Abstract

Localization microscopy achieves nanoscale spatial resolution by iterative localization of sparsely activated molecules, which generally leads to a long acquisition time. By implementing advanced algorithms to treat overlapping point spread functions (PSFs), imaging of densely activated molecules can improve the limited temporal resolution, as has been well demonstrated in two-dimensional imaging. However, three-dimensional (3D) localization of high-density data remains challenging since PSFs are far more similar along the axial dimension than the lateral dimensions. Here, we present a new, high-density 3D imaging system and algorithm. The hybrid system is implemented by combining astigmatic and biplane imaging. The proposed 3D reconstruction algorithm is extended from our state-of-the art 2D high-density localization algorithm. Using mutual coherence analysis of model PSFs, we validated that the hybrid system is more suitable than astigmatic or biplane imaging alone for 3D localization of high-density data. The efficacy of the proposed method was confirmed via simulation and real data of microtubules. Furthermore, we also successfully demonstrated fluorescent-protein-based live cell 3D localization microscopy with a temporal resolution of just 3 seconds, capturing fast dynamics of the endoplasmic recticulum.

© 2014 Optical Society of America

Full Article  |  PDF Article
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References

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2014 (4)

J. Min, C. Vonesch, H. Kirshner, L. Carlini, N. Olivier, S. Holden, S. Manley, J. C. Ye, and M. Unser, “FALCON: fast and unbiased reconstruction of high-density super-resolution microscopy data,” Sci. Rep. 4, 4577 (2014).
[Crossref]

L. Gu, Y. Sheng, Y. Chen, H. Chang, Y. Zhang, P. Lv, W. Ji, and T. Xu, “High-density 3D single molecular analysis based on compressed sensing,” Biophys. J. 106, 2443–2449 (2014).
[Crossref] [PubMed]

A. Barsic, G. Grover, and R. Piestun, “Three-dimensional super-resolution and localization of dense clusters of single molecules,” Sci. Rep. 4, 5388 (2014).
[Crossref] [PubMed]

S. Liu and K. A. Lidke, “A multiemitter localization comparison of 3d superresolution imaging modalities,” ChemPhysChem 15, 696–704 (2014).
[Crossref]

2013 (2)

N. Olivier, D. Keller, P. Gönczy, and S. Manley, “Resolution doubling in 3D-STORM imaging through improved buffers,” PloS one 8, e69004 (2013).
[Crossref] [PubMed]

F. Huang, T. M. P. Hartwich, F. E. Rivera-Molina, Y. Lin, W. C. Duim, P. D. U. Jane, J Long, J. R. Myers, M. A. Baird, W. Mothes, M. W. Davidson, D. Toomre, and J. Bewersdorf, “Video-rate nanoscopy using scmos camera-specific single-molecule localization algorithms,” Nat. Methods 10, 653–658 (2013).
[Crossref] [PubMed]

2012 (3)

L. Zhu, W. Zhang, D. Elnatan, and B. Huang, “Faster storm using compressed sensing,” Nat. Methods 9, 721–723 (2012).
[Crossref] [PubMed]

E. A. Mukamel, H. Babcock, and X. Zhuang, “Statistical deconvolution for superresolution fluorescence microscopy,” Biophys. J. 102, 2391–2400 (2012).
[Crossref] [PubMed]

H. Babcock, Y. M. Sigal, and X. Zhuang, “A high-density 3D localization algorithm for stochastic optical reconstruction microscopy,” Optical Nanoscopy 1, 1–10 (2012).
[Crossref]

2011 (5)

J. Hu, W. A. Prinz, and T. A. Rapoport, “Weaving the web of ER tubules,” Cell 147, 1226–1231 (2011).
[Crossref] [PubMed]

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

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

M. D. Lew, S. F. Lee, M. Badieirostami, and W. Moerner, “Corkscrew point spread function for far-field three-dimensional nanoscale localization of pointlike objects,” Opt. Lett. 36, 202–204 (2011).
[Crossref] [PubMed]

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, 1377–1393 (2011).
[Crossref] [PubMed]

2008 (3)

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

M. F. Juette, T. J. Gould, M. D. Lessard, M. J. Mlodzianoski, B. S. Nagpure, B. T. Bennett, S. T. Hess, and J. Bewersdorf, “Three-dimensional sub–100 nm resolution fluorescence microscopy of thick samples,” Nat. Methods 5, 527–529 (2008).
[Crossref] [PubMed]

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

2006 (3)

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

S. T. Hess, T. P. Girirajan, and M. D. Mason, “Ultra-high resolution imaging by fluorescence photoactivation localization microscopy,” Biophys. J. 91, 4258 (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, 1642–1645 (2006).
[Crossref] [PubMed]

2005 (1)

L. S. Churchman, Z. Ökten, R. S. Rock, J. F. Dawson, and J. A. Spudich, “Single molecule high-resolution colocalization of cy3 and cy5 attached to macromolecules measures intramolecular distances through time,” Proc. Natl. Acad. Sci. USA 102, 1419–1423 (2005).
[Crossref] [PubMed]

Amodaj, N.

