Abstract

Optical aberrations degrade image quality in fluorescence microscopy, including for single-molecule based techniques. These depend on post-processing to localize individual molecules in an image series. Using simulated data, we show the impact of optical aberrations on localization success, accuracy and precision. The peak intensity and the proportion of successful localizations strongly reduces when the aberration strength is greater than 1.0 rad RMS, while the precision of each of those localisations is halved. The number of false-positive localisations exceeded 10% of the number of true-positive localisations at an aberration strength of only ~0.6 rad RMS when using the ThunderSTORM package, but at greater than 1.0 rad RMS with the Radial Symmetry package. In the presence of coma, the localization error reaches 100 nm at ~0.6 rad RMS of aberration strength. The impact of noise and of astigmatism for axial resolution are also considered. Understanding the effect of aberrations is crucial when deciding whether the addition of adaptive optics to a single-molecule microscope could significantly increase the information obtainable from an image series.

© 2016 Optical Society of America

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  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(5793), 1642–1645 (2006).
    [Crossref] [PubMed]
  2. M. J. Rust, M. Bates, and X. Zhuang, “Sub-diffraction-limit imaging by stochastic optical reconstruction microscopy (STORM),” Nat. Methods 3(10), 793–796 (2006).
    [Crossref] [PubMed]
  3. S. T. Hess, T. P. K. Girirajan, and M. D. Mason, “Ultra-high resolution imaging by fluorescence photoactivation localization microscopy,” Biophys. J. 91(11), 4258–4272 (2006).
    [Crossref] [PubMed]
  4. A. Sharonov and R. M. Hochstrasser, “Wide-field subdiffraction imaging by accumulated binding of diffusing probes,” Proc. Natl. Acad. Sci. U.S.A. 103(50), 18911–18916 (2006).
    [Crossref] [PubMed]
  5. S. W. Hell, “Far-field optical nanoscopy,” Science 316(5828), 1153–1158 (2007).
    [Crossref] [PubMed]
  6. Adaptive Optics for Biological Imaging (CRC Press, 2013).
  7. R. Davies and M. Kasper, “Adaptive Optics for Astronomy,” Annu. Rev. Astron. Astrophys. 50(1), 305–351 (2012).
    [Crossref]
  8. M. J. Booth, “Adaptive optical microscopy: the ongoing quest for a perfect image,” Light Sci. Appl. 3, e165 (2014).
  9. T. J. Gould, D. Burke, J. Bewersdorf, and M. J. Booth, “Adaptive optics enables 3D STED microscopy in aberrating specimens,” Opt. Express 20(19), 20998–21009 (2012).
    [Crossref] [PubMed]
  10. J. Zeng, P. Mahou, M.-C. Schanne-Klein, E. Beaurepaire, and D. Débarre, “3D resolved mapping of optical aberrations in thick tissues,” Biomed. Opt. Express 3(8), 1898–1913 (2012).
    [Crossref] [PubMed]
  11. M. Schwertner, M. Booth, and T. Wilson, “Characterizing specimen induced aberrations for high NA adaptive optical microscopy,” Opt. Express 12(26), 6540–6552 (2004).
    [Crossref] [PubMed]
  12. I. Izeddin, M. El Beheiry, J. Andilla, D. Ciepielewski, X. Darzacq, and M. Dahan, “PSF shaping using adaptive optics for three-dimensional single-molecule super-resolution imaging and tracking,” Opt. Express 20(5), 4957–4967 (2012).
    [Crossref] [PubMed]
  13. X. Tao, A. Norton, M. Kissel, O. Azucena, and J. Kubby, “Adaptive optical two-photon microscopy using autofluorescent guide stars,” Opt. Lett. 38(23), 5075–5078 (2013).
    [Crossref] [PubMed]
  14. X. Tao, J. Crest, S. Kotadia, O. Azucena, D. C. Chen, W. Sullivan, and J. Kubby, “Live imaging using adaptive optics with fluorescent protein guide-stars,” Opt. Express 20(14), 15969–15982 (2012).
    [Crossref] [PubMed]
  15. D. Burke, B. Patton, F. Huang, J. Bewersdorf, and M. J. Booth, “Adaptive optics correction of specimen-induced aberrations in single-molecule switching microscopy,” Optica 2(2), 177–185 (2015).
