Abstract

Super-resolution fluorescence imaging techniques allow optical imaging of specimens beyond the diffraction limit of light. Super-resolution optical fluctuation imaging (SOFI) relies on computational analysis of stochastic blinking events to obtain a super-resolved image. As with some other super-resolution methods, this strong dependency on computational analysis can make it difficult to gauge how well the resulting images reflect the underlying sample structure. We herein report SOFIevaluator, an unbiased and parameter-free algorithm for calculating a set of metrics that describes the quality of super-resolution fluorescence imaging data for SOFI. We additionally demonstrate how SOFIevaluator can be used to identify fluorescent proteins that perform well for SOFI imaging under different imaging conditions.

© 2020 Optical Society of America under the terms of the OSA Open Access Publishing Agreement

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References

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    [Crossref]

2019 (4)

W. Vandenberg, M. Leutenegger, S. Duwe, and P. Dedecker, “An extended quantitative model for super-resolution optical fluctuation imaging (SOFI),” Opt. Express 27(18), 25749–25766 (2019).
[Crossref]

A. Descloux, K. S. Grußmayer, and A. Radenovic, “Parameter-free image resolution estimation based on decorrelation analysis,” Nat. Methods 16(9), 918–924 (2019).
[Crossref]

R. Van den Eynde, A. Sandmeyer, W. Vandenberg, S. Duwé, W. Hübner, T. Huser, P. Dedecker, and M. Müller, “Quantitative comparison of camera technologies for cost-effective super-resolution optical fluctuation imaging (SOFI),” J. Phys. Photonics 1(4), 044001 (2019).
[Crossref]

E. De Zitter, D. Thédié, V. Mönkemöller, S. Hugelier, J. Beaudouin, V. Adam, M. Byrdin, L. Van Meervelt, P. Dedecker, and D. Bourgeois, “Mechanistic investigation of mEos4b reveals a strategy to reduce track interruptions in sptPALM,” Nat. Methods 16(8), 707–710 (2019).
[Crossref]

2018 (3)

S. Culley, D. Albrecht, C. Jacobs, P. M. Pereira, C. Leterrier, J. Mercer, and R. Henriques, “Quantitative mapping and minimization of super-resolution optical imaging artifacts,” Nat. Methods 15(4), 263–266 (2018).
[Crossref]

B. Storti, E. Margheritis, G. Abbandonato, G. Domenichini, J. Dreier, I. Testa, G. Garau, R. Nifosì, and R. Bizzarri, “Role of Gln222 in Photoswitching of Aequorea Fluorescent Proteins: A Twisting and H-Bonding Affair?” ACS Chem. Biol. 13(8), 2082–2093 (2018).
[Crossref]

F. Pennacchietti, E. O. Serebrovskaya, A. R. Faro, I. I. Shemyakina, N. G. Bozhanova, A. A. Kotlobay, N. G. Gurskaya, A. Bodén, J. Dreier, D. M. Chudakov, K. A. Lukyanov, V. V. Verkhusha, A. S. Mishin, and I. Testa, “Fast reversibly photoswitching red fluorescent proteins for live-cell RESOLFT nanoscopy,” Nat. Methods 15(8), 601–604 (2018).
[Crossref]

2017 (4)

D. S. Bindels, L. Haarbosch, L. Van Weeren, M. Postma, K. E. Wiese, M. Mastop, S. Aumonier, G. Gotthard, A. Royant, M. A. Hink, and T. W. Gadella, “MScarlet: A bright monomeric red fluorescent protein for cellular imaging,” Nat. Methods 14(1), 53–56 (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]

P. Fox-Roberts, R. Marsh, K. Pfisterer, A. Jayo, M. Parsons, and S. Cox, “Local dimensionality determines imaging speed in localization microscopy,” Nat. Commun. 8(1), 13558–10 (2017).
[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]

2016 (2)

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 (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)

G. Ball, J. Demmerle, R. Kaufmann, I. Davis, I. M. Dobbie, and L. Schermelleh, “SIMcheck: A toolbox for successful super-resolution structured illumination microscopy,” Sci. Rep. 5(1), 15915–12 (2015).
[Crossref]

J. Demmerle, E. Wegel, L. Schermelleh, and I. M. Dobbie, “Assessing resolution in super-resolution imaging,” Methods 88, 3–10 (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]

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]

2014 (1)

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]

2013 (3)

N. C. Shaner, G. G. Lambert, A. Chammas, Y. Ni, P. J. Cranfill, M. A. Baird, B. R. Sell, J. R. Allen, R. N. Day, M. Israelsson, M. W. Davidson, and J. Wang, “A bright monomeric green fluorescent protein derived from Branchiostoma lanceolatum,” Nat. Methods 10(5), 407–409 (2013).
[Crossref]

N. Banterle, K. H. Bui, E. A. Lemke, and M. Beck, “Fourier ring correlation as a resolution criterion for super-resolution microscopy,” J. Struct. Biol. 183(3), 363–367 (2013).
[Crossref]

