Abstract

Super-resolution localization microscopy has revolutionized the observation of living structures at the cellular scale, by achieving a spatial resolution that is improved by more than an order of magnitude compared to the diffraction limit. These methods localize single events from isolated sources in repeated cycles in order to achieve super-resolution. The requirement for sparse distribution of simultaneously activated sources in the field of view dictates the acquisition of thousands of frames in order to construct the full super-resolution image. As a result, these methods have slow temporal resolution which is a major limitation when investigating live-cell dynamics. In this paper we present the use of a phase stretch transform for high-density super-resolution localization microscopy. This is a nonlinear frequency dependent transform that emulates the propagation of light through a physical medium with a specific warped diffractive property and applies a 2D phase function to the image in the frequency domain. By choosing properly the transform parameters and the phase kernel profile, the point spread function of each emitter can be sharpened and narrowed. This enables the localization of overlapping emitters, thus allowing a higher density of activated emitters as well as shorter data collection acquisition rates. The method is validated by numerical simulations and by experimental data obtained using a microtubule sample.

© 2016 Optical Society of America

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2015 (3)

M. H. Asghari and B. Jalali, “Edge Detection in Digital Images Using Dispersive Phase Stretch Transform,” Int. J. Biomed. Imaging 2015, 687819 (2015).
[Crossref] [PubMed]

B. Jalali and A. Mahjoubfar, “Tailoring wideband signals with a photonic hardware accelerator,” Proc. IEEE 103(7), 1071–1086 (2015).
[Crossref]

T. Ilovitsh, A. Weiss, A. Meiri, C. G. Ebeling, A. Amiel, H. Katz, B. Mannasse-Green, and Z. Zalevsky, “K-factor image deshadowing for three-dimensional fluorescence microscopy,” Sci. Rep. 5, 13724 (2015).
[Crossref] [PubMed]

2014 (3)

M. H. Asghari and B. Jalali, “Discrete anamorphic transform for image compression,” IEEE Signal Process. Lett. 21(7), 829–833 (2014).
[Crossref]

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] [PubMed]

T. Ilovitsh, A. Meiri, C. G. Ebeling, R. Menon, J. M. Gerton, E. M. Jorgensen, and Z. Zalevsky, “Improved localization accuracy in stochastic super-resolution fluorescence microscopy by K-factor image deshadowing,” Biomed. Opt. Express 5(1), 244–258 (2014).
[Crossref] [PubMed]

2013 (2)

K. Goda and B. Jalali, “Dispersive Fourier transformation for fast continuous single-shot measurements,” Nat. Photonics 7(2), 102–112 (2013).
[Crossref]

R. P. J. Nieuwenhuizen, K. A. Lidke, M. Bates, D. L. Puig, D. Grünwald, S. Stallinga, and B. Rieger, “Measuring image resolution in optical nanoscopy,” Nat. Methods 10(6), 557–562 (2013).
[Crossref] [PubMed]

2012 (2)

2011 (3)

2009 (1)

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

2008 (3)

M. Heilemann, S. van de Linde, M. Schüttpelz, R. Kasper, B. Seefeldt, A. Mukherjee, P. Tinnefeld, and M. Sauer, “Subdiffraction-resolution fluorescence imaging with conventional fluorescent probes,” Angew. Chem. Int. Ed. Engl. 47(33), 6172–6176 (2008).
[Crossref] [PubMed]

A. Sergé, N. Bertaux, H. Rigneault, and D. Marguet, “Dynamic multiple-target tracing to probe spatiotemporal cartography of cell membranes,” Nat. Methods 5(8), 687–694 (2008).
[Crossref] [PubMed]

L. Zhu, W. Zhang, D. Elnatan, and B. Huang, “Faster storm using compressed sensing,” Nat. Methods 141, 520–529 (2008).
[PubMed]

2007 (2)

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]

M. Bates, B. Huang, X. Zhuang, and T. Dempsey, “Multicolor Super-Resolution Imaging with Photo-Switchable Fluorescent Probes,” Science 317(5845), 1749–1753 (2007).
[Crossref] [PubMed]

2006 (3)

