Abstract

Stochastic optical reconstruction microscopy (STORM) can achieve resolutions of better than 20nm imaging single fluorescently labeled cells. However, when optical aberrations induced by larger biological samples degrade the point spread function (PSF), the localization accuracy and number of localizations are both reduced, destroying the resolution of STORM. Adaptive optics (AO) can be used to correct the wavefront, restoring the high resolution of STORM. A challenge for AO-STORM microscopy is the development of robust optimization algorithms which can efficiently correct the wavefront from stochastic raw STORM images. Here we present the implementation of a particle swarm optimization (PSO) approach with a Fourier metric for real-time correction of wavefront aberrations during STORM acquisition. We apply our approach to imaging boutons 100 μm deep inside the central nervous system (CNS) of Drosophila melanogaster larvae achieving a resolution of 146 nm.

© 2017 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).
    [PubMed]
  2. M. J. Rust, M. Bates, and X. Zhuang, “Sub-diffraction-limit imaging by stochastic optical reconstruction microscopy (STORM),” Nat. Methods 3(10), 793–795 (2006).
    [PubMed]
  3. A. G. York, A. Ghitani, A. Vaziri, M. W. Davidson, and H. Shroff, “Confined activation and subdiffractive localization enables whole-cell PALM with genetically expressed probes,” Nat. Methods 8(4), 327–333 (2011).
    [PubMed]
  4. B. Huang, S. A. Jones, B. Brandenburg, and X. Zhuang, “Whole-cell 3D STORM reveals interactions between cellular structures with nanometer-scale resolution,” Nat. Methods 5(12), 1047–1052 (2008).
    [PubMed]
  5. F. Cella Zanacchi, Z. Lavagnino, M. Perrone Donnorso, A. Del Bue, L. Furia, M. Faretta, and A. Diaspro, “Live-cell 3D super-resolution imaging in thick biological samples,” Nat. Methods 8(12), 1047–1049 (2011).
    [PubMed]
  6. F. Cella Zanacchi, Z. Lavagnino, M. Faretta, L. Furia, and A. Diaspro, “Light-Sheet Confined Super-Resolution Using Two-Photon Photoactivation,” PLoS One 8(7), e67667 (2013).
    [PubMed]
  7. M. B. M. Meddens, S. Liu, P. S. Finnegan, T. L. Edwards, C. D. James, and K. A. Lidke, “Single objective light-sheet microscopy for high-speed whole-cell 3D super-resolution,” Biomed. Opt. Express 7(6), 2219–2236 (2016).
    [PubMed]
  8. W. R. Legant, L. Shao, J. B. Grimm, T. A. Brown, D. E. Milkie, B. B. Avants, L. D. Lavis, and E. Betzig, “High-density three-dimensional localization microscopy across large volumes,” Nat. Methods 13(4), 359–365 (2016).
    [PubMed]
  9. 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).
    [PubMed]
  10. J. A. Kubby, ed., Adaptive Optics for Biological Imaging (CRC Press, New York, NY, 2013).
  11. M. J. Booth, “Wavefront sensorless adaptive optics for large aberrations,” Opt. Lett. 32(1), 5–7 (2007).
    [PubMed]
  12. D. Debarre, M. J. Booth, and T. Wilson, “Image based adaptive optics through optimisation of low spatial frequencies,” Opt. Express 15(13), 8176–8190 (2007).
    [PubMed]
  13. 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).
    [PubMed]
  14. M. J. Booth, M. A. Neil, R. Juskaitis, and T. Wilson, “Adaptive aberration correction in a confocal microscope,” Proc. Natl. Acad. Sci. U.S.A. 99(9), 5788–5792 (2002).
    [PubMed]
  15. D. Débarre, E. J. Botcherby, T. Watanabe, S. Srinivas, M. J. Booth, and T. Wilson, “Image-based adaptive optics for two-photon microscopy,” Opt. Lett. 34(16), 2495–2497 (2009).
    [PubMed]
  16. D. Débarre, E. J. Botcherby, M. J. Booth, and T. Wilson, “Adaptive optics for structured illumination microscopy,” Opt. Express 16(13), 9290–9305 (2008).
    [PubMed]
  17. B. Thomas, A. Wolstenholme, S. N. Chaudhari, E. T. Kipreos, and P. Kner, “Enhanced resolution through thick tissue with structured illumination and adaptive optics,” J. Biomed. Opt. 20(2), 26006 (2015).
    [PubMed]
  18. 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, 177–185 (2015).
  19. B. C. Coles, S. E. D. Webb, N. Schwartz, D. J. Rolfe, M. Martin-Fernandez, and V. Lo Schiavo, “Characterisation of the effects of optical aberrations in single molecule techniques,” Biomed. Opt. Express 7(5), 1755–1767 (2016).
    [PubMed]
  20. M. Booth, “Wave front sensor-less adaptive optics: a model-based approach using sphere packings,” Opt. Express 14(4), 1339–1352 (2006).
    [PubMed]
  21. A. J. Wright, D. Burns, B. A. Patterson, S. P. Poland, G. J. Valentine, and J. M. Girkin, “Exploration of the optimisation algorithms used in the implementation of adaptive optics in confocal and multiphoton microscopy,” Microsc. Res. Tech. 67(1), 36–44 (2005).
    [PubMed]
  22. O. Albert, L. Sherman, G. Mourou, T. B. Norris, and G. Vdovin, “Smart microscope: an adaptive optics learning system for aberration correction in multiphoton confocal microscopy,” Opt. Lett. 25(1), 52–54 (2000).
    [PubMed]
  23. R. Eberhart and J. Kennedy, “A new optimizer using particle swarm theory,” Proceedings of the Sixth International Symposium on Micro Machine and Human Science6, 39–43 (1995).
  24. K. Forouhesh Tehrani, and P. Kner, “Point spread function optimization for STORM using adaptive optics,” Proc. SPIE8978, 01–10 (2014).
  25. F.-A. Fortin, F.-M. D. Rainville, M.-A. Gardner, M. Parizeau, and C. Gagné, “DEAP: Evolutionary Algorithms Made Easy,” J. Mach. Learn. Res. 13, 2171–2175 (2012).
  26. L. Shao, P. Kner, E. H. Rego, and M. G. Gustafsson, “Super-resolution 3D microscopy of live whole cells using structured illumination,” Nat. Methods 8(12), 1044–1046 (2011).
    [PubMed]
  27. S. Wolter, M. Schüttpelz, M. Tscherepanow, S. VAN DE Linde, M. Heilemann, and M. Sauer, “Real-time computation of subdiffraction-resolution fluorescence images,” J. Microsc. 237(1), 12–22 (2010).
    [PubMed]
  28. J. Xu, K. F. Tehrani, and P. Kner, “Multicolor 3D Super-resolution Imaging by Quantum Dot Stochastic Optical Reconstruction Microscopy,” ACS Nano 9(3), 2917–2925 (2015).
    [PubMed]
  29. P. Shen and H. N. Cai, “Drosophila neuropeptide F mediates integration of chemosensory stimulation and conditioning of the nervous system by food,” J. Neurobiol. 47(1), 16–25 (2001).
    [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).
    [PubMed]
  31. R. W. Deming, “Phase retrieval from intensity-only data by relative entropy minimization,” J. Opt. Soc. Am. A 24(11), 3666–3679 (2007).
    [PubMed]
  32. J. C. Wyant, “Basic Wavefront Aberration Theory for Optical Metrology,” in Applied Optics and Optical Engineering, R. R. Shannon, and J. C. Wyant, eds. (Academic Press, 1992), pp. 28–39.
  33. P. Kner, L. Winoto, D. A. Agard, and J. W. Sedat, “Closed loop adaptive optics for microscopy without a wavefront sensor,” Proc SPIE Int Soc Opt Eng 7570, 6–9 (2010).
    [PubMed]
  34. 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).
    [PubMed]
  35. R. Hassan, B. Cohanim, O. d. Weck, and G. Venter, “A Comparison of Particle Swarm Optimization and the Genetic Algorithm,” 46th AIAA/ASME/ASCE/AHS/ASC Structures,Structural Dynamics and Materials Conference (2005).
  36. S. Panda and N. P. Padhy, “Comparison of particle swarm optimization and genetic algorithm for FACTS-based controller design,” Appl. Soft Comput. 8, 1418–1427 (2008).
  37. Y. Duan, R. G. Harley, and T. G. Habetler, “Comparison of Particle Swarm Optimization and Genetic Algorithm in the design of permanent magnet motors,” IEEE Power Electronics and Motion Control Conference6, 822–825 (2009).
  38. Q. Li, M. Reinig, D. Kamiyama, B. Huang, X. Tao, A. Bardales, and J. Kubby, “Woofer-tweeter adaptive optical structured illumination microscopy,” Photonics Research 5, 329–334 (2017).
  39. T. W. Wu and M. Cui, “Numerical study of multi-conjugate large area wavefront correction for deep tissue microscopy,” Opt. Express 23(6), 7463–7470 (2015).
    [PubMed]
  40. X. Zhang and P. Kner, “Binary wavefront optimization using a genetic algorithm,” J. Opt. 16, 125704 (2014).
  41. J.-H. Park, L. Kong, Y. Zhou, and M. Cui, “Large-field-of-view imaging by multi-pupil adaptive optics,” Nat. Methods 14(6), 581–583 (2017).
    [PubMed]

