Abstract

Single molecule localisation (SML) microscopy is a fundamental tool for biological discoveries; it provides sub-diffraction spatial resolution images by detecting and localizing “all” the fluorescent molecules labeling the structure of interest. For this reason, the effective resolution of SML microscopy strictly depends on the algorithm used to detect and localize the single molecules from the series of microscopy frames. To adapt to the different imaging conditions that can occur in a SML experiment, all current localisation algorithms request, from the microscopy users, the choice of different parameters. This choice is not always easy and their wrong selection can lead to poor performance. Here we overcome this weakness with the use of machine learning. We propose a parameter-free pipeline for SML learning based on support vector machine (SVM). This strategy requires a short supervised training that consists in selecting by the user few fluorescent molecules (∼ 10–20) from the frames under analysis. The algorithm has been extensively tested on both synthetic and real acquisitions. Results are qualitatively and quantitatively consistent with the state of the art in SML microscopy and demonstrate that the introduction of machine learning can lead to a new class of algorithms competitive and conceived from the user point of view.

© 2018 Optical Society of America under the terms of the OSA Open Access Publishing Agreement

Full Article  |  PDF Article

Corrections

3 April 2018: A typographical correction was made to the body text.


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  1. S. W. Hell, S. J. Sahl, M. Bates, X. Zhuang, R. Heintzmann, M. J. Booth, J. Bewersdorf, G. Shtengel, H. Hess, P. Tinnefeld, A. Honigmann, S. Jakobs, I. Testa, L. Cognet, B. Lounis, H. Ewers, S. J. Davis, C. Eggeling, D. Klenerman, K. I. Willig, G. Vicidomini, M. Castello, A. Diaspro, and T. Cordes, “The 2015 super-resolution microscopy roadmap,” J. Phys. D: Appl. Phys 48, 443001 (2015).
    [Crossref]
  2. S. J. Sahl, S. W. Hell, and S. Jakobs, “Fluorescence nanoscopy in cell biology,” Nat. Rev. Mol. Cell Biol. 18, 685–701 (2017).
    [Crossref] [PubMed]
  3. A. Small and S. Stahlheber, “Fluorophore localization algorithms for super-resolution microscopy,” Nat. Methods 11, 267–279 (2014).
    [Crossref] [PubMed]
  4. H. Deschout, F. C. Zanacchi, M. Mlodzianoski, A. Diaspro, J. Bewersdorf, S. T. Hess, and K. Braeckmans, “Precisely and accurately localizing single emitters in fluorescence microscopy,” Nat. Methods 11, 253–266 (2014).
    [Crossref] [PubMed]
  5. 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]
  6. M. J. Rust, M. Bates, and X. Zhuang, “Stochastic optical reconstruction microscopy (storm) provides sub-diffraction-limit image resolution,” Nat. Methods 3, 793 (2006).
    [Crossref] [PubMed]
  7. E. Abbe, “Beiträge zur theorie des mikroskops und der mikroskopischen wahrnehmung,” Archiv für mikroskopische Anatomie 9, 413–418 (1873).
    [Crossref]
  8. H. Shroff, C. G. Galbraith, J. A. Galbraith, and E. Betzig, “Live-cell photoactivated localization microscopy of nanoscale adhesion dynamics,” Nat. Methods 5, 417–423 (2008).
    [Crossref] [PubMed]
  9. H. Nyquist, “Certain topics in telegraph transmission theory,” Transactions of the American Institute of Electrical Engineers 47, 617–644 (1928).
    [Crossref]
  10. C. Cortes and V. Vapnik, “Support-vector networks,” Machine learning 20, 273–297 (1995).
    [Crossref]
  11. H. Guo, “A simple algorithm for fitting a gaussian function,” IEEE Signal Process. Mag. 28, 134–137 (2011).
    [Crossref]
  12. S. Colabrese, M. Castello, G. Vicidomini, and A. Del Bue, “Learning-based approach to boost detection rate and localisation accuracy in single molecule localisation microscopy,” in “Image Processing (ICIP), 2016 IEEE International Conference on,” (IEEE, 2016), pp. 3184–3188.
  13. M. Ovesnỳ, P. Křížek, J. Borkovec, Z. Švindrych, and G. M. Hagen, “Thunderstorm: a comprehensive imagej plug-in for palm and storm data analysis and super-resolution imaging,” Bioinformatics 30, 2389–2390 (2014).
    [Crossref]
  14. D. Sage, H. Kirshner, T. Pengo, N. Stuurman, J. Min, S. Manley, and M. Unser, “Quantitative evaluation of software packages for single-molecule localization microscopy,” Nat. Methods 12, 717–724 (2015).
    [Crossref] [PubMed]
  15. 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, 195–200 (2012).
    [Crossref]
  16. Y. S. Hu, X. Nan, P. Sengupta, J. Lippincott-Schwartz, and H. Cang, “Accelerating 3b single-molecule super-resolution microscopy with cloud computing,” Nat. Methods 10, 96–97 (2013).
    [Crossref] [PubMed]
  17. Y. Tang, J. Hendriks, T. Gensch, L. Dai, and J. Li, “Automatic bayesian single molecule identification for localization microscopy,” Scientific Reports 6, 33521 (2016).
  18. U. Köthe, F. Herrmannsdörfer, I. Kats, and F. A. Hamprecht, “SimpleSTORM: A fast, self-calibrating reconstruction algorithm for localization microscopy,” Histochem. Cell Biol. 141, 613–627 (2014).
    [Crossref] [PubMed]
  19. S. Boyd and L. Vandenberghe, Convex optimization (Cambridge university press, 2004).
    [Crossref]
  20. R.-E. Fan, K.-W. Chang, C.-J. Hsieh, X.-R. Wang, and C.-J. Lin, “Liblinear: A library for large linear classification,” J. Mach. Learn. Res. 9, 1871–1874 (2008).
  21. C. S. Smith, N. Joseph, B. Rieger, and K. A. Lidke, “Fast, single-molecule localization that achieves theoretically minimum uncertainty,” Nat. Methods 7, 373–375 (2010).
    [Crossref] [PubMed]
  22. “2013 isbi grand challenge localization microscopy,” http://bigwww.epfl.ch/smlm/challenge2013/index.html . Accessed: 12-12-2016.
  23. 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, 363–367 (2013).
    [Crossref] [PubMed]
  24. R. Nieuwenhuizen, K. Lidke, M. Bates, D. Puig, D. Grünwald, S. Stallinga, and B. Rieger, “Measuring image resolution in optical nanoscopy,” Nat. Methods 10, 557–562 (2013).
    [Crossref] [PubMed]
  25. S. Colabrese, “SVM for Single Molecule Localisation Microscopy,” https://doi.org/10.6084/m9.figshare.5977453. Accessed: 14-3-2018.

