Abstract

Localization-based super resolution microscopy holds superior performances in live cell imaging, but its widespread use is thus far mainly hindered by the slow image analysis speed. Here we show a powerful image analysis method based on the combination of the maximum likelihood algorithm and a Graphics Processing Unit (GPU). Results indicate that our method is fast enough for real-time processing of experimental images even from fast EMCCD cameras working at full frame rate without compromising localization precision or field of view. This newly developed method is also capable of revealing movements from the images immediately after data acquisition, which is of great benefit to live cell imaging.

© 2010 OSA

Full Article  |  PDF Article

References

  • View by:
  • |
  • |
  • |

  1. J. Lippincott-Schwartz and G. H. Patterson, “Development and use of fluorescent protein markers in living cells,” Science 300(5616), 87–91 (2003).
    [CrossRef] [PubMed]
  2. D. J. Stephens and V. J. Allan, “Light microscopy techniques for live cell imaging,” Science 300(5616), 82–86 (2003).
    [CrossRef] [PubMed]
  3. B. Huang, M. Bates, and X. W. Zhuang, “Super-resolution fluorescence microscopy,” Annu. Rev. Biochem. 78(1), 993–1016 (2009).
    [CrossRef] [PubMed]
  4. S. W. Hell, “Far-field optical nanoscopy,” Science 316(5828), 1153–1158 (2007).
    [CrossRef] [PubMed]
  5. H. Shroff, C. G. Galbraith, J. A. Galbraith, and E. Betzig, “Live-cell photoactivated localization microscopy of nanoscale adhesion dynamics,” Nat. Methods 5(5), 417–423 (2008).
    [CrossRef] [PubMed]
  6. T. J. Gould, V. V. Verkhusha, and S. T. Hess, “Imaging biological structures with fluorescence photoactivation localization microscopy,” Nat. Protoc. 4(3), 291–308 (2009).
    [CrossRef] [PubMed]
  7. P. N. Hedde, J. Fuchs, F. Oswald, J. Wiedenmann, and G. U. Nienhaus, “Online image analysis software for photoactivation localization microscopy,” Nat. Methods 6(10), 689–690 (2009).
    [CrossRef] [PubMed]
  8. S. B. Andersson, “Localization of a fluorescent source without numerical fitting,” Opt. Express 16(23), 18714–18724 (2008).
    [CrossRef]
  9. B. A. Wilt, L. D. Burns, E. T. Wei Ho, K. K. Ghosh, E. A. Mukamel, and M. J. Schnitzer, “Advances in light microscopy for neuroscience,” Annu. Rev. Neurosci. 32(1), 435–506 (2009).
    [CrossRef] [PubMed]
  10. S. A. McKinney, C. S. Murphy, K. L. Hazelwood, M. W. Davidson, and L. L. Looger, “A bright and photostable photoconvertible fluorescent protein,” Nat. Methods 6(2), 131–133 (2009).
    [CrossRef] [PubMed]
  11. J. D. Owens, D. Luebke, N. Govindaraju, M. Harris, J. Kruger, A. E. Lefohn, and T. J. Purcell, “A survey of general-purpose computation on graphics hardware,” Comput. Graph. Forum 26(1), 80–113 (2007).
    [CrossRef]
  12. G. Quan, T. Sun, and Y. Deng, “Fast reconstruction method based on common unified device architecture (CUDA) for micro-CT,” J. Innovative Opt. Health Sci. 3(1), 39–43 (2010).
    [CrossRef]
  13. C. von Middendorff, A. Egner, C. Geisler, S. W. Hell, and A. Schönle, “Isotropic 3D Nanoscopy based on single emitter switching,” Opt. Express 16(25), 20774–20788 (2008).
    [CrossRef] [PubMed]
  14. R. J. Ober, S. Ram, and E. S. Ward, “Localization accuracy in single-molecule microscopy,” Biophys. J. 86(2), 1185–1200 (2004).
    [CrossRef] [PubMed]
  15. P. H. Calamai and J. J. More, “Projected gradient methods for linearly constrained problems,” Math. Program. 39(1), 93–116 (1987).
    [CrossRef]
  16. D. Q. Mayne and E. Polak, “Feasible directions algorithm for optimization problems with equality and inequality constrains,” Math. Program. 11(1), 67–80 (1976).
    [CrossRef]
  17. A. R. Small, “Theoretical limits on errors and acquisition rates in localizing switchable fluorophores,” Biophys. J. 96(2), L16–L18 (2009).
    [CrossRef] [PubMed]
  18. 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]
  19. http://www.andor.com/scientific_cameras/ixon .
  20. 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]
  21. 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]
  22. M. J. Rust, M. Bates, and X. W. Zhuang, “Sub-diffraction-limit imaging by stochastic optical reconstruction microscopy (STORM),” Nat. Methods 3(10), 793–796 (2006).
    [CrossRef] [PubMed]

