenko, C. F. Schmidt, J. Enderlein, and A. I. Chizhik, “Super-resolution optical fluctuation bio-imaging with dual-color carbon nanodots,” Nano Lett. 16(1), 237–242 (2016).
[Crossref]

Dertinger, T.

A. Purohit, W. Vandenberg, T. Dertinger, P. Dedecker, and J. Enderlein, “Spatio-temporal correlation super-resolution optical fluctuation imaging,” EPL 125(2), 20005 (2019).
[Crossref]

P. Dedecker, G. C. Mo, T. Dertinger, and J. Zhang, “Widely accessible method for superresolution fluorescence imaging of living systems,” Proc. Natl. Acad. Sci. U. S. A. 109(27), 10909–10914 (2012).
[Crossref]

T. Dertinger, M. Heilemann, R. Vogel, M. Sauer, and S. Weiss, “Superresolution optical fluctuation imaging with organic dyes,” Angew. Chem., Int. Ed. 49(49), 9441–9443 (2010).
[Crossref]

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(18), 18875–18885 (2010).
[Crossref]

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. 106(52), 22287–22292 (2009).
[Crossref]

Deschout, H.

H. Deschout, T. Lukeš, A. Sharipov, D. Szlag, L. Feletti, W. Vandenberg, P. Dedecker, J. Hofkens, M. Leutenegger, T. Lasser, and A. Radenovic, “Complementarity of PALM and SOFI for super-resolution live-cell imaging of focal adhesions,” Nat. Commun. 7(1), 13693–00 (2016).
[Crossref]

Descloux, A.

A. Descloux, K. Grußmayer, E. Bostan, T. Lukeš, A. Bouwens, A. Sharipov, S. Geissbuehler, A. Mahul-Mellier, H. Lashuel, M. Leutenegger, and T. Lasser, “Combined multi-plane phase retrieval and super-resolution optical fluctuation imaging for 4D cell microscopy,” Nat. Photonics 12(3), 165–172 (2018).
[Crossref]

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(1), 5830 (2014).
[Crossref]

Duwé, S.

S. Duwé, W. Vandenberg, and P. Dedecker, “Live-cell monochromatic dual-label sub-diffraction microscopy by mt-pcSOFI,” Chem. Commun. 53(53), 7242–7245 (2017).
[Crossref]

Y. Peeters, W. Vandenberg, S. Duwé, A. Bouwens, T. Lukeš, C. Ruckebusch, T. Lasser, and P. Dedecker, “Correcting for photodestruction in super-resolution optical fluctuation imaging,” Sci. Rep. 7(1), 10470 (2017).
[Crossref]

W. Vandenberg, S. Duwé, M. Leutenegger, B. Moeyaert, B. Krajnik, T. Lasser, and P. Dedecker, “Model-free uncertainty estimation in stochastical optical fluctuation imaging (SOFI) leads to a doubled temporal resolution,” Biomed. Opt. Express 7(2), 467–480 (2016).
[Crossref]

F. Hertel, G. C. Mo, S. Duwé, P. Dedecker, and J. Zhang, “RefSOFI for mapping nanoscale organization of protein-protein interactions in living cells,” Cell Rep. 14(2), 390–400 (2016).
[Crossref]

S. Duwé, 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 9(10), 9528–9541 (2015).
[Crossref]

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(12), 126008 (2012).
[Crossref]

Enderlein, J.

A. Purohit, W. Vandenberg, T. Dertinger, P. Dedecker, and J. Enderlein, “Spatio-temporal correlation super-resolution optical fluctuation imaging,” EPL 125(2), 20005 (2019).
[Crossref]

A. M. Chizhik, S. Stein, M. O. Dekaliuk, C. Battle, W. Li, A. Huss, M. Platen, I. A. Schaap, I. Gregor, A. P. Demchenko, C. F. Schmidt, J. Enderlein, and A. I. Chizhik, “Super-resolution optical fluctuation bio-imaging with dual-color carbon nanodots,” Nano Lett. 16(1), 237–242 (2016).
[Crossref]

S. C. Stein, A. Huss, D. Hahnel, I. Gregor, and J. Enderlein, “Fourier interpolation stochastic optical fluctuation imaging,” Opt. Express 23(12), 16154–16163 (2015).
[Crossref]

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(1), 5830 (2014).
[Crossref]

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(18), 18875–18885 (2010).
[Crossref]

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. 106(52), 22287–22292 (2009).
[Crossref]

Feletti, L.

H. Deschout, T. Lukeš, A. Sharipov, D. Szlag, L. Feletti, W. Vandenberg, P. Dedecker, J. Hofkens, M. Leutenegger, T. Lasser, and A. Radenovic, “Complementarity of PALM and SOFI for super-resolution live-cell imaging of focal adhesions,” Nat. Commun. 7(1), 13693–00 (2016).
[Crossref]

Fleming, K. G.

G. C. Mo, B. Ross, F. Hertel, P. Manna, X. Yang, E. Greenwald, C. Booth, A. M. Plummer, B. Tenner, Z. Chen, Y. Wang, E. J. Kennedy, P. A. Cole, K. G. Fleming, A. Palmer, R. Jimenez, J. Xiao, P. Dedecker, and J. Zhang, “Genetically encoded biosensors for visualizing live-cell biochemical activity at super-resolution,” Nat. Methods 14(4), 427–434 (2017).
[Crossref]

Fliegel, K.

T. Lukeš, J. Pospíšil, K. Fliegel, T. Lasser, and G. Hagen, “Quantitative super-resolution single molecule microscopy dataset of YFP-tagged growth factor receptors,” GigaScience 7(3), giy002 (2018).
[Crossref]

Geissbuehler, S.

A. Descloux, K. Grußmayer, E. Bostan, T. Lukeš, A. Bouwens, A. Sharipov, S. Geissbuehler, A. Mahul-Mellier, H. Lashuel, M. Leutenegger, and T. Lasser, “Combined multi-plane phase retrieval and super-resolution optical fluctuation imaging for 4D cell microscopy,” Nat. Photonics 12(3), 165–172 (2018).
[Crossref]

A. Girsault, T. Lukeš, A. Sharipov, S. Geissbuehler, M. Leutenegger, W. Vandenberg, P. Dedecker, J. Hofkens, and T. Lasser, “SOFI simulation tool: a software package for simulating and testing super-resolution optical fluctuation imaging,” PLoS One 11(9), e0161602–0 (2016).
[Crossref]

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(1), 5830 (2014).
[Crossref]

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

S. Geissbuehler, C. Dellagiacoma, and T. Lasser, “Comparison between SOFI and STORM,” Biomed. Opt. Express 2(3), 408–420 (2011).
[Crossref]

Gielen, V.

S. Duwé, 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 9(10), 9528–9541 (2015).
[Crossref]

Girsault, A.

A. Girsault, T. Lukeš, A. Sharipov, S. Geissbuehler, M. Leutenegger, W. Vandenberg, P. Dedecker, J. Hofkens, and T. Lasser, “SOFI simulation tool: a software package for simulating and testing super-resolution optical fluctuation imaging,” PLoS One 11(9), e0161602–0 (2016).
[Crossref]

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(1), 5830 (2014).
[Crossref]

Glatzova, D.

T. Lukeš, D. Glatzova, Z. Kvicalova, F. Levet, A. Benda, T. Brdicka, T. Lasser, and M. Cebecauer, “Quantifying protein densities on cell membranes using super-resolution optical fluctuation imaging,” Nat. Commun. 8(1), 1731 (2017).
[Crossref]

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(1), 5830 (2014).
[Crossref]

Greenwald, E.

