Abstract

Three-dimensional (3D) particle localization at the nanometer scale plays a central role in 3D particle tracking and 3D localization-based super-resolution microscopy. Here we introduce a localization algorithm that is independent of theoretical models and therefore generally applicable to a large number of experimental realizations. Applying this algorithm and a convertible experimental setup we compare the performance of the two major 3D techniques based on astigmatic distortions and on multiplane detection. In both methods we obtain experimental 3D localization accuracies in agreement with theoretical predictions and characterize the depth dependence of the localization accuracy in detail.

© 2009 Optical Society of America

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    [CrossRef] [PubMed]
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    [CrossRef] [PubMed]
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    [CrossRef] [PubMed]

2009

S. W. Hell, "Microscopy and its focal switch," Nat. Methods 6, 24-32 (2009).
[CrossRef] [PubMed]

G. Shtengel, J. A. Galbraith, C. G. Galbraith, J. Lippincott-Schwartz, J. M. Gillette, S. Manley, R. Sougrat, C. M. Waterman, P. Kanchanawong, M. W. Davidson, R. D. Fetter, and H. F. Hess, "Interferometric fluorescent super-resolution microscopy resolves 3D cellular ultrastructure," Proc. Natl. Acad. Sci. USA 106, 3125-3130 (2009).
[CrossRef] [PubMed]

S. R. Pavani, M. A. Thompson, J. S. Biteen, S. J. Lord, N. Liu, R. J. Twieg, R. Piestun, and W. E. Moerner, "Three-dimensional, single-molecule fluorescence imaging beyond the diffraction limit by using a double-helix point spread function," Proc. Natl. Acad. Sci. USA 106, 2995-2999 (2009).
[CrossRef] [PubMed]

Y. Deng and J. W. Shaevitz, "Effect of aberration on height calibration in three-dimensional localization-based microscopy and particle tracking," Appl. Opt. 48, 1886-1890 (2009).
[CrossRef] [PubMed]

2008

C. von Middendorff, A. Egner, C. Geisler, S. W. Hell, and A. Schoenle, "Isotropic 3D Nanoscopy based on single emitter switching," Opt. Express 16, 20774-20788 (2008).
[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]

S. Ram, P. Prabhat, J. Chao, E. S. Ward, and R. J. Ober, "High Accuracy 3D Quantum Dot Tracking with Multifocal Plane Microscopy for the Study of Fast Intracellular Dynamics in Live Cells," Biophys. J. 95, 6025-6043 (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).

2007

S. Ram, J. Chao, P. Prabhat, E. S. Ward, and R. J. Ober, "A novel approach to determining the three-dimensional location of microscopic objects with applications to 3D particle tracking," Proc. SPIE 6443, 1-7 (2007).

P. Prabhat, Z. Gan, J. Chao, S. Ram, C. Vaccaro, S. Gibbons, R. J. Ober, and E. S. Ward, "Elucidation of intracellular recycling pathways leading to exocytosis of the Fc receptor, FcRn, by using multifocal plane microscopy," Proc. Natl. Acad. Sci. USA 104, 5889-5894 (2007).
[CrossRef] [PubMed]

E. Toprak, H. Balci, B. H. Blehm, and P. R. Selvin, "Three-dimensional particle tracking via bifocal imaging," Nano Lett. 7, 2043-2045 (2007).
[CrossRef] [PubMed]

L. Holtzer, T. Meckel, and T. Schmidt, "Nanometric three-dimensional tracking of individual quantum dots in cells," Appl. Phys. Lett. 90, 053902 (2007).
[CrossRef]

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

2006

J. Enderlein, E. Toprak, and P. R. Selvin, "Polarization effect on position accuracy of fluorophore localization," Opt. Express 14, 8111-8120 (2006).
[CrossRef] [PubMed]

S. T. Hess, T. P. K. Girirajan, and M. D. Mason, "Ultra-High Resolution Imaging by Fluorescence Photoactivation Localization Microscopy," Biophys. J. 91, 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, 1642-1645 (2006).
[CrossRef] [PubMed]

2005

S. Ram, E. S. Ward, and R. J. Ober, "How accurately can a single molecule be localized in three dimensions using a fluorescence microscope?," Proc. SPIE 5699, 426-435 (2005).
[CrossRef] [PubMed]

M. Wu, J. W. Roberts, and M. Buckley, "Three-dimensional fluorescent particle tracking at micron-scale using a single camera," Exp. Fluids 38, 461-465 (2005).
[CrossRef]

2004

P. Prabhat, S. Ram, E. S. Ward, and R. J. Ober, "Simultaneous imaging of different focal planes in fluorescence microscopy for the study of cellular dynamics in three dimensions," IEEE Trans. Nanobiosci. 3, 237-242 (2004).
[CrossRef]

K. Murase, T. Fujiwara, Y. Umemura, K. Suzuki, R. Iino, H. Yamashita, M. Saito, H. Murakoshi, K. Ritchie, and A. Kusumi, "Ultrafine membrane compartments for molecular diffusion as revealed by single molecule techniques," Biophys. J. 86, 4075-4093 (2004).
[CrossRef] [PubMed]