R. P. J. Nieuwenhuizen, K. a. Lidke, M. Bates, D. L. Puig, D. Grünwald, S. Stallinga, and B. Rieger, “Measuring image resolution in optical nanoscopy,” Nat. Methods 10(6), 557–562 (2013).
[Crossref]

2012 (7)

S. Cox, E. Rosten, J. Monypenny, T. Jovanovic-Talisman, D. T. Burnette, J. Lippincott-Schwartz, G. E. Jones, and R. Heintzmann, “Bayesian localization microscopy reveals nanoscale podosome dynamics,” Nat. Methods 9(2), 195–200 (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]

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)),” Opt Nanoscopy 1(1), 4 (2012).
[Crossref]

M. Zhang, H. Chang, Y. Zhang, J. Yu, L. Wu, W. Ji, J. Chen, B. Liu, J. Lu, Y. Liu, J. Zhang, P. Xu, and T. Xu, “Rational design of true monomeric and bright photoactivatable fluorescent proteins,” Nat. Methods 9(7), 727–729 (2012).
[Crossref]

S. Pletnev, F. V. Subach, Z. Dauter, A. Wlodawer, and V. V. Verkhusha, “A structural basis for reversible photoswitching of absorbance spectra in red fluorescent protein rsTagRFP,” J. Mol. Biol. 417(3), 144–151 (2012).
[Crossref]

J. Goedhart, D. von Stetten, M. Noirclerc-Savoye, M. Lelimousin, L. Joosen, M. a. Hink, L. van Weeren, T. W. J. Gadella, and A. Royant, “Structure-guided evolution of cyan fluorescent proteins towards a quantum yield of 93%,” Nat. Commun. 3(1), 751 (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)

O. M. Subach, P. J. Cranfill, M. W. Davidson, and V. V. Verkhusha, “An enhanced monomeric blue fluorescent protein with the high chemical stability of the chromophore,” PLoS One 6(12), e28674 (2011).
[Crossref]

2010 (1)

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]

2008 (2)

N. C. Shaner, M. Z. Lin, M. R. McKeown, P. A. Steinbach, K. L. Hazelwood, M. W. Davidson, and R. Y. Tsien, “Improving the photostability of bright monomeric orange and red fluorescent proteins,” Nat. Methods 5(6), 545–551 (2008).
[Crossref]

A. Sakaue-Sawano, H. Kurokawa, T. Morimura, A. Hanyu, H. Hama, H. Osawa, S. Kashiwagi, K. Fukami, T. Miyata, H. Miyoshi, T. Imamura, M. Ogawa, H. Masai, and A. Miyawaki, “Visualizing Spatiotemporal Dynamics of Multicellular Cell-Cycle Progression,” Cell 132(3), 487–498 (2008).
[Crossref]

2007 (1)

H.-W. Ai, N. C. Shaner, Z. Cheng, R. Y. Tsien, and R. E. Campbell, “Exploration of new chromophore structures leads to the identification of improved blue fluorescent proteins,” Biochemistry 46(20), 5904–5910 (2007).
[Crossref]

2006 (3)

H.-W. Ai, J. N. Henderson, S. J. Remington, and R. E. Campbell, “Directed evolution of a monomeric, bright and photostable version of Clavularia cyan fluorescent protein: structural characterization and applications in fluorescence imaging,” Biochem. J. 400(3), 531–540 (2006).
[Crossref]

N. G. Gurskaya, V. V. Verkhusha, A. S. Shcheglov, D. B. Staroverov, T. V. Chepurnykh, A. F. Fradkov, S. Lukyanov, and K. A. Lukyanov, “Engineering of a monomeric green-to-red photoactivatable fluorescent protein induced by blue light,” Nat. Biotechnol. 24(4), 461–465 (2006).
[Crossref]

E. Betzig, G. H. Patterson, R. Sougrat, O. W. Lindwasser, S. Olenych, J. S. Bonifacino, M. W. Davidson, J. Lippincott-Schwartz, and H. F. Hess, “Imaging intracellular fluorescent proteins at nanometer resolution,” Science 313(5793), 1642–1645 (2006).
[Crossref]

2005 (1)

M. A. Rizzo and D. W. Piston, “High-contrast imaging of fluorescent protein FRET by fluorescence polarization microscopy,” Biophys. J. 88(2), L14–L16 (2005).
[Crossref]

2002 (1)

D. A. Zacharias, J. D. Violin, A. C. Newton, and R. Y. Tsien, “Partitioning of lipid-modified monomeric GFPs into membrane microdomains of live cells,” Science 296(5569), 913–916 (2002).
[Crossref]

2000 (1)

M. G. L. Gustafsson, “Surpassing the lateral resolution limit by a factor of two using structured illumination microscopy,” J. Microsc. 198(2), 82–87 (2000).
[Crossref]

a. Hink, M.

J. Goedhart, D. von Stetten, M. Noirclerc-Savoye, M. Lelimousin, L. Joosen, M. a. Hink, L. van Weeren, T. W. J. Gadella, and A. Royant, “Structure-guided evolution of cyan fluorescent proteins towards a quantum yield of 93%,” Nat. Commun. 3(1), 751 (2012).
[Crossref]

a. Lidke, K.