G. C. Mo, B. Ross, F. Hertel, P. Manna, X. Yang, E. Greenwald, C. Booth, A. M. Plummer, B. Tenner, Z. Chen, Y. Wang, E. J. Kennedy, P. A. Cole, K. G. Fleming, A. Palmer, R. Jimenez, J. Xiao, P. Dedecker, and J. Zhang, “Genetically encoded biosensors for visualizing live-cell biochemical activity at super-resolution,” Nat. Methods 14(4), 427–434 (2017).
[Crossref]

Gregor, I.

A. M. Chizhik, S. Stein, M. O. Dekaliuk, C. Battle, W. Li, A. Huss, M. Platen, I. A. Schaap, I. Gregor, A. P. Demchenko, C. F. Schmidt, J. Enderlein, and A. I. Chizhik, “Super-resolution optical fluctuation bio-imaging with dual-color carbon nanodots,” Nano Lett. 16(1), 237–242 (2016).
[Crossref]

S. C. Stein, A. Huss, D. Hahnel, I. Gregor, and J. Enderlein, “Fourier interpolation stochastic optical fluctuation imaging,” Opt. Express 23(12), 16154–16163 (2015).
[Crossref]

Grotjohann, T.

S. Duwé, 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 9(10), 9528–9541 (2015).
[Crossref]

Grußmayer, K.

A. Descloux, K. Grußmayer, E. Bostan, T. Lukeš, A. Bouwens, A. Sharipov, S. Geissbuehler, A. Mahul-Mellier, H. Lashuel, M. Leutenegger, and T. Lasser, “Combined multi-plane phase retrieval and super-resolution optical fluctuation imaging for 4D cell microscopy,” Nat. Photonics 12(3), 165–172 (2018).
[Crossref]

Hagen, G.

T. Lukeš, J. Pospíšil, K. Fliegel, T. Lasser, and G. Hagen, “Quantitative super-resolution single molecule microscopy dataset of YFP-tagged growth factor receptors,” GigaScience 7(3), giy002 (2018).
[Crossref]

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. 49(49), 9441–9443 (2010).
[Crossref]

Hertel, F.

G. C. Mo, B. Ross, F. Hertel, P. Manna, X. Yang, E. Greenwald, C. Booth, A. M. Plummer, B. Tenner, Z. Chen, Y. Wang, E. J. Kennedy, P. A. Cole, K. G. Fleming, A. Palmer, R. Jimenez, J. Xiao, P. Dedecker, and J. Zhang, “Genetically encoded biosensors for visualizing live-cell biochemical activity at super-resolution,” Nat. Methods 14(4), 427–434 (2017).
[Crossref]

F. Hertel, G. C. Mo, S. Duwé, P. Dedecker, and J. Zhang, “RefSOFI for mapping nanoscale organization of protein-protein interactions in living cells,” Cell Rep. 14(2), 390–400 (2016).
[Crossref]

Hirsch, M.

M. Hirsch, R. J. Wareham, M. L. Martin-Fernandez, M. P. Hobson, and D. J. Rolfe, “A stochastic model for electron multiplication charge-coupled devices–from theory to practice,” PLoS One 8(1), e53671 (2013).
[Crossref]

Hobson, M. P.

M. Hirsch, R. J. Wareham, M. L. Martin-Fernandez, M. P. Hobson, and D. J. Rolfe, “A stochastic model for electron multiplication charge-coupled devices–from theory to practice,” PLoS One 8(1), e53671 (2013).
[Crossref]

Hofkens, J.

A. Girsault, T. Lukeš, A. Sharipov, S. Geissbuehler, M. Leutenegger, W. Vandenberg, P. Dedecker, J. Hofkens, and T. Lasser, “SOFI simulation tool: a software package for simulating and testing super-resolution optical fluctuation imaging,” PLoS One 11(9), e0161602–0 (2016).
[Crossref]

H. Deschout, T. Lukeš, A. Sharipov, D. Szlag, L. Feletti, W. Vandenberg, P. Dedecker, J. Hofkens, M. Leutenegger, T. Lasser, and A. Radenovic, “Complementarity of PALM and SOFI for super-resolution live-cell imaging of focal adhesions,” Nat. Commun. 7(1), 13693–00 (2016).
[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(1), 151–178 (2015).
[Crossref]

B. Moeyaert, N. Nguyen Bich, 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(2), 1664–1673 (2014).
[Crossref]

Hood, C. S.

E. Kirmani and C. S. Hood, “A new approach to analysis of interval availability,” in ARES 2008 - 3rd International Conference on Availability, Security, and Reliability, Proceedings, (IEEE Computer Society, 2008), pp. 479–483.

Huss, A.

A. M. Chizhik, S. Stein, M. O. Dekaliuk, C. Battle, W. Li, A. Huss, M. Platen, I. A. Schaap, I. Gregor, A. P. Demchenko, C. F. Schmidt, J. Enderlein, and A. I. Chizhik, “Super-resolution optical fluctuation bio-imaging with dual-color carbon nanodots,” Nano Lett. 16(1), 237–242 (2016).
[Crossref]

S. C. Stein, A. Huss, D. Hahnel, I. Gregor, and J. Enderlein, “Fourier interpolation stochastic optical fluctuation imaging,” Opt. Express 23(12), 16154–16163 (2015).
[Crossref]

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(1), 5830 (2014).
[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. 106(52), 22287–22292 (2009).
[Crossref]

Jakobs, S.

S. Duwé, 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 9(10), 9528–9541 (2015).
[Crossref]

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(1), 5830 (2014).
[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(1), 5830 (2014).
[Crossref]

Jimenez, R.

G. C. Mo, B. Ross, F. Hertel, P. Manna, X. Yang, E. Greenwald, C. Booth, A. M. Plummer, B. Tenner, Z. Chen, Y. Wang, E. J. Kennedy, P. A. Cole, K. G. Fleming, A. Palmer, R. Jimenez, J. Xiao, P. Dedecker, and J. Zhang, “Genetically encoded biosensors for visualizing live-cell biochemical activity at super-resolution,” Nat. Methods 14(4), 427–434 (2017).
[Crossref]

Kennedy, E. J.

G. C. Mo, B. Ross, F. Hertel, P. Manna, X. Yang, E. Greenwald, C. Booth, A. M. Plummer, B. Tenner, Z. Chen, Y. Wang, E. J. Kennedy, P. A. Cole, K. G. Fleming, A. Palmer, R. Jimenez, J. Xiao, P. Dedecker, and J. Zhang, “Genetically encoded biosensors for visualizing live-cell biochemical activity at super-resolution,” Nat. Methods 14(4), 427–434 (2017).
[Crossref]

Kirmani, E.

E. Kirmani and C. S. Hood, “A new approach to analysis of interval availability,” in ARES 2008 - 3rd International Conference on Availability, Security, and Reliability, Proceedings, (IEEE Computer Society, 2008), pp. 479–483.

Krajnik, B.

Kvicalova, Z.

T. Lukeš, D. Glatzova, Z. Kvicalova, F. Levet, A. Benda, T. Brdicka, T. Lasser, and M. Cebecauer, “Quantifying protein densities on cell membranes using super-resolution optical fluctuation imaging,” Nat. Commun. 8(1), 1731 (2017).
[Crossref]

Lashuel, H.