2003

A. Yildiz, J. N. Forkey, S. A. McKinney, T. Ha, Y. E. Goldman, and P. R. Selvin, "Myosin V walks hand-over-hand: single fluorophore imaging with 1.5-nm localization," Science 300, 2061-2065 (2003).
[CrossRef] [PubMed]

M. Speidel, A. Jonas, and E. L. Florin, "Three-dimensional tracking of fluorescent nanoparticles with subnanometer precision by use of off-focus imaging," Opt. Lett. 28, 69-71 (2003).
[CrossRef] [PubMed]

1994

H. P. Kao and A. S. Verkman, "Tracking of single fluorescent particles in three dimensions: use of cylindrical optics to encode particle position," Biophys. J. 67, 1291-1300 (1994).
[CrossRef] [PubMed]

1988

J. Gelles, B. J. Schnapp, and M. P. Sheetz, "Tracking kinesin-driven movements with nanometre-scale precision," Nature 331, 450-453 (1988).
[CrossRef] [PubMed]

Balci, H.

E. Toprak, H. Balci, B. H. Blehm, and P. R. Selvin, "Three-dimensional particle tracking via bifocal imaging," Nano Lett. 7, 2043-2045 (2007).
[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]

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).

Betzig, E.

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

Bewersdorf, 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).

Biteen, J. S.

S. R. Pavani, M. A. Thompson, J. S. Biteen, S. J. Lord, N. Liu, R. J. Twieg, R. Piestun, and W. E. Moerner, "Three-dimensional, single-molecule fluorescence imaging beyond the diffraction limit by using a double-helix point spread function," Proc. Natl. Acad. Sci. USA 106, 2995-2999 (2009).
[CrossRef] [PubMed]

Blehm, B. H.

E. Toprak, H. Balci, B. H. Blehm, and P. R. Selvin, "Three-dimensional particle tracking via bifocal imaging," Nano Lett. 7, 2043-2045 (2007).
[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]

Buckley, M.

M. Wu, J. W. Roberts, and M. Buckley, "Three-dimensional fluorescent particle tracking at micron-scale using a single camera," Exp. Fluids 38, 461-465 (2005).
[CrossRef]

Chao, J.

S. Ram, P. Prabhat, J. Chao, E. S. Ward, and R. J. Ober, "High Accuracy 3D Quantum Dot Tracking with Multifocal Plane Microscopy for the Study of Fast Intracellular Dynamics in Live Cells," Biophys. J. 95, 6025-6043 (2008).
[CrossRef] [PubMed]

P. Prabhat, Z. Gan, J. Chao, S. Ram, C. Vaccaro, S. Gibbons, R. J. Ober, and E. S. Ward, "Elucidation of intracellular recycling pathways leading to exocytosis of the Fc receptor, FcRn, by using multifocal plane microscopy," Proc. Natl. Acad. Sci. USA 104, 5889-5894 (2007).
[CrossRef] [PubMed]

S. Ram, J. Chao, P. Prabhat, E. S. Ward, and R. J. Ober, "A novel approach to determining the three-dimensional location of microscopic objects with applications to 3D particle tracking," Proc. SPIE 6443, 1-7 (2007).

Davidson, M. W.

G. Shtengel, J. A. Galbraith, C. G. Galbraith, J. Lippincott-Schwartz, J. M. Gillette, S. Manley, R. Sougrat, C. M. Waterman, P. Kanchanawong, M. W. Davidson, R. D. Fetter, and H. F. Hess, "Interferometric fluorescent super-resolution microscopy resolves 3D cellular ultrastructure," Proc. Natl. Acad. Sci. USA 106, 3125-3130 (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, 1642-1645 (2006).
[CrossRef] [PubMed]

Deng, Y.

Egner, A.

Enderlein, J.

Fetter, R. D.

G. Shtengel, J. A. Galbraith, C. G. Galbraith, J. Lippincott-Schwartz, J. M. Gillette, S. Manley, R. Sougrat, C. M. Waterman, P. Kanchanawong, M. W. Davidson, R. D. Fetter, and H. F. Hess, "Interferometric fluorescent super-resolution microscopy resolves 3D cellular ultrastructure," Proc. Natl. Acad. Sci. USA 106, 3125-3130 (2009).
[CrossRef] [PubMed]

Florin, E. L.

Forkey, J. N.

A. Yildiz, J. N. Forkey, S. A. McKinney, T. Ha, Y. E. Goldman, and P. R. Selvin, "Myosin V walks hand-over-hand: single fluorophore imaging with 1.5-nm localization," Science 300, 2061-2065 (2003).
[CrossRef] [PubMed]

Fujiwara, T.

K. Murase, T. Fujiwara, Y. Umemura, K. Suzuki, R. Iino, H. Yamashita, M. Saito, H. Murakoshi, K. Ritchie, and A. Kusumi, "Ultrafine membrane compartments for molecular diffusion as revealed by single molecule techniques," Biophys. J. 86, 4075-4093 (2004).
[CrossRef] [PubMed]

Galbraith, C. G.