2017 (1)

S. J. Sahl, S. W. Hell, and S. Jakobs, “Fluorescence nanoscopy in cell biology,” Nat. Rev. Mol. Cell Biol. 18, 685–701 (2017).
[Crossref] [PubMed]

2016 (1)

Y. Tang, J. Hendriks, T. Gensch, L. Dai, and J. Li, “Automatic bayesian single molecule identification for localization microscopy,” Scientific Reports 6, 33521 (2016).

2015 (2)

D. Sage, H. Kirshner, T. Pengo, N. Stuurman, J. Min, S. Manley, and M. Unser, “Quantitative evaluation of software packages for single-molecule localization microscopy,” Nat. Methods 12, 717–724 (2015).
[Crossref] [PubMed]

S. W. Hell, S. J. Sahl, M. Bates, X. Zhuang, R. Heintzmann, M. J. Booth, J. Bewersdorf, G. Shtengel, H. Hess, P. Tinnefeld, A. Honigmann, S. Jakobs, I. Testa, L. Cognet, B. Lounis, H. Ewers, S. J. Davis, C. Eggeling, D. Klenerman, K. I. Willig, G. Vicidomini, M. Castello, A. Diaspro, and T. Cordes, “The 2015 super-resolution microscopy roadmap,” J. Phys. D: Appl. Phys 48, 443001 (2015).
[Crossref]

2014 (4)

A. Small and S. Stahlheber, “Fluorophore localization algorithms for super-resolution microscopy,” Nat. Methods 11, 267–279 (2014).
[Crossref] [PubMed]

H. Deschout, F. C. Zanacchi, M. Mlodzianoski, A. Diaspro, J. Bewersdorf, S. T. Hess, and K. Braeckmans, “Precisely and accurately localizing single emitters in fluorescence microscopy,” Nat. Methods 11, 253–266 (2014).
[Crossref] [PubMed]

M. Ovesnỳ, P. Křížek, J. Borkovec, Z. Švindrych, and G. M. Hagen, “Thunderstorm: a comprehensive imagej plug-in for palm and storm data analysis and super-resolution imaging,” Bioinformatics 30, 2389–2390 (2014).
[Crossref]

U. Köthe, F. Herrmannsdörfer, I. Kats, and F. A. Hamprecht, “SimpleSTORM: A fast, self-calibrating reconstruction algorithm for localization microscopy,” Histochem. Cell Biol. 141, 613–627 (2014).
[Crossref] [PubMed]

2013 (3)

Y. S. Hu, X. Nan, P. Sengupta, J. Lippincott-Schwartz, and H. Cang, “Accelerating 3b single-molecule super-resolution microscopy with cloud computing,” Nat. Methods 10, 96–97 (2013).
[Crossref] [PubMed]

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, 363–367 (2013).
[Crossref] [PubMed]

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

2012 (1)

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, 195–200 (2012).
[Crossref]

2011 (1)

H. Guo, “A simple algorithm for fitting a gaussian function,” IEEE Signal Process. Mag. 28, 134–137 (2011).
[Crossref]

2010 (1)

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

2008 (2)

R.-E. Fan, K.-W. Chang, C.-J. Hsieh, X.-R. Wang, and C.-J. Lin, “Liblinear: A library for large linear classification,” J. Mach. Learn. Res. 9, 1871–1874 (2008).

H. Shroff, C. G. Galbraith, J. A. Galbraith, and E. Betzig, “Live-cell photoactivated localization microscopy of nanoscale adhesion dynamics,” Nat. Methods 5, 417–423 (2008).
[Crossref] [PubMed]

2006 (2)

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, “Stochastic optical reconstruction microscopy (storm) provides sub-diffraction-limit image resolution,” Nat. Methods 3, 793 (2006).
[Crossref] [PubMed]

1995 (1)

C. Cortes and V. Vapnik, “Support-vector networks,” Machine learning 20, 273–297 (1995).
[Crossref]

1928 (1)

H. Nyquist, “Certain topics in telegraph transmission theory,” Transactions of the American Institute of Electrical Engineers 47, 617–644 (1928).
[Crossref]

1873 (1)

E. Abbe, “Beiträge zur theorie des mikroskops und der mikroskopischen wahrnehmung,” Archiv für mikroskopische Anatomie 9, 413–418 (1873).
[Crossref]

Abbe, E.

E. Abbe, “Beiträge zur theorie des mikroskops und der mikroskopischen wahrnehmung,” Archiv für mikroskopische Anatomie 9, 413–418 (1873).
[Crossref]

Banterle, N.

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, 363–367 (2013).
[Crossref] [PubMed]

Bates, M.

S. W. Hell, S. J. Sahl, M. Bates, X. Zhuang, R. Heintzmann, M. J. Booth, J. Bewersdorf, G. Shtengel, H. Hess, P. Tinnefeld, A. Honigmann, S. Jakobs, I. Testa, L. Cognet, B. Lounis, H. Ewers, S. J. Davis, C. Eggeling, D. Klenerman, K. I. Willig, G. Vicidomini, M. Castello, A. Diaspro, and T. Cordes, “The 2015 super-resolution microscopy roadmap,” J. Phys. D: Appl. Phys 48, 443001 (2015).
[Crossref]

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

M. J. Rust, M. Bates, and X. Zhuang, “Stochastic optical reconstruction microscopy (storm) provides sub-diffraction-limit image resolution,” Nat. Methods 3, 793 (2006).
[Crossref] [PubMed]

Beck, M.

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, 363–367 (2013).
[Crossref] [PubMed]

Betzig, E.

H. Shroff, C. G. Galbraith, J. A. Galbraith, and E. Betzig, “Live-cell photoactivated localization microscopy of nanoscale adhesion dynamics,” Nat. Methods 5, 417–423 (2008).
[Crossref] [PubMed]

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

Bewersdorf, J.

S. W. Hell, S. J. Sahl, M. Bates, X. Zhuang, R. Heintzmann, M. J. Booth, J. Bewersdorf, G. Shtengel, H. Hess, P. Tinnefeld, A. Honigmann, S. Jakobs, I. Testa, L. Cognet, B. Lounis, H. Ewers, S. J. Davis, C. Eggeling, D. Klenerman, K. I. Willig, G. Vicidomini, M. Castello, A. Diaspro, and T. Cordes, “The 2015 super-resolution microscopy roadmap,” J. Phys. D: Appl. Phys 48, 443001 (2015).
[Crossref]

H. Deschout, F. C. Zanacchi, M. Mlodzianoski, A. Diaspro, J. Bewersdorf, S. T. Hess, and K. Braeckmans, “Precisely and accurately localizing single emitters in fluorescence microscopy,” Nat. Methods 11, 253–266 (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]

Booth, M. J.