A. Edelstein, N. Amodaj, K. Hoover, R. Vale, and N. Stuurman, Computer Control of Microscopes Using μManager (John Wiley & Sons, Inc., 2010).

Babcock, H.

H. Babcock, Y. M. Sigal, and X. Zhuang, “A high-density 3D localization algorithm for stochastic optical reconstruction microscopy,” Optical Nanoscopy 1, 1–10 (2012).
[Crossref]

E. A. Mukamel, H. Babcock, and X. Zhuang, “Statistical deconvolution for superresolution fluorescence microscopy,” Biophys. J. 102, 2391–2400 (2012).
[Crossref] [PubMed]

Badieirostami, M.

Baird, M. A.

F. Huang, T. M. P. Hartwich, F. E. Rivera-Molina, Y. Lin, W. C. Duim, P. D. U. Jane, J Long, J. R. Myers, M. A. Baird, W. Mothes, M. W. Davidson, D. Toomre, and J. Bewersdorf, “Video-rate nanoscopy using scmos camera-specific single-molecule localization algorithms,” Nat. Methods 10, 653–658 (2013).
[Crossref] [PubMed]

Barsic, A.

A. Barsic, G. Grover, and R. Piestun, “Three-dimensional super-resolution and localization of dense clusters of single molecules,” Sci. Rep. 4, 5388 (2014).
[Crossref] [PubMed]

Bates, M.

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

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

Bennett, B. T.

M. F. Juette, T. J. Gould, M. D. Lessard, M. J. Mlodzianoski, B. S. Nagpure, B. T. Bennett, S. T. Hess, and J. Bewersdorf, “Three-dimensional sub–100 nm resolution fluorescence microscopy of thick samples,” Nat. Methods 5, 527–529 (2008).
[Crossref] [PubMed]

Betzig, E.

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

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

Bewersdorf, J.

F. Huang, T. M. P. Hartwich, F. E. Rivera-Molina, Y. Lin, W. C. Duim, P. D. U. Jane, J Long, J. R. Myers, M. A. Baird, W. Mothes, M. W. Davidson, D. Toomre, and J. Bewersdorf, “Video-rate nanoscopy using scmos camera-specific single-molecule localization algorithms,” Nat. Methods 10, 653–658 (2013).
[Crossref] [PubMed]

M. F. Juette, T. J. Gould, M. D. Lessard, M. J. Mlodzianoski, B. S. Nagpure, B. T. Bennett, S. T. Hess, and J. Bewersdorf, “Three-dimensional sub–100 nm resolution fluorescence microscopy of thick samples,” Nat. Methods 5, 527–529 (2008).
[Crossref] [PubMed]

Bonifacino, J. S.

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

Byars, J. M.

Carlini, L.

J. Min, C. Vonesch, H. Kirshner, L. Carlini, N. Olivier, S. Holden, S. Manley, J. C. Ye, and M. Unser, “FALCON: fast and unbiased reconstruction of high-density super-resolution microscopy data,” Sci. Rep. 4, 4577 (2014).
[Crossref]

Chang, H.

L. Gu, Y. Sheng, Y. Chen, H. Chang, Y. Zhang, P. Lv, W. Ji, and T. Xu, “High-density 3D single molecular analysis based on compressed sensing,” Biophys. J. 106, 2443–2449 (2014).
[Crossref] [PubMed]

Chen, Y.

L. Gu, Y. Sheng, Y. Chen, H. Chang, Y. Zhang, P. Lv, W. Ji, and T. Xu, “High-density 3D single molecular analysis based on compressed sensing,” Biophys. J. 106, 2443–2449 (2014).
[Crossref] [PubMed]

Churchman, L. S.

L. S. Churchman, Z. Ökten, R. S. Rock, J. F. Dawson, and J. A. Spudich, “Single molecule high-resolution colocalization of cy3 and cy5 attached to macromolecules measures intramolecular distances through time,” Proc. Natl. Acad. Sci. USA 102, 1419–1423 (2005).
[Crossref] [PubMed]

Davidson, M. W.