R. P. J. Nieuwenhuizen, K. a. Lidke, M. Bates, D. L. Puig, D. Grünwald, S. Stallinga, and B. Rieger, “Measuring image resolution in optical nanoscopy,” Nat. Methods 10(6), 557–562 (2013).
[Crossref]

Abbandonato, G.

B. Storti, E. Margheritis, G. Abbandonato, G. Domenichini, J. Dreier, I. Testa, G. Garau, R. Nifosì, and R. Bizzarri, “Role of Gln222 in Photoswitching of Aequorea Fluorescent Proteins: A Twisting and H-Bonding Affair?” ACS Chem. Biol. 13(8), 2082–2093 (2018).
[Crossref]

Adam, V.

E. De Zitter, D. Thédié, V. Mönkemöller, S. Hugelier, J. Beaudouin, V. Adam, M. Byrdin, L. Van Meervelt, P. Dedecker, and D. Bourgeois, “Mechanistic investigation of mEos4b reveals a strategy to reduce track interruptions in sptPALM,” Nat. Methods 16(8), 707–710 (2019).
[Crossref]

Ai, H.-W.

H.-W. Ai, N. C. Shaner, Z. Cheng, R. Y. Tsien, and R. E. Campbell, “Exploration of new chromophore structures leads to the identification of improved blue fluorescent proteins,” Biochemistry 46(20), 5904–5910 (2007).
[Crossref]

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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).
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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).
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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).
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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).
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J. Demmerle, E. Wegel, L. Schermelleh, and I. M. Dobbie, “Assessing resolution in super-resolution imaging,” Methods 88, 3–10 (2015).
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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).
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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).
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G. Ball, J. Demmerle, R. Kaufmann, I. Davis, I. M. Dobbie, and L. Schermelleh, “SIMcheck: A toolbox for successful super-resolution structured illumination microscopy,” Sci. Rep. 5(1), 15915–12 (2015).
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B. Storti, E. Margheritis, G. Abbandonato, G. Domenichini, J. Dreier, I. Testa, G. Garau, R. Nifosì, and R. Bizzarri, “Role of Gln222 in Photoswitching of Aequorea Fluorescent Proteins: A Twisting and H-Bonding Affair?” ACS Chem. Biol. 13(8), 2082–2093 (2018).
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Duwe, S.

Duwé, S.

R. Van den Eynde, A. Sandmeyer, W. Vandenberg, S. Duwé, W. Hübner, T. Huser, P. Dedecker, and M. Müller, “Quantitative comparison of camera technologies for cost-effective super-resolution optical fluctuation imaging (SOFI),” J. Phys. Photonics 1(4), 044001 (2019).
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Opt. Express (2)

PLoS One (1)

O. M. Subach, P. J. Cranfill, M. W. Davidson, and V. V. Verkhusha, “An enhanced monomeric blue fluorescent protein with the high chemical stability of the chromophore,” PLoS One 6(12), e28674 (2011).
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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).
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Figures (3)

Fig. 1.
Fig. 1. Overview of the SOFIevaluator output. Green spheres represent data from SkylanS (imaging condition 2, images in Fig. 2(A)). Red squares represent data from rsGreen1 (imaging condition 6). (A) Time decorrelation graph representing the fraction of SOFI signal that is due to bleaching (baseline signal) and the rate constant of the emitter blinking (tau). (B) Histograms of the per-pixel signal-to-noise ratio without smoothing (darkest curve) to 1, 2 and 4 pixel smoothing (lighter curves). (C) Spatial decorrelation graph. Open markers are cross-cumulants as a function of the distance between the correlated pixels, filled markers are the autocumulant (cross-cumulant between the same detector pixel), curved line is a Gaussian fit of the cross-cumulant data and horizontal line is the value of the fit at infinite PSF width.
Fig. 2.
Fig. 2. Average and SOFI images of lyn-SkylanS-, lyn-rsGreen1-, lyn-mCherry- and lyn-mScarletI-expressing cells. (A) Representative lyn-SkylanS-expressing cell imaged with 39 W/cm2 488 nm excitation light and no 405 nm light (condition 2). (B-C) Cells with the best (B) and worst (C) SNR peak of the 10 lyn-SkylanS-expressing cells imaged using 3.3 W/cm2 488 nm light and 3.3 W/cm2 405 nm light (condition 8). Top: average image, bottom: SOFI image. (D) SOFI (top right) and average (bottom left) image of representative lyn-rsGreen1-expressing cell imaged with 3.3 W/cm2 488 nm light and 0.030 W/cm2 405 nm light (condition 4), lyn-mCherry-expressing cell imaged with 15 W/cm2 561 nm light and 0.030 W/cm2 405 nm light (condition 6) and lyn-mScarletI-expressing cell imaged with 43 W/cm2 561 nm light and 0.030 W/cm2 405 nm light (condition 7). Scale bar = 10 µm (large image) and 2.5 µm (inset)
Fig. 3.
Fig. 3. Summary of the imaging conditions

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