A. Descloux, K. Grußmayer, E. Bostan, T. Lukeš, A. Bouwens, A. Sharipov, S. Geissbuehler, A. Mahul-Mellier, H. Lashuel, M. Leutenegger, and T. Lasser, “Combined multi-plane phase retrieval and super-resolution optical fluctuation imaging for 4D cell microscopy,” Nat. Photonics 12(3), 165–172 (2018).
[Crossref]

Lasser, T.

A. Descloux, K. Grußmayer, E. Bostan, T. Lukeš, A. Bouwens, A. Sharipov, S. Geissbuehler, A. Mahul-Mellier, H. Lashuel, M. Leutenegger, and T. Lasser, “Combined multi-plane phase retrieval and super-resolution optical fluctuation imaging for 4D cell microscopy,” Nat. Photonics 12(3), 165–172 (2018).
[Crossref]

T. Lukeš, J. Pospíšil, K. Fliegel, T. Lasser, and G. Hagen, “Quantitative super-resolution single molecule microscopy dataset of YFP-tagged growth factor receptors,” GigaScience 7(3), giy002 (2018).
[Crossref]

T. Lukeš, D. Glatzova, Z. Kvicalova, F. Levet, A. Benda, T. Brdicka, T. Lasser, and M. Cebecauer, “Quantifying protein densities on cell membranes using super-resolution optical fluctuation imaging,” Nat. Commun. 8(1), 1731 (2017).
[Crossref]

Y. Peeters, W. Vandenberg, S. Duwé, A. Bouwens, T. Lukeš, C. Ruckebusch, T. Lasser, and P. Dedecker, “Correcting for photodestruction in super-resolution optical fluctuation imaging,” Sci. Rep. 7(1), 10470 (2017).
[Crossref]

W. Vandenberg, S. Duwé, M. Leutenegger, B. Moeyaert, B. Krajnik, T. Lasser, and P. Dedecker, “Model-free uncertainty estimation in stochastical optical fluctuation imaging (SOFI) leads to a doubled temporal resolution,” Biomed. Opt. Express 7(2), 467–480 (2016).
[Crossref]

A. Girsault, T. Lukeš, A. Sharipov, S. Geissbuehler, M. Leutenegger, W. Vandenberg, P. Dedecker, J. Hofkens, and T. Lasser, “SOFI simulation tool: a software package for simulating and testing super-resolution optical fluctuation imaging,” PLoS One 11(9), e0161602–0 (2016).
[Crossref]

H. Deschout, T. Lukeš, A. Sharipov, D. Szlag, L. Feletti, W. Vandenberg, P. Dedecker, J. Hofkens, M. Leutenegger, T. Lasser, and A. Radenovic, “Complementarity of PALM and SOFI for super-resolution live-cell imaging of focal adhesions,” Nat. Commun. 7(1), 13693–00 (2016).
[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(1), 151–178 (2015).
[Crossref]

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(1), 5830 (2014).
[Crossref]

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

S. Geissbuehler, C. Dellagiacoma, and T. Lasser, “Comparison between SOFI and STORM,” Biomed. Opt. Express 2(3), 408–420 (2011).
[Crossref]

Leutenegger, M.

A. Descloux, K. Grußmayer, E. Bostan, T. Lukeš, A. Bouwens, A. Sharipov, S. Geissbuehler, A. Mahul-Mellier, H. Lashuel, M. Leutenegger, and T. Lasser, “Combined multi-plane phase retrieval and super-resolution optical fluctuation imaging for 4D cell microscopy,” Nat. Photonics 12(3), 165–172 (2018).
[Crossref]

A. Girsault, T. Lukeš, A. Sharipov, S. Geissbuehler, M. Leutenegger, W. Vandenberg, P. Dedecker, J. Hofkens, and T. Lasser, “SOFI simulation tool: a software package for simulating and testing super-resolution optical fluctuation imaging,” PLoS One 11(9), e0161602–0 (2016).
[Crossref]

H. Deschout, T. Lukeš, A. Sharipov, D. Szlag, L. Feletti, W. Vandenberg, P. Dedecker, J. Hofkens, M. Leutenegger, T. Lasser, and A. Radenovic, “Complementarity of PALM and SOFI for super-resolution live-cell imaging of focal adhesions,” Nat. Commun. 7(1), 13693–00 (2016).
[Crossref]

W. Vandenberg, S. Duwé, M. Leutenegger, B. Moeyaert, B. Krajnik, T. Lasser, and P. Dedecker, “Model-free uncertainty estimation in stochastical optical fluctuation imaging (SOFI) leads to a doubled temporal resolution,” Biomed. Opt. Express 7(2), 467–480 (2016).
[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(1), 151–178 (2015).
[Crossref]

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(1), 5830 (2014).
[Crossref]

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

Levet, F.

T. Lukeš, D. Glatzova, Z. Kvicalova, F. Levet, A. Benda, T. Brdicka, T. Lasser, and M. Cebecauer, “Quantifying protein densities on cell membranes using super-resolution optical fluctuation imaging,” Nat. Commun. 8(1), 1731 (2017).
[Crossref]

Li, W.

A. M. Chizhik, S. Stein, M. O. Dekaliuk, C. Battle, W. Li, A. Huss, M. Platen, I. A. Schaap, I. Gregor, A. P. Demchenko, C. F. Schmidt, J. Enderlein, and A. I. Chizhik, “Super-resolution optical fluctuation bio-imaging with dual-color carbon nanodots,” Nano Lett. 16(1), 237–242 (2016).
[Crossref]

Lukeš, T.

A. Descloux, K. Grußmayer, E. Bostan, T. Lukeš, A. Bouwens, A. Sharipov, S. Geissbuehler, A. Mahul-Mellier, H. Lashuel, M. Leutenegger, and T. Lasser, “Combined multi-plane phase retrieval and super-resolution optical fluctuation imaging for 4D cell microscopy,” Nat. Photonics 12(3), 165–172 (2018).
[Crossref]

T. Lukeš, J. Pospíšil, K. Fliegel, T. Lasser, and G. Hagen, “Quantitative super-resolution single molecule microscopy dataset of YFP-tagged growth factor receptors,” GigaScience 7(3), giy002 (2018).
[Crossref]

T. Lukeš, D. Glatzova, Z. Kvicalova, F. Levet, A. Benda, T. Brdicka, T. Lasser, and M. Cebecauer, “Quantifying protein densities on cell membranes using super-resolution optical fluctuation imaging,” Nat. Commun. 8(1), 1731 (2017).
[Crossref]

Y. Peeters, W. Vandenberg, S. Duwé, A. Bouwens, T. Lukeš, C. Ruckebusch, T. Lasser, and P. Dedecker, “Correcting for photodestruction in super-resolution optical fluctuation imaging,” Sci. Rep. 7(1), 10470 (2017).
[Crossref]

H. Deschout, T. Lukeš, A. Sharipov, D. Szlag, L. Feletti, W. Vandenberg, P. Dedecker, J. Hofkens, M. Leutenegger, T. Lasser, and A. Radenovic, “Complementarity of PALM and SOFI for super-resolution live-cell imaging of focal adhesions,” Nat. Commun. 7(1), 13693–00 (2016).
[Crossref]

A. Girsault, T. Lukeš, A. Sharipov, S. Geissbuehler, M. Leutenegger, W. Vandenberg, P. Dedecker, J. Hofkens, and T. Lasser, “SOFI simulation tool: a software package for simulating and testing super-resolution optical fluctuation imaging,” PLoS One 11(9), e0161602–0 (2016).
[Crossref]

Mahul-Mellier, A.