2010

G. Quan, T. Sun, and Y. Deng, “Fast reconstruction method based on common unified device architecture (CUDA) for micro-CT,” J. Innovative Opt. Health Sci. 3(1), 39–43 (2010).
[CrossRef]

2009

A. R. Small, “Theoretical limits on errors and acquisition rates in localizing switchable fluorophores,” Biophys. J. 96(2), L16–L18 (2009).
[CrossRef] [PubMed]

B. Huang, M. Bates, and X. W. Zhuang, “Super-resolution fluorescence microscopy,” Annu. Rev. Biochem. 78(1), 993–1016 (2009).
[CrossRef] [PubMed]

T. J. Gould, V. V. Verkhusha, and S. T. Hess, “Imaging biological structures with fluorescence photoactivation localization microscopy,” Nat. Protoc. 4(3), 291–308 (2009).
[CrossRef] [PubMed]

P. N. Hedde, J. Fuchs, F. Oswald, J. Wiedenmann, and G. U. Nienhaus, “Online image analysis software for photoactivation localization microscopy,” Nat. Methods 6(10), 689–690 (2009).
[CrossRef] [PubMed]

B. A. Wilt, L. D. Burns, E. T. Wei Ho, K. K. Ghosh, E. A. Mukamel, and M. J. Schnitzer, “Advances in light microscopy for neuroscience,” Annu. Rev. Neurosci. 32(1), 435–506 (2009).
[CrossRef] [PubMed]

S. A. McKinney, C. S. Murphy, K. L. Hazelwood, M. W. Davidson, and L. L. Looger, “A bright and photostable photoconvertible fluorescent protein,” Nat. Methods 6(2), 131–133 (2009).
[CrossRef] [PubMed]

2008

2007

J. D. Owens, D. Luebke, N. Govindaraju, M. Harris, J. Kruger, A. E. Lefohn, and T. J. Purcell, “A survey of general-purpose computation on graphics hardware,” Comput. Graph. Forum 26(1), 80–113 (2007).
[CrossRef]

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

2006

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]

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. W. Zhuang, “Sub-diffraction-limit imaging by stochastic optical reconstruction microscopy (STORM),” Nat. Methods 3(10), 793–796 (2006).
[CrossRef] [PubMed]

2004

R. J. Ober, S. Ram, and E. S. Ward, “Localization accuracy in single-molecule microscopy,” Biophys. J. 86(2), 1185–1200 (2004).
[CrossRef] [PubMed]

2003

J. Lippincott-Schwartz and G. H. Patterson, “Development and use of fluorescent protein markers in living cells,” Science 300(5616), 87–91 (2003).
[CrossRef] [PubMed]

D. J. Stephens and V. J. Allan, “Light microscopy techniques for live cell imaging,” Science 300(5616), 82–86 (2003).
[CrossRef] [PubMed]

2002

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]

1987

P. H. Calamai and J. J. More, “Projected gradient methods for linearly constrained problems,” Math. Program. 39(1), 93–116 (1987).
[CrossRef]

1976

D. Q. Mayne and E. Polak, “Feasible directions algorithm for optimization problems with equality and inequality constrains,” Math. Program. 11(1), 67–80 (1976).
[CrossRef]

Allan, V. J.