    [Crossref]
  16. K. F. Tehrani, J. Xu, Y. Zhang, P. Shen, and P. Kner, “Adaptive optics stochastic optical reconstruction microscopy (AO-STORM) using a genetic algorithm,” Opt. Express 23(10), 13677–13692 (2015).
    [Crossref] [PubMed]
  17. L. Carlini, S. J. Holden, K. M. Douglass, and S. Manley, “Correction of a Depth-Dependent Lateral Distortion in 3D Super-Resolution Imaging,” PLoS One 10(11), e0142949 (2015).
    [Crossref] [PubMed]
  18. A. von Diezmann, M. Y. Lee, M. D. Lew, and W. E. Moerner, “Correcting field-dependent aberrations with nanoscale accuracy in three-dimensional single-molecule localization microscopy,” Optica 2(11), 985–993 (2015).
    [Crossref] [PubMed]
  19. R. McGorty, J. Schnitzbauer, W. Zhang, and B. Huang, “Correction of depth-dependent aberrations in 3D single-molecule localization and super-resolution microscopy,” Opt. Lett. 39(2), 275–278 (2014).
    [Crossref] [PubMed]
  20. Z. Cao and K. Wang, “Effects of astigmatism and coma on rotating point spread function,” Appl. Opt. 53(31), 7325–7330 (2014).
    [Crossref] [PubMed]
  21. S. Ghosh and C. Preza, “Characterization of a three-dimensional double-helix point-spread function for fluorescence microscopy in the presence of spherical aberration,” J. Biomed. Opt. 18(3), 036010 (2013).
    [Crossref] [PubMed]
  22. B. Huang, W. Wang, M. Bates, and X. Zhuang, “Three-dimensional super-resolution imaging by stochastic optical reconstruction microscopy,” Science 319(5864), 810–813 (2008).
    [Crossref] [PubMed]
  23. G. Clouvel, A. Jasaitis, J. Sillibourne, I. Izeddin, M. El Beheiry, X. Levecq, M. Dahan, M. Bornens, and X. Darzacq, “Dual-color 3D PALM/dSTORM imaging of centrosomal proteins using MicAO 3DSR,” in Conference on Single Molecule Spectroscopy and Superresolution Imaging VI(San Francisco, CA, 2013).
    [Crossref]
  24. M. Born and E. Wolf, Principles of Optics (John Wiley, 1999).
  25. V. N. Mahajan, “Strehl ratio for primary aberrations in terms of their aberration variance,” J. Opt. Soc. Am. 73(6), 860–861 (1983).
    [Crossref]
  26. M. Ovesný, P. Křížek, J. Borkovec, Z. Svindrych, and G. M. Hagen, “ThunderSTORM: a comprehensive ImageJ plug-in for PALM and STORM data analysis and super-resolution imaging,” Bioinformatics 30(16), 2389–2390 (2014).
    [Crossref] [PubMed]
  27. R. Parthasarathy, “Rapid, accurate particle tracking by calculation of radial symmetry centers,” Nat. Methods 9(7), 724–726 (2012).
    [Crossref] [PubMed]
  28. 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(8), 717–724 (2015).
    [Crossref] [PubMed]
  29. R. E. Thompson, D. R. Larson, and W. W. Webb, “Precise nanometer localization analysis for individual fluorescent probes,” Biophys. J. 82(5), 2775–2783 (2002).
    [Crossref] [PubMed]
  30. G. T. Dempsey, J. C. Vaughan, K. H. Chen, M. Bates, and X. Zhuang, “Evaluation of fluorophores for optimal performance in localization-based super-resolution imaging,” Nat. Methods 8(12), 1027–1036 (2011).
    [Crossref] [PubMed]
  31. P. Kner, J. W. Sedat, D. A. Agard, and Z. Kam, “High-resolution wide-field microscopy with adaptive optics for spherical aberration correction and motionless focusing,” J. Microsc. 237(2), 136–147 (2010).
    [Crossref] [PubMed]
  32. J. M. Murray, P. L. Appleton, J. R. Swedlow, and J. C. Waters, “Evaluating performance in three-dimensional fluorescence microscopy,” J. Microsc. 228(3), 390–405 (2007).
    [Crossref] [PubMed]
  33. D. E. Wolf, C. Samarasekera, and J. R. Swedlow, “Quantitative analysis of digital microscope images,” in Digital Microscopy, 3rd ed. (Elsevier, 2007) 81, pp. 365–396.
  34. J. Mertz, H. Paudel, and T. G. Bifano, “Field of view advantage of conjugate adaptive optics in microscopy applications,” Appl. Opt. 54(11), 3498–3506 (2015).
    [Crossref] [PubMed]