F. Huang, T. M. P. Hartwich, F. E. Rivera-Molina, Y. Lin, W. C. Duim, P. D. U. Jane, J Long, J. R. Myers, M. A. Baird, W. Mothes, M. W. Davidson, D. Toomre, and J. Bewersdorf, “Video-rate nanoscopy using scmos camera-specific single-molecule localization algorithms,” Nat. Methods 10, 653–658 (2013).
[Crossref] [PubMed]

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

Dawson, J. F.

L. S. Churchman, Z. Ökten, R. S. Rock, J. F. Dawson, and J. A. Spudich, “Single molecule high-resolution colocalization of cy3 and cy5 attached to macromolecules measures intramolecular distances through time,” Proc. Natl. Acad. Sci. USA 102, 1419–1423 (2005).
[Crossref] [PubMed]

Duim, W. C.

F. Huang, T. M. P. Hartwich, F. E. Rivera-Molina, Y. Lin, W. C. Duim, P. D. U. Jane, J Long, J. R. Myers, M. A. Baird, W. Mothes, M. W. Davidson, D. Toomre, and J. Bewersdorf, “Video-rate nanoscopy using scmos camera-specific single-molecule localization algorithms,” Nat. Methods 10, 653–658 (2013).
[Crossref] [PubMed]

Edelstein, A.

A. Edelstein, N. Amodaj, K. Hoover, R. Vale, and N. Stuurman, Computer Control of Microscopes Using μManager (John Wiley & Sons, Inc., 2010).

Elnatan, D.

L. Zhu, W. Zhang, D. Elnatan, and B. Huang, “Faster storm using compressed sensing,” Nat. Methods 9, 721–723 (2012).
[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, 417–423 (2008).
[Crossref] [PubMed]

Galbraith, J. A.

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

Girirajan, T. P.

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

Gönczy, P.

N. Olivier, D. Keller, P. Gönczy, and S. Manley, “Resolution doubling in 3D-STORM imaging through improved buffers,” PloS one 8, e69004 (2013).
[Crossref] [PubMed]

Gould, T. J.

M. F. Juette, T. J. Gould, M. D. Lessard, M. J. Mlodzianoski, B. S. Nagpure, B. T. Bennett, S. T. Hess, and J. Bewersdorf, “Three-dimensional sub–100 nm resolution fluorescence microscopy of thick samples,” Nat. Methods 5, 527–529 (2008).
[Crossref] [PubMed]

Grover, G.

A. Barsic, G. Grover, and R. Piestun, “Three-dimensional super-resolution and localization of dense clusters of single molecules,” Sci. Rep. 4, 5388 (2014).
[Crossref] [PubMed]

Gu, L.

L. Gu, Y. Sheng, Y. Chen, H. Chang, Y. Zhang, P. Lv, W. Ji, and T. Xu, “High-density 3D single molecular analysis based on compressed sensing,” Biophys. J. 106, 2443–2449 (2014).
[Crossref] [PubMed]

Hartwich, T. M. P.

F. Huang, T. M. P. Hartwich, F. E. Rivera-Molina, Y. Lin, W. C. Duim, P. D. U. Jane, J Long, J. R. Myers, M. A. Baird, W. Mothes, M. W. Davidson, D. Toomre, and J. Bewersdorf, “Video-rate nanoscopy using scmos camera-specific single-molecule localization algorithms,” Nat. Methods 10, 653–658 (2013).
[Crossref] [PubMed]

He, J.

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

Hess, H. F.

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

Hess, S. T.

M. F. Juette, T. J. Gould, M. D. Lessard, M. J. Mlodzianoski, B. S. Nagpure, B. T. Bennett, S. T. Hess, and J. Bewersdorf, “Three-dimensional sub–100 nm resolution fluorescence microscopy of thick samples,” Nat. Methods 5, 527–529 (2008).
[Crossref] [PubMed]

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

Holden, S.

J. Min, C. Vonesch, H. Kirshner, L. Carlini, N. Olivier, S. Holden, S. Manley, J. C. Ye, and M. Unser, “FALCON: fast and unbiased reconstruction of high-density super-resolution microscopy data,” Sci. Rep. 4, 4577 (2014).
[Crossref]

Holden., S. J.

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

Hoover, K.

A. Edelstein, N. Amodaj, K. Hoover, R. Vale, and N. Stuurman, Computer Control of Microscopes Using μManager (John Wiley & Sons, Inc., 2010).

Hu, J.

J. Hu, W. A. Prinz, and T. A. Rapoport, “Weaving the web of ER tubules,” Cell 147, 1226–1231 (2011).
[Crossref] [PubMed]

Huang, B.

L. Zhu, W. Zhang, D. Elnatan, and B. Huang, “Faster storm using compressed sensing,” Nat. Methods 9, 721–723 (2012).
[Crossref] [PubMed]

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

Huang, F.