D. J. Stephens and V. J. Allan, “Light microscopy techniques for live cell imaging,” Science 300(5616), 82–86 (2003).
[CrossRef] [PubMed]

Andersson, S. B.

Bates, M.

B. Huang, M. Bates, and X. W. Zhuang, “Super-resolution fluorescence microscopy,” Annu. Rev. Biochem. 78(1), 993–1016 (2009).
[CrossRef] [PubMed]

M. J. Rust, M. Bates, and X. W. Zhuang, “Sub-diffraction-limit imaging by stochastic optical reconstruction microscopy (STORM),” Nat. Methods 3(10), 793–796 (2006).
[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(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(5793), 1642–1645 (2006).
[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(5793), 1642–1645 (2006).
[CrossRef] [PubMed]

Burns, L. D.

B. A. Wilt, L. D. Burns, E. T. Wei Ho, K. K. Ghosh, E. A. Mukamel, and M. J. Schnitzer, “Advances in light microscopy for neuroscience,” Annu. Rev. Neurosci. 32(1), 435–506 (2009).
[CrossRef] [PubMed]

Calamai, P. H.

P. H. Calamai and J. J. More, “Projected gradient methods for linearly constrained problems,” Math. Program. 39(1), 93–116 (1987).
[CrossRef]

Davidson, M. W.

S. A. McKinney, C. S. Murphy, K. L. Hazelwood, M. W. Davidson, and L. L. Looger, “A bright and photostable photoconvertible fluorescent protein,” Nat. Methods 6(2), 131–133 (2009).
[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]

Deng, Y.

G. Quan, T. Sun, and Y. Deng, “Fast reconstruction method based on common unified device architecture (CUDA) for micro-CT,” J. Innovative Opt. Health Sci. 3(1), 39–43 (2010).
[CrossRef]

Egner, A.

Fuchs, J.

P. N. Hedde, J. Fuchs, F. Oswald, J. Wiedenmann, and G. U. Nienhaus, “Online image analysis software for photoactivation localization microscopy,” Nat. Methods 6(10), 689–690 (2009).
[CrossRef] [PubMed]

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(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(5), 417–423 (2008).
[CrossRef] [PubMed]

Geisler, C.

Ghosh, K. K.

B. A. Wilt, L. D. Burns, E. T. Wei Ho, K. K. Ghosh, E. A. Mukamel, and M. J. Schnitzer, “Advances in light microscopy for neuroscience,” Annu. Rev. Neurosci. 32(1), 435–506 (2009).
[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.

T. J. Gould, V. V. Verkhusha, and S. T. Hess, “Imaging biological structures with fluorescence photoactivation localization microscopy,” Nat. Protoc. 4(3), 291–308 (2009).
[CrossRef] [PubMed]

Govindaraju, N.

J. D. Owens, D. Luebke, N. Govindaraju, M. Harris, J. Kruger, A. E. Lefohn, and T. J. Purcell, “A survey of general-purpose computation on graphics hardware,” Comput. Graph. Forum 26(1), 80–113 (2007).
[CrossRef]

Harris, M.

J. D. Owens, D. Luebke, N. Govindaraju, M. Harris, J. Kruger, A. E. Lefohn, and T. J. Purcell, “A survey of general-purpose computation on graphics hardware,” Comput. Graph. Forum 26(1), 80–113 (2007).
[CrossRef]

Hazelwood, K. L.

S. A. McKinney, C. S. Murphy, K. L. Hazelwood, M. W. Davidson, and L. L. Looger, “A bright and photostable photoconvertible fluorescent protein,” Nat. Methods 6(2), 131–133 (2009).
[CrossRef] [PubMed]

Hedde, P. N.

P. N. Hedde, J. Fuchs, F. Oswald, J. Wiedenmann, and G. U. Nienhaus, “Online image analysis software for photoactivation localization microscopy,” Nat. Methods 6(10), 689–690 (2009).
[CrossRef] [PubMed]

Hell, S. W.