2015 (6)

2014 (4)

M. Ovesný, P. Křížek, J. Borkovec, Z. Svindrych, and G. M. Hagen, “ThunderSTORM: a comprehensive ImageJ plug-in for PALM and STORM data analysis and super-resolution imaging,” Bioinformatics 30(16), 2389–2390 (2014).
[Crossref] [PubMed]

R. McGorty, J. Schnitzbauer, W. Zhang, and B. Huang, “Correction of depth-dependent aberrations in 3D single-molecule localization and super-resolution microscopy,” Opt. Lett. 39(2), 275–278 (2014).
[Crossref] [PubMed]

Z. Cao and K. Wang, “Effects of astigmatism and coma on rotating point spread function,” Appl. Opt. 53(31), 7325–7330 (2014).
[Crossref] [PubMed]

M. J. Booth, “Adaptive optical microscopy: the ongoing quest for a perfect image,” Light Sci. Appl. 3, e165 (2014).

2013 (2)

S. Ghosh and C. Preza, “Characterization of a three-dimensional double-helix point-spread function for fluorescence microscopy in the presence of spherical aberration,” J. Biomed. Opt. 18(3), 036010 (2013).
[Crossref] [PubMed]

X. Tao, A. Norton, M. Kissel, O. Azucena, and J. Kubby, “Adaptive optical two-photon microscopy using autofluorescent guide stars,” Opt. Lett. 38(23), 5075–5078 (2013).
[Crossref] [PubMed]

2012 (6)

2011 (1)

G. T. Dempsey, J. C. Vaughan, K. H. Chen, M. Bates, and X. Zhuang, “Evaluation of fluorophores for optimal performance in localization-based super-resolution imaging,” Nat. Methods 8(12), 1027–1036 (2011).
[Crossref] [PubMed]

2010 (1)

P. Kner, J. W. Sedat, D. A. Agard, and Z. Kam, “High-resolution wide-field microscopy with adaptive optics for spherical aberration correction and motionless focusing,” J. Microsc. 237(2), 136–147 (2010).
[Crossref] [PubMed]

2008 (1)

B. Huang, W. Wang, M. Bates, and X. Zhuang, “Three-dimensional super-resolution imaging by stochastic optical reconstruction microscopy,” Science 319(5864), 810–813 (2008).
[Crossref] [PubMed]

2007 (2)

J. M. Murray, P. L. Appleton, J. R. Swedlow, and J. C. Waters, “Evaluating performance in three-dimensional fluorescence microscopy,” J. Microsc. 228(3), 390–405 (2007).
[Crossref] [PubMed]

S. W. Hell, “Far-field optical nanoscopy,” Science 316(5828), 1153–1158 (2007).
[Crossref] [PubMed]

2006 (4)

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

M. J. Rust, M. Bates, and X. Zhuang, “Sub-diffraction-limit imaging by stochastic optical reconstruction microscopy (STORM),” Nat. Methods 3(10), 793–796 (2006).
[Crossref] [PubMed]

S. T. Hess, T. P. K. Girirajan, and M. D. Mason, “Ultra-high resolution imaging by fluorescence photoactivation localization microscopy,” Biophys. J. 91(11), 4258–4272 (2006).
[Crossref] [PubMed]

A. Sharonov and R. M. Hochstrasser, “Wide-field subdiffraction imaging by accumulated binding of diffusing probes,” Proc. Natl. Acad. Sci. U.S.A. 103(50), 18911–18916 (2006).
[Crossref] [PubMed]

2004 (1)

2002 (1)

R. E. Thompson, D. R. Larson, and W. W. Webb, “Precise nanometer localization analysis for individual fluorescent probes,” Biophys. J. 82(5), 2775–2783 (2002).
[Crossref] [PubMed]

1983 (1)

Agard, D. A.

P. Kner, J. W. Sedat, D. A. Agard, and Z. Kam, “High-resolution wide-field microscopy with adaptive optics for spherical aberration correction and motionless focusing,” J. Microsc. 237(2), 136–147 (2010).
[Crossref] [PubMed]

Andilla, J.

Appleton, P. L.

J. M. Murray, P. L. Appleton, J. R. Swedlow, and J. C. Waters, “Evaluating performance in three-dimensional fluorescence microscopy,” J. Microsc. 228(3), 390–405 (2007).
[Crossref] [PubMed]

Azucena, O.

Bates, M.

G. T. Dempsey, J. C. Vaughan, K. H. Chen, M. Bates, and X. Zhuang, “Evaluation of fluorophores for optimal performance in localization-based super-resolution imaging,” Nat. Methods 8(12), 1027–1036 (2011).
[Crossref] [PubMed]

B. Huang, W. Wang, M. Bates, and X. Zhuang, “Three-dimensional super-resolution imaging by stochastic optical reconstruction microscopy,” Science 319(5864), 810–813 (2008).
[Crossref] [PubMed]

M. J. Rust, M. Bates, and X. Zhuang, “Sub-diffraction-limit imaging by stochastic optical reconstruction microscopy (STORM),” Nat. Methods 3(10), 793–796 (2006).
[Crossref] [PubMed]

Beaurepaire, E.

Betzig, E.

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

Bewersdorf, J.

Bifano, T. G.

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(5793), 1642–1645 (2006).
[Crossref] [PubMed]

Booth, M.

Booth, M. J.

Borkovec, J.

M. Ovesný, P. Křížek, J. Borkovec, Z. Svindrych, and G. M. Hagen, “ThunderSTORM: a comprehensive ImageJ plug-in for PALM and STORM data analysis and super-resolution imaging,” Bioinformatics 30(16), 2389–2390 (2014).
[Crossref] [PubMed]

Bornens, M.

G. Clouvel, A. Jasaitis, J. Sillibourne, I. Izeddin, M. El Beheiry, X. Levecq, M. Dahan, M. Bornens, and X. Darzacq, “Dual-color 3D PALM/dSTORM imaging of centrosomal proteins using MicAO 3DSR,” in Conference on Single Molecule Spectroscopy and Superresolution Imaging VI(San Francisco, CA, 2013).
[Crossref]

Burke, D.

Cao, Z.

Carlini, L.