F. Huang, T. M. P. Hartwich, F. E. Rivera-Molina, Y. Lin, W. C. Duim, P. D. U. Jane, J Long, J. R. Myers, M. A. Baird, W. Mothes, M. W. Davidson, D. Toomre, and J. Bewersdorf, “Video-rate nanoscopy using scmos camera-specific single-molecule localization algorithms,” Nat. Methods 10, 653–658 (2013).
[Crossref] [PubMed]

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, 1377–1393 (2011).
[Crossref] [PubMed]

Jane, P. D. U.

F. Huang, T. M. P. Hartwich, F. E. Rivera-Molina, Y. Lin, W. C. Duim, P. D. U. Jane, J Long, J. R. Myers, M. A. Baird, W. Mothes, M. W. Davidson, D. Toomre, and J. Bewersdorf, “Video-rate nanoscopy using scmos camera-specific single-molecule localization algorithms,” Nat. Methods 10, 653–658 (2013).
[Crossref] [PubMed]

Ji, W.

L. Gu, Y. Sheng, Y. Chen, H. Chang, Y. Zhang, P. Lv, W. Ji, and T. Xu, “High-density 3D single molecular analysis based on compressed sensing,” Biophys. J. 106, 2443–2449 (2014).
[Crossref] [PubMed]

Jones, S. A.

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

Juette, M. F.

M. F. Juette, T. J. Gould, M. D. Lessard, M. J. Mlodzianoski, B. S. Nagpure, B. T. Bennett, S. T. Hess, and J. Bewersdorf, “Three-dimensional sub–100 nm resolution fluorescence microscopy of thick samples,” Nat. Methods 5, 527–529 (2008).
[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, 279–280 (2011).
[Crossref] [PubMed]

Keller, D.

N. Olivier, D. Keller, P. Gönczy, and S. Manley, “Resolution doubling in 3D-STORM imaging through improved buffers,” PloS one 8, e69004 (2013).
[Crossref] [PubMed]

Kirshner, H.

J. Min, C. Vonesch, H. Kirshner, L. Carlini, N. Olivier, S. Holden, S. Manley, J. C. Ye, and M. Unser, “FALCON: fast and unbiased reconstruction of high-density super-resolution microscopy data,” Sci. Rep. 4, 4577 (2014).
[Crossref]

Lee, S. F.

Lessard, M. D.

M. F. Juette, T. J. Gould, M. D. Lessard, M. J. Mlodzianoski, B. S. Nagpure, B. T. Bennett, S. T. Hess, and J. Bewersdorf, “Three-dimensional sub–100 nm resolution fluorescence microscopy of thick samples,” Nat. Methods 5, 527–529 (2008).
[Crossref] [PubMed]

Lew, M. D.

Lidke, K. A.

S. Liu and K. A. Lidke, “A multiemitter localization comparison of 3d superresolution imaging modalities,” ChemPhysChem 15, 696–704 (2014).
[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, 1377–1393 (2011).
[Crossref] [PubMed]

Lin, Y.

F. Huang, T. M. P. Hartwich, F. E. Rivera-Molina, Y. Lin, W. C. Duim, P. D. U. Jane, J Long, J. R. Myers, M. A. Baird, W. Mothes, M. W. Davidson, D. Toomre, and J. Bewersdorf, “Video-rate nanoscopy using scmos camera-specific single-molecule localization algorithms,” Nat. Methods 10, 653–658 (2013).
[Crossref] [PubMed]

Lindwasser, O. W.

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

Lippincott-Schwartz, J.

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

Liu, S.

S. Liu and K. A. Lidke, “A multiemitter localization comparison of 3d superresolution imaging modalities,” ChemPhysChem 15, 696–704 (2014).
[Crossref]

Long, J

F. Huang, T. M. P. Hartwich, F. E. Rivera-Molina, Y. Lin, W. C. Duim, P. D. U. Jane, J Long, J. R. Myers, M. A. Baird, W. Mothes, M. W. Davidson, D. Toomre, and J. Bewersdorf, “Video-rate nanoscopy using scmos camera-specific single-molecule localization algorithms,” Nat. Methods 10, 653–658 (2013).
[Crossref] [PubMed]

Lv, P.

L. Gu, Y. Sheng, Y. Chen, H. Chang, Y. Zhang, P. Lv, W. Ji, and T. Xu, “High-density 3D single molecular analysis based on compressed sensing,” Biophys. J. 106, 2443–2449 (2014).
[Crossref] [PubMed]

Manley, S.