S. W. Hell, S. J. Sahl, M. Bates, X. Zhuang, R. Heintzmann, M. J. Booth, J. Bewersdorf, G. Shtengel, H. Hess, P. Tinnefeld, A. Honigmann, S. Jakobs, I. Testa, L. Cognet, B. Lounis, H. Ewers, S. J. Davis, C. Eggeling, D. Klenerman, K. I. Willig, G. Vicidomini, M. Castello, A. Diaspro, and T. Cordes, “The 2015 super-resolution microscopy roadmap,” J. Phys. D: Appl. Phys 48, 443001 (2015).
[Crossref]

Borkovec, J.

M. Ovesnỳ, P. Křížek, J. Borkovec, Z. Švindrych, and G. M. Hagen, “Thunderstorm: a comprehensive imagej plug-in for palm and storm data analysis and super-resolution imaging,” Bioinformatics 30, 2389–2390 (2014).
[Crossref]

Boyd, S.

S. Boyd and L. Vandenberghe, Convex optimization (Cambridge university press, 2004).
[Crossref]

Braeckmans, K.

H. Deschout, F. C. Zanacchi, M. Mlodzianoski, A. Diaspro, J. Bewersdorf, S. T. Hess, and K. Braeckmans, “Precisely and accurately localizing single emitters in fluorescence microscopy,” Nat. Methods 11, 253–266 (2014).
[Crossref] [PubMed]

Bui, K. H.

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, 363–367 (2013).
[Crossref] [PubMed]

Burnette, D. T.

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, 195–200 (2012).
[Crossref]

Cang, H.

Y. S. Hu, X. Nan, P. Sengupta, J. Lippincott-Schwartz, and H. Cang, “Accelerating 3b single-molecule super-resolution microscopy with cloud computing,” Nat. Methods 10, 96–97 (2013).
[Crossref] [PubMed]

Castello, M.

S. W. Hell, S. J. Sahl, M. Bates, X. Zhuang, R. Heintzmann, M. J. Booth, J. Bewersdorf, G. Shtengel, H. Hess, P. Tinnefeld, A. Honigmann, S. Jakobs, I. Testa, L. Cognet, B. Lounis, H. Ewers, S. J. Davis, C. Eggeling, D. Klenerman, K. I. Willig, G. Vicidomini, M. Castello, A. Diaspro, and T. Cordes, “The 2015 super-resolution microscopy roadmap,” J. Phys. D: Appl. Phys 48, 443001 (2015).
[Crossref]

S. Colabrese, M. Castello, G. Vicidomini, and A. Del Bue, “Learning-based approach to boost detection rate and localisation accuracy in single molecule localisation microscopy,” in “Image Processing (ICIP), 2016 IEEE International Conference on,” (IEEE, 2016), pp. 3184–3188.

Chang, K.-W.

R.-E. Fan, K.-W. Chang, C.-J. Hsieh, X.-R. Wang, and C.-J. Lin, “Liblinear: A library for large linear classification,” J. Mach. Learn. Res. 9, 1871–1874 (2008).

Cognet, L.

S. W. Hell, S. J. Sahl, M. Bates, X. Zhuang, R. Heintzmann, M. J. Booth, J. Bewersdorf, G. Shtengel, H. Hess, P. Tinnefeld, A. Honigmann, S. Jakobs, I. Testa, L. Cognet, B. Lounis, H. Ewers, S. J. Davis, C. Eggeling, D. Klenerman, K. I. Willig, G. Vicidomini, M. Castello, A. Diaspro, and T. Cordes, “The 2015 super-resolution microscopy roadmap,” J. Phys. D: Appl. Phys 48, 443001 (2015).
[Crossref]

Colabrese, S.

S. Colabrese, M. Castello, G. Vicidomini, and A. Del Bue, “Learning-based approach to boost detection rate and localisation accuracy in single molecule localisation microscopy,” in “Image Processing (ICIP), 2016 IEEE International Conference on,” (IEEE, 2016), pp. 3184–3188.

Cordes, T.

S. W. Hell, S. J. Sahl, M. Bates, X. Zhuang, R. Heintzmann, M. J. Booth, J. Bewersdorf, G. Shtengel, H. Hess, P. Tinnefeld, A. Honigmann, S. Jakobs, I. Testa, L. Cognet, B. Lounis, H. Ewers, S. J. Davis, C. Eggeling, D. Klenerman, K. I. Willig, G. Vicidomini, M. Castello, A. Diaspro, and T. Cordes, “The 2015 super-resolution microscopy roadmap,” J. Phys. D: Appl. Phys 48, 443001 (2015).
[Crossref]

Cortes, C.

C. Cortes and V. Vapnik, “Support-vector networks,” Machine learning 20, 273–297 (1995).
[Crossref]

Cox, S.

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, 195–200 (2012).
[Crossref]

Dai, L.

Y. Tang, J. Hendriks, T. Gensch, L. Dai, and J. Li, “Automatic bayesian single molecule identification for localization microscopy,” Scientific Reports 6, 33521 (2016).

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]

Davis, S. J.

S. W. Hell, S. J. Sahl, M. Bates, X. Zhuang, R. Heintzmann, M. J. Booth, J. Bewersdorf, G. Shtengel, H. Hess, P. Tinnefeld, A. Honigmann, S. Jakobs, I. Testa, L. Cognet, B. Lounis, H. Ewers, S. J. Davis, C. Eggeling, D. Klenerman, K. I. Willig, G. Vicidomini, M. Castello, A. Diaspro, and T. Cordes, “The 2015 super-resolution microscopy roadmap,” J. Phys. D: Appl. Phys 48, 443001 (2015).
[Crossref]

Del Bue, A.

S. Colabrese, M. Castello, G. Vicidomini, and A. Del Bue, “Learning-based approach to boost detection rate and localisation accuracy in single molecule localisation microscopy,” in “Image Processing (ICIP), 2016 IEEE International Conference on,” (IEEE, 2016), pp. 3184–3188.

Deschout, H.

H. Deschout, F. C. Zanacchi, M. Mlodzianoski, A. Diaspro, J. Bewersdorf, S. T. Hess, and K. Braeckmans, “Precisely and accurately localizing single emitters in fluorescence microscopy,” Nat. Methods 11, 253–266 (2014).
[Crossref] [PubMed]

Diaspro, A.