2017 (2)

Q. Li, M. Reinig, D. Kamiyama, B. Huang, X. Tao, A. Bardales, and J. Kubby, “Woofer-tweeter adaptive optical structured illumination microscopy,” Photonics Research 5, 329–334 (2017).

J.-H. Park, L. Kong, Y. Zhou, and M. Cui, “Large-field-of-view imaging by multi-pupil adaptive optics,” Nat. Methods 14(6), 581–583 (2017).
[PubMed]

2016 (3)

2015 (5)

2014 (1)

X. Zhang and P. Kner, “Binary wavefront optimization using a genetic algorithm,” J. Opt. 16, 125704 (2014).

2013 (2)

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).
[PubMed]

F. Cella Zanacchi, Z. Lavagnino, M. Faretta, L. Furia, and A. Diaspro, “Light-Sheet Confined Super-Resolution Using Two-Photon Photoactivation,” PLoS One 8(7), e67667 (2013).
[PubMed]

2012 (1)

F.-A. Fortin, F.-M. D. Rainville, M.-A. Gardner, M. Parizeau, and C. Gagné, “DEAP: Evolutionary Algorithms Made Easy,” J. Mach. Learn. Res. 13, 2171–2175 (2012).

2011 (4)

L. Shao, P. Kner, E. H. Rego, and M. G. Gustafsson, “Super-resolution 3D microscopy of live whole cells using structured illumination,” Nat. Methods 8(12), 1044–1046 (2011).
[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).
[PubMed]

F. Cella Zanacchi, Z. Lavagnino, M. Perrone Donnorso, A. Del Bue, L. Furia, M. Faretta, and A. Diaspro, “Live-cell 3D super-resolution imaging in thick biological samples,” Nat. Methods 8(12), 1047–1049 (2011).
[PubMed]

A. G. York, A. Ghitani, A. Vaziri, M. W. Davidson, and H. Shroff, “Confined activation and subdiffractive localization enables whole-cell PALM with genetically expressed probes,” Nat. Methods 8(4), 327–333 (2011).
[PubMed]

2010 (3)

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).
[PubMed]

P. Kner, L. Winoto, D. A. Agard, and J. W. Sedat, “Closed loop adaptive optics for microscopy without a wavefront sensor,” Proc SPIE Int Soc Opt Eng 7570, 6–9 (2010).
[PubMed]

S. Wolter, M. Schüttpelz, M. Tscherepanow, S. VAN DE Linde, M. Heilemann, and M. Sauer, “Real-time computation of subdiffraction-resolution fluorescence images,” J. Microsc. 237(1), 12–22 (2010).
[PubMed]

2009 (1)

2008 (3)

D. Débarre, E. J. Botcherby, M. J. Booth, and T. Wilson, “Adaptive optics for structured illumination microscopy,” Opt. Express 16(13), 9290–9305 (2008).
[PubMed]

B. Huang, S. A. Jones, B. Brandenburg, and X. Zhuang, “Whole-cell 3D STORM reveals interactions between cellular structures with nanometer-scale resolution,” Nat. Methods 5(12), 1047–1052 (2008).
[PubMed]

S. Panda and N. P. Padhy, “Comparison of particle swarm optimization and genetic algorithm for FACTS-based controller design,” Appl. Soft Comput. 8, 1418–1427 (2008).