J. Min, C. Vonesch, H. Kirshner, L. Carlini, N. Olivier, S. Holden, S. Manley, J. C. Ye, and M. Unser, “FALCON: fast and unbiased reconstruction of high-density super-resolution microscopy data,” Sci. Rep. 4, 4577 (2014).
[Crossref]

N. Olivier, D. Keller, P. Gönczy, and S. Manley, “Resolution doubling in 3D-STORM imaging through improved buffers,” PloS one 8, e69004 (2013).
[Crossref] [PubMed]

Mason, M. D.

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

Min, J.

J. Min, C. Vonesch, H. Kirshner, L. Carlini, N. Olivier, S. Holden, S. Manley, J. C. Ye, and M. Unser, “FALCON: fast and unbiased reconstruction of high-density super-resolution microscopy data,” Sci. Rep. 4, 4577 (2014).
[Crossref]

Mlodzianoski, M. J.

M. F. Juette, T. J. Gould, M. D. Lessard, M. J. Mlodzianoski, B. S. Nagpure, B. T. Bennett, S. T. Hess, and J. Bewersdorf, “Three-dimensional sub–100 nm resolution fluorescence microscopy of thick samples,” Nat. Methods 5, 527–529 (2008).
[Crossref] [PubMed]

Moerner, W.

Mothes, W.

F. Huang, T. M. P. Hartwich, F. E. Rivera-Molina, Y. Lin, W. C. Duim, P. D. U. Jane, J Long, J. R. Myers, M. A. Baird, W. Mothes, M. W. Davidson, D. Toomre, and J. Bewersdorf, “Video-rate nanoscopy using scmos camera-specific single-molecule localization algorithms,” Nat. Methods 10, 653–658 (2013).
[Crossref] [PubMed]

Mukamel, E. A.

E. A. Mukamel, H. Babcock, and X. Zhuang, “Statistical deconvolution for superresolution fluorescence microscopy,” Biophys. J. 102, 2391–2400 (2012).
[Crossref] [PubMed]

Myers, J. R.

F. Huang, T. M. P. Hartwich, F. E. Rivera-Molina, Y. Lin, W. C. Duim, P. D. U. Jane, J Long, J. R. Myers, M. A. Baird, W. Mothes, M. W. Davidson, D. Toomre, and J. Bewersdorf, “Video-rate nanoscopy using scmos camera-specific single-molecule localization algorithms,” Nat. Methods 10, 653–658 (2013).
[Crossref] [PubMed]

Nagpure, B. S.

M. F. Juette, T. J. Gould, M. D. Lessard, M. J. Mlodzianoski, B. S. Nagpure, B. T. Bennett, S. T. Hess, and J. Bewersdorf, “Three-dimensional sub–100 nm resolution fluorescence microscopy of thick samples,” Nat. Methods 5, 527–529 (2008).
[Crossref] [PubMed]

Ökten, Z.

L. S. Churchman, Z. Ökten, R. S. Rock, J. F. Dawson, and J. A. Spudich, “Single molecule high-resolution colocalization of cy3 and cy5 attached to macromolecules measures intramolecular distances through time,” Proc. Natl. Acad. Sci. USA 102, 1419–1423 (2005).
[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, 1642–1645 (2006).
[Crossref] [PubMed]

Olivier, N.

J. Min, C. Vonesch, H. Kirshner, L. Carlini, N. Olivier, S. Holden, S. Manley, J. C. Ye, and M. Unser, “FALCON: fast and unbiased reconstruction of high-density super-resolution microscopy data,” Sci. Rep. 4, 4577 (2014).
[Crossref]

N. Olivier, D. Keller, P. Gönczy, and S. Manley, “Resolution doubling in 3D-STORM imaging through improved buffers,” PloS one 8, e69004 (2013).
[Crossref] [PubMed]

Patterson, G. H.

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

Piestun, R.

A. Barsic, G. Grover, and R. Piestun, “Three-dimensional super-resolution and localization of dense clusters of single molecules,” Sci. Rep. 4, 5388 (2014).
[Crossref] [PubMed]

Prinz, W. A.

J. Hu, W. A. Prinz, and T. A. Rapoport, “Weaving the web of ER tubules,” Cell 147, 1226–1231 (2011).
[Crossref] [PubMed]

Rapoport, T. A.

J. Hu, W. A. Prinz, and T. A. Rapoport, “Weaving the web of ER tubules,” Cell 147, 1226–1231 (2011).
[Crossref] [PubMed]

Rivera-Molina, F. E.

F. Huang, T. M. P. Hartwich, F. E. Rivera-Molina, Y. Lin, W. C. Duim, P. D. U. Jane, J Long, J. R. Myers, M. A. Baird, W. Mothes, M. W. Davidson, D. Toomre, and J. Bewersdorf, “Video-rate nanoscopy using scmos camera-specific single-molecule localization algorithms,” Nat. Methods 10, 653–658 (2013).
[Crossref] [PubMed]

Rock, R. S.