S. W. Hell, S. J. Sahl, M. Bates, X. Zhuang, R. Heintzmann, M. J. Booth, J. Bewersdorf, G. Shtengel, H. Hess, P. Tinnefeld, A. Honigmann, S. Jakobs, I. Testa, L. Cognet, B. Lounis, H. Ewers, S. J. Davis, C. Eggeling, D. Klenerman, K. I. Willig, G. Vicidomini, M. Castello, A. Diaspro, and T. Cordes, “The 2015 super-resolution microscopy roadmap,” J. Phys. D: Appl. Phys 48, 443001 (2015).
[Crossref]

H. Deschout, F. C. Zanacchi, M. Mlodzianoski, A. Diaspro, J. Bewersdorf, S. T. Hess, and K. Braeckmans, “Precisely and accurately localizing single emitters in fluorescence microscopy,” Nat. Methods 11, 253–266 (2014).
[Crossref] [PubMed]

Eggeling, C.

S. W. Hell, S. J. Sahl, M. Bates, X. Zhuang, R. Heintzmann, M. J. Booth, J. Bewersdorf, G. Shtengel, H. Hess, P. Tinnefeld, A. Honigmann, S. Jakobs, I. Testa, L. Cognet, B. Lounis, H. Ewers, S. J. Davis, C. Eggeling, D. Klenerman, K. I. Willig, G. Vicidomini, M. Castello, A. Diaspro, and T. Cordes, “The 2015 super-resolution microscopy roadmap,” J. Phys. D: Appl. Phys 48, 443001 (2015).
[Crossref]

Ewers, H.

S. W. Hell, S. J. Sahl, M. Bates, X. Zhuang, R. Heintzmann, M. J. Booth, J. Bewersdorf, G. Shtengel, H. Hess, P. Tinnefeld, A. Honigmann, S. Jakobs, I. Testa, L. Cognet, B. Lounis, H. Ewers, S. J. Davis, C. Eggeling, D. Klenerman, K. I. Willig, G. Vicidomini, M. Castello, A. Diaspro, and T. Cordes, “The 2015 super-resolution microscopy roadmap,” J. Phys. D: Appl. Phys 48, 443001 (2015).
[Crossref]

Fan, R.-E.

R.-E. Fan, K.-W. Chang, C.-J. Hsieh, X.-R. Wang, and C.-J. Lin, “Liblinear: A library for large linear classification,” J. Mach. Learn. Res. 9, 1871–1874 (2008).

Galbraith, C. G.

H. Shroff, C. G. Galbraith, J. A. Galbraith, and E. Betzig, “Live-cell photoactivated localization microscopy of nanoscale adhesion dynamics,” Nat. Methods 5, 417–423 (2008).
[Crossref] [PubMed]

Galbraith, J. A.

H. Shroff, C. G. Galbraith, J. A. Galbraith, and E. Betzig, “Live-cell photoactivated localization microscopy of nanoscale adhesion dynamics,” Nat. Methods 5, 417–423 (2008).
[Crossref] [PubMed]

Gensch, T.

Y. Tang, J. Hendriks, T. Gensch, L. Dai, and J. Li, “Automatic bayesian single molecule identification for localization microscopy,” Scientific Reports 6, 33521 (2016).

Grünwald, D.

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

Guo, H.

H. Guo, “A simple algorithm for fitting a gaussian function,” IEEE Signal Process. Mag. 28, 134–137 (2011).
[Crossref]

Hagen, G. M.

M. Ovesnỳ, P. Křížek, J. Borkovec, Z. Švindrych, and G. M. Hagen, “Thunderstorm: a comprehensive imagej plug-in for palm and storm data analysis and super-resolution imaging,” Bioinformatics 30, 2389–2390 (2014).
[Crossref]

Hamprecht, F. A.

U. Köthe, F. Herrmannsdörfer, I. Kats, and F. A. Hamprecht, “SimpleSTORM: A fast, self-calibrating reconstruction algorithm for localization microscopy,” Histochem. Cell Biol. 141, 613–627 (2014).
[Crossref] [PubMed]

Heintzmann, R.

S. W. Hell, S. J. Sahl, M. Bates, X. Zhuang, R. Heintzmann, M. J. Booth, J. Bewersdorf, G. Shtengel, H. Hess, P. Tinnefeld, A. Honigmann, S. Jakobs, I. Testa, L. Cognet, B. Lounis, H. Ewers, S. J. Davis, C. Eggeling, D. Klenerman, K. I. Willig, G. Vicidomini, M. Castello, A. Diaspro, and T. Cordes, “The 2015 super-resolution microscopy roadmap,” J. Phys. D: Appl. Phys 48, 443001 (2015).
[Crossref]

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, 195–200 (2012).
[Crossref]

Hell, S. W.

S. J. Sahl, S. W. Hell, and S. Jakobs, “Fluorescence nanoscopy in cell biology,” Nat. Rev. Mol. Cell Biol. 18, 685–701 (2017).
[Crossref] [PubMed]

S. W. Hell, S. J. Sahl, M. Bates, X. Zhuang, R. Heintzmann, M. J. Booth, J. Bewersdorf, G. Shtengel, H. Hess, P. Tinnefeld, A. Honigmann, S. Jakobs, I. Testa, L. Cognet, B. Lounis, H. Ewers, S. J. Davis, C. Eggeling, D. Klenerman, K. I. Willig, G. Vicidomini, M. Castello, A. Diaspro, and T. Cordes, “The 2015 super-resolution microscopy roadmap,” J. Phys. D: Appl. Phys 48, 443001 (2015).
[Crossref]

Hendriks, J.

Y. Tang, J. Hendriks, T. Gensch, L. Dai, and J. Li, “Automatic bayesian single molecule identification for localization microscopy,” Scientific Reports 6, 33521 (2016).

Herrmannsdörfer, F.

U. Köthe, F. Herrmannsdörfer, I. Kats, and F. A. Hamprecht, “SimpleSTORM: A fast, self-calibrating reconstruction algorithm for localization microscopy,” Histochem. Cell Biol. 141, 613–627 (2014).
[Crossref] [PubMed]

Hess, H.

S. W. Hell, S. J. Sahl, M. Bates, X. Zhuang, R. Heintzmann, M. J. Booth, J. Bewersdorf, G. Shtengel, H. Hess, P. Tinnefeld, A. Honigmann, S. Jakobs, I. Testa, L. Cognet, B. Lounis, H. Ewers, S. J. Davis, C. Eggeling, D. Klenerman, K. I. Willig, G. Vicidomini, M. Castello, A. Diaspro, and T. Cordes, “The 2015 super-resolution microscopy roadmap,” J. Phys. D: Appl. Phys 48, 443001 (2015).
[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.

H. Deschout, F. C. Zanacchi, M. Mlodzianoski, A. Diaspro, J. Bewersdorf, S. T. Hess, and K. Braeckmans, “Precisely and accurately localizing single emitters in fluorescence microscopy,” Nat. Methods 11, 253–266 (2014).
[Crossref] [PubMed]

Honigmann, A.