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.

T. J. Gould, V. V. Verkhusha, and S. T. Hess, “Imaging biological structures with fluorescence photoactivation localization microscopy,” Nat. Protoc. 4(3), 291–308 (2009).
[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]

Huang, B.

B. Huang, M. Bates, and X. W. Zhuang, “Super-resolution fluorescence microscopy,” Annu. Rev. Biochem. 78(1), 993–1016 (2009).
[CrossRef] [PubMed]

Kruger, J.

J. D. Owens, D. Luebke, N. Govindaraju, M. Harris, J. Kruger, A. E. Lefohn, and T. J. Purcell, “A survey of general-purpose computation on graphics hardware,” Comput. Graph. Forum 26(1), 80–113 (2007).
[CrossRef]

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]

Lefohn, A. E.

J. D. Owens, D. Luebke, N. Govindaraju, M. Harris, J. Kruger, A. E. Lefohn, and T. J. Purcell, “A survey of general-purpose computation on graphics hardware,” Comput. Graph. Forum 26(1), 80–113 (2007).
[CrossRef]

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]

J. Lippincott-Schwartz and G. H. Patterson, “Development and use of fluorescent protein markers in living cells,” Science 300(5616), 87–91 (2003).
[CrossRef] [PubMed]

Looger, L. L.

S. A. McKinney, C. S. Murphy, K. L. Hazelwood, M. W. Davidson, and L. L. Looger, “A bright and photostable photoconvertible fluorescent protein,” Nat. Methods 6(2), 131–133 (2009).
[CrossRef] [PubMed]

Luebke, D.

J. D. Owens, D. Luebke, N. Govindaraju, M. Harris, J. Kruger, A. E. Lefohn, and T. J. Purcell, “A survey of general-purpose computation on graphics hardware,” Comput. Graph. Forum 26(1), 80–113 (2007).
[CrossRef]

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]

Mayne, D. Q.

D. Q. Mayne and E. Polak, “Feasible directions algorithm for optimization problems with equality and inequality constrains,” Math. Program. 11(1), 67–80 (1976).
[CrossRef]

McKinney, S. A.

S. A. McKinney, C. S. Murphy, K. L. Hazelwood, M. W. Davidson, and L. L. Looger, “A bright and photostable photoconvertible fluorescent protein,” Nat. Methods 6(2), 131–133 (2009).
[CrossRef] [PubMed]

More, J. J.

P. H. Calamai and J. J. More, “Projected gradient methods for linearly constrained problems,” Math. Program. 39(1), 93–116 (1987).
[CrossRef]

Mukamel, E. A.

B. A. Wilt, L. D. Burns, E. T. Wei Ho, K. K. Ghosh, E. A. Mukamel, and M. J. Schnitzer, “Advances in light microscopy for neuroscience,” Annu. Rev. Neurosci. 32(1), 435–506 (2009).
[CrossRef] [PubMed]

Murphy, C. S.

S. A. McKinney, C. S. Murphy, K. L. Hazelwood, M. W. Davidson, and L. L. Looger, “A bright and photostable photoconvertible fluorescent protein,” Nat. Methods 6(2), 131–133 (2009).
[CrossRef] [PubMed]

Nienhaus, G. U.

P. N. Hedde, J. Fuchs, F. Oswald, J. Wiedenmann, and G. U. Nienhaus, “Online image analysis software for photoactivation localization microscopy,” Nat. Methods 6(10), 689–690 (2009).
[CrossRef] [PubMed]

Ober, R. J.

R. J. Ober, S. Ram, and E. S. Ward, “Localization accuracy in single-molecule microscopy,” Biophys. J. 86(2), 1185–1200 (2004).
[CrossRef] [PubMed]

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]

Oswald, F.