L. Carlini, S. J. Holden, K. M. Douglass, and S. Manley, “Correction of a Depth-Dependent Lateral Distortion in 3D Super-Resolution Imaging,” PLoS One 10(11), e0142949 (2015).
[Crossref] [PubMed]

Chen, D. C.

Chen, K. H.

G. T. Dempsey, J. C. Vaughan, K. H. Chen, M. Bates, and X. Zhuang, “Evaluation of fluorophores for optimal performance in localization-based super-resolution imaging,” Nat. Methods 8(12), 1027–1036 (2011).
[Crossref] [PubMed]

Ciepielewski, D.

Clouvel, G.

G. Clouvel, A. Jasaitis, J. Sillibourne, I. Izeddin, M. El Beheiry, X. Levecq, M. Dahan, M. Bornens, and X. Darzacq, “Dual-color 3D PALM/dSTORM imaging of centrosomal proteins using MicAO 3DSR,” in Conference on Single Molecule Spectroscopy and Superresolution Imaging VI(San Francisco, CA, 2013).
[Crossref]

Crest, J.

Dahan, M.

I. Izeddin, M. El Beheiry, J. Andilla, D. Ciepielewski, X. Darzacq, and M. Dahan, “PSF shaping using adaptive optics for three-dimensional single-molecule super-resolution imaging and tracking,” Opt. Express 20(5), 4957–4967 (2012).
[Crossref] [PubMed]

G. Clouvel, A. Jasaitis, J. Sillibourne, I. Izeddin, M. El Beheiry, X. Levecq, M. Dahan, M. Bornens, and X. Darzacq, “Dual-color 3D PALM/dSTORM imaging of centrosomal proteins using MicAO 3DSR,” in Conference on Single Molecule Spectroscopy and Superresolution Imaging VI(San Francisco, CA, 2013).
[Crossref]

Darzacq, X.

I. Izeddin, M. El Beheiry, J. Andilla, D. Ciepielewski, X. Darzacq, and M. Dahan, “PSF shaping using adaptive optics for three-dimensional single-molecule super-resolution imaging and tracking,” Opt. Express 20(5), 4957–4967 (2012).
[Crossref] [PubMed]

G. Clouvel, A. Jasaitis, J. Sillibourne, I. Izeddin, M. El Beheiry, X. Levecq, M. Dahan, M. Bornens, and X. Darzacq, “Dual-color 3D PALM/dSTORM imaging of centrosomal proteins using MicAO 3DSR,” in Conference on Single Molecule Spectroscopy and Superresolution Imaging VI(San Francisco, CA, 2013).
[Crossref]

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(5793), 1642–1645 (2006).
[Crossref] [PubMed]

Davies, R.

R. Davies and M. Kasper, “Adaptive Optics for Astronomy,” Annu. Rev. Astron. Astrophys. 50(1), 305–351 (2012).
[Crossref]

Débarre, D.

Dempsey, G. T.

G. T. Dempsey, J. C. Vaughan, K. H. Chen, M. Bates, and X. Zhuang, “Evaluation of fluorophores for optimal performance in localization-based super-resolution imaging,” Nat. Methods 8(12), 1027–1036 (2011).
[Crossref] [PubMed]

Douglass, K. M.

L. Carlini, S. J. Holden, K. M. Douglass, and S. Manley, “Correction of a Depth-Dependent Lateral Distortion in 3D Super-Resolution Imaging,” PLoS One 10(11), e0142949 (2015).
[Crossref] [PubMed]

El Beheiry, M.

I. Izeddin, M. El Beheiry, J. Andilla, D. Ciepielewski, X. Darzacq, and M. Dahan, “PSF shaping using adaptive optics for three-dimensional single-molecule super-resolution imaging and tracking,” Opt. Express 20(5), 4957–4967 (2012).
[Crossref] [PubMed]

G. Clouvel, A. Jasaitis, J. Sillibourne, I. Izeddin, M. El Beheiry, X. Levecq, M. Dahan, M. Bornens, and X. Darzacq, “Dual-color 3D PALM/dSTORM imaging of centrosomal proteins using MicAO 3DSR,” in Conference on Single Molecule Spectroscopy and Superresolution Imaging VI(San Francisco, CA, 2013).
[Crossref]

Ghosh, S.

S. Ghosh and C. Preza, “Characterization of a three-dimensional double-helix point-spread function for fluorescence microscopy in the presence of spherical aberration,” J. Biomed. Opt. 18(3), 036010 (2013).
[Crossref] [PubMed]

Girirajan, T. P. K.

S. T. Hess, T. P. K. Girirajan, and M. D. Mason, “Ultra-high resolution imaging by fluorescence photoactivation localization microscopy,” Biophys. J. 91(11), 4258–4272 (2006).
[Crossref] [PubMed]

Gould, T. J.

Hagen, G. M.

M. Ovesný, P. Křížek, J. Borkovec, Z. Svindrych, and G. M. Hagen, “ThunderSTORM: a comprehensive ImageJ plug-in for PALM and STORM data analysis and super-resolution imaging,” Bioinformatics 30(16), 2389–2390 (2014).
[Crossref] [PubMed]

Hell, S. W.