2007 (3)

2006 (3)

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

M. J. Rust, M. Bates, and X. Zhuang, “Sub-diffraction-limit imaging by stochastic optical reconstruction microscopy (STORM),” Nat. Methods 3(10), 793–795 (2006).
[PubMed]

M. Booth, “Wave front sensor-less adaptive optics: a model-based approach using sphere packings,” Opt. Express 14(4), 1339–1352 (2006).
[PubMed]

2005 (1)

A. J. Wright, D. Burns, B. A. Patterson, S. P. Poland, G. J. Valentine, and J. M. Girkin, “Exploration of the optimisation algorithms used in the implementation of adaptive optics in confocal and multiphoton microscopy,” Microsc. Res. Tech. 67(1), 36–44 (2005).
[PubMed]

2002 (1)

M. J. Booth, M. A. Neil, R. Juskaitis, and T. Wilson, “Adaptive aberration correction in a confocal microscope,” Proc. Natl. Acad. Sci. U.S.A. 99(9), 5788–5792 (2002).
[PubMed]

2001 (1)

P. Shen and H. N. Cai, “Drosophila neuropeptide F mediates integration of chemosensory stimulation and conditioning of the nervous system by food,” J. Neurobiol. 47(1), 16–25 (2001).
[PubMed]

2000 (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).
[PubMed]

P. Kner, L. Winoto, D. A. Agard, and J. W. Sedat, “Closed loop adaptive optics for microscopy without a wavefront sensor,” Proc SPIE Int Soc Opt Eng 7570, 6–9 (2010).
[PubMed]

Albert, O.

Avants, B. B.

W. R. Legant, L. Shao, J. B. Grimm, T. A. Brown, D. E. Milkie, B. B. Avants, L. D. Lavis, and E. Betzig, “High-density three-dimensional localization microscopy across large volumes,” Nat. Methods 13(4), 359–365 (2016).
[PubMed]

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(3), 363–367 (2013).
[PubMed]

Bardales, A.

Q. Li, M. Reinig, D. Kamiyama, B. Huang, X. Tao, A. Bardales, and J. Kubby, “Woofer-tweeter adaptive optical structured illumination microscopy,” Photonics Research 5, 329–334 (2017).

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).
[PubMed]

M. J. Rust, M. Bates, and X. Zhuang, “Sub-diffraction-limit imaging by stochastic optical reconstruction microscopy (STORM),” Nat. Methods 3(10), 793–795 (2006).
[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(3), 363–367 (2013).
[PubMed]

Betzig, E.

W. R. Legant, L. Shao, J. B. Grimm, T. A. Brown, D. E. Milkie, B. B. Avants, L. D. Lavis, and E. Betzig, “High-density three-dimensional localization microscopy across large volumes,” Nat. Methods 13(4), 359–365 (2016).
[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).
[PubMed]

Bewersdorf, J.

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).
[PubMed]

Booth, M.

Booth, M. J.

Botcherby, E. J.

Brandenburg, B.

B. Huang, S. A. Jones, B. Brandenburg, and X. Zhuang, “Whole-cell 3D STORM reveals interactions between cellular structures with nanometer-scale resolution,” Nat. Methods 5(12), 1047–1052 (2008).
[PubMed]

Brown, T. A.

W. R. Legant, L. Shao, J. B. Grimm, T. A. Brown, D. E. Milkie, B. B. Avants, L. D. Lavis, and E. Betzig, “High-density three-dimensional localization microscopy across large volumes,” Nat. Methods 13(4), 359–365 (2016).
[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(3), 363–367 (2013).
[PubMed]

Burke, D.

Burns, D.

A. J. Wright, D. Burns, B. A. Patterson, S. P. Poland, G. J. Valentine, and J. M. Girkin, “Exploration of the optimisation algorithms used in the implementation of adaptive optics in confocal and multiphoton microscopy,” Microsc. Res. Tech. 67(1), 36–44 (2005).
[PubMed]

Cai, H. N.

P. Shen and H. N. Cai, “Drosophila neuropeptide F mediates integration of chemosensory stimulation and conditioning of the nervous system by food,” J. Neurobiol. 47(1), 16–25 (2001).
[PubMed]

Cella Zanacchi, F.

F. Cella Zanacchi, Z. Lavagnino, M. Faretta, L. Furia, and A. Diaspro, “Light-Sheet Confined Super-Resolution Using Two-Photon Photoactivation,” PLoS One 8(7), e67667 (2013).
[PubMed]

F. Cella Zanacchi, Z. Lavagnino, M. Perrone Donnorso, A. Del Bue, L. Furia, M. Faretta, and A. Diaspro, “Live-cell 3D super-resolution imaging in thick biological samples,” Nat. Methods 8(12), 1047–1049 (2011).
[PubMed]

Chaudhari, S. N.

B. Thomas, A. Wolstenholme, S. N. Chaudhari, E. T. Kipreos, and P. Kner, “Enhanced resolution through thick tissue with structured illumination and adaptive optics,” J. Biomed. Opt. 20(2), 26006 (2015).
[PubMed]

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).
[PubMed]

Coles, B. C.

Cui, M.

J.-H. Park, L. Kong, Y. Zhou, and M. Cui, “Large-field-of-view imaging by multi-pupil adaptive optics,” Nat. Methods 14(6), 581–583 (2017).
[PubMed]

T. W. Wu and M. Cui, “Numerical study of multi-conjugate large area wavefront correction for deep tissue microscopy,” Opt. Express 23(6), 7463–7470 (2015).
[PubMed]

Davidson, M. W.

A. G. York, A. Ghitani, A. Vaziri, M. W. Davidson, and H. Shroff, “Confined activation and subdiffractive localization enables whole-cell PALM with genetically expressed probes,” Nat. Methods 8(4), 327–333 (2011).
[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).
[PubMed]

Debarre, D.

Débarre, D.

Del Bue, A.