G. Shtengel, J. A. Galbraith, C. G. Galbraith, J. Lippincott-Schwartz, J. M. Gillette, S. Manley, R. Sougrat, C. M. Waterman, P. Kanchanawong, M. W. Davidson, R. D. Fetter, and H. F. Hess, "Interferometric fluorescent super-resolution microscopy resolves 3D cellular ultrastructure," Proc. Natl. Acad. Sci. USA 106, 3125-3130 (2009).
[CrossRef] [PubMed]

Galbraith, J. A.

G. Shtengel, J. A. Galbraith, C. G. Galbraith, J. Lippincott-Schwartz, J. M. Gillette, S. Manley, R. Sougrat, C. M. Waterman, P. Kanchanawong, M. W. Davidson, R. D. Fetter, and H. F. Hess, "Interferometric fluorescent super-resolution microscopy resolves 3D cellular ultrastructure," Proc. Natl. Acad. Sci. USA 106, 3125-3130 (2009).
[CrossRef] [PubMed]

Gan, Z.

P. Prabhat, Z. Gan, J. Chao, S. Ram, C. Vaccaro, S. Gibbons, R. J. Ober, and E. S. Ward, "Elucidation of intracellular recycling pathways leading to exocytosis of the Fc receptor, FcRn, by using multifocal plane microscopy," Proc. Natl. Acad. Sci. USA 104, 5889-5894 (2007).
[CrossRef] [PubMed]

Geisler, C.

Gelles, J.

J. Gelles, B. J. Schnapp, and M. P. Sheetz, "Tracking kinesin-driven movements with nanometre-scale precision," Nature 331, 450-453 (1988).
[CrossRef] [PubMed]

Gibbons, S.

P. Prabhat, Z. Gan, J. Chao, S. Ram, C. Vaccaro, S. Gibbons, R. J. Ober, and E. S. Ward, "Elucidation of intracellular recycling pathways leading to exocytosis of the Fc receptor, FcRn, by using multifocal plane microscopy," Proc. Natl. Acad. Sci. USA 104, 5889-5894 (2007).
[CrossRef] [PubMed]

Gillette, J. M.

G. Shtengel, J. A. Galbraith, C. G. Galbraith, J. Lippincott-Schwartz, J. M. Gillette, S. Manley, R. Sougrat, C. M. Waterman, P. Kanchanawong, M. W. Davidson, R. D. Fetter, and H. F. Hess, "Interferometric fluorescent super-resolution microscopy resolves 3D cellular ultrastructure," Proc. Natl. Acad. Sci. USA 106, 3125-3130 (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, 4258-4272 (2006).
[CrossRef] [PubMed]

Goldman, Y. E.

A. Yildiz, J. N. Forkey, S. A. McKinney, T. Ha, Y. E. Goldman, and P. R. Selvin, "Myosin V walks hand-over-hand: single fluorophore imaging with 1.5-nm localization," Science 300, 2061-2065 (2003).
[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).

Ha, T.

A. Yildiz, J. N. Forkey, S. A. McKinney, T. Ha, Y. E. Goldman, and P. R. Selvin, "Myosin V walks hand-over-hand: single fluorophore imaging with 1.5-nm localization," Science 300, 2061-2065 (2003).
[CrossRef] [PubMed]

Hell, S. W.

S. W. Hell, "Microscopy and its focal switch," Nat. Methods 6, 24-32 (2009).
[CrossRef] [PubMed]

C. von Middendorff, A. Egner, C. Geisler, S. W. Hell, and A. Schoenle, "Isotropic 3D Nanoscopy based on single emitter switching," Opt. Express 16, 20774-20788 (2008).
[CrossRef] [PubMed]

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

Hess, H. F.

G. Shtengel, J. A. Galbraith, C. G. Galbraith, J. Lippincott-Schwartz, J. M. Gillette, S. Manley, R. Sougrat, C. M. Waterman, P. Kanchanawong, M. W. Davidson, R. D. Fetter, and H. F. Hess, "Interferometric fluorescent super-resolution microscopy resolves 3D cellular ultrastructure," Proc. Natl. Acad. Sci. USA 106, 3125-3130 (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, 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).

S. T. Hess, T. P. K. Girirajan, and M. D. Mason, "Ultra-High Resolution Imaging by Fluorescence Photoactivation Localization Microscopy," Biophys. J. 91, 4258-4272 (2006).
[CrossRef] [PubMed]

Holtzer, L.

L. Holtzer, T. Meckel, and T. Schmidt, "Nanometric three-dimensional tracking of individual quantum dots in cells," Appl. Phys. Lett. 90, 053902 (2007).
[CrossRef]

Huang, B.

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]

Iino, R.

K. Murase, T. Fujiwara, Y. Umemura, K. Suzuki, R. Iino, H. Yamashita, M. Saito, H. Murakoshi, K. Ritchie, and A. Kusumi, "Ultrafine membrane compartments for molecular diffusion as revealed by single molecule techniques," Biophys. J. 86, 4075-4093 (2004).
[CrossRef] [PubMed]

Jonas, A.

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).

Kanchanawong, P.