L. S. Churchman, Z. Ökten, R. S. Rock, J. F. Dawson, and J. A. Spudich, “Single molecule high-resolution colocalization of cy3 and cy5 attached to macromolecules measures intramolecular distances through time,” Proc. Natl. Acad. Sci. USA 102, 1419–1423 (2005).
[Crossref] [PubMed]

Rust, M. J.

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

Schwartz, S. L.

Sheng, Y.

L. Gu, Y. Sheng, Y. Chen, H. Chang, Y. Zhang, P. Lv, W. Ji, and T. Xu, “High-density 3D single molecular analysis based on compressed sensing,” Biophys. J. 106, 2443–2449 (2014).
[Crossref] [PubMed]

Shim, S.-H.

S. A. Jones, S.-H. Shim, J. He, and X. Zhuang, “Fast, three-dimensional super-resolution imaging of live cells,” Nat. Methods 8, 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, 417–423 (2008).
[Crossref] [PubMed]

Sigal, Y. M.

H. Babcock, Y. M. Sigal, and X. Zhuang, “A high-density 3D localization algorithm for stochastic optical reconstruction microscopy,” Optical Nanoscopy 1, 1–10 (2012).
[Crossref]

Snapp, E. L.

E. L. Snapp, ER biogenesis: proliferation and differentiation. The Biogenesis of Cellular Organelles (Landes Bioscience and KluwerAcademic/Plenum Publishers, 2004).

Sougrat, R.

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

Spudich, J. A.

L. S. Churchman, Z. Ökten, R. S. Rock, J. F. Dawson, and J. A. Spudich, “Single molecule high-resolution colocalization of cy3 and cy5 attached to macromolecules measures intramolecular distances through time,” Proc. Natl. Acad. Sci. USA 102, 1419–1423 (2005).
[Crossref] [PubMed]

Stuurman, N.

A. Edelstein, N. Amodaj, K. Hoover, R. Vale, and N. Stuurman, Computer Control of Microscopes Using μManager (John Wiley & Sons, Inc., 2010).

Toomre, D.

F. Huang, T. M. P. Hartwich, F. E. Rivera-Molina, Y. Lin, W. C. Duim, P. D. U. Jane, J Long, J. R. Myers, M. A. Baird, W. Mothes, M. W. Davidson, D. Toomre, and J. Bewersdorf, “Video-rate nanoscopy using scmos camera-specific single-molecule localization algorithms,” Nat. Methods 10, 653–658 (2013).
[Crossref] [PubMed]

Unser, M.

J. Min, C. Vonesch, H. Kirshner, L. Carlini, N. Olivier, S. Holden, S. Manley, J. C. Ye, and M. Unser, “FALCON: fast and unbiased reconstruction of high-density super-resolution microscopy data,” Sci. Rep. 4, 4577 (2014).
[Crossref]

Uphoff., S.

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

Vale, R.

A. Edelstein, N. Amodaj, K. Hoover, R. Vale, and N. Stuurman, Computer Control of Microscopes Using μManager (John Wiley & Sons, Inc., 2010).

Vonesch, C.

J. Min, C. Vonesch, H. Kirshner, L. Carlini, N. Olivier, S. Holden, S. Manley, J. C. Ye, and M. Unser, “FALCON: fast and unbiased reconstruction of high-density super-resolution microscopy data,” Sci. Rep. 4, 4577 (2014).
[Crossref]

Wang, W.

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

Xu, T.

L. Gu, Y. Sheng, Y. Chen, H. Chang, Y. Zhang, P. Lv, W. Ji, and T. Xu, “High-density 3D single molecular analysis based on compressed sensing,” Biophys. J. 106, 2443–2449 (2014).
[Crossref] [PubMed]

Ye, J. C.

J. Min, C. Vonesch, H. Kirshner, L. Carlini, N. Olivier, S. Holden, S. Manley, J. C. Ye, and M. Unser, “FALCON: fast and unbiased reconstruction of high-density super-resolution microscopy data,” Sci. Rep. 4, 4577 (2014).
[Crossref]

Zhang, W.

L. Zhu, W. Zhang, D. Elnatan, and B. Huang, “Faster storm using compressed sensing,” Nat. Methods 9, 721–723 (2012).
[Crossref] [PubMed]

Zhang, Y.

L. Gu, Y. Sheng, Y. Chen, H. Chang, Y. Zhang, P. Lv, W. Ji, and T. Xu, “High-density 3D single molecular analysis based on compressed sensing,” Biophys. J. 106, 2443–2449 (2014).
[Crossref] [PubMed]

Zhu, L.

