Abstract

Developing methods for high-density localization of multiple emitters is a promising approach for enhancing the temporal resolution of localization microscopy while maintaining a desired spatial resolution, but the widespread use of this approach is thus far mainly obstructed by the slow image analysis speed. Here we present a high-density localization method based on the combination of Graphics Processing Unit (GPU) parallel computation, multiple-emitter fitting, and model recommendation via Bayesian Information Criterion (BIC). This method, called PALMER, exhibits satisfactory localization accuracy comparable with the previous reported SSM_BIC method, while executes more than two orders of magnitudes faster. Meanwhile, compared to the conventional localization microscopy which is based on sparse emitter localization, high-density localization microscopy based the PALMER method allows a speed gain of up to ~14-fold in obtaining a super-resolution image with the same Nyquist resolution.

© 2012 OSA

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References

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    [Crossref] [PubMed]

2012 (1)

L. Zhu, W. Zhang, D. Elnatan, and B. Huang, “Faster STORM using compressed sensing,” Nat Methods (2012), doi:.
[Crossref] [PubMed]

2011 (7)

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

S. J. Holden, S. Uphoff, and A. N. Kapanidis, “DAOSTORM: an algorithm for high- density super-resolution microscopy,” Nat. Methods 8(4), 279–280 (2011).
[Crossref] [PubMed]

S. Cox, E. Rosten, J. Monypenny, T. Jovanovic-Talisman, D. T. Burnette, J. Lippincott-Schwartz, G. E. Jones, and R. Heintzmann, “Bayesian localization microscopy reveals nanoscale podosome dynamics,” Nat. Methods 9(2), 195–200 (2011).
[Crossref] [PubMed]

S. A. Jones, S. H. Shim, J. He, and X. W. Zhuang, “Fast, three-dimensional super-resolution imaging of live cells,” Nat. Methods 8(6), 499–505 (2011).
[Crossref] [PubMed]

E. Pastrana, “Fast 3D super-resolution fluorescence microscopy,” Nat. Methods 8(1), 46 (2011).
[Crossref]

F. Huang, S. L. Schwartz, J. M. Byars, and K. A. Lidke, “Simultaneous multiple-emitter fitting for single molecule super-resolution imaging,” Biomed. Opt. Express 2(5), 1377–1393 (2011).
[Crossref] [PubMed]

T. W. Quan, H. Y. Zhu, X. M. Liu, Y. F. Liu, J. P. Ding, S. Q. Zeng, and Z. L. Huang, “High-density localization of active molecules using Structured Sparse Model and Bayesian Information Criterion,” Opt. Express 19(18), 16963–16974 (2011).
[Crossref] [PubMed]

2010 (3)

2009 (1)

K. R. Chi, “Super-resolution microscopy: breaking the limits,” Nat. Methods 6(1), 15–18 (2009).
[Crossref]

2008 (1)

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]

2007 (3)

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

M. A. T. Figueiredo, R. D. Nowak, and S. J. Wright, “Gradient projection for sparse reconstruction: application to compressed sensing and other inverse problems,” IEEE J. Sel. Top. Signal Process. 1(4), 586–597 (2007).
[Crossref]

B. Zhang, J. Zerubia, and J. C. Olivo-Marin, “Gaussian approximations of fluorescence microscope point-spread function models,” Appl. Opt. 46(10), 1819–1829 (2007).
[Crossref] [PubMed]

2005 (1)

K. Nienhaus, G. U. Nienhaus, J. Wiedenmann, and H. Nar, “Structural basis for photo-induced protein cleavage and green-to-red conversion of fluorescent protein EosFP,” Proc. Natl. Acad. Sci. U.S.A. 102(26), 9156–9159 (2005).
[Crossref] [PubMed]

1996 (1)

Z. Gao, Y. Lai, and Z. Hu, “A generalized gradient projection method for optimization problems with equality and inequality constraints about arbitrary initial point,” Acta Appl. Math. 12(1), 40–49 (1996).
[Crossref]

1995 (1)

Y. Cheng, “Mean shift, mode seeking, and clustering,” IEEE Trans. Pattern Anal. Mach. Intell. 17(8), 790–799 (1995).
[Crossref]

Bates, M.

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

Bewersdorf, J.

D. Toomre and J. Bewersdorf, “A new wave of cellular imaging,” Annu. Rev. Cell Dev. Biol. 26(1), 285–314 (2010).
[Crossref] [PubMed]

Burnette, D. T.