S. T. Hess, T. P. K. Girirajan, and M. D. Mason, “Ultra-high resolution imaging by fluorescence photoactivation localization microscopy,” Biophys. J. 91(11), 4258–4272 (2006).
[Crossref] [PubMed]

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

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

2004 (2)

M. P. Gordon, T. Ha, and P. R. Selvin, “Single-molecule high-resolution imaging with photobleaching,” Proc. Natl. Acad. Sci. U.S.A. 101(17), 6462–6465 (2004).
[Crossref] [PubMed]

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

2003 (2)

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(5628), 2061–2065 (2003).
[Crossref] [PubMed]

Y. Han and B. Jalali, “Photonic time-stretched analog-to-digital converter: fundamental concepts and practical considerations,” J. Lightwave Technol. 21(12), 3085–3103 (2003).
[Crossref]

2002 (1)

R. E. Thompson, D. R. Larson, and W. W. Webb, “Precise nanometer localization analysis for individual fluorescent probes,” Biophys. J. 82(5), 2775–2783 (2002).
[Crossref] [PubMed]

2001 (1)

M. K. Cheezum, W. F. Walker, and W. H. Guilford, “Quantitative comparison of algorithms for tracking single fluorescent particles,” Biophys. J. 81(4), 2378–2388 (2001).
[Crossref] [PubMed]

1994 (1)

R. N. Ghosh and W. W. Webb, “Automated detection and tracking of individual and clustered cell surface low density lipoprotein receptor molecules,” Biophys. J. 66(5), 1301–1318 (1994).
[Crossref] [PubMed]

1991 (1)

E. Betzig, J. K. Trautman, T. D. Harris, J. S. Weiner, and R. L. Kostelak, “Breaking the diffraction barrier: optical microscopy on a nanometric scale,” Science 251(5000), 1468–1470 (1991).
[Crossref] [PubMed]

1986 (1)

N. Bobroff, “Position measurement with a resolution and noise-limited instrument,” Rev. Sci. Instrum. 57(6), 1152 (1986).
[Crossref]

1982 (1)

L. A. Shepp and Y. Vardi, “Maximum likelihood reconstruction for emission tomography,” IEEE Trans. Med. Imaging 1(2), 113–122 (1982).
[Crossref] [PubMed]

1944 (1)

1896 (1)

L. Rayleigh, “On the theory of optical images, with special reference to the microscope,” London, Edinburgh, Dublin Philos. Mag. J. Sci. 42, 167–195 (1896).
[Crossref]

1873 (1)

E. Abbe, “Beitrage zur theorie des mikroskops und der mikroskopischen Wahrnehmung,” Arch. für mikroskopische Anat. 9(1), 413–418 (1873).
[Crossref]

Abbe, E.

E. Abbe, “Beitrage zur theorie des mikroskops und der mikroskopischen Wahrnehmung,” Arch. für mikroskopische Anat. 9(1), 413–418 (1873).
[Crossref]

Amiel, A.

T. Ilovitsh, A. Weiss, A. Meiri, C. G. Ebeling, A. Amiel, H. Katz, B. Mannasse-Green, and Z. Zalevsky, “K-factor image deshadowing for three-dimensional fluorescence microscopy,” Sci. Rep. 5, 13724 (2015).
[Crossref] [PubMed]

Asghari, M. H.

M. H. Asghari and B. Jalali, “Edge Detection in Digital Images Using Dispersive Phase Stretch Transform,” Int. J. Biomed. Imaging 2015, 687819 (2015).
[Crossref] [PubMed]

M. H. Asghari and B. Jalali, “Discrete anamorphic transform for image compression,” IEEE Signal Process. Lett. 21(7), 829–833 (2014).
[Crossref]

Babcock, H.

E. A. Mukamel, H. Babcock, and X. Zhuang, “Statistical deconvolution for superresolution fluorescence microscopy,” Biophys. J. 102(10), 2391–2400 (2012).
[Crossref] [PubMed]

Bates, M.