F. Cella Zanacchi, Z. Lavagnino, M. Perrone Donnorso, A. Del Bue, L. Furia, M. Faretta, and A. Diaspro, “Live-cell 3D super-resolution imaging in thick biological samples,” Nat. Methods 8(12), 1047–1049 (2011).
[PubMed]

Deming, R. W.

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).
[PubMed]

Diaspro, A.

F. Cella Zanacchi, Z. Lavagnino, M. Faretta, L. Furia, and A. Diaspro, “Light-Sheet Confined Super-Resolution Using Two-Photon Photoactivation,” PLoS One 8(7), e67667 (2013).
[PubMed]

F. Cella Zanacchi, Z. Lavagnino, M. Perrone Donnorso, A. Del Bue, L. Furia, M. Faretta, and A. Diaspro, “Live-cell 3D super-resolution imaging in thick biological samples,” Nat. Methods 8(12), 1047–1049 (2011).
[PubMed]

Duan, Y.

Y. Duan, R. G. Harley, and T. G. Habetler, “Comparison of Particle Swarm Optimization and Genetic Algorithm in the design of permanent magnet motors,” IEEE Power Electronics and Motion Control Conference6, 822–825 (2009).

Eberhart, R.

R. Eberhart and J. Kennedy, “A new optimizer using particle swarm theory,” Proceedings of the Sixth International Symposium on Micro Machine and Human Science6, 39–43 (1995).

Edwards, T. L.

Faretta, M.

F. Cella Zanacchi, Z. Lavagnino, M. Faretta, L. Furia, and A. Diaspro, “Light-Sheet Confined Super-Resolution Using Two-Photon Photoactivation,” PLoS One 8(7), e67667 (2013).
[PubMed]

F. Cella Zanacchi, Z. Lavagnino, M. Perrone Donnorso, A. Del Bue, L. Furia, M. Faretta, and A. Diaspro, “Live-cell 3D super-resolution imaging in thick biological samples,” Nat. Methods 8(12), 1047–1049 (2011).
[PubMed]

Finnegan, P. S.

Fortin, F.-A.

F.-A. Fortin, F.-M. D. Rainville, M.-A. Gardner, M. Parizeau, and C. Gagné, “DEAP: Evolutionary Algorithms Made Easy,” J. Mach. Learn. Res. 13, 2171–2175 (2012).

Furia, L.

F. Cella Zanacchi, Z. Lavagnino, M. Faretta, L. Furia, and A. Diaspro, “Light-Sheet Confined Super-Resolution Using Two-Photon Photoactivation,” PLoS One 8(7), e67667 (2013).
[PubMed]

F. Cella Zanacchi, Z. Lavagnino, M. Perrone Donnorso, A. Del Bue, L. Furia, M. Faretta, and A. Diaspro, “Live-cell 3D super-resolution imaging in thick biological samples,” Nat. Methods 8(12), 1047–1049 (2011).
[PubMed]

Gagné, C.

F.-A. Fortin, F.-M. D. Rainville, M.-A. Gardner, M. Parizeau, and C. Gagné, “DEAP: Evolutionary Algorithms Made Easy,” J. Mach. Learn. Res. 13, 2171–2175 (2012).

Gardner, M.-A.

F.-A. Fortin, F.-M. D. Rainville, M.-A. Gardner, M. Parizeau, and C. Gagné, “DEAP: Evolutionary Algorithms Made Easy,” J. Mach. Learn. Res. 13, 2171–2175 (2012).

Ghitani, A.

A. G. York, A. Ghitani, A. Vaziri, M. W. Davidson, and H. Shroff, “Confined activation and subdiffractive localization enables whole-cell PALM with genetically expressed probes,” Nat. Methods 8(4), 327–333 (2011).
[PubMed]

Girkin, J. M.

A. J. Wright, D. Burns, B. A. Patterson, S. P. Poland, G. J. Valentine, and J. M. Girkin, “Exploration of the optimisation algorithms used in the implementation of adaptive optics in confocal and multiphoton microscopy,” Microsc. Res. Tech. 67(1), 36–44 (2005).
[PubMed]

Grimm, J. B.

W. R. Legant, L. Shao, J. B. Grimm, T. A. Brown, D. E. Milkie, B. B. Avants, L. D. Lavis, and E. Betzig, “High-density three-dimensional localization microscopy across large volumes,” Nat. Methods 13(4), 359–365 (2016).
[PubMed]

Gustafsson, M. G.

L. Shao, P. Kner, E. H. Rego, and M. G. Gustafsson, “Super-resolution 3D microscopy of live whole cells using structured illumination,” Nat. Methods 8(12), 1044–1046 (2011).
[PubMed]

Habetler, T. G.

Y. Duan, R. G. Harley, and T. G. Habetler, “Comparison of Particle Swarm Optimization and Genetic Algorithm in the design of permanent magnet motors,” IEEE Power Electronics and Motion Control Conference6, 822–825 (2009).

Harley, R. G.

Y. Duan, R. G. Harley, and T. G. Habetler, “Comparison of Particle Swarm Optimization and Genetic Algorithm in the design of permanent magnet motors,” IEEE Power Electronics and Motion Control Conference6, 822–825 (2009).

Heilemann, M.

S. Wolter, M. Schüttpelz, M. Tscherepanow, S. VAN DE Linde, M. Heilemann, and M. Sauer, “Real-time computation of subdiffraction-resolution fluorescence images,” J. Microsc. 237(1), 12–22 (2010).
[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).
[PubMed]

Huang, B.

Q. Li, M. Reinig, D. Kamiyama, B. Huang, X. Tao, A. Bardales, and J. Kubby, “Woofer-tweeter adaptive optical structured illumination microscopy,” Photonics Research 5, 329–334 (2017).

B. Huang, S. A. Jones, B. Brandenburg, and X. Zhuang, “Whole-cell 3D STORM reveals interactions between cellular structures with nanometer-scale resolution,” Nat. Methods 5(12), 1047–1052 (2008).
[PubMed]

Huang, F.

James, C. D.

Jones, S. A.

B. Huang, S. A. Jones, B. Brandenburg, and X. Zhuang, “Whole-cell 3D STORM reveals interactions between cellular structures with nanometer-scale resolution,” Nat. Methods 5(12), 1047–1052 (2008).
[PubMed]

Juskaitis, R.