S. W. Hell, “Far-field optical nanoscopy,” Science 316(5828), 1153–1158 (2007).
[Crossref] [PubMed]

Hess, H. F.

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

Hess, S. T.

S. T. Hess, T. P. K. Girirajan, and M. D. Mason, “Ultra-high resolution imaging by fluorescence photoactivation localization microscopy,” Biophys. J. 91(11), 4258–4272 (2006).
[Crossref] [PubMed]

Hochstrasser, R. M.

A. Sharonov and R. M. Hochstrasser, “Wide-field subdiffraction imaging by accumulated binding of diffusing probes,” Proc. Natl. Acad. Sci. U.S.A. 103(50), 18911–18916 (2006).
[Crossref] [PubMed]

Holden, S. J.

L. Carlini, S. J. Holden, K. M. Douglass, and S. Manley, “Correction of a Depth-Dependent Lateral Distortion in 3D Super-Resolution Imaging,” PLoS One 10(11), e0142949 (2015).
[Crossref] [PubMed]

Huang, B.

R. McGorty, J. Schnitzbauer, W. Zhang, and B. Huang, “Correction of depth-dependent aberrations in 3D single-molecule localization and super-resolution microscopy,” Opt. Lett. 39(2), 275–278 (2014).
[Crossref] [PubMed]

B. Huang, W. Wang, M. Bates, and X. Zhuang, “Three-dimensional super-resolution imaging by stochastic optical reconstruction microscopy,” Science 319(5864), 810–813 (2008).
[Crossref] [PubMed]

Huang, F.

Izeddin, I.

I. Izeddin, M. El Beheiry, J. Andilla, D. Ciepielewski, X. Darzacq, and M. Dahan, “PSF shaping using adaptive optics for three-dimensional single-molecule super-resolution imaging and tracking,” Opt. Express 20(5), 4957–4967 (2012).
[Crossref] [PubMed]

G. Clouvel, A. Jasaitis, J. Sillibourne, I. Izeddin, M. El Beheiry, X. Levecq, M. Dahan, M. Bornens, and X. Darzacq, “Dual-color 3D PALM/dSTORM imaging of centrosomal proteins using MicAO 3DSR,” in Conference on Single Molecule Spectroscopy and Superresolution Imaging VI(San Francisco, CA, 2013).
[Crossref]

Jasaitis, A.

G. Clouvel, A. Jasaitis, J. Sillibourne, I. Izeddin, M. El Beheiry, X. Levecq, M. Dahan, M. Bornens, and X. Darzacq, “Dual-color 3D PALM/dSTORM imaging of centrosomal proteins using MicAO 3DSR,” in Conference on Single Molecule Spectroscopy and Superresolution Imaging VI(San Francisco, CA, 2013).
[Crossref]

Kam, Z.

P. Kner, J. W. Sedat, D. A. Agard, and Z. Kam, “High-resolution wide-field microscopy with adaptive optics for spherical aberration correction and motionless focusing,” J. Microsc. 237(2), 136–147 (2010).
[Crossref] [PubMed]

Kasper, M.

R. Davies and M. Kasper, “Adaptive Optics for Astronomy,” Annu. Rev. Astron. Astrophys. 50(1), 305–351 (2012).
[Crossref]

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(8), 717–724 (2015).
[Crossref] [PubMed]

Kissel, M.

Kner, P.

K. F. Tehrani, J. Xu, Y. Zhang, P. Shen, and P. Kner, “Adaptive optics stochastic optical reconstruction microscopy (AO-STORM) using a genetic algorithm,” Opt. Express 23(10), 13677–13692 (2015).
[Crossref] [PubMed]

P. Kner, J. W. Sedat, D. A. Agard, and Z. Kam, “High-resolution wide-field microscopy with adaptive optics for spherical aberration correction and motionless focusing,” J. Microsc. 237(2), 136–147 (2010).
[Crossref] [PubMed]

Kotadia, S.

Krížek, P.

M. Ovesný, P. Křížek, J. Borkovec, Z. Svindrych, and G. M. Hagen, “ThunderSTORM: a comprehensive ImageJ plug-in for PALM and STORM data analysis and super-resolution imaging,” Bioinformatics 30(16), 2389–2390 (2014).
[Crossref] [PubMed]

Kubby, J.

Larson, D. R.

R. E. Thompson, D. R. Larson, and W. W. Webb, “Precise nanometer localization analysis for individual fluorescent probes,” Biophys. J. 82(5), 2775–2783 (2002).
[Crossref] [PubMed]

Lee, M. Y.

Levecq, X.

G. Clouvel, A. Jasaitis, J. Sillibourne, I. Izeddin, M. El Beheiry, X. Levecq, M. Dahan, M. Bornens, and X. Darzacq, “Dual-color 3D PALM/dSTORM imaging of centrosomal proteins using MicAO 3DSR,” in Conference on Single Molecule Spectroscopy and Superresolution Imaging VI(San Francisco, CA, 2013).
[Crossref]

Lew, M. D.