S. W. Hell, S. J. Sahl, M. Bates, X. Zhuang, R. Heintzmann, M. J. Booth, J. Bewersdorf, G. Shtengel, H. Hess, P. Tinnefeld, A. Honigmann, S. Jakobs, I. Testa, L. Cognet, B. Lounis, H. Ewers, S. J. Davis, C. Eggeling, D. Klenerman, K. I. Willig, G. Vicidomini, M. Castello, A. Diaspro, and T. Cordes, “The 2015 super-resolution microscopy roadmap,” J. Phys. D: Appl. Phys 48, 443001 (2015).
[Crossref]

Hsieh, C.-J.

R.-E. Fan, K.-W. Chang, C.-J. Hsieh, X.-R. Wang, and C.-J. Lin, “Liblinear: A library for large linear classification,” J. Mach. Learn. Res. 9, 1871–1874 (2008).

Hu, Y. S.

Y. S. Hu, X. Nan, P. Sengupta, J. Lippincott-Schwartz, and H. Cang, “Accelerating 3b single-molecule super-resolution microscopy with cloud computing,” Nat. Methods 10, 96–97 (2013).
[Crossref] [PubMed]

Jakobs, S.

S. J. Sahl, S. W. Hell, and S. Jakobs, “Fluorescence nanoscopy in cell biology,” Nat. Rev. Mol. Cell Biol. 18, 685–701 (2017).
[Crossref] [PubMed]

S. W. Hell, S. J. Sahl, M. Bates, X. Zhuang, R. Heintzmann, M. J. Booth, J. Bewersdorf, G. Shtengel, H. Hess, P. Tinnefeld, A. Honigmann, S. Jakobs, I. Testa, L. Cognet, B. Lounis, H. Ewers, S. J. Davis, C. Eggeling, D. Klenerman, K. I. Willig, G. Vicidomini, M. Castello, A. Diaspro, and T. Cordes, “The 2015 super-resolution microscopy roadmap,” J. Phys. D: Appl. Phys 48, 443001 (2015).
[Crossref]

Jones, G. E.

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, 195–200 (2012).
[Crossref]

Joseph, N.

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

Jovanovic-Talisman, T.

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, 195–200 (2012).
[Crossref]

Kats, I.

U. Köthe, F. Herrmannsdörfer, I. Kats, and F. A. Hamprecht, “SimpleSTORM: A fast, self-calibrating reconstruction algorithm for localization microscopy,” Histochem. Cell Biol. 141, 613–627 (2014).
[Crossref] [PubMed]

Kirshner, H.

D. Sage, H. Kirshner, T. Pengo, N. Stuurman, J. Min, S. Manley, and M. Unser, “Quantitative evaluation of software packages for single-molecule localization microscopy,” Nat. Methods 12, 717–724 (2015).
[Crossref] [PubMed]

Klenerman, D.

S. W. Hell, S. J. Sahl, M. Bates, X. Zhuang, R. Heintzmann, M. J. Booth, J. Bewersdorf, G. Shtengel, H. Hess, P. Tinnefeld, A. Honigmann, S. Jakobs, I. Testa, L. Cognet, B. Lounis, H. Ewers, S. J. Davis, C. Eggeling, D. Klenerman, K. I. Willig, G. Vicidomini, M. Castello, A. Diaspro, and T. Cordes, “The 2015 super-resolution microscopy roadmap,” J. Phys. D: Appl. Phys 48, 443001 (2015).
[Crossref]

Köthe, U.

U. Köthe, F. Herrmannsdörfer, I. Kats, and F. A. Hamprecht, “SimpleSTORM: A fast, self-calibrating reconstruction algorithm for localization microscopy,” Histochem. Cell Biol. 141, 613–627 (2014).
[Crossref] [PubMed]

Krížek, P.

M. Ovesnỳ, P. Křížek, J. Borkovec, Z. Švindrych, and G. M. Hagen, “Thunderstorm: a comprehensive imagej plug-in for palm and storm data analysis and super-resolution imaging,” Bioinformatics 30, 2389–2390 (2014).
[Crossref]

Lemke, E. A.

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, 363–367 (2013).
[Crossref] [PubMed]

Li, J.

Y. Tang, J. Hendriks, T. Gensch, L. Dai, and J. Li, “Automatic bayesian single molecule identification for localization microscopy,” Scientific Reports 6, 33521 (2016).

Lidke, K.

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

Lidke, K. A.

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

Lin, C.-J.

R.-E. Fan, K.-W. Chang, C.-J. Hsieh, X.-R. Wang, and C.-J. Lin, “Liblinear: A library for large linear classification,” J. Mach. Learn. Res. 9, 1871–1874 (2008).

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.

Y. S. Hu, X. Nan, P. Sengupta, J. Lippincott-Schwartz, and H. Cang, “Accelerating 3b single-molecule super-resolution microscopy with cloud computing,” Nat. Methods 10, 96–97 (2013).
[Crossref] [PubMed]

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, 195–200 (2012).
[Crossref]

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

Lounis, B.

S. W. Hell, S. J. Sahl, M. Bates, X. Zhuang, R. Heintzmann, M. J. Booth, J. Bewersdorf, G. Shtengel, H. Hess, P. Tinnefeld, A. Honigmann, S. Jakobs, I. Testa, L. Cognet, B. Lounis, H. Ewers, S. J. Davis, C. Eggeling, D. Klenerman, K. I. Willig, G. Vicidomini, M. Castello, A. Diaspro, and T. Cordes, “The 2015 super-resolution microscopy roadmap,” J. Phys. D: Appl. Phys 48, 443001 (2015).
[Crossref]

Manley, S.

D. Sage, H. Kirshner, T. Pengo, N. Stuurman, J. Min, S. Manley, and M. Unser, “Quantitative evaluation of software packages for single-molecule localization microscopy,” Nat. Methods 12, 717–724 (2015).
[Crossref] [PubMed]

Min, J.

D. Sage, H. Kirshner, T. Pengo, N. Stuurman, J. Min, S. Manley, and M. Unser, “Quantitative evaluation of software packages for single-molecule localization microscopy,” Nat. Methods 12, 717–724 (2015).
[Crossref] [PubMed]

Mlodzianoski, M.

H. Deschout, F. C. Zanacchi, M. Mlodzianoski, A. Diaspro, J. Bewersdorf, S. T. Hess, and K. Braeckmans, “Precisely and accurately localizing single emitters in fluorescence microscopy,” Nat. Methods 11, 253–266 (2014).
[Crossref] [PubMed]

Monypenny, J.

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, 195–200 (2012).
[Crossref]

Nan, X.