G. Shtengel, J. A. Galbraith, C. G. Galbraith, J. Lippincott-Schwartz, J. M. Gillette, S. Manley, R. Sougrat, C. M. Waterman, P. Kanchanawong, M. W. Davidson, R. D. Fetter, and H. F. Hess, "Interferometric fluorescent super-resolution microscopy resolves 3D cellular ultrastructure," Proc. Natl. Acad. Sci. USA 106, 3125-3130 (2009).
[CrossRef] [PubMed]

Kao, H. P.

H. P. Kao and A. S. Verkman, "Tracking of single fluorescent particles in three dimensions: use of cylindrical optics to encode particle position," Biophys. J. 67, 1291-1300 (1994).
[CrossRef] [PubMed]

Kusumi, A.

K. Murase, T. Fujiwara, Y. Umemura, K. Suzuki, R. Iino, H. Yamashita, M. Saito, H. Murakoshi, K. Ritchie, and A. Kusumi, "Ultrafine membrane compartments for molecular diffusion as revealed by single molecule techniques," Biophys. J. 86, 4075-4093 (2004).
[CrossRef] [PubMed]

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).

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.

G. Shtengel, J. A. Galbraith, C. G. Galbraith, J. Lippincott-Schwartz, J. M. Gillette, S. Manley, R. Sougrat, C. M. Waterman, P. Kanchanawong, M. W. Davidson, R. D. Fetter, and H. F. Hess, "Interferometric fluorescent super-resolution microscopy resolves 3D cellular ultrastructure," Proc. Natl. Acad. Sci. USA 106, 3125-3130 (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, 1642-1645 (2006).
[CrossRef] [PubMed]

Liu, N.

S. R. Pavani, M. A. Thompson, J. S. Biteen, S. J. Lord, N. Liu, R. J. Twieg, R. Piestun, and W. E. Moerner, "Three-dimensional, single-molecule fluorescence imaging beyond the diffraction limit by using a double-helix point spread function," Proc. Natl. Acad. Sci. USA 106, 2995-2999 (2009).
[CrossRef] [PubMed]

Lord, S. J.

S. R. Pavani, M. A. Thompson, J. S. Biteen, S. J. Lord, N. Liu, R. J. Twieg, R. Piestun, and W. E. Moerner, "Three-dimensional, single-molecule fluorescence imaging beyond the diffraction limit by using a double-helix point spread function," Proc. Natl. Acad. Sci. USA 106, 2995-2999 (2009).
[CrossRef] [PubMed]

Manley, S.

G. Shtengel, J. A. Galbraith, C. G. Galbraith, J. Lippincott-Schwartz, J. M. Gillette, S. Manley, R. Sougrat, C. M. Waterman, P. Kanchanawong, M. W. Davidson, R. D. Fetter, and H. F. Hess, "Interferometric fluorescent super-resolution microscopy resolves 3D cellular ultrastructure," Proc. Natl. Acad. Sci. USA 106, 3125-3130 (2009).
[CrossRef] [PubMed]

Mason, M. D.

S. T. Hess, T. P. K. Girirajan, and M. D. Mason, "Ultra-High Resolution Imaging by Fluorescence Photoactivation Localization Microscopy," Biophys. J. 91, 4258-4272 (2006).
[CrossRef] [PubMed]

McKinney, S. A.

A. Yildiz, J. N. Forkey, S. A. McKinney, T. Ha, Y. E. Goldman, and P. R. Selvin, "Myosin V walks hand-over-hand: single fluorophore imaging with 1.5-nm localization," Science 300, 2061-2065 (2003).
[CrossRef] [PubMed]

Meckel, T.

L. Holtzer, T. Meckel, and T. Schmidt, "Nanometric three-dimensional tracking of individual quantum dots in cells," Appl. Phys. Lett. 90, 053902 (2007).
[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).

Moerner, W. E.

S. R. Pavani, M. A. Thompson, J. S. Biteen, S. J. Lord, N. Liu, R. J. Twieg, R. Piestun, and W. E. Moerner, "Three-dimensional, single-molecule fluorescence imaging beyond the diffraction limit by using a double-helix point spread function," Proc. Natl. Acad. Sci. USA 106, 2995-2999 (2009).
[CrossRef] [PubMed]

Murakoshi, H.

K. Murase, T. Fujiwara, Y. Umemura, K. Suzuki, R. Iino, H. Yamashita, M. Saito, H. Murakoshi, K. Ritchie, and A. Kusumi, "Ultrafine membrane compartments for molecular diffusion as revealed by single molecule techniques," Biophys. J. 86, 4075-4093 (2004).
[CrossRef] [PubMed]

Murase, K.

K. Murase, T. Fujiwara, Y. Umemura, K. Suzuki, R. Iino, H. Yamashita, M. Saito, H. Murakoshi, K. Ritchie, and A. Kusumi, "Ultrafine membrane compartments for molecular diffusion as revealed by single molecule techniques," Biophys. J. 86, 4075-4093 (2004).
[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).

Ober, R. J.