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(5793), 1642–1645 (2006).
[Crossref] [PubMed]

Lippincott-Schwartz, J.

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

Mahajan, V. N.

Mahou, P.

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(8), 717–724 (2015).
[Crossref] [PubMed]

L. Carlini, S. J. Holden, K. M. Douglass, and S. Manley, “Correction of a Depth-Dependent Lateral Distortion in 3D Super-Resolution Imaging,” PLoS One 10(11), e0142949 (2015).
[Crossref] [PubMed]

Mason, M. D.

S. T. Hess, T. P. K. Girirajan, and M. D. Mason, “Ultra-high resolution imaging by fluorescence photoactivation localization microscopy,” Biophys. J. 91(11), 4258–4272 (2006).
[Crossref] [PubMed]

McGorty, R.

Mertz, J.

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(8), 717–724 (2015).
[Crossref] [PubMed]

Moerner, W. E.

Murray, J. M.

J. M. Murray, P. L. Appleton, J. R. Swedlow, and J. C. Waters, “Evaluating performance in three-dimensional fluorescence microscopy,” J. Microsc. 228(3), 390–405 (2007).
[Crossref] [PubMed]

Norton, A.

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(5793), 1642–1645 (2006).
[Crossref] [PubMed]

Ovesný, M.

M. Ovesný, P. Křížek, J. Borkovec, Z. Svindrych, and G. M. Hagen, “ThunderSTORM: a comprehensive ImageJ plug-in for PALM and STORM data analysis and super-resolution imaging,” Bioinformatics 30(16), 2389–2390 (2014).
[Crossref] [PubMed]

Parthasarathy, R.

R. Parthasarathy, “Rapid, accurate particle tracking by calculation of radial symmetry centers,” Nat. Methods 9(7), 724–726 (2012).
[Crossref] [PubMed]

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(5793), 1642–1645 (2006).
[Crossref] [PubMed]

Patton, B.

Paudel, H.

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(8), 717–724 (2015).
[Crossref] [PubMed]

Preza, C.

S. Ghosh and C. Preza, “Characterization of a three-dimensional double-helix point-spread function for fluorescence microscopy in the presence of spherical aberration,” J. Biomed. Opt. 18(3), 036010 (2013).
[Crossref] [PubMed]

Rust, M. J.

M. J. Rust, M. Bates, and X. Zhuang, “Sub-diffraction-limit imaging by stochastic optical reconstruction microscopy (STORM),” Nat. Methods 3(10), 793–796 (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(8), 717–724 (2015).
[Crossref] [PubMed]

Schanne-Klein, M.-C.

Schnitzbauer, J.

Schwertner, M.

Sedat, J. W.

P. Kner, J. W. Sedat, D. A. Agard, and Z. Kam, “High-resolution wide-field microscopy with adaptive optics for spherical aberration correction and motionless focusing,” J. Microsc. 237(2), 136–147 (2010).
[Crossref] [PubMed]

Sharonov, A.

A. Sharonov and R. M. Hochstrasser, “Wide-field subdiffraction imaging by accumulated binding of diffusing probes,” Proc. Natl. Acad. Sci. U.S.A. 103(50), 18911–18916 (2006).
[Crossref] [PubMed]

Shen, P.

Sillibourne, J.

G. Clouvel, A. Jasaitis, J. Sillibourne, I. Izeddin, M. El Beheiry, X. Levecq, M. Dahan, M. Bornens, and X. Darzacq, “Dual-color 3D PALM/dSTORM imaging of centrosomal proteins using MicAO 3DSR,” in Conference on Single Molecule Spectroscopy and Superresolution Imaging VI(San Francisco, CA, 2013).
[Crossref]

Sougrat, R.

E. Betzig, G. H. Patterson, R. Sougrat, O. W. Lindwasser, S. Olenych, J. S. Bonifacino, M. W. Davidson, J. Lippincott-Schwartz, and H. F. Hess, “Imaging intracellular fluorescent proteins at nanometer resolution,” Science 313(5793), 1642–1645 (2006).
[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(8), 717–724 (2015).
[Crossref] [PubMed]

Sullivan, W.

Svindrych, Z.

M. Ovesný, P. Křížek, J. Borkovec, Z. Svindrych, and G. M. Hagen, “ThunderSTORM: a comprehensive ImageJ plug-in for PALM and STORM data analysis and super-resolution imaging,” Bioinformatics 30(16), 2389–2390 (2014).
[Crossref] [PubMed]

Swedlow, J. R.

J. M. Murray, P. L. Appleton, J. R. Swedlow, and J. C. Waters, “Evaluating performance in three-dimensional fluorescence microscopy,” J. Microsc. 228(3), 390–405 (2007).
[Crossref] [PubMed]

Tao, X.

Tehrani, K. F.

Thompson, R. E.

R. E. Thompson, D. R. Larson, and W. W. Webb, “Precise nanometer localization analysis for individual fluorescent probes,” Biophys. J. 82(5), 2775–2783 (2002).
[Crossref] [PubMed]

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(8), 717–724 (2015).
[Crossref] [PubMed]

Vaughan, J. C.