A. Descloux, K. Grußmayer, E. Bostan, T. Lukeš, A. Bouwens, A. Sharipov, S. Geissbuehler, A. Mahul-Mellier, H. Lashuel, M. Leutenegger, and T. Lasser, “Combined multi-plane phase retrieval and super-resolution optical fluctuation imaging for 4D cell microscopy,” Nat. Photonics 12(3), 165–172 (2018).
[Crossref]

Manna, P.

G. C. Mo, B. Ross, F. Hertel, P. Manna, X. Yang, E. Greenwald, C. Booth, A. M. Plummer, B. Tenner, Z. Chen, Y. Wang, E. J. Kennedy, P. A. Cole, K. G. Fleming, A. Palmer, R. Jimenez, J. Xiao, P. Dedecker, and J. Zhang, “Genetically encoded biosensors for visualizing live-cell biochemical activity at super-resolution,” Nat. Methods 14(4), 427–434 (2017).
[Crossref]

Martin-Fernandez, M. L.

M. Hirsch, R. J. Wareham, M. L. Martin-Fernandez, M. P. Hobson, and D. J. Rolfe, “A stochastic model for electron multiplication charge-coupled devices–from theory to practice,” PLoS One 8(1), e53671 (2013).
[Crossref]

Mizuno, H.

B. Moeyaert, N. Nguyen Bich, 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(2), 1664–1673 (2014).
[Crossref]

Mo, G. C.

G. C. Mo, B. Ross, F. Hertel, P. Manna, X. Yang, E. Greenwald, C. Booth, A. M. Plummer, B. Tenner, Z. Chen, Y. Wang, E. J. Kennedy, P. A. Cole, K. G. Fleming, A. Palmer, R. Jimenez, J. Xiao, P. Dedecker, and J. Zhang, “Genetically encoded biosensors for visualizing live-cell biochemical activity at super-resolution,” Nat. Methods 14(4), 427–434 (2017).
[Crossref]

F. Hertel, G. C. Mo, S. Duwé, P. Dedecker, and J. Zhang, “RefSOFI for mapping nanoscale organization of protein-protein interactions in living cells,” Cell Rep. 14(2), 390–400 (2016).
[Crossref]

P. Dedecker, G. C. Mo, T. Dertinger, and J. Zhang, “Widely accessible method for superresolution fluorescence imaging of living systems,” Proc. Natl. Acad. Sci. U. S. A. 109(27), 10909–10914 (2012).
[Crossref]

Moeyaert, B.

W. Vandenberg, S. Duwé, M. Leutenegger, B. Moeyaert, B. Krajnik, T. Lasser, and P. Dedecker, “Model-free uncertainty estimation in stochastical optical fluctuation imaging (SOFI) leads to a doubled temporal resolution,” Biomed. Opt. Express 7(2), 467–480 (2016).
[Crossref]

S. Duwé, 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 9(10), 9528–9541 (2015).
[Crossref]

B. Moeyaert, N. Nguyen Bich, 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(2), 1664–1673 (2014).
[Crossref]

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(12), 126008 (2012).
[Crossref]

Nguyen Bich, N.

B. Moeyaert, N. Nguyen Bich, 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(2), 1664–1673 (2014).
[Crossref]

Ord, K.

A. Stuart and K. Ord, Kendall’s advanced theory of statistics, vol. I (Wiley, 2009).

Palmer, A.

G. C. Mo, B. Ross, F. Hertel, P. Manna, X. Yang, E. Greenwald, C. Booth, A. M. Plummer, B. Tenner, Z. Chen, Y. Wang, E. J. Kennedy, P. A. Cole, K. G. Fleming, A. Palmer, R. Jimenez, J. Xiao, P. Dedecker, and J. Zhang, “Genetically encoded biosensors for visualizing live-cell biochemical activity at super-resolution,” Nat. Methods 14(4), 427–434 (2017).
[Crossref]

Peeters, Y.

Y. Peeters, W. Vandenberg, S. Duwé, A. Bouwens, T. Lukeš, C. Ruckebusch, T. Lasser, and P. Dedecker, “Correcting for photodestruction in super-resolution optical fluctuation imaging,” Sci. Rep. 7(1), 10470 (2017).
[Crossref]

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(3), 2659–2667 (2015).
[Crossref]

Platen, M.

A. M. Chizhik, S. Stein, M. O. Dekaliuk, C. Battle, W. Li, A. Huss, M. Platen, I. A. Schaap, I. Gregor, A. P. Demchenko, C. F. Schmidt, J. Enderlein, and A. I. Chizhik, “Super-resolution optical fluctuation bio-imaging with dual-color carbon nanodots,” Nano Lett. 16(1), 237–242 (2016).
[Crossref]

Plummer, A. M.

G. C. Mo, B. Ross, F. Hertel, P. Manna, X. Yang, E. Greenwald, C. Booth, A. M. Plummer, B. Tenner, Z. Chen, Y. Wang, E. J. Kennedy, P. A. Cole, K. G. Fleming, A. Palmer, R. Jimenez, J. Xiao, P. Dedecker, and J. Zhang, “Genetically encoded biosensors for visualizing live-cell biochemical activity at super-resolution,” Nat. Methods 14(4), 427–434 (2017).
[Crossref]

Pospíšil, J.

T. Lukeš, J. Pospíšil, K. Fliegel, T. Lasser, and G. Hagen, “Quantitative super-resolution single molecule microscopy dataset of YFP-tagged growth factor receptors,” GigaScience 7(3), giy002 (2018).
[Crossref]

Purohit, A.

A. Purohit, W. Vandenberg, T. Dertinger, P. Dedecker, and J. Enderlein, “Spatio-temporal correlation super-resolution optical fluctuation imaging,” EPL 125(2), 20005 (2019).
[Crossref]

Radenovic, A.

H. Deschout, T. Lukeš, A. Sharipov, D. Szlag, L. Feletti, W. Vandenberg, P. Dedecker, J. Hofkens, M. Leutenegger, T. Lasser, and A. Radenovic, “Complementarity of PALM and SOFI for super-resolution live-cell imaging of focal adhesions,” Nat. Commun. 7(1), 13693–00 (2016).
[Crossref]

Rocha, S.

B. Moeyaert, N. Nguyen Bich, 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(2), 1664–1673 (2014).
[Crossref]

Rolfe, D. J.

M. Hirsch, R. J. Wareham, M. L. Martin-Fernandez, M. P. Hobson, and D. J. Rolfe, “A stochastic model for electron multiplication charge-coupled devices–from theory to practice,” PLoS One 8(1), e53671 (2013).
[Crossref]

Ross, B.

G. C. Mo, B. Ross, F. Hertel, P. Manna, X. Yang, E. Greenwald, C. Booth, A. M. Plummer, B. Tenner, Z. Chen, Y. Wang, E. J. Kennedy, P. A. Cole, K. G. Fleming, A. Palmer, R. Jimenez, J. Xiao, P. Dedecker, and J. Zhang, “Genetically encoded biosensors for visualizing live-cell biochemical activity at super-resolution,” Nat. Methods 14(4), 427–434 (2017).
[Crossref]

Ruckebusch, C.

Y. Peeters, W. Vandenberg, S. Duwé, A. Bouwens, T. Lukeš, C. Ruckebusch, T. Lasser, and P. Dedecker, “Correcting for photodestruction in super-resolution optical fluctuation imaging,” Sci. Rep. 7(1), 10470 (2017).
[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(1), 5830 (2014).
[Crossref]

Sauer, M.