S. Ram, P. Prabhat, J. Chao, E. S. Ward, and R. J. Ober, "High Accuracy 3D Quantum Dot Tracking with Multifocal Plane Microscopy for the Study of Fast Intracellular Dynamics in Live Cells," Biophys. J. 95, 6025-6043 (2008).
[CrossRef] [PubMed]

P. Prabhat, Z. Gan, J. Chao, S. Ram, C. Vaccaro, S. Gibbons, R. J. Ober, and E. S. Ward, "Elucidation of intracellular recycling pathways leading to exocytosis of the Fc receptor, FcRn, by using multifocal plane microscopy," Proc. Natl. Acad. Sci. USA 104, 5889-5894 (2007).
[CrossRef] [PubMed]

S. Ram, J. Chao, P. Prabhat, E. S. Ward, and R. J. Ober, "A novel approach to determining the three-dimensional location of microscopic objects with applications to 3D particle tracking," Proc. SPIE 6443, 1-7 (2007).

S. Ram, E. S. Ward, and R. J. Ober, "How accurately can a single molecule be localized in three dimensions using a fluorescence microscope?," Proc. SPIE 5699, 426-435 (2005).
[CrossRef] [PubMed]

P. Prabhat, S. Ram, E. S. Ward, and R. J. Ober, "Simultaneous imaging of different focal planes in fluorescence microscopy for the study of cellular dynamics in three dimensions," IEEE Trans. Nanobiosci. 3, 237-242 (2004).
[CrossRef]

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]

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]

Pavani, S. R.

S. R. Pavani, M. A. Thompson, J. S. Biteen, S. J. Lord, N. Liu, R. J. Twieg, R. Piestun, and W. E. Moerner, "Three-dimensional, single-molecule fluorescence imaging beyond the diffraction limit by using a double-helix point spread function," Proc. Natl. Acad. Sci. USA 106, 2995-2999 (2009).
[CrossRef] [PubMed]

Piestun, R.

S. R. Pavani, M. A. Thompson, J. S. Biteen, S. J. Lord, N. Liu, R. J. Twieg, R. Piestun, and W. E. Moerner, "Three-dimensional, single-molecule fluorescence imaging beyond the diffraction limit by using a double-helix point spread function," Proc. Natl. Acad. Sci. USA 106, 2995-2999 (2009).
[CrossRef] [PubMed]

Prabhat, P.

S. Ram, P. Prabhat, J. Chao, E. S. Ward, and R. J. Ober, "High Accuracy 3D Quantum Dot Tracking with Multifocal Plane Microscopy for the Study of Fast Intracellular Dynamics in Live Cells," Biophys. J. 95, 6025-6043 (2008).
[CrossRef] [PubMed]

P. Prabhat, Z. Gan, J. Chao, S. Ram, C. Vaccaro, S. Gibbons, R. J. Ober, and E. S. Ward, "Elucidation of intracellular recycling pathways leading to exocytosis of the Fc receptor, FcRn, by using multifocal plane microscopy," Proc. Natl. Acad. Sci. USA 104, 5889-5894 (2007).
[CrossRef] [PubMed]

S. Ram, J. Chao, P. Prabhat, E. S. Ward, and R. J. Ober, "A novel approach to determining the three-dimensional location of microscopic objects with applications to 3D particle tracking," Proc. SPIE 6443, 1-7 (2007).

P. Prabhat, S. Ram, E. S. Ward, and R. J. Ober, "Simultaneous imaging of different focal planes in fluorescence microscopy for the study of cellular dynamics in three dimensions," IEEE Trans. Nanobiosci. 3, 237-242 (2004).
[CrossRef]

Ram, S.

S. Ram, P. Prabhat, J. Chao, E. S. Ward, and R. J. Ober, "High Accuracy 3D Quantum Dot Tracking with Multifocal Plane Microscopy for the Study of Fast Intracellular Dynamics in Live Cells," Biophys. J. 95, 6025-6043 (2008).
[CrossRef] [PubMed]

P. Prabhat, Z. Gan, J. Chao, S. Ram, C. Vaccaro, S. Gibbons, R. J. Ober, and E. S. Ward, "Elucidation of intracellular recycling pathways leading to exocytosis of the Fc receptor, FcRn, by using multifocal plane microscopy," Proc. Natl. Acad. Sci. USA 104, 5889-5894 (2007).
[CrossRef] [PubMed]

S. Ram, J. Chao, P. Prabhat, E. S. Ward, and R. J. Ober, "A novel approach to determining the three-dimensional location of microscopic objects with applications to 3D particle tracking," Proc. SPIE 6443, 1-7 (2007).

S. Ram, E. S. Ward, and R. J. Ober, "How accurately can a single molecule be localized in three dimensions using a fluorescence microscope?," Proc. SPIE 5699, 426-435 (2005).
[CrossRef] [PubMed]

P. Prabhat, S. Ram, E. S. Ward, and R. J. Ober, "Simultaneous imaging of different focal planes in fluorescence microscopy for the study of cellular dynamics in three dimensions," IEEE Trans. Nanobiosci. 3, 237-242 (2004).
[CrossRef]

Ritchie, K.

K. Murase, T. Fujiwara, Y. Umemura, K. Suzuki, R. Iino, H. Yamashita, M. Saito, H. Murakoshi, K. Ritchie, and A. Kusumi, "Ultrafine membrane compartments for molecular diffusion as revealed by single molecule techniques," Biophys. J. 86, 4075-4093 (2004).
[CrossRef] [PubMed]

Roberts, J. W.