S. Cox, E. Rosten, J. Monypenny, T. Jovanovic-Talisman, D. T. Burnette, J. Lippincott-Schwartz, G. E. Jones, and R. Heintzmann, “Bayesian localization microscopy reveals nanoscale podosome dynamics,” Nat. Methods 9(2), 195–200 (2011).
[Crossref] [PubMed]

Byars, J. M.

Chen, K. H.

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

Cheng, Y.

Y. Cheng, “Mean shift, mode seeking, and clustering,” IEEE Trans. Pattern Anal. Mach. Intell. 17(8), 790–799 (1995).
[Crossref]

Chi, K. R.

K. R. Chi, “Super-resolution microscopy: breaking the limits,” Nat. Methods 6(1), 15–18 (2009).
[Crossref]

Cox, S.

S. Cox, E. Rosten, J. Monypenny, T. Jovanovic-Talisman, D. T. Burnette, J. Lippincott-Schwartz, G. E. Jones, and R. Heintzmann, “Bayesian localization microscopy reveals nanoscale podosome dynamics,” Nat. Methods 9(2), 195–200 (2011).
[Crossref] [PubMed]

Dempsey, G. T.

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

Ding, J. P.

Elnatan, D.

L. Zhu, W. Zhang, D. Elnatan, and B. Huang, “Faster STORM using compressed sensing,” Nat Methods (2012), doi:.
[Crossref] [PubMed]

Figueiredo, M. A. T.

M. A. T. Figueiredo, R. D. Nowak, and S. J. Wright, “Gradient projection for sparse reconstruction: application to compressed sensing and other inverse problems,” IEEE J. Sel. Top. Signal Process. 1(4), 586–597 (2007).
[Crossref]

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]

Gao, Z.

Z. Gao, Y. Lai, and Z. Hu, “A generalized gradient projection method for optimization problems with equality and inequality constraints about arbitrary initial point,” Acta Appl. Math. 12(1), 40–49 (1996).
[Crossref]

He, J.

S. A. Jones, S. H. Shim, J. He, and X. W. Zhuang, “Fast, three-dimensional super-resolution imaging of live cells,” Nat. Methods 8(6), 499–505 (2011).
[Crossref] [PubMed]

Hedde, P. N.

Heintzmann, R.

S. Cox, E. Rosten, J. Monypenny, T. Jovanovic-Talisman, D. T. Burnette, J. Lippincott-Schwartz, G. E. Jones, and R. Heintzmann, “Bayesian localization microscopy reveals nanoscale podosome dynamics,” Nat. Methods 9(2), 195–200 (2011).
[Crossref] [PubMed]

Hell, S. W.

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

Holden, S. J.

S. J. Holden, S. Uphoff, and A. N. Kapanidis, “DAOSTORM: an algorithm for high- density super-resolution microscopy,” Nat. Methods 8(4), 279–280 (2011).
[Crossref] [PubMed]

Hu, Z.

Z. Gao, Y. Lai, and Z. Hu, “A generalized gradient projection method for optimization problems with equality and inequality constraints about arbitrary initial point,” Acta Appl. Math. 12(1), 40–49 (1996).
[Crossref]

Huang, B.

L. Zhu, W. Zhang, D. Elnatan, and B. Huang, “Faster STORM using compressed sensing,” Nat Methods (2012), doi:.
[Crossref] [PubMed]

Huang, F.

Huang, Z. L.

Jones, G. E.

S. Cox, E. Rosten, J. Monypenny, T. Jovanovic-Talisman, D. T. Burnette, J. Lippincott-Schwartz, G. E. Jones, and R. Heintzmann, “Bayesian localization microscopy reveals nanoscale podosome dynamics,” Nat. Methods 9(2), 195–200 (2011).
[Crossref] [PubMed]

Jones, S. A.

S. A. Jones, S. H. Shim, J. He, and X. W. Zhuang, “Fast, three-dimensional super-resolution imaging of live cells,” Nat. Methods 8(6), 499–505 (2011).
[Crossref] [PubMed]

Jovanovic-Talisman, T.

S. Cox, E. Rosten, J. Monypenny, T. Jovanovic-Talisman, D. T. Burnette, J. Lippincott-Schwartz, G. E. Jones, and R. Heintzmann, “Bayesian localization microscopy reveals nanoscale podosome dynamics,” Nat. Methods 9(2), 195–200 (2011).
[Crossref] [PubMed]

Kapanidis, A. N.