L. Zhu, W. Zhang, D. Elnatan, and B. Huang, “Faster storm using compressed sensing,” Nat. Methods 9, 721–723 (2012).
[Crossref] [PubMed]

Zhuang, X.

H. Babcock, Y. M. Sigal, and X. Zhuang, “A high-density 3D localization algorithm for stochastic optical reconstruction microscopy,” Optical Nanoscopy 1, 1–10 (2012).
[Crossref]

E. A. Mukamel, H. Babcock, and X. Zhuang, “Statistical deconvolution for superresolution fluorescence microscopy,” Biophys. J. 102, 2391–2400 (2012).
[Crossref] [PubMed]

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

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

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

Biomed. Opt. Express (1)

Biophys. J. (3)

E. A. Mukamel, H. Babcock, and X. Zhuang, “Statistical deconvolution for superresolution fluorescence microscopy,” Biophys. J. 102, 2391–2400 (2012).
[Crossref] [PubMed]

L. Gu, Y. Sheng, Y. Chen, H. Chang, Y. Zhang, P. Lv, W. Ji, and T. Xu, “High-density 3D single molecular analysis based on compressed sensing,” Biophys. J. 106, 2443–2449 (2014).
[Crossref] [PubMed]

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

Cell (1)

J. Hu, W. A. Prinz, and T. A. Rapoport, “Weaving the web of ER tubules,” Cell 147, 1226–1231 (2011).
[Crossref] [PubMed]

ChemPhysChem (1)

S. Liu and K. A. Lidke, “A multiemitter localization comparison of 3d superresolution imaging modalities,” ChemPhysChem 15, 696–704 (2014).
[Crossref]

Nat. Methods (7)

L. Zhu, W. Zhang, D. Elnatan, and B. Huang, “Faster storm using compressed sensing,” Nat. Methods 9, 721–723 (2012).
[Crossref] [PubMed]

M. F. Juette, T. J. Gould, M. D. Lessard, M. J. Mlodzianoski, B. S. Nagpure, B. T. Bennett, S. T. Hess, and J. Bewersdorf, “Three-dimensional sub–100 nm resolution fluorescence microscopy of thick samples,” Nat. Methods 5, 527–529 (2008).
[Crossref] [PubMed]

F. Huang, T. M. P. Hartwich, F. E. Rivera-Molina, Y. Lin, W. C. Duim, P. D. U. Jane, J Long, J. R. Myers, M. A. Baird, W. Mothes, M. W. Davidson, D. Toomre, and J. Bewersdorf, “Video-rate nanoscopy using scmos camera-specific single-molecule localization algorithms,” Nat. Methods 10, 653–658 (2013).
[Crossref] [PubMed]

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

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

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

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

Opt. Lett. (1)

Optical Nanoscopy (1)

H. Babcock, Y. M. Sigal, and X. Zhuang, “A high-density 3D localization algorithm for stochastic optical reconstruction microscopy,” Optical Nanoscopy 1, 1–10 (2012).
[Crossref]

PloS one (1)

N. Olivier, D. Keller, P. Gönczy, and S. Manley, “Resolution doubling in 3D-STORM imaging through improved buffers,” PloS one 8, e69004 (2013).
[Crossref] [PubMed]

Proc. Natl. Acad. Sci. USA (1)

L. S. Churchman, Z. Ökten, R. S. Rock, J. F. Dawson, and J. A. Spudich, “Single molecule high-resolution colocalization of cy3 and cy5 attached to macromolecules measures intramolecular distances through time,” Proc. Natl. Acad. Sci. USA 102, 1419–1423 (2005).
[Crossref] [PubMed]

Sci. Rep. (2)

A. Barsic, G. Grover, and R. Piestun, “Three-dimensional super-resolution and localization of dense clusters of single molecules,” Sci. Rep. 4, 5388 (2014).
[Crossref] [PubMed]

J. Min, C. Vonesch, H. Kirshner, L. Carlini, N. Olivier, S. Holden, S. Manley, J. C. Ye, and M. Unser, “FALCON: fast and unbiased reconstruction of high-density super-resolution microscopy data,” Sci. Rep. 4, 4577 (2014).
[Crossref]

Science (2)

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

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

Other (2)

E. L. Snapp, ER biogenesis: proliferation and differentiation. The Biogenesis of Cellular Organelles (Landes Bioscience and KluwerAcademic/Plenum Publishers, 2004).

A. Edelstein, N. Amodaj, K. Hoover, R. Vale, and N. Stuurman, Computer Control of Microscopes Using μManager (John Wiley & Sons, Inc., 2010).