M. Wu, J. W. Roberts, and M. Buckley, "Three-dimensional fluorescent particle tracking at micron-scale using a single camera," Exp. Fluids 38, 461-465 (2005).
[CrossRef]

Saito, M.

K. Murase, T. Fujiwara, Y. Umemura, K. Suzuki, R. Iino, H. Yamashita, M. Saito, H. Murakoshi, K. Ritchie, and A. Kusumi, "Ultrafine membrane compartments for molecular diffusion as revealed by single molecule techniques," Biophys. J. 86, 4075-4093 (2004).
[CrossRef] [PubMed]

Schmidt, T.

L. Holtzer, T. Meckel, and T. Schmidt, "Nanometric three-dimensional tracking of individual quantum dots in cells," Appl. Phys. Lett. 90, 053902 (2007).
[CrossRef]

Schnapp, B. J.

J. Gelles, B. J. Schnapp, and M. P. Sheetz, "Tracking kinesin-driven movements with nanometre-scale precision," Nature 331, 450-453 (1988).
[CrossRef] [PubMed]

Schoenle, A.

Selvin, P. R.

E. Toprak, H. Balci, B. H. Blehm, and P. R. Selvin, "Three-dimensional particle tracking via bifocal imaging," Nano Lett. 7, 2043-2045 (2007).
[CrossRef] [PubMed]

J. Enderlein, E. Toprak, and P. R. Selvin, "Polarization effect on position accuracy of fluorophore localization," Opt. Express 14, 8111-8120 (2006).
[CrossRef] [PubMed]

A. Yildiz, J. N. Forkey, S. A. McKinney, T. Ha, Y. E. Goldman, and P. R. Selvin, "Myosin V walks hand-over-hand: single fluorophore imaging with 1.5-nm localization," Science 300, 2061-2065 (2003).
[CrossRef] [PubMed]

Shaevitz, J. W.

Sheetz, M. P.

J. Gelles, B. J. Schnapp, and M. P. Sheetz, "Tracking kinesin-driven movements with nanometre-scale precision," Nature 331, 450-453 (1988).
[CrossRef] [PubMed]

Shtengel, G.

G. Shtengel, J. A. Galbraith, C. G. Galbraith, J. Lippincott-Schwartz, J. M. Gillette, S. Manley, R. Sougrat, C. M. Waterman, P. Kanchanawong, M. W. Davidson, R. D. Fetter, and H. F. Hess, "Interferometric fluorescent super-resolution microscopy resolves 3D cellular ultrastructure," Proc. Natl. Acad. Sci. USA 106, 3125-3130 (2009).
[CrossRef] [PubMed]

Sougrat, R.

G. Shtengel, J. A. Galbraith, C. G. Galbraith, J. Lippincott-Schwartz, J. M. Gillette, S. Manley, R. Sougrat, C. M. Waterman, P. Kanchanawong, M. W. Davidson, R. D. Fetter, and H. F. Hess, "Interferometric fluorescent super-resolution microscopy resolves 3D cellular ultrastructure," Proc. Natl. Acad. Sci. USA 106, 3125-3130 (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, 1642-1645 (2006).
[CrossRef] [PubMed]

Speidel, M.

Suzuki, K.

K. Murase, T. Fujiwara, Y. Umemura, K. Suzuki, R. Iino, H. Yamashita, M. Saito, H. Murakoshi, K. Ritchie, and A. Kusumi, "Ultrafine membrane compartments for molecular diffusion as revealed by single molecule techniques," Biophys. J. 86, 4075-4093 (2004).
[CrossRef] [PubMed]

Thompson, M. A.

S. R. Pavani, M. A. Thompson, J. S. Biteen, S. J. Lord, N. Liu, R. J. Twieg, R. Piestun, and W. E. Moerner, "Three-dimensional, single-molecule fluorescence imaging beyond the diffraction limit by using a double-helix point spread function," Proc. Natl. Acad. Sci. USA 106, 2995-2999 (2009).
[CrossRef] [PubMed]

Toprak, E.

E. Toprak, H. Balci, B. H. Blehm, and P. R. Selvin, "Three-dimensional particle tracking via bifocal imaging," Nano Lett. 7, 2043-2045 (2007).
[CrossRef] [PubMed]

J. Enderlein, E. Toprak, and P. R. Selvin, "Polarization effect on position accuracy of fluorophore localization," Opt. Express 14, 8111-8120 (2006).
[CrossRef] [PubMed]

Twieg, R. J.

S. R. Pavani, M. A. Thompson, J. S. Biteen, S. J. Lord, N. Liu, R. J. Twieg, R. Piestun, and W. E. Moerner, "Three-dimensional, single-molecule fluorescence imaging beyond the diffraction limit by using a double-helix point spread function," Proc. Natl. Acad. Sci. USA 106, 2995-2999 (2009).
[CrossRef] [PubMed]

Umemura, Y.

K. Murase, T. Fujiwara, Y. Umemura, K. Suzuki, R. Iino, H. Yamashita, M. Saito, H. Murakoshi, K. Ritchie, and A. Kusumi, "Ultrafine membrane compartments for molecular diffusion as revealed by single molecule techniques," Biophys. J. 86, 4075-4093 (2004).
[CrossRef] [PubMed]

Vaccaro, C.