S. J. Holden, S. Uphoff, and A. N. Kapanidis, “DAOSTORM: an algorithm for high- density super-resolution microscopy,” Nat. Methods 8(4), 279–280 (2011).
[Crossref] [PubMed]

Lai, Y.

Z. Gao, Y. Lai, and Z. Hu, “A generalized gradient projection method for optimization problems with equality and inequality constraints about arbitrary initial point,” Acta Appl. Math. 12(1), 40–49 (1996).
[Crossref]

Li, P. C.

Lidke, K. A.

Lippincott-Schwartz, J.

S. Cox, E. Rosten, J. Monypenny, T. Jovanovic-Talisman, D. T. Burnette, J. Lippincott-Schwartz, G. E. Jones, and R. Heintzmann, “Bayesian localization microscopy reveals nanoscale podosome dynamics,” Nat. Methods 9(2), 195–200 (2011).
[Crossref] [PubMed]

Liu, X. M.

Liu, Y. F.

Long, F.

Luo, Q. M.

Monypenny, J.

S. Cox, E. Rosten, J. Monypenny, T. Jovanovic-Talisman, D. T. Burnette, J. Lippincott-Schwartz, G. E. Jones, and R. Heintzmann, “Bayesian localization microscopy reveals nanoscale podosome dynamics,” Nat. Methods 9(2), 195–200 (2011).
[Crossref] [PubMed]

Nar, H.

K. Nienhaus, G. U. Nienhaus, J. Wiedenmann, and H. Nar, “Structural basis for photo-induced protein cleavage and green-to-red conversion of fluorescent protein EosFP,” Proc. Natl. Acad. Sci. U.S.A. 102(26), 9156–9159 (2005).
[Crossref] [PubMed]

Nienhaus, G. U.

T. W. Quan, P. C. Li, F. Long, S. Q. Zeng, Q. M. Luo, P. N. Hedde, G. U. Nienhaus, and Z. L. Huang, “Ultra-fast, high-precision image analysis for localization-based super resolution microscopy,” Opt. Express 18(11), 11867–11876 (2010).
[Crossref] [PubMed]

K. Nienhaus, G. U. Nienhaus, J. Wiedenmann, and H. Nar, “Structural basis for photo-induced protein cleavage and green-to-red conversion of fluorescent protein EosFP,” Proc. Natl. Acad. Sci. U.S.A. 102(26), 9156–9159 (2005).
[Crossref] [PubMed]

Nienhaus, K.

K. Nienhaus, G. U. Nienhaus, J. Wiedenmann, and H. Nar, “Structural basis for photo-induced protein cleavage and green-to-red conversion of fluorescent protein EosFP,” Proc. Natl. Acad. Sci. U.S.A. 102(26), 9156–9159 (2005).
[Crossref] [PubMed]

Nowak, R. D.

M. A. T. Figueiredo, R. D. Nowak, and S. J. Wright, “Gradient projection for sparse reconstruction: application to compressed sensing and other inverse problems,” IEEE J. Sel. Top. Signal Process. 1(4), 586–597 (2007).
[Crossref]

Olivo-Marin, J. C.

Pastrana, E.

E. Pastrana, “Fast 3D super-resolution fluorescence microscopy,” Nat. Methods 8(1), 46 (2011).
[Crossref]

Quan, T. W.

Rieger, B.

Rosten, E.

S. Cox, E. Rosten, J. Monypenny, T. Jovanovic-Talisman, D. T. Burnette, J. Lippincott-Schwartz, G. E. Jones, and R. Heintzmann, “Bayesian localization microscopy reveals nanoscale podosome dynamics,” Nat. Methods 9(2), 195–200 (2011).
[Crossref] [PubMed]

Schwartz, S. L.

Shim, S. H.

S. A. Jones, S. H. Shim, J. He, and X. W. Zhuang, “Fast, three-dimensional super-resolution imaging of live cells,” Nat. Methods 8(6), 499–505 (2011).
[Crossref] [PubMed]

Shroff, H.

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

Stallinga, S.

Toomre, D.

D. Toomre and J. Bewersdorf, “A new wave of cellular imaging,” Annu. Rev. Cell Dev. Biol. 26(1), 285–314 (2010).
[Crossref] [PubMed]

Uphoff, S.

S. J. Holden, S. Uphoff, and A. N. Kapanidis, “DAOSTORM: an algorithm for high- density super-resolution microscopy,” Nat. Methods 8(4), 279–280 (2011).
[Crossref] [PubMed]

Vaughan, J. C.