Supplementary Material (2)

» Media 1: AVI (781 KB)     
» Media 2: AVI (506 KB)     

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Figures (7)

Fig. 1
Fig. 1

Hybrid imaging system implemented by inserting a cylindrical lens in one channel of a biplane imaging system. Experimentally measured PSF model on the right side. Obj: objective lens, DM: dichroic mirror, EM: emission filter, CL: cylindrical lens, BS: beam splitter.

Fig. 2
Fig. 2

Channel alignment analysis: an LWM transform T is constructed after collecting paired points (ρ1, ρ2) from the two channels, where ρi = (xi, yi). Registration errors were calculated by e = ρ1T (ρ2).

Fig. 3
Fig. 3

PSF analysis: mutual correlation values between PSF1(0,0,z1) and PSF2(dx,dy,z2) over ranges of −1μm < dx, dy < 1μm and −600nm < z1, z1 < 600nm. The left three columns correspond to lateral analysis of mutual coherence, and the rightmost column represents the axial analysis.

Fig. 4
Fig. 4

Simulation analysis in comparison with least-square fitting method with molecular activation density from 0.1 to 7 μm−2. Analysis results of the highest-photon emission rates (a–c), mid-photon emission rates (d–f) and the lowest-photon emission rates (g–i): lateral localization accuracy (a,d,g), axial localization accuracy (b,e,h) and recall rates (c,f,i). At each imaging density, the analysis was repeated 50 times, and the error bar denotes standard deviation.

Fig. 5
Fig. 5

3D super-resolution reconstruction of fixed microtubule data. Alpha tubulin subunits of microtubules (MTs) labeled with Alexa 647 in COS-7 cells were imaged with a 30 ms exposure time. (a) a single raw high-density image. (b) a conventional wide-field image acquired from 150 raw frames. (c) a SR image of LS fitting and (d) a SR image of FALCON3D by using 150 frames of raw high density data. (e–g) close-up images from the regions of solid white boxes in (b–d), respectively. (h–j) close-up images from the regions of dotted white boxes in (b–d), respectively. (k) lateral and axial line profiles of the microtubules highlighted by the yellow arrows in (c–d). (l) lateral and axial line profiles, respectively, measured from (g). (m) lateral and axial line profiles respectively, measured from (j). The colors in (l) and (m) correspond to the profiles of microtubules highlighted by the arrows of the same colors in (g) and (j), respectively. The widths of the microtubules are indicated as full width at half maximum. Scale bars are 2 μm in (a–d), and 500nm in (e–j)

Fig. 6
Fig. 6

3D super-resolution reconstruction of live ER data. The endoplasmic reticulum proteins, reticulon-4 fused to tdEos in a COS 7 cell were imaged with a 30 ms exposure time. (a) conventional wide-field images generated by averaging 100 frames of raw high-density data from a non-astigmatism channel for each image, (b) SR images of LS fitting (see Media 2), (c) SR images of FALCON3D (see Media 1) with a temporal resolution of 3 seconds. (d–f) close-up images corresponding to the regions of white boxes (d), green boxes (e), and yellow boxes (f), respectively. Scale bars in (a–c) are 2 μm, and scale bars in (d–f) are 500nm

Fig. 7
Fig. 7

Experimentally measured PSFs for astigmatic imaging (Astigmatism) and biplane imaging (Biplane)

Equations (10)

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

S ( ρ ) = k = 1 K c k δ ( ρ ρ k ) ,
f 1 [ n ] = ( k = 1 K c k h 1 ( n ρ k ) ) + b 1 ( n ) + e 1 ( n ) , f 2 [ n ] = ( k = 1 K c k h 2 ( n ρ k ) ) + b 2 ( n ) + e 2 ( n ) .
n [ ( f 1 [ n ] b 1 [ n ] k = 1 K c k h 1 ( n ρ k ) ) 2 + ( f 2 [ n ] b 2 [ n ] k = 1 K c k h 2 ( n ρ k ) ) 2 ] .
f = Hc + b
min c 0 f Hc b 2 2 + ϕ ( c ) .
ρ k = m k + ε k .
h ( x ρ k ) h ( x m k ) ε k T h ( x m k ) .
J ( c , ε ) = n ( f 1 [ n ] b 1 k = 1 K c [ m k ] [ h 1 ( n m k ) ε k T h 1 ( n m k ) ] ) 2 + n ( f 2 [ n ] b 2 k = 1 K c [ m k ] [ h 2 ( n m k ) ε k T h 2 ( n m k ) ] ) 2 .
min c > 0 f Hc b 2 2 + ϕ ( c )
min c > 0 , | ε | Δ J ( c , ε ) .

Metrics