T. Dertinger, M. Heilemann, R. Vogel, M. Sauer, and S. Weiss, “Superresolution optical fluctuation imaging with organic dyes,” Angew. Chem., Int. Ed. 49(49), 9441–9443 (2010).
[Crossref]

Schaap, I. A.

A. M. Chizhik, S. Stein, M. O. Dekaliuk, C. Battle, W. Li, A. Huss, M. Platen, I. A. Schaap, I. Gregor, A. P. Demchenko, C. F. Schmidt, J. Enderlein, and A. I. Chizhik, “Super-resolution optical fluctuation bio-imaging with dual-color carbon nanodots,” Nano Lett. 16(1), 237–242 (2016).
[Crossref]

Schmidt, C. F.

A. M. Chizhik, S. Stein, M. O. Dekaliuk, C. Battle, W. Li, A. Huss, M. Platen, I. A. Schaap, I. Gregor, A. P. Demchenko, C. F. Schmidt, J. Enderlein, and A. I. Chizhik, “Super-resolution optical fluctuation bio-imaging with dual-color carbon nanodots,” Nano Lett. 16(1), 237–242 (2016).
[Crossref]

Sharipov, A.

A. Descloux, K. Grußmayer, E. Bostan, T. Lukeš, A. Bouwens, A. Sharipov, S. Geissbuehler, A. Mahul-Mellier, H. Lashuel, M. Leutenegger, and T. Lasser, “Combined multi-plane phase retrieval and super-resolution optical fluctuation imaging for 4D cell microscopy,” Nat. Photonics 12(3), 165–172 (2018).
[Crossref]

A. Girsault, T. Lukeš, A. Sharipov, S. Geissbuehler, M. Leutenegger, W. Vandenberg, P. Dedecker, J. Hofkens, and T. Lasser, “SOFI simulation tool: a software package for simulating and testing super-resolution optical fluctuation imaging,” PLoS One 11(9), e0161602–0 (2016).
[Crossref]

H. Deschout, T. Lukeš, A. Sharipov, D. Szlag, L. Feletti, W. Vandenberg, P. Dedecker, J. Hofkens, M. Leutenegger, T. Lasser, and A. Radenovic, “Complementarity of PALM and SOFI for super-resolution live-cell imaging of focal adhesions,” Nat. Commun. 7(1), 13693–00 (2016).
[Crossref]

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(1), 5830 (2014).
[Crossref]

Stein, S.

A. M. Chizhik, S. Stein, M. O. Dekaliuk, C. Battle, W. Li, A. Huss, M. Platen, I. A. Schaap, I. Gregor, A. P. Demchenko, C. F. Schmidt, J. Enderlein, and A. I. Chizhik, “Super-resolution optical fluctuation bio-imaging with dual-color carbon nanodots,” Nano Lett. 16(1), 237–242 (2016).
[Crossref]

Stein, S. C.

Stuart, A.

A. Stuart and K. Ord, Kendall’s advanced theory of statistics, vol. I (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(3), 2659–2667 (2015).
[Crossref]

Szlag, D.

H. Deschout, T. Lukeš, A. Sharipov, D. Szlag, L. Feletti, W. Vandenberg, P. Dedecker, J. Hofkens, M. Leutenegger, T. Lasser, and A. Radenovic, “Complementarity of PALM and SOFI for super-resolution live-cell imaging of focal adhesions,” Nat. Commun. 7(1), 13693–00 (2016).
[Crossref]

Tenner, B.

G. C. Mo, B. Ross, F. Hertel, P. Manna, X. Yang, E. Greenwald, C. Booth, A. M. Plummer, B. Tenner, Z. Chen, Y. Wang, E. J. Kennedy, P. A. Cole, K. G. Fleming, A. Palmer, R. Jimenez, J. Xiao, P. Dedecker, and J. Zhang, “Genetically encoded biosensors for visualizing live-cell biochemical activity at super-resolution,” Nat. Methods 14(4), 427–434 (2017).
[Crossref]

Van Meervelt, L.

S. Duwé, 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 9(10), 9528–9541 (2015).
[Crossref]

B. Moeyaert, N. Nguyen Bich, 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(2), 1664–1673 (2014).
[Crossref]

Vandenberg, W.

A. Purohit, W. Vandenberg, T. Dertinger, P. Dedecker, and J. Enderlein, “Spatio-temporal correlation super-resolution optical fluctuation imaging,” EPL 125(2), 20005 (2019).
[Crossref]

S. Duwé, W. Vandenberg, and P. Dedecker, “Live-cell monochromatic dual-label sub-diffraction microscopy by mt-pcSOFI,” Chem. Commun. 53(53), 7242–7245 (2017).
[Crossref]

Y. Peeters, W. Vandenberg, S. Duwé, A. Bouwens, T. Lukeš, C. Ruckebusch, T. Lasser, and P. Dedecker, “Correcting for photodestruction in super-resolution optical fluctuation imaging,” Sci. Rep. 7(1), 10470 (2017).
[Crossref]

W. Vandenberg and P. Dedecker, “Effect of probe diffusion on the SOFi imaging accuracy,” Sci. Rep. 7(1), 44665 (2017).
[Crossref]

W. Vandenberg, S. Duwé, M. Leutenegger, B. Moeyaert, B. Krajnik, T. Lasser, and P. Dedecker, “Model-free uncertainty estimation in stochastical optical fluctuation imaging (SOFI) leads to a doubled temporal resolution,” Biomed. Opt. Express 7(2), 467–480 (2016).
[Crossref]

A. Girsault, T. Lukeš, A. Sharipov, S. Geissbuehler, M. Leutenegger, W. Vandenberg, P. Dedecker, J. Hofkens, and T. Lasser, “SOFI simulation tool: a software package for simulating and testing super-resolution optical fluctuation imaging,” PLoS One 11(9), e0161602–0 (2016).
[Crossref]

H. Deschout, T. Lukeš, A. Sharipov, D. Szlag, L. Feletti, W. Vandenberg, P. Dedecker, J. Hofkens, M. Leutenegger, T. Lasser, and A. Radenovic, “Complementarity of PALM and SOFI for super-resolution live-cell imaging of focal adhesions,” Nat. Commun. 7(1), 13693–00 (2016).
[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(1), 151–178 (2015).
[Crossref]

S. Duwé, 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 9(10), 9528–9541 (2015).
[Crossref]

Vogel, R.

T. Dertinger, M. Heilemann, R. Vogel, M. Sauer, and S. Weiss, “Superresolution optical fluctuation imaging with organic dyes,” Angew. Chem., Int. Ed. 49(49), 9441–9443 (2010).
[Crossref]

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(18), 18875–18885 (2010).
[Crossref]

Wang, Y.

G. C. Mo, B. Ross, F. Hertel, P. Manna, X. Yang, E. Greenwald, C. Booth, A. M. Plummer, B. Tenner, Z. Chen, Y. Wang, E. J. Kennedy, P. A. Cole, K. G. Fleming, A. Palmer, R. Jimenez, J. Xiao, P. Dedecker, and J. Zhang, “Genetically encoded biosensors for visualizing live-cell biochemical activity at super-resolution,” Nat. Methods 14(4), 427–434 (2017).
[Crossref]

Wareham, R. J.

M. Hirsch, R. J. Wareham, M. L. Martin-Fernandez, M. P. Hobson, and D. J. Rolfe, “A stochastic model for electron multiplication charge-coupled devices–from theory to practice,” PLoS One 8(1), e53671 (2013).
[Crossref]

Weiss, S.