G. T. Dempsey, J. C. Vaughan, K. H. Chen, M. Bates, and X. Zhuang, “Evaluation of fluorophores for optimal performance in localization-based super-resolution imaging,” Nat. Methods 8(12), 1027–1036 (2011).
[Crossref] [PubMed]

von Diezmann, A.

Wang, K.

Wang, W.

B. Huang, W. Wang, M. Bates, and X. Zhuang, “Three-dimensional super-resolution imaging by stochastic optical reconstruction microscopy,” Science 319(5864), 810–813 (2008).
[Crossref] [PubMed]

Waters, J. C.

J. M. Murray, P. L. Appleton, J. R. Swedlow, and J. C. Waters, “Evaluating performance in three-dimensional fluorescence microscopy,” J. Microsc. 228(3), 390–405 (2007).
[Crossref] [PubMed]

Webb, W. W.

R. E. Thompson, D. R. Larson, and W. W. Webb, “Precise nanometer localization analysis for individual fluorescent probes,” Biophys. J. 82(5), 2775–2783 (2002).
[Crossref] [PubMed]

Wilson, T.

Xu, J.

Zeng, J.

Zhang, W.

Zhang, Y.

Zhuang, X.

G. T. Dempsey, J. C. Vaughan, K. H. Chen, M. Bates, and X. Zhuang, “Evaluation of fluorophores for optimal performance in localization-based super-resolution imaging,” Nat. Methods 8(12), 1027–1036 (2011).
[Crossref] [PubMed]

B. Huang, W. Wang, M. Bates, and X. Zhuang, “Three-dimensional super-resolution imaging by stochastic optical reconstruction microscopy,” Science 319(5864), 810–813 (2008).
[Crossref] [PubMed]

M. J. Rust, M. Bates, and X. Zhuang, “Sub-diffraction-limit imaging by stochastic optical reconstruction microscopy (STORM),” Nat. Methods 3(10), 793–796 (2006).
[Crossref] [PubMed]

Annu. Rev. Astron. Astrophys. (1)

R. Davies and M. Kasper, “Adaptive Optics for Astronomy,” Annu. Rev. Astron. Astrophys. 50(1), 305–351 (2012).
[Crossref]

Appl. Opt. (2)

Bioinformatics (1)

M. Ovesný, P. Křížek, J. Borkovec, Z. Svindrych, and G. M. Hagen, “ThunderSTORM: a comprehensive ImageJ plug-in for PALM and STORM data analysis and super-resolution imaging,” Bioinformatics 30(16), 2389–2390 (2014).
[Crossref] [PubMed]

Biomed. Opt. Express (1)

Biophys. J. (2)

S. T. Hess, T. P. K. Girirajan, and M. D. Mason, “Ultra-high resolution imaging by fluorescence photoactivation localization microscopy,” Biophys. J. 91(11), 4258–4272 (2006).
[Crossref] [PubMed]

R. E. Thompson, D. R. Larson, and W. W. Webb, “Precise nanometer localization analysis for individual fluorescent probes,” Biophys. J. 82(5), 2775–2783 (2002).
[Crossref] [PubMed]

J. Biomed. Opt. (1)

S. Ghosh and C. Preza, “Characterization of a three-dimensional double-helix point-spread function for fluorescence microscopy in the presence of spherical aberration,” J. Biomed. Opt. 18(3), 036010 (2013).
[Crossref] [PubMed]

J. Microsc. (2)

P. Kner, J. W. Sedat, D. A. Agard, and Z. Kam, “High-resolution wide-field microscopy with adaptive optics for spherical aberration correction and motionless focusing,” J. Microsc. 237(2), 136–147 (2010).
[Crossref] [PubMed]

J. M. Murray, P. L. Appleton, J. R. Swedlow, and J. C. Waters, “Evaluating performance in three-dimensional fluorescence microscopy,” J. Microsc. 228(3), 390–405 (2007).
[Crossref] [PubMed]

J. Opt. Soc. Am. (1)

Light Sci. Appl. (1)

M. J. Booth, “Adaptive optical microscopy: the ongoing quest for a perfect image,” Light Sci. Appl. 3, e165 (2014).

Nat. Methods (4)

M. J. Rust, M. Bates, and X. Zhuang, “Sub-diffraction-limit imaging by stochastic optical reconstruction microscopy (STORM),” Nat. Methods 3(10), 793–796 (2006).
[Crossref] [PubMed]

G. T. Dempsey, J. C. Vaughan, K. H. Chen, M. Bates, and X. Zhuang, “Evaluation of fluorophores for optimal performance in localization-based super-resolution imaging,” Nat. Methods 8(12), 1027–1036 (2011).
[Crossref] [PubMed]

R. Parthasarathy, “Rapid, accurate particle tracking by calculation of radial symmetry centers,” Nat. Methods 9(7), 724–726 (2012).
[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(8), 717–724 (2015).
[Crossref] [PubMed]

Opt. Express (5)

Opt. Lett. (2)