M. J. Booth, M. A. Neil, R. Juskaitis, and T. Wilson, “Adaptive aberration correction in a confocal microscope,” Proc. Natl. Acad. Sci. U.S.A. 99(9), 5788–5792 (2002).
[PubMed]

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).
[PubMed]

Kamiyama, D.

Q. Li, M. Reinig, D. Kamiyama, B. Huang, X. Tao, A. Bardales, and J. Kubby, “Woofer-tweeter adaptive optical structured illumination microscopy,” Photonics Research 5, 329–334 (2017).

Kennedy, J.

R. Eberhart and J. Kennedy, “A new optimizer using particle swarm theory,” Proceedings of the Sixth International Symposium on Micro Machine and Human Science6, 39–43 (1995).

Kipreos, E. T.

B. Thomas, A. Wolstenholme, S. N. Chaudhari, E. T. Kipreos, and P. Kner, “Enhanced resolution through thick tissue with structured illumination and adaptive optics,” J. Biomed. Opt. 20(2), 26006 (2015).
[PubMed]

Kner, P.

B. Thomas, A. Wolstenholme, S. N. Chaudhari, E. T. Kipreos, and P. Kner, “Enhanced resolution through thick tissue with structured illumination and adaptive optics,” J. Biomed. Opt. 20(2), 26006 (2015).
[PubMed]

J. Xu, K. F. Tehrani, and P. Kner, “Multicolor 3D Super-resolution Imaging by Quantum Dot Stochastic Optical Reconstruction Microscopy,” ACS Nano 9(3), 2917–2925 (2015).
[PubMed]

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).
[PubMed]

X. Zhang and P. Kner, “Binary wavefront optimization using a genetic algorithm,” J. Opt. 16, 125704 (2014).

L. Shao, P. Kner, E. H. Rego, and M. G. Gustafsson, “Super-resolution 3D microscopy of live whole cells using structured illumination,” Nat. Methods 8(12), 1044–1046 (2011).
[PubMed]

P. Kner, L. Winoto, D. A. Agard, and J. W. Sedat, “Closed loop adaptive optics for microscopy without a wavefront sensor,” Proc SPIE Int Soc Opt Eng 7570, 6–9 (2010).
[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).
[PubMed]

Kong, L.

J.-H. Park, L. Kong, Y. Zhou, and M. Cui, “Large-field-of-view imaging by multi-pupil adaptive optics,” Nat. Methods 14(6), 581–583 (2017).
[PubMed]

Kubby, J.

Q. Li, M. Reinig, D. Kamiyama, B. Huang, X. Tao, A. Bardales, and J. Kubby, “Woofer-tweeter adaptive optical structured illumination microscopy,” Photonics Research 5, 329–334 (2017).

Lavagnino, Z.

F. Cella Zanacchi, Z. Lavagnino, M. Faretta, L. Furia, and A. Diaspro, “Light-Sheet Confined Super-Resolution Using Two-Photon Photoactivation,” PLoS One 8(7), e67667 (2013).
[PubMed]

F. Cella Zanacchi, Z. Lavagnino, M. Perrone Donnorso, A. Del Bue, L. Furia, M. Faretta, and A. Diaspro, “Live-cell 3D super-resolution imaging in thick biological samples,” Nat. Methods 8(12), 1047–1049 (2011).
[PubMed]

Lavis, L. D.

W. R. Legant, L. Shao, J. B. Grimm, T. A. Brown, D. E. Milkie, B. B. Avants, L. D. Lavis, and E. Betzig, “High-density three-dimensional localization microscopy across large volumes,” Nat. Methods 13(4), 359–365 (2016).
[PubMed]

Legant, W. R.

W. R. Legant, L. Shao, J. B. Grimm, T. A. Brown, D. E. Milkie, B. B. Avants, L. D. Lavis, and E. Betzig, “High-density three-dimensional localization microscopy across large volumes,” Nat. Methods 13(4), 359–365 (2016).
[PubMed]

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(3), 363–367 (2013).
[PubMed]

Li, Q.

Q. Li, M. Reinig, D. Kamiyama, B. Huang, X. Tao, A. Bardales, and J. Kubby, “Woofer-tweeter adaptive optical structured illumination microscopy,” Photonics Research 5, 329–334 (2017).

Lidke, K. A.

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).
[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).
[PubMed]

Liu, S.

Lo Schiavo, V.

Martin-Fernandez, M.

Meddens, M. B. M.

Milkie, D. E.

W. R. Legant, L. Shao, J. B. Grimm, T. A. Brown, D. E. Milkie, B. B. Avants, L. D. Lavis, and E. Betzig, “High-density three-dimensional localization microscopy across large volumes,” Nat. Methods 13(4), 359–365 (2016).
[PubMed]

Mourou, G.

Neil, M. A.

M. J. Booth, M. A. Neil, R. Juskaitis, and T. Wilson, “Adaptive aberration correction in a confocal microscope,” Proc. Natl. Acad. Sci. U.S.A. 99(9), 5788–5792 (2002).
[PubMed]

Norris, T. B.

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).
[PubMed]

Padhy, N. P.

S. Panda and N. P. Padhy, “Comparison of particle swarm optimization and genetic algorithm for FACTS-based controller design,” Appl. Soft Comput. 8, 1418–1427 (2008).

Panda, S.

S. Panda and N. P. Padhy, “Comparison of particle swarm optimization and genetic algorithm for FACTS-based controller design,” Appl. Soft Comput. 8, 1418–1427 (2008).

Parizeau, M.

F.-A. Fortin, F.-M. D. Rainville, M.-A. Gardner, M. Parizeau, and C. Gagné, “DEAP: Evolutionary Algorithms Made Easy,” J. Mach. Learn. Res. 13, 2171–2175 (2012).

Park, J.-H.

J.-H. Park, L. Kong, Y. Zhou, and M. Cui, “Large-field-of-view imaging by multi-pupil adaptive optics,” Nat. Methods 14(6), 581–583 (2017).
[PubMed]

Patterson, B. A.

A. J. Wright, D. Burns, B. A. Patterson, S. P. Poland, G. J. Valentine, and J. M. Girkin, “Exploration of the optimisation algorithms used in the implementation of adaptive optics in confocal and multiphoton microscopy,” Microsc. Res. Tech. 67(1), 36–44 (2005).
[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).
[PubMed]

Patton, B.