P. N. Hedde, J. Fuchs, F. Oswald, J. Wiedenmann, and G. U. Nienhaus, “Online image analysis software for photoactivation localization microscopy,” Nat. Methods 6(10), 689–690 (2009).
[CrossRef] [PubMed]

Owens, J. D.

J. D. Owens, D. Luebke, N. Govindaraju, M. Harris, J. Kruger, A. E. Lefohn, and T. J. Purcell, “A survey of general-purpose computation on graphics hardware,” Comput. Graph. Forum 26(1), 80–113 (2007).
[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(5793), 1642–1645 (2006).
[CrossRef] [PubMed]

J. Lippincott-Schwartz and G. H. Patterson, “Development and use of fluorescent protein markers in living cells,” Science 300(5616), 87–91 (2003).
[CrossRef] [PubMed]

Polak, E.

D. Q. Mayne and E. Polak, “Feasible directions algorithm for optimization problems with equality and inequality constrains,” Math. Program. 11(1), 67–80 (1976).
[CrossRef]

Purcell, T. J.

J. D. Owens, D. Luebke, N. Govindaraju, M. Harris, J. Kruger, A. E. Lefohn, and T. J. Purcell, “A survey of general-purpose computation on graphics hardware,” Comput. Graph. Forum 26(1), 80–113 (2007).
[CrossRef]

Quan, G.

G. Quan, T. Sun, and Y. Deng, “Fast reconstruction method based on common unified device architecture (CUDA) for micro-CT,” J. Innovative Opt. Health Sci. 3(1), 39–43 (2010).
[CrossRef]

Ram, S.

R. J. Ober, S. Ram, and E. S. Ward, “Localization accuracy in single-molecule microscopy,” Biophys. J. 86(2), 1185–1200 (2004).
[CrossRef] [PubMed]

Rust, M. J.

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

Schnitzer, M. J.

B. A. Wilt, L. D. Burns, E. T. Wei Ho, K. K. Ghosh, E. A. Mukamel, and M. J. Schnitzer, “Advances in light microscopy for neuroscience,” Annu. Rev. Neurosci. 32(1), 435–506 (2009).
[CrossRef] [PubMed]

Schönle, A.

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(5), 417–423 (2008).
[CrossRef] [PubMed]

Small, A. R.

A. R. Small, “Theoretical limits on errors and acquisition rates in localizing switchable fluorophores,” Biophys. J. 96(2), L16–L18 (2009).
[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(5793), 1642–1645 (2006).
[CrossRef] [PubMed]

Stephens, D. J.

D. J. Stephens and V. J. Allan, “Light microscopy techniques for live cell imaging,” Science 300(5616), 82–86 (2003).
[CrossRef] [PubMed]

Sun, T.

G. Quan, T. Sun, and Y. Deng, “Fast reconstruction method based on common unified device architecture (CUDA) for micro-CT,” J. Innovative Opt. Health Sci. 3(1), 39–43 (2010).
[CrossRef]

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]

Verkhusha, V. V.

T. J. Gould, V. V. Verkhusha, and S. T. Hess, “Imaging biological structures with fluorescence photoactivation localization microscopy,” Nat. Protoc. 4(3), 291–308 (2009).
[CrossRef] [PubMed]

von Middendorff, C.

Ward, E. S.

R. J. Ober, S. Ram, and E. S. Ward, “Localization accuracy in single-molecule microscopy,” Biophys. J. 86(2), 1185–1200 (2004).
[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]

Wei Ho, E. T.

B. A. Wilt, L. D. Burns, E. T. Wei Ho, K. K. Ghosh, E. A. Mukamel, and M. J. Schnitzer, “Advances in light microscopy for neuroscience,” Annu. Rev. Neurosci. 32(1), 435–506 (2009).
[CrossRef] [PubMed]

Wiedenmann, J.

P. N. Hedde, J. Fuchs, F. Oswald, J. Wiedenmann, and G. U. Nienhaus, “Online image analysis software for photoactivation localization microscopy,” Nat. Methods 6(10), 689–690 (2009).
[CrossRef] [PubMed]

Wilt, B. A.