R. P. J. Nieuwenhuizen, K. A. Lidke, M. Bates, D. L. Puig, D. Grünwald, S. Stallinga, and B. Rieger, “Measuring image resolution in optical nanoscopy,” Nat. Methods 10(6), 557–562 (2013).
[Crossref] [PubMed]

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

M. Bates, B. Huang, X. Zhuang, and T. Dempsey, “Multicolor Super-Resolution Imaging with Photo-Switchable Fluorescent Probes,” Science 317(5845), 1749–1753 (2007).
[Crossref] [PubMed]

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

Bertaux, N.

A. Sergé, N. Bertaux, H. Rigneault, and D. Marguet, “Dynamic multiple-target tracing to probe spatiotemporal cartography of cell membranes,” Nat. Methods 5(8), 687–694 (2008).
[Crossref] [PubMed]

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(5793), 1642–1645 (2006).
[Crossref] [PubMed]

E. Betzig, J. K. Trautman, T. D. Harris, J. S. Weiner, and R. L. Kostelak, “Breaking the diffraction barrier: optical microscopy on a nanometric scale,” Science 251(5000), 1468–1470 (1991).
[Crossref] [PubMed]

Bobroff, N.

N. Bobroff, “Position measurement with a resolution and noise-limited instrument,” Rev. Sci. Instrum. 57(6), 1152 (1986).
[Crossref]

Bonifacino, J. S.

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

Boulanger, J.

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] [PubMed]

Cheezum, M. K.

M. K. Cheezum, W. F. Walker, and W. H. Guilford, “Quantitative comparison of algorithms for tracking single fluorescent particles,” Biophys. J. 81(4), 2378–2388 (2001).
[Crossref] [PubMed]

Choquet, D.

Dahan, M.

Davidson, M. W.

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

Dempsey, T.

M. Bates, B. Huang, X. Zhuang, and T. Dempsey, “Multicolor Super-Resolution Imaging with Photo-Switchable Fluorescent Probes,” Science 317(5845), 1749–1753 (2007).
[Crossref] [PubMed]

Dempster, W. T.

Ebeling, C. G.

T. Ilovitsh, A. Weiss, A. Meiri, C. G. Ebeling, A. Amiel, H. Katz, B. Mannasse-Green, and Z. Zalevsky, “K-factor image deshadowing for three-dimensional fluorescence microscopy,” Sci. Rep. 5, 13724 (2015).
[Crossref] [PubMed]

T. Ilovitsh, A. Meiri, C. G. Ebeling, R. Menon, J. M. Gerton, E. M. Jorgensen, and Z. Zalevsky, “Improved localization accuracy in stochastic super-resolution fluorescence microscopy by K-factor image deshadowing,” Biomed. Opt. Express 5(1), 244–258 (2014).
[Crossref] [PubMed]

Elnatan, D.

L. Zhu, W. Zhang, D. Elnatan, and B. Huang, “Faster storm using compressed sensing,” Nat. Methods 141, 520–529 (2008).
[PubMed]

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(5628), 2061–2065 (2003).
[Crossref] [PubMed]

Gerton, J. M.

Ghosh, R. N.

R. N. Ghosh and W. W. Webb, “Automated detection and tracking of individual and clustered cell surface low density lipoprotein receptor molecules,” Biophys. J. 66(5), 1301–1318 (1994).
[Crossref] [PubMed]

Girirajan, T. P. K.

S. T. Hess, T. P. K. Girirajan, and M. D. Mason, “Ultra-high resolution imaging by fluorescence photoactivation localization microscopy,” Biophys. J. 91(11), 4258–4272 (2006).
[Crossref] [PubMed]

Goda, K.

K. Goda and B. Jalali, “Dispersive Fourier transformation for fast continuous single-shot measurements,” Nat. Photonics 7(2), 102–112 (2013).
[Crossref]

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(5628), 2061–2065 (2003).
[Crossref] [PubMed]

Gordon, M. P.

M. P. Gordon, T. Ha, and P. R. Selvin, “Single-molecule high-resolution imaging with photobleaching,” Proc. Natl. Acad. Sci. U.S.A. 101(17), 6462–6465 (2004).
[Crossref] [PubMed]

Griffiths, C.

R. Henriques, C. Griffiths, E. Hesper Rego, and M. M. Mhlanga, “PALM and STORM: unlocking live-cell super-resolution,” Biopolymers 95(5), 322–331 (2011).
[Crossref] [PubMed]

Grünwald, D.