T. Dertinger, M. Heilemann, R. Vogel, M. Sauer, and S. Weiss, “Superresolution optical fluctuation imaging with organic dyes,” Angew. Chem., Int. Ed. 49(49), 9441–9443 (2010).
[Crossref]

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(18), 18875–18885 (2010).
[Crossref]

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. 106(52), 22287–22292 (2009).
[Crossref]

Widengren, J.

J. Widengren, “Fluorescence-based transient state monitoring for biomolecular spectroscopy and imaging,” J. R. Soc., Interface 7(49), 1135–1144 (2010).
[Crossref]

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(3), 2659–2667 (2015).
[Crossref]

Xiao, J.

G. C. Mo, B. Ross, F. Hertel, P. Manna, X. Yang, E. Greenwald, C. Booth, A. M. Plummer, B. Tenner, Z. Chen, Y. Wang, E. J. Kennedy, P. A. Cole, K. G. Fleming, A. Palmer, R. Jimenez, J. Xiao, P. Dedecker, and J. Zhang, “Genetically encoded biosensors for visualizing live-cell biochemical activity at super-resolution,” Nat. Methods 14(4), 427–434 (2017).
[Crossref]

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(3), 2659–2667 (2015).
[Crossref]

Yang, X.

G. C. Mo, B. Ross, F. Hertel, P. Manna, X. Yang, E. Greenwald, C. Booth, A. M. Plummer, B. Tenner, Z. Chen, Y. Wang, E. J. Kennedy, P. A. Cole, K. G. Fleming, A. Palmer, R. Jimenez, J. Xiao, P. Dedecker, and J. Zhang, “Genetically encoded biosensors for visualizing live-cell biochemical activity at super-resolution,” Nat. Methods 14(4), 427–434 (2017).
[Crossref]

Zeng, Z.

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(3), 2659–2667 (2015).
[Crossref]

Zhang, J.

G. C. Mo, B. Ross, F. Hertel, P. Manna, X. Yang, E. Greenwald, C. Booth, A. M. Plummer, B. Tenner, Z. Chen, Y. Wang, E. J. Kennedy, P. A. Cole, K. G. Fleming, A. Palmer, R. Jimenez, J. Xiao, P. Dedecker, and J. Zhang, “Genetically encoded biosensors for visualizing live-cell biochemical activity at super-resolution,” Nat. Methods 14(4), 427–434 (2017).
[Crossref]

F. Hertel, G. C. Mo, S. Duwé, P. Dedecker, and J. Zhang, “RefSOFI for mapping nanoscale organization of protein-protein interactions in living cells,” Cell Rep. 14(2), 390–400 (2016).
[Crossref]

P. Dedecker, G. C. Mo, T. Dertinger, and J. Zhang, “Widely accessible method for superresolution fluorescence imaging of living systems,” Proc. Natl. Acad. Sci. U. S. A. 109(27), 10909–10914 (2012).
[Crossref]

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(12), 126008 (2012).
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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(3), 2659–2667 (2015).
[Crossref]

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(3), 2659–2667 (2015).
[Crossref]

ACS Nano (3)

B. Moeyaert, N. Nguyen Bich, 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(2), 1664–1673 (2014).
[Crossref]

S. Duwé, 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 9(10), 9528–9541 (2015).
[Crossref]

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(3), 2659–2667 (2015).
[Crossref]

Angew. Chem., Int. Ed. (1)

T. Dertinger, M. Heilemann, R. Vogel, M. Sauer, and S. Weiss, “Superresolution optical fluctuation imaging with organic dyes,” Angew. Chem., Int. Ed. 49(49), 9441–9443 (2010).
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Biomed. Opt. Express (2)

Biomed. Opt. Phase Microsc. Nanosc. (1)

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

Cell Rep. (1)

F. Hertel, G. C. Mo, S. Duwé, P. Dedecker, and J. Zhang, “RefSOFI for mapping nanoscale organization of protein-protein interactions in living cells,” Cell Rep. 14(2), 390–400 (2016).
[Crossref]

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(1), 151–178 (2015).
[Crossref]

Chem. Commun. (1)

S. Duwé, W. Vandenberg, and P. Dedecker, “Live-cell monochromatic dual-label sub-diffraction microscopy by mt-pcSOFI,” Chem. Commun. 53(53), 7242–7245 (2017).
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EPL (1)

A. Purohit, W. Vandenberg, T. Dertinger, P. Dedecker, and J. Enderlein, “Spatio-temporal correlation super-resolution optical fluctuation imaging,” EPL 125(2), 20005 (2019).
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GigaScience (1)

T. Lukeš, J. Pospíšil, K. Fliegel, T. Lasser, and G. Hagen, “Quantitative super-resolution single molecule microscopy dataset of YFP-tagged growth factor receptors,” GigaScience 7(3), giy002 (2018).
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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(12), 126008 (2012).
[Crossref]

J. R. Soc., Interface (1)

J. Widengren, “Fluorescence-based transient state monitoring for biomolecular spectroscopy and imaging,” J. R. Soc., Interface 7(49), 1135–1144 (2010).
[Crossref]

Nano Lett. (1)

A. M. Chizhik, S. Stein, M. O. Dekaliuk, C. Battle, W. Li, A. Huss, M. Platen, I. A. Schaap, I. Gregor, A. P. Demchenko, C. F. Schmidt, J. Enderlein, and A. I. Chizhik, “Super-resolution optical fluctuation bio-imaging with dual-color carbon nanodots,” Nano Lett. 16(1), 237–242 (2016).
[Crossref]

Nat. Commun. (3)

T. Lukeš, D. Glatzova, Z. Kvicalova, F. Levet, A. Benda, T. Brdicka, T. Lasser, and M. Cebecauer, “Quantifying protein densities on cell membranes using super-resolution optical fluctuation imaging,” Nat. Commun. 8(1), 1731 (2017).
[Crossref]

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(1), 5830 (2014).
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H. Deschout, T. Lukeš, A. Sharipov, D. Szlag, L. Feletti, W. Vandenberg, P. Dedecker, J. Hofkens, M. Leutenegger, T. Lasser, and A. Radenovic, “Complementarity of PALM and SOFI for super-resolution live-cell imaging of focal adhesions,” Nat. Commun. 7(1), 13693–00 (2016).
[Crossref]

Nat. Methods (1)

G. C. Mo, B. Ross, F. Hertel, P. Manna, X. Yang, E. Greenwald, C. Booth, A. M. Plummer, B. Tenner, Z. Chen, Y. Wang, E. J. Kennedy, P. A. Cole, K. G. Fleming, A. Palmer, R. Jimenez, J. Xiao, P. Dedecker, and J. Zhang, “Genetically encoded biosensors for visualizing live-cell biochemical activity at super-resolution,” Nat. Methods 14(4), 427–434 (2017).
[Crossref]

Nat. Photonics (1)

A. Descloux, K. Grußmayer, E. Bostan, T. Lukeš, A. Bouwens, A. Sharipov, S. Geissbuehler, A. Mahul-Mellier, H. Lashuel, M. Leutenegger, and T. Lasser, “Combined multi-plane phase retrieval and super-resolution optical fluctuation imaging for 4D cell microscopy,” Nat. Photonics 12(3), 165–172 (2018).
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Opt. Express (2)

PLoS One (2)

M. Hirsch, R. J. Wareham, M. L. Martin-Fernandez, M. P. Hobson, and D. J. Rolfe, “A stochastic model for electron multiplication charge-coupled devices–from theory to practice,” PLoS One 8(1), e53671 (2013).
[Crossref]