B. A. Wilt, L. D. Burns, E. T. Wei Ho, K. K. Ghosh, E. A. Mukamel, and M. J. Schnitzer, “Advances in light microscopy for neuroscience,” Annu. Rev. Neurosci. 32(1), 435–506 (2009).
[CrossRef] [PubMed]

Zhuang, X. W.

B. Huang, M. Bates, and X. W. Zhuang, “Super-resolution fluorescence microscopy,” Annu. Rev. Biochem. 78(1), 993–1016 (2009).
[CrossRef] [PubMed]

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

Annu. Rev. Biochem.

B. Huang, M. Bates, and X. W. Zhuang, “Super-resolution fluorescence microscopy,” Annu. Rev. Biochem. 78(1), 993–1016 (2009).
[CrossRef] [PubMed]

Annu. Rev. Neurosci.

B. A. Wilt, L. D. Burns, E. T. Wei Ho, K. K. Ghosh, E. A. Mukamel, and M. J. Schnitzer, “Advances in light microscopy for neuroscience,” Annu. Rev. Neurosci. 32(1), 435–506 (2009).
[CrossRef] [PubMed]

Biophys. J.

R. J. Ober, S. Ram, and E. S. Ward, “Localization accuracy in single-molecule microscopy,” Biophys. J. 86(2), 1185–1200 (2004).
[CrossRef] [PubMed]

A. R. Small, “Theoretical limits on errors and acquisition rates in localizing switchable fluorophores,” Biophys. J. 96(2), L16–L18 (2009).
[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]

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]

Comput. Graph. Forum

J. D. Owens, D. Luebke, N. Govindaraju, M. Harris, J. Kruger, A. E. Lefohn, and T. J. Purcell, “A survey of general-purpose computation on graphics hardware,” Comput. Graph. Forum 26(1), 80–113 (2007).
[CrossRef]

J. Innovative Opt. Health Sci.

G. Quan, T. Sun, and Y. Deng, “Fast reconstruction method based on common unified device architecture (CUDA) for micro-CT,” J. Innovative Opt. Health Sci. 3(1), 39–43 (2010).
[CrossRef]

Math. Program.

P. H. Calamai and J. J. More, “Projected gradient methods for linearly constrained problems,” Math. Program. 39(1), 93–116 (1987).
[CrossRef]

D. Q. Mayne and E. Polak, “Feasible directions algorithm for optimization problems with equality and inequality constrains,” Math. Program. 11(1), 67–80 (1976).
[CrossRef]

Nat. Methods

S. A. McKinney, C. S. Murphy, K. L. Hazelwood, M. W. Davidson, and L. L. Looger, “A bright and photostable photoconvertible fluorescent protein,” Nat. Methods 6(2), 131–133 (2009).
[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(5), 417–423 (2008).
[CrossRef] [PubMed]

P. N. Hedde, J. Fuchs, F. Oswald, J. Wiedenmann, and G. U. Nienhaus, “Online image analysis software for photoactivation localization microscopy,” Nat. Methods 6(10), 689–690 (2009).
[CrossRef] [PubMed]

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

Nat. Protoc.

T. J. Gould, V. V. Verkhusha, and S. T. Hess, “Imaging biological structures with fluorescence photoactivation localization microscopy,” Nat. Protoc. 4(3), 291–308 (2009).
[CrossRef] [PubMed]

Opt. Express

Science

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

J. Lippincott-Schwartz and G. H. Patterson, “Development and use of fluorescent protein markers in living cells,” Science 300(5616), 87–91 (2003).
[CrossRef] [PubMed]

D. J. Stephens and V. J. Allan, “Light microscopy techniques for live cell imaging,” Science 300(5616), 82–86 (2003).
[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]

Other

http://www.andor.com/scientific_cameras/ixon .

Cited By

OSA participates in CrossRef's Cited-By Linking service. Citing articles from OSA journals and other participating publishers are listed here.

Alert me when this article is cited.


Figures (7)

Fig. 1
Fig. 1

The entire PALM image analysis routine.