Y. S. Hu, X. Nan, P. Sengupta, J. Lippincott-Schwartz, and H. Cang, “Accelerating 3b single-molecule super-resolution microscopy with cloud computing,” Nat. Methods 10, 96–97 (2013).
[Crossref] [PubMed]

Nieuwenhuizen, R.

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

Nyquist, H.

H. Nyquist, “Certain topics in telegraph transmission theory,” Transactions of the American Institute of Electrical Engineers 47, 617–644 (1928).
[Crossref]

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]

Ovesn?, M.

M. Ovesnỳ, P. Křížek, J. Borkovec, Z. Švindrych, and G. M. Hagen, “Thunderstorm: a comprehensive imagej plug-in for palm and storm data analysis and super-resolution imaging,” Bioinformatics 30, 2389–2390 (2014).
[Crossref]

Patterson, G. H.

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

Pengo, T.

D. Sage, H. Kirshner, T. Pengo, N. Stuurman, J. Min, S. Manley, and M. Unser, “Quantitative evaluation of software packages for single-molecule localization microscopy,” Nat. Methods 12, 717–724 (2015).
[Crossref] [PubMed]

Puig, D.

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

Rieger, B.

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

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

Rosten, E.

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, 195–200 (2012).
[Crossref]

Rust, M. J.

M. J. Rust, M. Bates, and X. Zhuang, “Stochastic optical reconstruction microscopy (storm) provides sub-diffraction-limit image resolution,” Nat. Methods 3, 793 (2006).
[Crossref] [PubMed]

Sage, D.

D. Sage, H. Kirshner, T. Pengo, N. Stuurman, J. Min, S. Manley, and M. Unser, “Quantitative evaluation of software packages for single-molecule localization microscopy,” Nat. Methods 12, 717–724 (2015).
[Crossref] [PubMed]

Sahl, S. J.

S. J. Sahl, S. W. Hell, and S. Jakobs, “Fluorescence nanoscopy in cell biology,” Nat. Rev. Mol. Cell Biol. 18, 685–701 (2017).
[Crossref] [PubMed]

S. W. Hell, S. J. Sahl, M. Bates, X. Zhuang, R. Heintzmann, M. J. Booth, J. Bewersdorf, G. Shtengel, H. Hess, P. Tinnefeld, A. Honigmann, S. Jakobs, I. Testa, L. Cognet, B. Lounis, H. Ewers, S. J. Davis, C. Eggeling, D. Klenerman, K. I. Willig, G. Vicidomini, M. Castello, A. Diaspro, and T. Cordes, “The 2015 super-resolution microscopy roadmap,” J. Phys. D: Appl. Phys 48, 443001 (2015).
[Crossref]

Sengupta, P.

Y. S. Hu, X. Nan, P. Sengupta, J. Lippincott-Schwartz, and H. Cang, “Accelerating 3b single-molecule super-resolution microscopy with cloud computing,” Nat. Methods 10, 96–97 (2013).
[Crossref] [PubMed]

Shroff, H.

H. Shroff, C. G. Galbraith, J. A. Galbraith, and E. Betzig, “Live-cell photoactivated localization microscopy of nanoscale adhesion dynamics,” Nat. Methods 5, 417–423 (2008).
[Crossref] [PubMed]

Shtengel, G.

S. W. Hell, S. J. Sahl, M. Bates, X. Zhuang, R. Heintzmann, M. J. Booth, J. Bewersdorf, G. Shtengel, H. Hess, P. Tinnefeld, A. Honigmann, S. Jakobs, I. Testa, L. Cognet, B. Lounis, H. Ewers, S. J. Davis, C. Eggeling, D. Klenerman, K. I. Willig, G. Vicidomini, M. Castello, A. Diaspro, and T. Cordes, “The 2015 super-resolution microscopy roadmap,” J. Phys. D: Appl. Phys 48, 443001 (2015).
[Crossref]

Small, A.

A. Small and S. Stahlheber, “Fluorophore localization algorithms for super-resolution microscopy,” Nat. Methods 11, 267–279 (2014).
[Crossref] [PubMed]

Smith, C. S.

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

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]

Stahlheber, S.

A. Small and S. Stahlheber, “Fluorophore localization algorithms for super-resolution microscopy,” Nat. Methods 11, 267–279 (2014).
[Crossref] [PubMed]

Stallinga, S.

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

Stuurman, N.

D. Sage, H. Kirshner, T. Pengo, N. Stuurman, J. Min, S. Manley, and M. Unser, “Quantitative evaluation of software packages for single-molecule localization microscopy,” Nat. Methods 12, 717–724 (2015).
[Crossref] [PubMed]

Švindrych, Z.

M. Ovesnỳ, P. Křížek, J. Borkovec, Z. Švindrych, and G. M. Hagen, “Thunderstorm: a comprehensive imagej plug-in for palm and storm data analysis and super-resolution imaging,” Bioinformatics 30, 2389–2390 (2014).
[Crossref]

Tang, Y.

Y. Tang, J. Hendriks, T. Gensch, L. Dai, and J. Li, “Automatic bayesian single molecule identification for localization microscopy,” Scientific Reports 6, 33521 (2016).

Testa, I.

S. W. Hell, S. J. Sahl, M. Bates, X. Zhuang, R. Heintzmann, M. J. Booth, J. Bewersdorf, G. Shtengel, H. Hess, P. Tinnefeld, A. Honigmann, S. Jakobs, I. Testa, L. Cognet, B. Lounis, H. Ewers, S. J. Davis, C. Eggeling, D. Klenerman, K. I. Willig, G. Vicidomini, M. Castello, A. Diaspro, and T. Cordes, “The 2015 super-resolution microscopy roadmap,” J. Phys. D: Appl. Phys 48, 443001 (2015).
[Crossref]

Tinnefeld, P.

S. W. Hell, S. J. Sahl, M. Bates, X. Zhuang, R. Heintzmann, M. J. Booth, J. Bewersdorf, G. Shtengel, H. Hess, P. Tinnefeld, A. Honigmann, S. Jakobs, I. Testa, L. Cognet, B. Lounis, H. Ewers, S. J. Davis, C. Eggeling, D. Klenerman, K. I. Willig, G. Vicidomini, M. Castello, A. Diaspro, and T. Cordes, “The 2015 super-resolution microscopy roadmap,” J. Phys. D: Appl. Phys 48, 443001 (2015).
[Crossref]

Unser, M.

D. Sage, H. Kirshner, T. Pengo, N. Stuurman, J. Min, S. Manley, and M. Unser, “Quantitative evaluation of software packages for single-molecule localization microscopy,” Nat. Methods 12, 717–724 (2015).
[Crossref] [PubMed]

Vandenberghe, L.

S. Boyd and L. Vandenberghe, Convex optimization (Cambridge university press, 2004).
[Crossref]

Vapnik, V.