R. P. J. Nieuwenhuizen, K. A. Lidke, M. Bates, D. L. Puig, D. Grünwald, S. Stallinga, and B. Rieger, “Measuring image resolution in optical nanoscopy,” Nat. Methods 10(6), 557–562 (2013).
[Crossref] [PubMed]

Guilford, W. H.

M. K. Cheezum, W. F. Walker, and W. H. Guilford, “Quantitative comparison of algorithms for tracking single fluorescent particles,” Biophys. J. 81(4), 2378–2388 (2001).
[Crossref] [PubMed]

Ha, T.

M. P. Gordon, T. Ha, and P. R. Selvin, “Single-molecule high-resolution imaging with photobleaching,” Proc. Natl. Acad. Sci. U.S.A. 101(17), 6462–6465 (2004).
[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(5628), 2061–2065 (2003).
[Crossref] [PubMed]

Hagen, G. M.

Han, Y.

Harris, T. D.

E. Betzig, J. K. Trautman, T. D. Harris, J. S. Weiner, and R. L. Kostelak, “Breaking the diffraction barrier: optical microscopy on a nanometric scale,” Science 251(5000), 1468–1470 (1991).
[Crossref] [PubMed]

Heilemann, M.

M. Heilemann, S. van de Linde, M. Schüttpelz, R. Kasper, B. Seefeldt, A. Mukherjee, P. Tinnefeld, and M. Sauer, “Subdiffraction-resolution fluorescence imaging with conventional fluorescent probes,” Angew. Chem. Int. Ed. Engl. 47(33), 6172–6176 (2008).
[Crossref] [PubMed]

Henriques, R.

R. Henriques, C. Griffiths, E. Hesper Rego, and M. M. Mhlanga, “PALM and STORM: unlocking live-cell super-resolution,” Biopolymers 95(5), 322–331 (2011).
[Crossref] [PubMed]

Hesper Rego, E.

R. Henriques, C. Griffiths, E. Hesper Rego, and M. M. Mhlanga, “PALM and STORM: unlocking live-cell super-resolution,” Biopolymers 95(5), 322–331 (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(5793), 1642–1645 (2006).
[Crossref] [PubMed]

Hess, S. T.

S. T. Hess, T. P. K. Girirajan, and M. D. Mason, “Ultra-high resolution imaging by fluorescence photoactivation localization microscopy,” Biophys. J. 91(11), 4258–4272 (2006).
[Crossref] [PubMed]

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] [PubMed]

Huang, B.

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

L. Zhu, W. Zhang, D. Elnatan, and B. Huang, “Faster storm using compressed sensing,” Nat. Methods 141, 520–529 (2008).
[PubMed]

M. Bates, B. Huang, X. Zhuang, and T. Dempsey, “Multicolor Super-Resolution Imaging with Photo-Switchable Fluorescent Probes,” Science 317(5845), 1749–1753 (2007).
[Crossref] [PubMed]

Huang, F.

Ilovitsh, T.

T. Ilovitsh, A. Weiss, A. Meiri, C. G. Ebeling, A. Amiel, H. Katz, B. Mannasse-Green, and Z. Zalevsky, “K-factor image deshadowing for three-dimensional fluorescence microscopy,” Sci. Rep. 5, 13724 (2015).
[Crossref] [PubMed]

T. Ilovitsh, A. Meiri, C. G. Ebeling, R. Menon, J. M. Gerton, E. M. Jorgensen, and Z. Zalevsky, “Improved localization accuracy in stochastic super-resolution fluorescence microscopy by K-factor image deshadowing,” Biomed. Opt. Express 5(1), 244–258 (2014).
[Crossref] [PubMed]

Izeddin, I.

Jalali, B.