P. Prabhat, Z. Gan, J. Chao, S. Ram, C. Vaccaro, S. Gibbons, R. J. Ober, and E. S. Ward, "Elucidation of intracellular recycling pathways leading to exocytosis of the Fc receptor, FcRn, by using multifocal plane microscopy," Proc. Natl. Acad. Sci. USA 104, 5889-5894 (2007).
[CrossRef] [PubMed]

Verkman, A. S.

H. P. Kao and A. S. Verkman, "Tracking of single fluorescent particles in three dimensions: use of cylindrical optics to encode particle position," Biophys. J. 67, 1291-1300 (1994).
[CrossRef] [PubMed]

von Middendorff, C.

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]

Ward, E. S.

S. Ram, P. Prabhat, J. Chao, E. S. Ward, and R. J. Ober, "High Accuracy 3D Quantum Dot Tracking with Multifocal Plane Microscopy for the Study of Fast Intracellular Dynamics in Live Cells," Biophys. J. 95, 6025-6043 (2008).
[CrossRef] [PubMed]

P. Prabhat, Z. Gan, J. Chao, S. Ram, C. Vaccaro, S. Gibbons, R. J. Ober, and E. S. Ward, "Elucidation of intracellular recycling pathways leading to exocytosis of the Fc receptor, FcRn, by using multifocal plane microscopy," Proc. Natl. Acad. Sci. USA 104, 5889-5894 (2007).
[CrossRef] [PubMed]

S. Ram, J. Chao, P. Prabhat, E. S. Ward, and R. J. Ober, "A novel approach to determining the three-dimensional location of microscopic objects with applications to 3D particle tracking," Proc. SPIE 6443, 1-7 (2007).

S. Ram, E. S. Ward, and R. J. Ober, "How accurately can a single molecule be localized in three dimensions using a fluorescence microscope?," Proc. SPIE 5699, 426-435 (2005).
[CrossRef] [PubMed]

P. Prabhat, S. Ram, E. S. Ward, and R. J. Ober, "Simultaneous imaging of different focal planes in fluorescence microscopy for the study of cellular dynamics in three dimensions," IEEE Trans. Nanobiosci. 3, 237-242 (2004).
[CrossRef]

Waterman, C. M.

G. Shtengel, J. A. Galbraith, C. G. Galbraith, J. Lippincott-Schwartz, J. M. Gillette, S. Manley, R. Sougrat, C. M. Waterman, P. Kanchanawong, M. W. Davidson, R. D. Fetter, and H. F. Hess, "Interferometric fluorescent super-resolution microscopy resolves 3D cellular ultrastructure," Proc. Natl. Acad. Sci. USA 106, 3125-3130 (2009).
[CrossRef] [PubMed]

Wu, M.

M. Wu, J. W. Roberts, and M. Buckley, "Three-dimensional fluorescent particle tracking at micron-scale using a single camera," Exp. Fluids 38, 461-465 (2005).
[CrossRef]

Yamashita, H.

K. Murase, T. Fujiwara, Y. Umemura, K. Suzuki, R. Iino, H. Yamashita, M. Saito, H. Murakoshi, K. Ritchie, and A. Kusumi, "Ultrafine membrane compartments for molecular diffusion as revealed by single molecule techniques," Biophys. J. 86, 4075-4093 (2004).
[CrossRef] [PubMed]

Yildiz, A.

A. Yildiz, J. N. Forkey, S. A. McKinney, T. Ha, Y. E. Goldman, and P. R. Selvin, "Myosin V walks hand-over-hand: single fluorophore imaging with 1.5-nm localization," Science 300, 2061-2065 (2003).
[CrossRef] [PubMed]

Zhuang, X.

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]

Appl. Opt.

Appl. Phys. Lett.

L. Holtzer, T. Meckel, and T. Schmidt, "Nanometric three-dimensional tracking of individual quantum dots in cells," Appl. Phys. Lett. 90, 053902 (2007).
[CrossRef]

Biophys. J.

H. P. Kao and A. S. Verkman, "Tracking of single fluorescent particles in three dimensions: use of cylindrical optics to encode particle position," Biophys. J. 67, 1291-1300 (1994).
[CrossRef] [PubMed]

S. Ram, P. Prabhat, J. Chao, E. S. Ward, and R. J. Ober, "High Accuracy 3D Quantum Dot Tracking with Multifocal Plane Microscopy for the Study of Fast Intracellular Dynamics in Live Cells," Biophys. J. 95, 6025-6043 (2008).
[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, 4258-4272 (2006).
[CrossRef] [PubMed]

K. Murase, T. Fujiwara, Y. Umemura, K. Suzuki, R. Iino, H. Yamashita, M. Saito, H. Murakoshi, K. Ritchie, and A. Kusumi, "Ultrafine membrane compartments for molecular diffusion as revealed by single molecule techniques," Biophys. J. 86, 4075-4093 (2004).
[CrossRef] [PubMed]

Exp. Fluids

M. Wu, J. W. Roberts, and M. Buckley, "Three-dimensional fluorescent particle tracking at micron-scale using a single camera," Exp. Fluids 38, 461-465 (2005).
[CrossRef]

IEEE Trans. Nanobiosci.