A. Girsault, T. Lukeš, A. Sharipov, S. Geissbuehler, M. Leutenegger, W. Vandenberg, P. Dedecker, J. Hofkens, and T. Lasser, “SOFI simulation tool: a software package for simulating and testing super-resolution optical fluctuation imaging,” PLoS One 11(9), e0161602–0 (2016).
[Crossref]

Proc. Natl. Acad. Sci. (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. 106(52), 22287–22292 (2009).
[Crossref]

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

P. Dedecker, G. C. Mo, T. Dertinger, and J. Zhang, “Widely accessible method for superresolution fluorescence imaging of living systems,” Proc. Natl. Acad. Sci. U. S. A. 109(27), 10909–10914 (2012).
[Crossref]

Sci. Rep. (2)

W. Vandenberg and P. Dedecker, “Effect of probe diffusion on the SOFi imaging accuracy,” Sci. Rep. 7(1), 44665 (2017).
[Crossref]

Y. Peeters, W. Vandenberg, S. Duwé, A. Bouwens, T. Lukeš, C. Ruckebusch, T. Lasser, and P. Dedecker, “Correcting for photodestruction in super-resolution optical fluctuation imaging,” Sci. Rep. 7(1), 10470 (2017).
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A. Stuart and K. Ord, Kendall’s advanced theory of statistics, vol. I (Wiley, 2009).

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Figures (4)

Fig. 1.
Fig. 1. Cumulants of the Bernoulli distribution and correction factors for fast switching fluorophores. Even though the correction factor for time-lagged second-order SOFI is positive, the absolute signal for a time-lagged cumulant will always be smaller than that of the non-lagged version.
Fig. 2.
Fig. 2. The effect of limited measurement duration on the correction factor on the Bernoulli model, taking both fast switching and a limited measurement duration into account.
Fig. 3.
Fig. 3. The effect of limited measurement duration on the correction factor on the Bernoulli model, taking both fast switching and a limited measurement duration into account.
Fig. 4.
Fig. 4. Measured SOFI signal on a live HeLa cell expressing rsGreen1, and as a function of time lag (full details can be found in Appendix D). The signal from a single detector pixel is shown. Also shown are the best fits of this data using the previous SOFI, the model presented here, and numerical simulations.

Equations (62)