M. H. Asghari and B. Jalali, “Edge Detection in Digital Images Using Dispersive Phase Stretch Transform,” Int. J. Biomed. Imaging 2015, 687819 (2015).
[Crossref] [PubMed]

B. Jalali and A. Mahjoubfar, “Tailoring wideband signals with a photonic hardware accelerator,” Proc. IEEE 103(7), 1071–1086 (2015).
[Crossref]

M. H. Asghari and B. Jalali, “Discrete anamorphic transform for image compression,” IEEE Signal Process. Lett. 21(7), 829–833 (2014).
[Crossref]

K. Goda and B. Jalali, “Dispersive Fourier transformation for fast continuous single-shot measurements,” Nat. Photonics 7(2), 102–112 (2013).
[Crossref]

Y. Han and B. Jalali, “Photonic time-stretched analog-to-digital converter: fundamental concepts and practical considerations,” J. Lightwave Technol. 21(12), 3085–3103 (2003).
[Crossref]

Jorgensen, E. M.

Kasper, R.

M. Heilemann, S. van de Linde, M. Schüttpelz, R. Kasper, B. Seefeldt, A. Mukherjee, P. Tinnefeld, and M. Sauer, “Subdiffraction-resolution fluorescence imaging with conventional fluorescent probes,” Angew. Chem. Int. Ed. Engl. 47(33), 6172–6176 (2008).
[Crossref] [PubMed]

Katz, H.

T. Ilovitsh, A. Weiss, A. Meiri, C. G. Ebeling, A. Amiel, H. Katz, B. Mannasse-Green, and Z. Zalevsky, “K-factor image deshadowing for three-dimensional fluorescence microscopy,” Sci. Rep. 5, 13724 (2015).
[Crossref] [PubMed]

Kechkar, A.

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] [PubMed]

Kostelak, R. L.

E. Betzig, J. K. Trautman, T. D. Harris, J. S. Weiner, and R. L. Kostelak, “Breaking the diffraction barrier: optical microscopy on a nanometric scale,” Science 251(5000), 1468–1470 (1991).
[Crossref] [PubMed]

Krížek, P.

Larson, D. R.

R. E. Thompson, D. R. Larson, and W. W. Webb, “Precise nanometer localization analysis for individual fluorescent probes,” Biophys. J. 82(5), 2775–2783 (2002).
[Crossref] [PubMed]

Lidke, K. A.

R. P. J. Nieuwenhuizen, K. A. Lidke, M. Bates, D. L. Puig, D. Grünwald, S. Stallinga, and B. Rieger, “Measuring image resolution in optical nanoscopy,” Nat. Methods 10(6), 557–562 (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(5), 1377–1393 (2011).
[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(5793), 1642–1645 (2006).
[Crossref] [PubMed]

Lippincott-Schwartz, J.

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

Mahjoubfar, A.

B. Jalali and A. Mahjoubfar, “Tailoring wideband signals with a photonic hardware accelerator,” Proc. IEEE 103(7), 1071–1086 (2015).
[Crossref]

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] [PubMed]

Mannasse-Green, B.

T. Ilovitsh, A. Weiss, A. Meiri, C. G. Ebeling, A. Amiel, H. Katz, B. Mannasse-Green, and Z. Zalevsky, “K-factor image deshadowing for three-dimensional fluorescence microscopy,” Sci. Rep. 5, 13724 (2015).
[Crossref] [PubMed]

Marguet, D.

A. Sergé, N. Bertaux, H. Rigneault, and D. Marguet, “Dynamic multiple-target tracing to probe spatiotemporal cartography of cell membranes,” Nat. Methods 5(8), 687–694 (2008).
[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(11), 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(5628), 2061–2065 (2003).
[Crossref] [PubMed]

Meiri, A.

T. Ilovitsh, A. Weiss, A. Meiri, C. G. Ebeling, A. Amiel, H. Katz, B. Mannasse-Green, and Z. Zalevsky, “K-factor image deshadowing for three-dimensional fluorescence microscopy,” Sci. Rep. 5, 13724 (2015).
[Crossref] [PubMed]

T. Ilovitsh, A. Meiri, C. G. Ebeling, R. Menon, J. M. Gerton, E. M. Jorgensen, and Z. Zalevsky, “Improved localization accuracy in stochastic super-resolution fluorescence microscopy by K-factor image deshadowing,” Biomed. Opt. Express 5(1), 244–258 (2014).
[Crossref] [PubMed]

Menon, R.