P. Prabhat, S. Ram, E. S. Ward, and R. J. Ober, "Simultaneous imaging of different focal planes in fluorescence microscopy for the study of cellular dynamics in three dimensions," IEEE Trans. Nanobiosci. 3, 237-242 (2004).
[CrossRef]

Nano Lett.

E. Toprak, H. Balci, B. H. Blehm, and P. R. Selvin, "Three-dimensional particle tracking via bifocal imaging," Nano Lett. 7, 2043-2045 (2007).
[CrossRef] [PubMed]

Nat. Methods

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).

S. W. Hell, "Microscopy and its focal switch," Nat. Methods 6, 24-32 (2009).
[CrossRef] [PubMed]

Nature

J. Gelles, B. J. Schnapp, and M. P. Sheetz, "Tracking kinesin-driven movements with nanometre-scale precision," Nature 331, 450-453 (1988).
[CrossRef] [PubMed]

Opt. Express

Opt. Lett.

Proc. Natl. Acad. Sci. USA

G. Shtengel, J. A. Galbraith, C. G. Galbraith, J. Lippincott-Schwartz, J. M. Gillette, S. Manley, R. Sougrat, C. M. Waterman, P. Kanchanawong, M. W. Davidson, R. D. Fetter, and H. F. Hess, "Interferometric fluorescent super-resolution microscopy resolves 3D cellular ultrastructure," Proc. Natl. Acad. Sci. USA 106, 3125-3130 (2009).
[CrossRef] [PubMed]

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Figures (5)

Fig. 1.
Fig. 1.

Schematic of combined biplane and astigmatism 3D localization setup. FA – Field aperture; L – lens; obj – objective; N – neutral beamsplitter cube; M – mirrors; CL – cylindrical lens; D- dichroic; TL – tube lens; FP – focal plane; F – band pass filter. Not shown: laser beam expansion, shutter and mirrors in front of the field aperture. The dashed box in (a) can be configured as shown in (b) and (c).

Fig. 2.
Fig. 2.

Experimental point-spread functions and their profiles for biplane detection (a-c) and astigmatic detection (d-f). (a) Scanning a single point-like particle in z-direction with the biplane detection scheme yields two 3D data stacks depicted by their center cross sections. Due to the different image planes of the beam paths the particle is in focus at different axial positions. (b) Profiles of the PSFs along the optic axis for the transmitted (black) and reflected (red) light paths. Due to the 42:58 splitting ratio of the beamsplitter cube, the reflected PSF shows a lower intensity. (c) FWHM of both PSFs in x and y-direction as a function of the axial position. (d), (e) and (f) show the same information as depicted in (a), (b) and (c), respectively, for the astigmatic detection case. Please note, that in this case only one PSF is created. The small cuts in (d) show sections in yz and x-z orientation through the PSF center. Scale bar in (a) and (d) 500 nm. The data displayed in (c) and (f) is averaged over 12 PSFs. The color tables in (a) and (d) are normalized to the individual maximum values in the 3D stacks.

Fig. 3.
Fig. 3.

Localization of fluorescent beads with the biplane detection scheme at plane distances of 400 nm (a-b), 500 nm (c-d) and 600 nm (e-f) in the sample. 100 images were taken at each objective z-position with 50 nm z-steps in between. (a, c, e) show the results of a single bead localized by the fit algorithm. Determined x, y and z-positions are shown in blue, green and red, respectively. The dark gray points show the z-position corrected for the actual z-movement of the objective. All position values are offset by a constant, arbitrary value to avoid overlap between the curves. The insets show the area depicted by the black rectangles enlarged to give a better view of the data. (b, d, f) show the localization accuracy determined as standard deviation σ from the 100 images taken at each z-position. The gray area denotes the fraction Φ of images in which the fit properly converged and the bead could be located.

Fig. 4.
Fig. 4.

Localization of fluorescent beads with the astigmatic detection scheme at distances Δ of 375 nm (a-b), 475 nm (c-d) and 575 nm (e-f) between the planes of maximum x and y-focusing in the sample. Data was analyzed and is presented as described for Fig. 3.

Fig. 5.
Fig. 5.

Localization accuracy, σ, and axial localization range, ALR, as a function of particle brightness. Every data point represents the results of the imaging series of a single bead. (a, b) Localization accuracy in x, y and z-direction for the biplane and the astigmatism detection scheme, respectively, follow a square root dependence on the number of detected photons for 180 photons and above. The values stem from beads centered between the detection planes (biplane) and a plane where ellipticity is small (astigmatism). (c, d) The axial range over which each particle could be properly localized in at least 50% of the recorded frames. The different symbols used in (a-d) represent measurements at different focal plane distances Δ as specified in the figure legends.

Tables (1)

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Table 1. FWHM of measured PSFs

Equations (3)

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χ2(v,b,a)=j(njFv,b,a(xj)σj)2
ha(xj)=h0(ξl) δ(ξlDa(xj))
FT{ha(xj)}=H0(κl) ×eiκlDa(xj)

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