Optica (2)

PLoS One (1)

L. Carlini, S. J. Holden, K. M. Douglass, and S. Manley, “Correction of a Depth-Dependent Lateral Distortion in 3D Super-Resolution Imaging,” PLoS One 10(11), e0142949 (2015).
[Crossref] [PubMed]

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

A. Sharonov and R. M. Hochstrasser, “Wide-field subdiffraction imaging by accumulated binding of diffusing probes,” Proc. Natl. Acad. Sci. U.S.A. 103(50), 18911–18916 (2006).
[Crossref] [PubMed]

Science (3)

S. W. Hell, “Far-field optical nanoscopy,” Science 316(5828), 1153–1158 (2007).
[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(5793), 1642–1645 (2006).
[Crossref] [PubMed]

B. Huang, W. Wang, M. Bates, and X. Zhuang, “Three-dimensional super-resolution imaging by stochastic optical reconstruction microscopy,” Science 319(5864), 810–813 (2008).
[Crossref] [PubMed]

Other (4)

G. Clouvel, A. Jasaitis, J. Sillibourne, I. Izeddin, M. El Beheiry, X. Levecq, M. Dahan, M. Bornens, and X. Darzacq, “Dual-color 3D PALM/dSTORM imaging of centrosomal proteins using MicAO 3DSR,” in Conference on Single Molecule Spectroscopy and Superresolution Imaging VI(San Francisco, CA, 2013).
[Crossref]

M. Born and E. Wolf, Principles of Optics (John Wiley, 1999).

D. E. Wolf, C. Samarasekera, and J. R. Swedlow, “Quantitative analysis of digital microscope images,” in Digital Microscopy, 3rd ed. (Elsevier, 2007) 81, pp. 365–396.

Adaptive Optics for Biological Imaging (CRC Press, 2013).

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Figures (9)

Fig. 1
Fig. 1

Formation and processing of simulated single-molecule fluorescence images. A random field of single molecules – the’ground truth’ – is convolved with aberrated point-spread functions with a range of aberration strengths, and noise added. Following localisation by a single molecule software package, the calculated co-ordinates are compared with those of the ground truth.

Fig. 2
Fig. 2

Aberrations in single-molecule imaging. (a) Lateral form of PSFs with (left) 1.57 and (right) 2.51 rad RMS spherical aberration applied; (b) Lateral form of PSFs with increasing levels of coma applied in the x-axis (from left to right: 0.06, 0.31, 0.63 and 1.26 rad RMS); (c) Lateral form of PSFs with 2.51 rad RMS of 45° astigmatism at various depths (from left to right: 0 nm, 250 nm and 500 nm depth)

Fig. 3
Fig. 3

Effects of aberrations on single molecule images. (a) Strehl ratios for the simulated data sets as a function of aberration strength in units rad RMS; (b) Profiles of the spherically aberrated PSFs in Fig. 2(a).

Fig. 4
Fig. 4

Localisation success in the presence of aberrations. Proportion of successfully localised ground truths, after analysis using (a, b) ThunderSTORM, (c, d) Radial Symmetry and defining a localization as successful if it is within (a, c) 250 nm or (b, d) 20 nm of the ground truth location. (e) Proportion of successfully localized ground truths, in the presence of coma, within 480 nm of the ground truth.

Fig. 5
Fig. 5

Localisation accuracy and precision. (a, b) Accuracy (along x-axis) after analysis using (a) ThunderSTORM, and (b) Radial Symmetry for localisations within 480 nm of the ground truth; (c-f) Precision using (c, d) ThunderSTORM and (e, f) Radial Symmetry for localisations within (c, e) 250 nm and (d, f) 20 nm of the ground truth; (g) Profiles of the plots in Fig. 2(b).

Fig. 6
Fig. 6

False-positive detection. Mean number of false-positive single-molecule detections per frame using (a, c) ThunderSTORM and (b, c) Radial Symmetry for a localization radius of (a, b) 250 nm and (c) 480 nm. Note that the number of ground truths is 1000.

Fig. 7
Fig. 7

Astigmatic single molecule detection at different depths using ThunderSTORM, with a localization radius of 250 nm. (a) Number of successful localisations at various depths in the presence of defocus or trefoil aberrations; (b) Mean number of false-positive localisations exhibiting astigmatism aberrations, as a function of sample depth; (c) Accuracy (along x-axis) and (d) lateral precision for PSFs exhibiting defocus or trefoil aberrations as a function of depth; (e) Profiles of the plots in Fig. 2(c), along the major axis of the elliptical PSF.

Fig. 8
Fig. 8

Combined effects of aberrations and image noise on single molecule detection. With a 250 nm localization radius, the (a) proportion of ground truths successfully localized and (b) precision, with increasing levels of background noise in the presence of astigmatism in the x-axis, was determined using ThunderSTORM.

Fig. 9
Fig. 9

Effects of aggregated aberrations typical of biological samples. Simulated point spread functions containing (left) no aberrations and (right) specimen-induced aberrations when imaging microtubules in cells. Red crosses mark localization co-ordinates.

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