Mets, L.

X. Qu, D. Wu, L. Mets, and N. Scherer, “Nanometer-localized multiple single-molecule fluorescence microscopy,” in Proceedings of the National Academy of Sciences of the United States of America (2004), pp. 11298–11303.

Mhlanga, M. M.

R. Henriques, C. Griffiths, E. Hesper Rego, and M. M. Mhlanga, “PALM and STORM: unlocking live-cell super-resolution,” Biopolymers 95(5), 322–331 (2011).
[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] [PubMed]

Mukamel, E. A.

E. A. Mukamel, H. Babcock, and X. Zhuang, “Statistical deconvolution for superresolution fluorescence microscopy,” Biophys. J. 102(10), 2391–2400 (2012).
[Crossref] [PubMed]

Mukherjee, A.

M. Heilemann, S. van de Linde, M. Schüttpelz, R. Kasper, B. Seefeldt, A. Mukherjee, P. Tinnefeld, and M. Sauer, “Subdiffraction-resolution fluorescence imaging with conventional fluorescent probes,” Angew. Chem. Int. Ed. Engl. 47(33), 6172–6176 (2008).
[Crossref] [PubMed]

Nair, D.

Nieuwenhuizen, R. P. J.

R. P. J. Nieuwenhuizen, K. A. Lidke, M. Bates, D. L. Puig, D. Grünwald, S. Stallinga, and B. Rieger, “Measuring image resolution in optical nanoscopy,” Nat. Methods 10(6), 557–562 (2013).
[Crossref] [PubMed]

Ober, R. J.

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

Olenych, S.

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

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] [PubMed]

Olivo-Marin, J. C.

Patterson, G. H.

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

Puig, D. L.

R. P. J. Nieuwenhuizen, K. A. Lidke, M. Bates, D. L. Puig, D. Grünwald, S. Stallinga, and B. Rieger, “Measuring image resolution in optical nanoscopy,” Nat. Methods 10(6), 557–562 (2013).
[Crossref] [PubMed]

Qu, X.

X. Qu, D. Wu, L. Mets, and N. Scherer, “Nanometer-localized multiple single-molecule fluorescence microscopy,” in Proceedings of the National Academy of Sciences of the United States of America (2004), pp. 11298–11303.

Racine, V.

Ram, S.

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

Raška, I.

Rayleigh, L.

L. Rayleigh, “On the theory of optical images, with special reference to the microscope,” London, Edinburgh, Dublin Philos. Mag. J. Sci. 42, 167–195 (1896).
[Crossref]

Rieger, B.

R. P. J. Nieuwenhuizen, K. A. Lidke, M. Bates, D. L. Puig, D. Grünwald, S. Stallinga, and B. Rieger, “Measuring image resolution in optical nanoscopy,” Nat. Methods 10(6), 557–562 (2013).
[Crossref] [PubMed]

Rigneault, H.

A. Sergé, N. Bertaux, H. Rigneault, and D. Marguet, “Dynamic multiple-target tracing to probe spatiotemporal cartography of cell membranes,” Nat. Methods 5(8), 687–694 (2008).
[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(10), 793–796 (2006).
[Crossref] [PubMed]

Sauer, M.

M. Heilemann, S. van de Linde, M. Schüttpelz, R. Kasper, B. Seefeldt, A. Mukherjee, P. Tinnefeld, and M. Sauer, “Subdiffraction-resolution fluorescence imaging with conventional fluorescent probes,” Angew. Chem. Int. Ed. Engl. 47(33), 6172–6176 (2008).
[Crossref] [PubMed]

Scherer, N.

X. Qu, D. Wu, L. Mets, and N. Scherer, “Nanometer-localized multiple single-molecule fluorescence microscopy,” in Proceedings of the National Academy of Sciences of the United States of America (2004), pp. 11298–11303.

Schüttpelz, M.

M. Heilemann, S. van de Linde, M. Schüttpelz, R. Kasper, B. Seefeldt, A. Mukherjee, P. Tinnefeld, and M. Sauer, “Subdiffraction-resolution fluorescence imaging with conventional fluorescent probes,” Angew. Chem. Int. Ed. Engl. 47(33), 6172–6176 (2008).
[Crossref] [PubMed]

Schwartz, S. L.