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F ( r , t ) = j = 1 M P S F ( r r j ) ϵ j s j ( t )
κ 2 ( r + ξ 2 ) = C 2 ( F ( r , t ) , F ( r + ξ , t + δ ) ) = P S F ( ξ 2 ) j M P S F 2 ( r + ξ 2 r j ) ϵ j 2 C 2 ( δ ) ,
C k ( j F j ) = j C k ( F j )
C G F ( t 1 , t 2 , ) = log ( C F ( t 1 , t 2 , ) ) ,
C F ( t 1 , t 2 , ) = E { exp ( i t 1 X 1 + i t 2 X 2 + ) }
C k ( X 1 m , X 2 n , ) = i k [ m t 1 m n t 2 n C G F ( t 1 , t 2 , ) ] t 1 , t 2 , = 0
C G F poisson ( t ) = λ ( e i t 1 ) ,
C G F nn ( t 1 , t 2 , ) = j λ j ( e i t j 1 )
C F gamma = ( 1 γ i t ) η ,
C F em = η = 0 ( 1 γ i t ) η λ η e λ η ! = e λ η = 0 ( λ / ( 1 γ i t ) ) η η ! = exp ( λ γ i t 1 γ i t )
C G F em ( t 1 , t 2 , ) = j λ j γ i t j 1 γ i t j ,
SNR = g t CGF 2 t 2 CGF | t = 0
C G F linear detector = j λ j f ( t j )
ρ ( t ) = 1 T t t + T s ( t ) d t ,
C G F det ( t 1 , t 2 , ) = log ( 0 1 exp ( ρ C G F det ( t 1 , t 2 , ) ) ϕ ( ρ ) d ρ ) ,
C G F det ( t 1 , t 2 , ) = C G F ρ ( i 1 C G F det ( t 1 , t 2 , ) )
C G F nn ( t 1 , t 2 , ) = C G F ρ ( 1 i j λ j ( e i t j 1 ) ) .
C G F em ( t 1 , t 2 , ) = C G F ρ ( j λ j γ t j 1 γ i t j ) .
C 2 ( X 1 , X 2 ) = λ 1 λ 2 C 2 ( ρ )
C 3 ( X 1 , X 2 , X 3 ) = λ 1 λ 2 λ 3 C 3 ( ρ )
C 4 ( X 1 , X 2 , X 3 , X 4 ) = λ 1 λ 2 λ 3 λ 4 C 4 ( ρ )
C 2 ( X 1 , X 1 , δ 1 ) = λ 1 2 C 2 ( ρ , ρ δ 1 )
C 2 ( X 1 , X 2 , δ 1 ) = λ 1 λ 2 C 2 ( ρ , ρ δ 1 )
C 3 ( X 1 , X 1 , δ 1 , X 1 , δ 2 ) = λ 1 3 C 3 ( ρ , ρ δ 1 , ρ δ 2 )
C 3 ( X 1 , X 2 , X 3 , δ 1 ) = λ 1 λ 2 λ 3 C 3 ( ρ , ρ , ρ δ 1 )
C 3 ( X 1 , X 1 , δ 1 , X 2 ) = λ 1 2 λ 2 C 3 ( ρ , ρ , ρ δ 1 )
C k , em = γ k C k , nn
C 2 ( X 1 , X 2 ) = E { X 1 X 2 } E { X 1 } E { X 2 }
c 2 ( X 1 , X 2 ) = 1 N n = 1 N ( X 1 , n X 2 , n ) 1 N 2 n = 1 N X 1 , n n = 1 N X 2 , n
E { c 2 ( X 1 , X 2 ) } = N 1 N E { X 1 , t X 2 , t } n = 1 N 1 N n N 2 ( E { X 1 , t + n X 2 , t } + E { X 1 , t X 2 , t + n } )
E { c 2 ( X 1 , X 2 ) } = N 1 N C 2 ( X 1 , X 2 ) n = 1 N 1 2 N n N 2 C 2 ( X 1 , X 2 , δ n )
E { c 2 ( X 1 , X 2 , δ s ) } = C 2 ( X 1 , X 2 , δ s ) N | s | N 2 C 2 ( X 1 , X 2 ) n = 1 | s | 2 N | s | N 2 C 2 ( X 1 , X 2 , δ n ) n = | s | + 1 N | s | 2 N n N 2 C 2 ( X 1 , X 2 , δ n ) n = N | s | + 1 N 1 N n N 2 C 2 ( X 1 , X 2 , δ n )
λ j = ϵ f r A j P S F ( r f r ) d r ,
λ j = ϵ f P S F ( r f r j ) .
λ j = ϵ f [ Φ ( x j x f + d / 2 σ ) Φ ( x j x f d / 2 σ ) ] × [ Φ ( y j y f + d / 2 σ ) Φ ( y j y f d / 2 σ ) ]
1 / τ = k on off + k off on
ρ ^ = k off on k on off + k off on
C 3 ( X 1 , X 1 , X 1 , δ 1 ) = λ 1 3 C 3 ( ρ , ρ , ρ δ 1 ) + C 2 ( X 1 , X 1 , δ 1 )
C 3 ( X 1 , X 1 , X 2 ) = λ 1 2 λ 2 C 3 ( ρ ) + C 2 ( X 1 , X 2 )
C 4 ( X 1 , X 1 , X 1 , X 1 , δ 1 ) = λ 1 4 C 4 ( ρ , ρ , ρ , ρ δ 1 ) + 3 C 3 ( X 1 , X 1 , X δ 1 ) 2 C 2 ( X 1 , X 1 , δ 1 )
C 4 ( X 1 , X 1 , X 1 , X 2 ) = λ 1 3 λ 2 C 4 ( ρ ) + 3 C 3 ( X 1 , X 1 , X 2 ) 2 C 2 ( X 1 , X 2 )
C 4 ( X 1 , X 1 , X 2 , X 2 ) = λ 1 2 λ 2 2 C 4 ( ρ ) + C 3 ( X 1 , X 1 , X 2 ) + C 3 ( X 1 , X 2 , X 2 ) C 2 ( X 1 , X 2 )
C 4 ( X 1 , X 1 , X 2 , X 3 ) = λ 1 2 λ 2 λ 3 C 4 ( ρ ) + C 3 ( X 1 , X 2 , X 3 )
C 4 ( X 1 , X 1 , X 1 , δ 1 , X 1 , δ 2 ) = λ 1 4 C 4 ( ρ , ρ , ρ δ 1 , ρ δ 2 ) + C 3 ( X 1 , X 1 , δ 1 , X 1 , δ 2 )
C 3 ( X 1 , X 1 , X 1 , δ 1 ) = γ 3 λ 1 3 C 3 ( ρ , ρ , ρ δ 1 ) + 2 γ C 2 ( X 1 , X 1 , δ 1 )
C 3 ( X 1 , X 1 , X 2 ) = γ 3 λ 1 2 λ 2 C 3 ( ρ ) + 2 γ C 2 ( X 1 , X 2 )
C 4 ( X 1 , X 1 , X 1 , X 1 , δ 1 ) = γ 4 λ 1 4 C 4 ( ρ , ρ , ρ , ρ δ 1 ) + 6 γ C 3 ( X 1 , X 1 , X δ 1 ) 6 γ 2 C 3 ( X 1 , X 1 , δ 1 )
C 4 ( X 1 , X 1 , X 1 , X 2 ) = γ 4 λ 1 3 λ 2 C 4 ( ρ ) + 6 γ C 3 ( X 1 , X 1 , X 2 ) 6 γ 2 C 3 ( X 1 , X 2 )
C 4 ( X 1 , X 1 , X 2 , X 2 ) = γ 4 λ 1 2 λ 2 2 C 4 ( ρ ) + 2 γ C 3 ( X 1 , X 1 , X 2 ) + 2 γ C 3 ( X 1 , X 2 , X 2 ) 4 γ 2 C 2 ( X 1 , X 2 )
C 4 ( X 1 , X 1 , X 2 , X 3 ) = γ 4 λ 1 2 λ 2 λ 3 C 4 ( ρ ) + 2 γ C 3 ( X 1 , X 2 , X 3 )
C 4 ( X 1 , X 1 , X 1 , δ 1 , X 1 , δ 2 ) = γ 4 λ 1 4 C 4 ( ρ , ρ , ρ δ 1 , ρ δ 2 ) + 2 γ C 3 ( X 1 , X 1 , δ 1 , X 1 , δ 2 )
C 3 ( X 1 , X 2 , X 3 ) = E { X 1 X 2 X 3 } + 2 E { X 1 } E { X 2 } E { X 3 } E { X 1 X 2 } E { X 3 } E { X 1 X 3 } E { X 2 } E { X 2 X 3 } E { X 1 }
c 3 ( X 1 , X 2 , X 3 ) = 1 N n = 1 N ( X 1 , n X 2 , n X 3 , n ) + 2 N 3 n = 1 N X 1 , n n = 1 N X 2 , n n = 1 N X 3 , n 1 N 2 n = 1 N ( X 1 , n X 2 , n ) n = 1 N X 3 , n 1 N 2 n = 1 N ( X 1 , n X 3 , n ) n = 1 N X 2 , n 1 N 2 n = 1 N ( X 2 , n X 3 , n ) n = 1 N X 1 , n
E { c 3 ( X 1 , X 2 , X 3 ) } = 1 N E { X 1 , t X 2 , t X 3 , t } + 2 N 3 i = 1 N j = 1 N k = 1 N E { X 1 X 2 , ( j i ) X 3 , ( k i ) } 1 N 2 i = 1 N j = 1 N ( E { X 1 X 2 X 3 , ( j i ) } + E { X 1 X 2 , ( j i ) X 3 } + E { X 1 , ( j i ) X 2 X 3 } )
E { X 1 , i X 2 , j X 3 , k } = C 3 ( X 1 , i , X 2 , j , X 3 , k ) 2 E { X 1 } E { X 2 } E { X 3 } E { X 1 , i X 2 , j } E { X 3 } E { X 1 , i X 3 , k } E { X 2 } E { X 2 , j X 3 , k } E { X 1 }
E { c 3 ( X 1 , X 2 , X 3 ) } = ( n n + 2 n n 3 3 n n 2 ) C 3 ( X 1 , X 2 , X 3 ) + j = 1 j = n 1 ( 2 ( n j ) n 3 n j n 2 ) ( C 3 ( X 1 , X 2 , δ j , X 3 ) + C 3 ( X 1 , X 2 , δ j , X 3 ) ) + j = 1 j = n 1 ( 2 ( n j ) n 3 n j n 2 ) ( C 3 ( X 1 , X 2 , X 3 , δ j ) + C 3 ( X 1 , X 2 , X 3 , δ j ) ) + j = 1 j = n 1 ( 2 ( n j ) n 3 n j n 2 ) ( C 3 ( X 1 , X 2 , δ j , X 3 , δ j ) + C 3 ( X 1 , X 2 , δ j , X 3 , δ j ) ) + i = 1 i = n 1 j = i + 1 j = n 1 2 ( n j ) n 3 ( C 3 ( X 1 , X 2 , δ i , X 3 , δ j ) + C 3 ( X 1 , X 2 , δ j , X 3 , δ i ) ) + i = 1 i = n 1 j = i + 1 j = n 1 2 ( n j ) n 3 ( C 3 ( X 1 , X 2 , δ i , X 3 , δ j i ) + C 3 ( X 1 , X 2 , δ j , X 3 , δ i j ) ) + i = 1 i = n 1 j = i + 1 j = n 1 2 ( n j ) n 3 ( C 3 ( X 1 , X 2 , δ j i , X 3 , δ i ) + C 3 ( X 1 , X 2 , δ i j , X 3 , δ j ) )
E off { ( 1 ρ ) n } E on { ρ n }  with swapped  k o n o f f  and  k o f f o n .
E off { 1 ρ } = 1 E off { ρ } E off { ρ } = 1 E off { 1 ρ }
E off { ( 1 ρ ) 2 } = 1 2 E off { ρ } + E off { ρ 2 } E off { ρ 2 } = 1 2 E off { 1 ρ } + E off { ( 1 ρ ) 2 }
E { ρ n } = ρ ^ E on { ρ n } + ( 1 ρ ^ ) E off { ρ n }
E { ρ m ρ δ n } = E on { ρ m } ρ ^ E on { ρ n } + E off { ρ m } ( 1 ρ ^ ) E off { ρ n }
E { ρ m ρ δ n } = ρ ^ E on { ρ m } P o n o n ( δ ) E on { ρ n } + ρ ^ E on { ρ m } P o n o f f ( δ ) E off { ρ n } + ( 1 ρ ^ ) E off { ρ m } P o f f o n ( δ ) E on { ρ n } + ( 1 ρ ^ ) E off { ρ m } P o f f o f f ( δ ) E off { ρ n }

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