C. Cortes and V. Vapnik, “Support-vector networks,” Machine learning 20, 273–297 (1995).
[Crossref]

Vicidomini, G.

S. W. Hell, S. J. Sahl, M. Bates, X. Zhuang, R. Heintzmann, M. J. Booth, J. Bewersdorf, G. Shtengel, H. Hess, P. Tinnefeld, A. Honigmann, S. Jakobs, I. Testa, L. Cognet, B. Lounis, H. Ewers, S. J. Davis, C. Eggeling, D. Klenerman, K. I. Willig, G. Vicidomini, M. Castello, A. Diaspro, and T. Cordes, “The 2015 super-resolution microscopy roadmap,” J. Phys. D: Appl. Phys 48, 443001 (2015).
[Crossref]

S. Colabrese, M. Castello, G. Vicidomini, and A. Del Bue, “Learning-based approach to boost detection rate and localisation accuracy in single molecule localisation microscopy,” in “Image Processing (ICIP), 2016 IEEE International Conference on,” (IEEE, 2016), pp. 3184–3188.

Wang, X.-R.

R.-E. Fan, K.-W. Chang, C.-J. Hsieh, X.-R. Wang, and C.-J. Lin, “Liblinear: A library for large linear classification,” J. Mach. Learn. Res. 9, 1871–1874 (2008).

Willig, K. I.

S. W. Hell, S. J. Sahl, M. Bates, X. Zhuang, R. Heintzmann, M. J. Booth, J. Bewersdorf, G. Shtengel, H. Hess, P. Tinnefeld, A. Honigmann, S. Jakobs, I. Testa, L. Cognet, B. Lounis, H. Ewers, S. J. Davis, C. Eggeling, D. Klenerman, K. I. Willig, G. Vicidomini, M. Castello, A. Diaspro, and T. Cordes, “The 2015 super-resolution microscopy roadmap,” J. Phys. D: Appl. Phys 48, 443001 (2015).
[Crossref]

Zanacchi, F. C.

H. Deschout, F. C. Zanacchi, M. Mlodzianoski, A. Diaspro, J. Bewersdorf, S. T. Hess, and K. Braeckmans, “Precisely and accurately localizing single emitters in fluorescence microscopy,” Nat. Methods 11, 253–266 (2014).
[Crossref] [PubMed]

Zhuang, X.

S. W. Hell, S. J. Sahl, M. Bates, X. Zhuang, R. Heintzmann, M. J. Booth, J. Bewersdorf, G. Shtengel, H. Hess, P. Tinnefeld, A. Honigmann, S. Jakobs, I. Testa, L. Cognet, B. Lounis, H. Ewers, S. J. Davis, C. Eggeling, D. Klenerman, K. I. Willig, G. Vicidomini, M. Castello, A. Diaspro, and T. Cordes, “The 2015 super-resolution microscopy roadmap,” J. Phys. D: Appl. Phys 48, 443001 (2015).
[Crossref]

M. J. Rust, M. Bates, and X. Zhuang, “Stochastic optical reconstruction microscopy (storm) provides sub-diffraction-limit image resolution,” Nat. Methods 3, 793 (2006).
[Crossref] [PubMed]

Archiv für mikroskopische Anatomie (1)

E. Abbe, “Beiträge zur theorie des mikroskops und der mikroskopischen wahrnehmung,” Archiv für mikroskopische Anatomie 9, 413–418 (1873).
[Crossref]

Bioinformatics (1)

M. Ovesnỳ, P. Křížek, J. Borkovec, Z. Švindrych, and G. M. Hagen, “Thunderstorm: a comprehensive imagej plug-in for palm and storm data analysis and super-resolution imaging,” Bioinformatics 30, 2389–2390 (2014).
[Crossref]

Histochem. Cell Biol. (1)

U. Köthe, F. Herrmannsdörfer, I. Kats, and F. A. Hamprecht, “SimpleSTORM: A fast, self-calibrating reconstruction algorithm for localization microscopy,” Histochem. Cell Biol. 141, 613–627 (2014).
[Crossref] [PubMed]

IEEE Signal Process. Mag. (1)

H. Guo, “A simple algorithm for fitting a gaussian function,” IEEE Signal Process. Mag. 28, 134–137 (2011).
[Crossref]

J. Mach. Learn. Res. (1)

R.-E. Fan, K.-W. Chang, C.-J. Hsieh, X.-R. Wang, and C.-J. Lin, “Liblinear: A library for large linear classification,” J. Mach. Learn. Res. 9, 1871–1874 (2008).

J. Phys. D: Appl. Phys (1)

S. W. Hell, S. J. Sahl, M. Bates, X. Zhuang, R. Heintzmann, M. J. Booth, J. Bewersdorf, G. Shtengel, H. Hess, P. Tinnefeld, A. Honigmann, S. Jakobs, I. Testa, L. Cognet, B. Lounis, H. Ewers, S. J. Davis, C. Eggeling, D. Klenerman, K. I. Willig, G. Vicidomini, M. Castello, A. Diaspro, and T. Cordes, “The 2015 super-resolution microscopy roadmap,” J. Phys. D: Appl. Phys 48, 443001 (2015).
[Crossref]

J. Struct. Biol. (1)

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, 363–367 (2013).
[Crossref] [PubMed]

Machine learning (1)

C. Cortes and V. Vapnik, “Support-vector networks,” Machine learning 20, 273–297 (1995).
[Crossref]

Nat. Methods (9)

M. J. Rust, M. Bates, and X. Zhuang, “Stochastic optical reconstruction microscopy (storm) provides sub-diffraction-limit image resolution,” Nat. Methods 3, 793 (2006).
[Crossref] [PubMed]

H. Shroff, C. G. Galbraith, J. A. Galbraith, and E. Betzig, “Live-cell photoactivated localization microscopy of nanoscale adhesion dynamics,” Nat. Methods 5, 417–423 (2008).
[Crossref] [PubMed]

A. Small and S. Stahlheber, “Fluorophore localization algorithms for super-resolution microscopy,” Nat. Methods 11, 267–279 (2014).
[Crossref] [PubMed]

H. Deschout, F. C. Zanacchi, M. Mlodzianoski, A. Diaspro, J. Bewersdorf, S. T. Hess, and K. Braeckmans, “Precisely and accurately localizing single emitters in fluorescence microscopy,” Nat. Methods 11, 253–266 (2014).
[Crossref] [PubMed]

D. Sage, H. Kirshner, T. Pengo, N. Stuurman, J. Min, S. Manley, and M. Unser, “Quantitative evaluation of software packages for single-molecule localization microscopy,” Nat. Methods 12, 717–724 (2015).
[Crossref] [PubMed]

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, 195–200 (2012).
[Crossref]

Y. S. Hu, X. Nan, P. Sengupta, J. Lippincott-Schwartz, and H. Cang, “Accelerating 3b single-molecule super-resolution microscopy with cloud computing,” Nat. Methods 10, 96–97 (2013).
[Crossref] [PubMed]

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

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

Nat. Rev. Mol. Cell Biol. (1)

S. J. Sahl, S. W. Hell, and S. Jakobs, “Fluorescence nanoscopy in cell biology,” Nat. Rev. Mol. Cell Biol. 18, 685–701 (2017).
[Crossref] [PubMed]

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]

Scientific Reports (1)

Y. Tang, J. Hendriks, T. Gensch, L. Dai, and J. Li, “Automatic bayesian single molecule identification for localization microscopy,” Scientific Reports 6, 33521 (2016).