Seefeldt, B.

M. Heilemann, S. van de Linde, M. Schüttpelz, R. Kasper, B. Seefeldt, A. Mukherjee, P. Tinnefeld, and M. Sauer, “Subdiffraction-resolution fluorescence imaging with conventional fluorescent probes,” Angew. Chem. Int. Ed. Engl. 47(33), 6172–6176 (2008).
[Crossref] [PubMed]

Selvin, P. R.

M. P. Gordon, T. Ha, and P. R. Selvin, “Single-molecule high-resolution imaging with photobleaching,” Proc. Natl. Acad. Sci. U.S.A. 101(17), 6462–6465 (2004).
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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(5628), 2061–2065 (2003).
[Crossref] [PubMed]

Sergé, A.

A. Sergé, N. Bertaux, H. Rigneault, and D. Marguet, “Dynamic multiple-target tracing to probe spatiotemporal cartography of cell membranes,” Nat. Methods 5(8), 687–694 (2008).
[Crossref] [PubMed]

Shepp, L. A.

L. A. Shepp and Y. Vardi, “Maximum likelihood reconstruction for emission tomography,” IEEE Trans. Med. Imaging 1(2), 113–122 (1982).
[Crossref] [PubMed]

Sibarita, J. B.

Sougrat, R.

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

Specht, C. G.

Stallinga, S.

R. P. J. Nieuwenhuizen, K. A. Lidke, M. Bates, D. L. Puig, D. Grünwald, S. Stallinga, and B. Rieger, “Measuring image resolution in optical nanoscopy,” Nat. Methods 10(6), 557–562 (2013).
[Crossref] [PubMed]

Thompson, R. E.

R. E. Thompson, D. R. Larson, and W. W. Webb, “Precise nanometer localization analysis for individual fluorescent probes,” Biophys. J. 82(5), 2775–2783 (2002).
[Crossref] [PubMed]

Tinnefeld, P.

M. Heilemann, S. van de Linde, M. Schüttpelz, R. Kasper, B. Seefeldt, A. Mukherjee, P. Tinnefeld, and M. Sauer, “Subdiffraction-resolution fluorescence imaging with conventional fluorescent probes,” Angew. Chem. Int. Ed. Engl. 47(33), 6172–6176 (2008).
[Crossref] [PubMed]

Trautman, J. K.

E. Betzig, J. K. Trautman, T. D. Harris, J. S. Weiner, and R. L. Kostelak, “Breaking the diffraction barrier: optical microscopy on a nanometric scale,” Science 251(5000), 1468–1470 (1991).
[Crossref] [PubMed]

Triller, A.

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] [PubMed]

van de Linde, S.

M. Heilemann, S. van de Linde, M. Schüttpelz, R. Kasper, B. Seefeldt, A. Mukherjee, P. Tinnefeld, and M. Sauer, “Subdiffraction-resolution fluorescence imaging with conventional fluorescent probes,” Angew. Chem. Int. Ed. Engl. 47(33), 6172–6176 (2008).
[Crossref] [PubMed]

Vardi, Y.

L. A. Shepp and Y. Vardi, “Maximum likelihood reconstruction for emission tomography,” IEEE Trans. Med. Imaging 1(2), 113–122 (1982).
[Crossref] [PubMed]

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] [PubMed]

Walker, W. F.

M. K. Cheezum, W. F. Walker, and W. H. Guilford, “Quantitative comparison of algorithms for tracking single fluorescent particles,” Biophys. J. 81(4), 2378–2388 (2001).
[Crossref] [PubMed]

Ward, E. S.

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

Webb, W. W.

R. E. Thompson, D. R. Larson, and W. W. Webb, “Precise nanometer localization analysis for individual fluorescent probes,” Biophys. J. 82(5), 2775–2783 (2002).
[Crossref] [PubMed]

R. N. Ghosh and W. W. Webb, “Automated detection and tracking of individual and clustered cell surface low density lipoprotein receptor molecules,” Biophys. J. 66(5), 1301–1318 (1994).
[Crossref] [PubMed]

Weiner, J. S.