Perrone Donnorso, M.

F. Cella Zanacchi, Z. Lavagnino, M. Perrone Donnorso, A. Del Bue, L. Furia, M. Faretta, and A. Diaspro, “Live-cell 3D super-resolution imaging in thick biological samples,” Nat. Methods 8(12), 1047–1049 (2011).
[PubMed]

Poland, S. P.

A. J. Wright, D. Burns, B. A. Patterson, S. P. Poland, G. J. Valentine, and J. M. Girkin, “Exploration of the optimisation algorithms used in the implementation of adaptive optics in confocal and multiphoton microscopy,” Microsc. Res. Tech. 67(1), 36–44 (2005).
[PubMed]

Rainville, F.-M. D.

F.-A. Fortin, F.-M. D. Rainville, M.-A. Gardner, M. Parizeau, and C. Gagné, “DEAP: Evolutionary Algorithms Made Easy,” J. Mach. Learn. Res. 13, 2171–2175 (2012).

Rego, E. H.

L. Shao, P. Kner, E. H. Rego, and M. G. Gustafsson, “Super-resolution 3D microscopy of live whole cells using structured illumination,” Nat. Methods 8(12), 1044–1046 (2011).
[PubMed]

Reinig, M.

Q. Li, M. Reinig, D. Kamiyama, B. Huang, X. Tao, A. Bardales, and J. Kubby, “Woofer-tweeter adaptive optical structured illumination microscopy,” Photonics Research 5, 329–334 (2017).

Rolfe, D. J.

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), 793–795 (2006).
[PubMed]

Sauer, M.

S. Wolter, M. Schüttpelz, M. Tscherepanow, S. VAN DE Linde, M. Heilemann, and M. Sauer, “Real-time computation of subdiffraction-resolution fluorescence images,” J. Microsc. 237(1), 12–22 (2010).
[PubMed]

Schüttpelz, M.

S. Wolter, M. Schüttpelz, M. Tscherepanow, S. VAN DE Linde, M. Heilemann, and M. Sauer, “Real-time computation of subdiffraction-resolution fluorescence images,” J. Microsc. 237(1), 12–22 (2010).
[PubMed]

Schwartz, N.

Sedat, J. W.

P. Kner, L. Winoto, D. A. Agard, and J. W. Sedat, “Closed loop adaptive optics for microscopy without a wavefront sensor,” Proc SPIE Int Soc Opt Eng 7570, 6–9 (2010).
[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).
[PubMed]

Shao, L.

W. R. Legant, L. Shao, J. B. Grimm, T. A. Brown, D. E. Milkie, B. B. Avants, L. D. Lavis, and E. Betzig, “High-density three-dimensional localization microscopy across large volumes,” Nat. Methods 13(4), 359–365 (2016).
[PubMed]

L. Shao, P. Kner, E. H. Rego, and M. G. Gustafsson, “Super-resolution 3D microscopy of live whole cells using structured illumination,” Nat. Methods 8(12), 1044–1046 (2011).
[PubMed]

Shen, 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).
[PubMed]

P. Shen and H. N. Cai, “Drosophila neuropeptide F mediates integration of chemosensory stimulation and conditioning of the nervous system by food,” J. Neurobiol. 47(1), 16–25 (2001).
[PubMed]

Sherman, L.

Shroff, H.

A. G. York, A. Ghitani, A. Vaziri, M. W. Davidson, and H. Shroff, “Confined activation and subdiffractive localization enables whole-cell PALM with genetically expressed probes,” Nat. Methods 8(4), 327–333 (2011).
[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(5793), 1642–1645 (2006).
[PubMed]

Srinivas, S.

Tao, X.

Q. Li, M. Reinig, D. Kamiyama, B. Huang, X. Tao, A. Bardales, and J. Kubby, “Woofer-tweeter adaptive optical structured illumination microscopy,” Photonics Research 5, 329–334 (2017).

Tehrani, K. F.

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).
[PubMed]

J. Xu, K. F. Tehrani, and P. Kner, “Multicolor 3D Super-resolution Imaging by Quantum Dot Stochastic Optical Reconstruction Microscopy,” ACS Nano 9(3), 2917–2925 (2015).
[PubMed]

Thomas, B.

B. Thomas, A. Wolstenholme, S. N. Chaudhari, E. T. Kipreos, and P. Kner, “Enhanced resolution through thick tissue with structured illumination and adaptive optics,” J. Biomed. Opt. 20(2), 26006 (2015).
[PubMed]

Tscherepanow, M.

S. Wolter, M. Schüttpelz, M. Tscherepanow, S. VAN DE Linde, M. Heilemann, and M. Sauer, “Real-time computation of subdiffraction-resolution fluorescence images,” J. Microsc. 237(1), 12–22 (2010).
[PubMed]

Valentine, G. J.

A. J. Wright, D. Burns, B. A. Patterson, S. P. Poland, G. J. Valentine, and J. M. Girkin, “Exploration of the optimisation algorithms used in the implementation of adaptive optics in confocal and multiphoton microscopy,” Microsc. Res. Tech. 67(1), 36–44 (2005).
[PubMed]

VAN DE Linde, S.

S. Wolter, M. Schüttpelz, M. Tscherepanow, S. VAN DE Linde, M. Heilemann, and M. Sauer, “Real-time computation of subdiffraction-resolution fluorescence images,” J. Microsc. 237(1), 12–22 (2010).
[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).
[PubMed]

Vaziri, A.

A. G. York, A. Ghitani, A. Vaziri, M. W. Davidson, and H. Shroff, “Confined activation and subdiffractive localization enables whole-cell PALM with genetically expressed probes,” Nat. Methods 8(4), 327–333 (2011).
[PubMed]

Vdovin, G.

Watanabe, T.

Webb, S. E. D.

Wilson, T.

Winoto, L.

P. Kner, L. Winoto, D. A. Agard, and J. W. Sedat, “Closed loop adaptive optics for microscopy without a wavefront sensor,” Proc SPIE Int Soc Opt Eng 7570, 6–9 (2010).
[PubMed]

Wolstenholme, A.

B. Thomas, A. Wolstenholme, S. N. Chaudhari, E. T. Kipreos, and P. Kner, “Enhanced resolution through thick tissue with structured illumination and adaptive optics,” J. Biomed. Opt. 20(2), 26006 (2015).
[PubMed]

Wolter, S.