Transactions of the American Institute of Electrical Engineers (1)

H. Nyquist, “Certain topics in telegraph transmission theory,” Transactions of the American Institute of Electrical Engineers 47, 617–644 (1928).
[Crossref]

Other (4)

S. Colabrese, M. Castello, G. Vicidomini, and A. Del Bue, “Learning-based approach to boost detection rate and localisation accuracy in single molecule localisation microscopy,” in “Image Processing (ICIP), 2016 IEEE International Conference on,” (IEEE, 2016), pp. 3184–3188.

S. Boyd and L. Vandenberghe, Convex optimization (Cambridge university press, 2004).
[Crossref]

“2013 isbi grand challenge localization microscopy,” http://bigwww.epfl.ch/smlm/challenge2013/index.html . Accessed: 12-12-2016.

S. Colabrese, “SVM for Single Molecule Localisation Microscopy,” https://doi.org/10.6084/m9.figshare.5977453. Accessed: 14-3-2018.

Supplementary Material (1)

NameDescription
» Code 1       SVM for Single Molecule Localisation Microscopy

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Figures (6)

Fig. 1
Fig. 1 Pipeline for SML. The standard solution is presented on top (red arrows) while our proposal is at the bottom, underlined with green arrows. The Support Vector Machine block aims at substituting the red blocks of Pre-Processing and Detection, localisation is a common step instead.
Fig. 2
Fig. 2 Quantitative results over the synthetic dataset Tubulin I. The measurements taken into account are, clock wise starting from top-left: Jaccard, Accuracy, Precision and Recall.
Fig. 3
Fig. 3 Results over the synthetic datasets Bundled Of Tubulin (top), Tubulin I (centre) and Tubulin II (bottom). Our software is run neglecting the ground truth. Column wise, detail of super-resolved images obtained by ThunderSTORM, by the SVM with half of the available images for the training and by the SVM with 20 selections. The scale bar values are 0.3 µm for Bundled Of Tubulin (top), and 1.2 µm for Tubulin I and Tubulin II.
Fig. 4
Fig. 4 Quantitative comparison of our algorithm with ThunderSTORM. The FRC is computed for the synthetic datasets, clock-wise starting from top-left: Bundled Of Tubulin, Tubulin I and Tubulin II.
Fig. 5
Fig. 5 Results over the real datasets TubulinAF647 (top) and TubulinsLS (bottom). Column wise, from left to righ: super-resolved images obtained by ThunderSTORM, upper left corner, and our SVM-based algorithm, scale bar 1 µm (top) and 0.7 µm (bottom); a detail of ThunderSTORM reconstruction and a detail of our SVM-based algorithm, scale bar 0.6 µm (top) and 0.3 µm (bottom).
Fig. 6
Fig. 6 Quantitative results (FRC) over the real datasets TubulinAF647 and TubulinsLS.

Tables (3)

Tables Icon

Table 1 Properties of the synthetic datasets in use, for detailed informations on the acquisition settings refer to [22].

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Table 2 Properties of the real datasets in use, for other information (frame rate, laser wavelength, etc.) refer to [22].

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Table 3 Performance comparison among ThunderSTORM (TS), our SVM-based approach with half of the acquired stack used for the training (SVM-half) and the same SVM approach using for training only 20 activations (SVM-few).

Equations (14)

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w T x + b = 0 ,
min w 1 2 w T w + C i = 1 M ψ ( f ( x i , { w , b } ) , y i ) ,
G ( x , y ) = k 2 π σ x σ y e ( x μ x ) 2 2 σ x 2 ( y μ y ) 2 2 σ y 2 , k +
G ^ ( x , y ) = ln { k 2 π σ x σ y } ( x μ x ) 2 2 σ x 2 ( y μ y ) 2 2 σ y 2 = A + B x + C y + D x 2 + E y 2 ,
{ A ln { k 2 π σ x σ y } μ x 2 2 σ x 2 μ y 2 2 σ y 2 B μ x σ x 2 C μ x σ y 2 D 1 2 σ x 2 E 1 2 σ y 2 .
{ A , B > = 0 C > = 0 D < 0 E < 0 .
i = 1 N ϵ i 2 = i = 1 N [ I ^ i G ^ ( x i , y i ) ] 2 ,
M ( A B C D E ) = ( ln z i x i ln z i y i ln z i x i 2 ln z i y i 2 ln z i ) ,
M = ( N 1 x i y i x i 2 y i 2 x i x i 2 x i y i x i 3 x i y i 2 y i x i y i y i 2 x i 2 y i y i 3 x i 2 x i 3 x i 2 y i x i 4 x i 2 y i 2 y i 2 x i y i 2 y i 3 x i 2 y i 2 y i 4 ) .
i = 1 N w i 2 ϵ i 2 = i = 1 N w i 2 [ I ^ i G ^ k ( x i , y i ) ] 2 = i = 1 N | G k 1 ( x i , y i ) | 4 [ I ^ i G ^ k ( x i , y i ) ] 2 , if k > 1
M ^ ( A B C D E ) = ( w i ln I i w i x i ln I i w i y i ln I i w i x i 2 ln I i w i y i 2 ln I i ) ,
M ^ = ( w i w i x i w i y i w i x i 2 w i y i 2 w i x i w i x i 2 w i x i y i w i x i 3 w i x i y i 2 w i y i w i x i y i w i y i 2 w i x i 2 y i w i y i 3 w i x i 2 w i x i 3 w i x i 2 y i w i x i 4 w i x i 2 y i 2 w i y i 2 w i x i y i 2 w i y i 3 w i x i 2 y i 2 w i y i 4 ) ,
w i = { | G k 1 ( x i , y i ) | 2 if k > 1 | G 0 ( x i , y i ) | 2 if k = 1 ,
a 2 = 1 N n = 1 N ( x n T e s t x n R e f ) 2 + ( y n T e s t y n R e f ) 2 ,

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