Fig. 5
Fig. 5

Capability of detecting intracellular motions with the MaLiang method. The full image in (a) was overlaid from four PALM images reconstructed from data sets 1, 3, 5 and 7. The green region in (a) was enlarged to (b), and the latter was cleaned up (c) and further analyzed (d). Individual PALM images for data set 1 (blue), 3 (green), 5 (red) and 7 (black) are shown in (c), where data points heavily deviating from the mean contour lines were eliminated (see Section 2.5 for details). The projection of all molecules in (c) to an orthogonal direction of the mean contour line from data set 1 is shown in (d). Similarly, (e)-(f) are for the yellow region in (a). The bead marked with a magenta circle in (a) was used to correct sample drift. The scale bar is 3 μm for (a) and 500 nm for (b) and (e).

Fig. 2
Fig. 2

Localization performance of Gaussian fitting (GF), fluoroBancroft (FB), and MaLiang (MLG) methods for real image frames (a-f) and simulations (g-h). Overlay of the first 1000 original image frames is shown in (a). Super resolution images were reconstructed by GF (b), FB (c) and MLG (d) method, respectively. (e) Normalized distributions of fluorescent molecules deviating from their mean contour lines for the first 1000 image frames (data set 1). (f) The full width at half maximum (FWHM) of the distribution for all image frames (data sets 1-8). The frames were grouped into 8 consecutive data sets with 1000 frames each. The mean absolute error (g) and standard deviation (h) as a function of signal-to-noise (SNR) are also presented.

Fig. 3
Fig. 3

Time consumption in localization (a) and full routine (b) for the three methods using simulated data. Simulated images (512 x 512 pixels) with different number of molecules (10-100) were used. Each data point was calculated from 30 simulated images. Speed gains for the localization (c) and full routine (d) are also provided.

Fig. 4
Fig. 4

Optimization of the number of iterations with simulation (a-b) and experimental data (c-d). (a) Iteration error is shown for simulation data with different signal-noise-ratio (SNR) levels. The iteration error was computed as the difference between the molecule positions provided in the (k)-th and (k-1)-th iteration step. (b) Comparison of localization precisions by using different iteration times (N). (c) Overlay of the first 900 experimental image frames used to optimize the number of iterations. (d) The relations between iteration number (N) and the distributions of fluorescent molecules around their mean contour line.

Fig. 6
Fig. 6

Sample drift correction. (a) Sample drift was determined by tracking a luminescent bead during the entire PALM image acquisition process. The smooth drifts were used in the sample drift correction, so that the influence from localization error to the localization precision of the PALM data could be minimized. Localization of the bead before (b) and after (c) drift correction indicates that the drift-based contribution to position errors in PALM data is significantly reduced. The standard deviation of the bead position in (c) is 7.5 nm.

Fig. 7
Fig. 7

Comparison of the motion detection sensitivity between the MaLiang (MLG) and fluoroBancroft (FB) methods. The motion detection sensitivity is characterized by Z-statistics (y-axis), where bigger value represents larger difference between two data sets. Movement between data set 1 and 3 is represented as motion 1, while motion 2 and 3 corresponding to movements from data set 3 to 5, and 5 to 7, respectively.

Tables (2)

Tables Icon

Table 1 Comparison of the maximum number of molecules that need to be localized in PALM imaging with different detectors.

Tables Icon

Table 2 Time consumption in different image analysis steps for experimental and simulated image data. a

Equations (4)

Equations on this page are rendered with MathJax. Learn more.

I i , j = A exp ( ( i x 0 ) 2 + ( j y 0 ) 2 2 σ 2 ) + b
P ( I i , j = q i , j ) = I i , j q i , j exp ( I i , j ) q i , j !
i , j P ( I i , j = q i , j )
min L = ( 1 i , j n I i , j ) 1 i , j n q i , j log ( I i , j ) s . t   A > 0 , x 0 > 0 , y 0 > 0 , σ > 0 , b > 0

Metrics