S. Wolter, M. Schüttpelz, M. Tscherepanow, S. VAN DE Linde, M. Heilemann, and M. Sauer, “Real-time computation of subdiffraction-resolution fluorescence images,” J. Microsc. 237(1), 12–22 (2010).
[PubMed]

Wright, A. J.

A. J. Wright, D. Burns, B. A. Patterson, S. P. Poland, G. J. Valentine, and J. M. Girkin, “Exploration of the optimisation algorithms used in the implementation of adaptive optics in confocal and multiphoton microscopy,” Microsc. Res. Tech. 67(1), 36–44 (2005).
[PubMed]

Wu, T. W.

Xu, J.

J. Xu, K. F. Tehrani, and P. Kner, “Multicolor 3D Super-resolution Imaging by Quantum Dot Stochastic Optical Reconstruction Microscopy,” ACS Nano 9(3), 2917–2925 (2015).
[PubMed]

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).
[PubMed]

York, A. G.

A. G. York, A. Ghitani, A. Vaziri, M. W. Davidson, and H. Shroff, “Confined activation and subdiffractive localization enables whole-cell PALM with genetically expressed probes,” Nat. Methods 8(4), 327–333 (2011).
[PubMed]

Zhang, X.

X. Zhang and P. Kner, “Binary wavefront optimization using a genetic algorithm,” J. Opt. 16, 125704 (2014).

Zhang, Y.

Zhou, Y.

J.-H. Park, L. Kong, Y. Zhou, and M. Cui, “Large-field-of-view imaging by multi-pupil adaptive optics,” Nat. Methods 14(6), 581–583 (2017).
[PubMed]

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).
[PubMed]

B. Huang, S. A. Jones, B. Brandenburg, and X. Zhuang, “Whole-cell 3D STORM reveals interactions between cellular structures with nanometer-scale resolution,” Nat. Methods 5(12), 1047–1052 (2008).
[PubMed]

M. J. Rust, M. Bates, and X. Zhuang, “Sub-diffraction-limit imaging by stochastic optical reconstruction microscopy (STORM),” Nat. Methods 3(10), 793–795 (2006).
[PubMed]

ACS Nano (1)

J. Xu, K. F. Tehrani, and P. Kner, “Multicolor 3D Super-resolution Imaging by Quantum Dot Stochastic Optical Reconstruction Microscopy,” ACS Nano 9(3), 2917–2925 (2015).
[PubMed]

Appl. Soft Comput. (1)

S. Panda and N. P. Padhy, “Comparison of particle swarm optimization and genetic algorithm for FACTS-based controller design,” Appl. Soft Comput. 8, 1418–1427 (2008).

Biomed. Opt. Express (2)

J. Biomed. Opt. (1)

B. Thomas, A. Wolstenholme, S. N. Chaudhari, E. T. Kipreos, and P. Kner, “Enhanced resolution through thick tissue with structured illumination and adaptive optics,” J. Biomed. Opt. 20(2), 26006 (2015).
[PubMed]

J. Mach. Learn. Res. (1)

F.-A. Fortin, F.-M. D. Rainville, M.-A. Gardner, M. Parizeau, and C. Gagné, “DEAP: Evolutionary Algorithms Made Easy,” J. Mach. Learn. Res. 13, 2171–2175 (2012).

J. Microsc. (2)

S. Wolter, M. Schüttpelz, M. Tscherepanow, S. VAN DE Linde, M. Heilemann, and M. Sauer, “Real-time computation of subdiffraction-resolution fluorescence images,” J. Microsc. 237(1), 12–22 (2010).
[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).
[PubMed]

J. Neurobiol. (1)

P. Shen and H. N. Cai, “Drosophila neuropeptide F mediates integration of chemosensory stimulation and conditioning of the nervous system by food,” J. Neurobiol. 47(1), 16–25 (2001).
[PubMed]

J. Opt. (1)

X. Zhang and P. Kner, “Binary wavefront optimization using a genetic algorithm,” J. Opt. 16, 125704 (2014).

J. Opt. Soc. Am. A (1)

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(3), 363–367 (2013).
[PubMed]

Microsc. Res. Tech. (1)

A. J. Wright, D. Burns, B. A. Patterson, S. P. Poland, G. J. Valentine, and J. M. Girkin, “Exploration of the optimisation algorithms used in the implementation of adaptive optics in confocal and multiphoton microscopy,” Microsc. Res. Tech. 67(1), 36–44 (2005).
[PubMed]

Nat. Methods (8)

L. Shao, P. Kner, E. H. Rego, and M. G. Gustafsson, “Super-resolution 3D microscopy of live whole cells using structured illumination,” Nat. Methods 8(12), 1044–1046 (2011).
[PubMed]

W. R. Legant, L. Shao, J. B. Grimm, T. A. Brown, D. E. Milkie, B. B. Avants, L. D. Lavis, and E. Betzig, “High-density three-dimensional localization microscopy across large volumes,” Nat. Methods 13(4), 359–365 (2016).
[PubMed]

M. J. Rust, M. Bates, and X. Zhuang, “Sub-diffraction-limit imaging by stochastic optical reconstruction microscopy (STORM),” Nat. Methods 3(10), 793–795 (2006).
[PubMed]

A. G. York, A. Ghitani, A. Vaziri, M. W. Davidson, and H. Shroff, “Confined activation and subdiffractive localization enables whole-cell PALM with genetically expressed probes,” Nat. Methods 8(4), 327–333 (2011).
[PubMed]

B. Huang, S. A. Jones, B. Brandenburg, and X. Zhuang, “Whole-cell 3D STORM reveals interactions between cellular structures with nanometer-scale resolution,” Nat. Methods 5(12), 1047–1052 (2008).
[PubMed]

F. Cella Zanacchi, Z. Lavagnino, M. Perrone Donnorso, A. Del Bue, L. Furia, M. Faretta, and A. Diaspro, “Live-cell 3D super-resolution imaging in thick biological samples,” Nat. Methods 8(12), 1047–1049 (2011).
[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).
[PubMed]

J.-H. Park, L. Kong, Y. Zhou, and M. Cui, “Large-field-of-view imaging by multi-pupil adaptive optics,” Nat. Methods 14(6), 581–583 (2017).
[PubMed]

Opt. Express (5)

Opt. Lett. (3)

Optica (1)

Photonics Research (1)

Q. Li, M. Reinig, D. Kamiyama, B. Huang, X. Tao, A. Bardales, and J. Kubby, “Woofer-tweeter adaptive optical structured illumination microscopy,” Photonics Research 5, 329–334 (2017).