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

Wiedenmann, J.

K. Nienhaus, G. U. Nienhaus, J. Wiedenmann, and H. Nar, “Structural basis for photo-induced protein cleavage and green-to-red conversion of fluorescent protein EosFP,” Proc. Natl. Acad. Sci. U.S.A. 102(26), 9156–9159 (2005).
[Crossref] [PubMed]

Wright, S. J.

M. A. T. Figueiredo, R. D. Nowak, and S. J. Wright, “Gradient projection for sparse reconstruction: application to compressed sensing and other inverse problems,” IEEE J. Sel. Top. Signal Process. 1(4), 586–597 (2007).
[Crossref]

Zeng, S. Q.

Zerubia, J.

Zhang, B.

Zhang, W.

L. Zhu, W. Zhang, D. Elnatan, and B. Huang, “Faster STORM using compressed sensing,” Nat Methods (2012), doi:.
[Crossref] [PubMed]

Zhu, H. Y.

Zhu, L.

L. Zhu, W. Zhang, D. Elnatan, and B. Huang, “Faster STORM using compressed sensing,” Nat Methods (2012), doi:.
[Crossref] [PubMed]

Zhuang, X. W.

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

S. A. Jones, S. H. Shim, J. He, and X. W. Zhuang, “Fast, three-dimensional super-resolution imaging of live cells,” Nat. Methods 8(6), 499–505 (2011).
[Crossref] [PubMed]

Acta Appl. Math. (1)

Z. Gao, Y. Lai, and Z. Hu, “A generalized gradient projection method for optimization problems with equality and inequality constraints about arbitrary initial point,” Acta Appl. Math. 12(1), 40–49 (1996).
[Crossref]

Annu. Rev. Cell Dev. Biol. (1)

D. Toomre and J. Bewersdorf, “A new wave of cellular imaging,” Annu. Rev. Cell Dev. Biol. 26(1), 285–314 (2010).
[Crossref] [PubMed]

Appl. Opt. (1)

Biomed. Opt. Express (1)

IEEE J. Sel. Top. Signal Process. (1)

M. A. T. Figueiredo, R. D. Nowak, and S. J. Wright, “Gradient projection for sparse reconstruction: application to compressed sensing and other inverse problems,” IEEE J. Sel. Top. Signal Process. 1(4), 586–597 (2007).
[Crossref]

IEEE Trans. Pattern Anal. Mach. Intell. (1)

Y. Cheng, “Mean shift, mode seeking, and clustering,” IEEE Trans. Pattern Anal. Mach. Intell. 17(8), 790–799 (1995).
[Crossref]

Nat Methods (1)

L. Zhu, W. Zhang, D. Elnatan, and B. Huang, “Faster STORM using compressed sensing,” Nat Methods (2012), doi:.
[Crossref] [PubMed]

Nat. Methods (7)

K. R. Chi, “Super-resolution microscopy: breaking the limits,” Nat. Methods 6(1), 15–18 (2009).
[Crossref]

S. A. Jones, S. H. Shim, J. He, and X. W. Zhuang, “Fast, three-dimensional super-resolution imaging of live cells,” Nat. Methods 8(6), 499–505 (2011).
[Crossref] [PubMed]

E. Pastrana, “Fast 3D super-resolution fluorescence microscopy,” Nat. Methods 8(1), 46 (2011).
[Crossref]

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]

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

S. J. Holden, S. Uphoff, and A. N. Kapanidis, “DAOSTORM: an algorithm for high- density super-resolution microscopy,” Nat. Methods 8(4), 279–280 (2011).
[Crossref] [PubMed]

S. Cox, E. Rosten, J. Monypenny, T. Jovanovic-Talisman, D. T. Burnette, J. Lippincott-Schwartz, G. E. Jones, and R. Heintzmann, “Bayesian localization microscopy reveals nanoscale podosome dynamics,” Nat. Methods 9(2), 195–200 (2011).
[Crossref] [PubMed]

Opt. Express (3)

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

K. Nienhaus, G. U. Nienhaus, J. Wiedenmann, and H. Nar, “Structural basis for photo-induced protein cleavage and green-to-red conversion of fluorescent protein EosFP,” Proc. Natl. Acad. Sci. U.S.A. 102(26), 9156–9159 (2005).
[Crossref] [PubMed]

Science (1)

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

Other (1)

“GPU computing SDK, ” http://developer.nvidia.com/gpu-computing-sdk , accessed March 2012.

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