PLoS One (1)

F. Cella Zanacchi, Z. Lavagnino, M. Faretta, L. Furia, and A. Diaspro, “Light-Sheet Confined Super-Resolution Using Two-Photon Photoactivation,” PLoS One 8(7), e67667 (2013).
[PubMed]

Proc SPIE Int Soc Opt Eng (1)

P. Kner, L. Winoto, D. A. Agard, and J. W. Sedat, “Closed loop adaptive optics for microscopy without a wavefront sensor,” Proc SPIE Int Soc Opt Eng 7570, 6–9 (2010).
[PubMed]

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

M. J. Booth, M. A. Neil, R. Juskaitis, and T. Wilson, “Adaptive aberration correction in a confocal microscope,” Proc. Natl. Acad. Sci. U.S.A. 99(9), 5788–5792 (2002).
[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(5793), 1642–1645 (2006).
[PubMed]

Other (6)

R. Eberhart and J. Kennedy, “A new optimizer using particle swarm theory,” Proceedings of the Sixth International Symposium on Micro Machine and Human Science6, 39–43 (1995).

K. Forouhesh Tehrani, and P. Kner, “Point spread function optimization for STORM using adaptive optics,” Proc. SPIE8978, 01–10 (2014).

J. A. Kubby, ed., Adaptive Optics for Biological Imaging (CRC Press, New York, NY, 2013).

J. C. Wyant, “Basic Wavefront Aberration Theory for Optical Metrology,” in Applied Optics and Optical Engineering, R. R. Shannon, and J. C. Wyant, eds. (Academic Press, 1992), pp. 28–39.

R. Hassan, B. Cohanim, O. d. Weck, and G. Venter, “A Comparison of Particle Swarm Optimization and the Genetic Algorithm,” 46th AIAA/ASME/ASCE/AHS/ASC Structures,Structural Dynamics and Materials Conference (2005).

Y. Duan, R. G. Harley, and T. G. Habetler, “Comparison of Particle Swarm Optimization and Genetic Algorithm in the design of permanent magnet motors,” IEEE Power Electronics and Motion Control Conference6, 822–825 (2009).

Supplementary Material (1)

NameDescription
» Visualization 1       PSO-AO correction on a single 200nm yellow-green fluorescent microsphere. The experiment was performed with particles placed in the position range from -5 to 5 radians. The velocity range was -0.5 to 0.5. The population size was 50 and the optimizati

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Figures (7)

Fig. 1
Fig. 1 A demonstration of Particle Swarm Optimization in a 2 dimensional space. The red particles are searching for the minimum of the surface. (a-c) show early, mid, and late stages of the convergence.
Fig. 2
Fig. 2 Simulation of AO-STORM using PSO for correction of random wavefront aberrations. (a) shows a graph of the metric values and rms wavefront error plotted against the generation. (b-e) show individual frames at generations 0, 13, 41, and 51 respectively. (f) is the reconstructed image from 2000 frames after convergence of the algorithm. Scale bars for are 1 μm for (b-e) and 200 nm for (f).
Fig. 3
Fig. 3 - Diagram of the microscope. L1: 350mm efl achromat. L2: 350mm efl achromat. L3: 100mm efl achromat. L4: 300mm efl achromat. L5 and L6: 7.86 mm. DiM1: multiband dichroic mirror. DiM2: 550 nm long pass.
Fig. 4
Fig. 4 PSO-AO correction on a single fluorescent microsphere. (a) PSF before correction. (b) The final frame of the optimization showing the corrected PSF. (c) Zernike coefficients of the correction (Noll ordering). The experiment was performed with particles placed in the position range from −5 to 5 radians. The velocity range was −0.5 to 0.5. The population size was 50. Values of r 1 and r 2 were both 2.0. Sigma for the metric was 0.1 μm−1. The exposure time was 50 ms. A 470 nm LED was used for illumination. Scale bars are 1 µm. A video of this process is shown in supplemental Visualization 1.
Fig. 5
Fig. 5 200nm YG beads under a C. elegans roundworm. The ROI used for correction is shown as a box in (a) and (b). The aberrated image is shown in (a). The bead images under the worm are distorted. After correction, the bead images under the worm are corrected as shown in (b). (a) and (b) are shown using the same intensity scale. We can see the increase in intensity under the center of the worm in (b). (c) shows the coefficients of the Zernike modes applied to the wavefront by the PSO algorithm (Noll ordering). Scale bars are 5 µm.
Fig. 6
Fig. 6 Correction of aberrations caused by the nucleus of a Hela cell. (a) shows a widefield image of microtubules labeled with 565nm Quantum Dots before correction. The correction ROI is shown in the white box. In (b), an average of all frames from the STORM data set after AO correction is shown. (c) shows the final STORM image, reconstructed using the frames after correction. (d) shows the coefficients of the Zernike modes applied to the wavefront. (e) The cross-section of a microtubule specified with an arrow in (c), shows a FWHM of 32 nm. Scale bars are 2 µm.
Fig. 7
Fig. 7 PSO-AO-STORM microscopy applied to a Bouton in the ventral nerve cord of the Drosophila larva. A system-corrected widefield image before PSO-AO is shown in (a). After correction widefield image (b) is generated by averaging all the frames in the STORM data set. (c) shows the PSO-AO- STORM image reconstructed using 10,000 frames after convergence of the algorithm. (d) shows the coefficients of the Zernike modes. Scale bars are 2 µm.

Equations (3)

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v ¯ i ( t+1 )= v ¯ i ( t )+ r 1 ( p ¯ i best p ¯ i ( t ) )+ r 2 ( p ¯ g best p ¯ i ( t ) )
p ¯ i ( t+1 )= p ¯ i ( t )+ v ¯ i ( t )
Δx= s N 1 p + 4 π sdx(1p) p 2 A

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