E. Betzig, J. K. Trautman, T. D. Harris, J. S. Weiner, and R. L. Kostelak, “Breaking the diffraction barrier: optical microscopy on a nanometric scale,” Science 251(5000), 1468–1470 (1991).
[Crossref] [PubMed]

Weiss, A.

T. Ilovitsh, A. Weiss, A. Meiri, C. G. Ebeling, A. Amiel, H. Katz, B. Mannasse-Green, and Z. Zalevsky, “K-factor image deshadowing for three-dimensional fluorescence microscopy,” Sci. Rep. 5, 13724 (2015).
[Crossref] [PubMed]

Wu, D.

X. Qu, D. Wu, L. Mets, and N. Scherer, “Nanometer-localized multiple single-molecule fluorescence microscopy,” in Proceedings of the National Academy of Sciences of the United States of America (2004), pp. 11298–11303.

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] [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(5628), 2061–2065 (2003).
[Crossref] [PubMed]

Zalevsky, Z.

T. Ilovitsh, A. Weiss, A. Meiri, C. G. Ebeling, A. Amiel, H. Katz, B. Mannasse-Green, and Z. Zalevsky, “K-factor image deshadowing for three-dimensional fluorescence microscopy,” Sci. Rep. 5, 13724 (2015).
[Crossref] [PubMed]

T. Ilovitsh, A. Meiri, C. G. Ebeling, R. Menon, J. M. Gerton, E. M. Jorgensen, and Z. Zalevsky, “Improved localization accuracy in stochastic super-resolution fluorescence microscopy by K-factor image deshadowing,” Biomed. Opt. Express 5(1), 244–258 (2014).
[Crossref] [PubMed]

Zerubia, J.

Zhang, B.

Zhang, W.

L. Zhu, W. Zhang, D. Elnatan, and B. Huang, “Faster storm using compressed sensing,” Nat. Methods 141, 520–529 (2008).
[PubMed]

Zhu, L.

L. Zhu, W. Zhang, D. Elnatan, and B. Huang, “Faster storm using compressed sensing,” Nat. Methods 141, 520–529 (2008).
[PubMed]

Zhuang, X.

E. A. Mukamel, H. Babcock, and X. Zhuang, “Statistical deconvolution for superresolution fluorescence microscopy,” Biophys. J. 102(10), 2391–2400 (2012).
[Crossref] [PubMed]

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

M. Bates, B. Huang, X. Zhuang, and T. Dempsey, “Multicolor Super-Resolution Imaging with Photo-Switchable Fluorescent Probes,” Science 317(5845), 1749–1753 (2007).
[Crossref] [PubMed]

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

Angew. Chem. Int. Ed. Engl. (1)

M. Heilemann, S. van de Linde, M. Schüttpelz, R. Kasper, B. Seefeldt, A. Mukherjee, P. Tinnefeld, and M. Sauer, “Subdiffraction-resolution fluorescence imaging with conventional fluorescent probes,” Angew. Chem. Int. Ed. Engl. 47(33), 6172–6176 (2008).
[Crossref] [PubMed]

Annu. Rev. Biochem. (1)

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

Appl. Opt. (1)

Arch. für mikroskopische Anat. (1)

E. Abbe, “Beitrage zur theorie des mikroskops und der mikroskopischen Wahrnehmung,” Arch. für mikroskopische Anat. 9(1), 413–418 (1873).
[Crossref]

Biomed. Opt. Express (2)

Biophys. J. (6)

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

S. T. Hess, T. P. K. Girirajan, and M. D. Mason, “Ultra-high resolution imaging by fluorescence photoactivation localization microscopy,” Biophys. J. 91(11), 4258–4272 (2006).
[Crossref] [PubMed]

R. E. Thompson, D. R. Larson, and W. W. Webb, “Precise nanometer localization analysis for individual fluorescent probes,” Biophys. J. 82(5), 2775–2783 (2002).
[Crossref] [PubMed]

E. A. Mukamel, H. Babcock, and X. Zhuang, “Statistical deconvolution for superresolution fluorescence microscopy,” Biophys. J. 102(10), 2391–2400 (2012).
[Crossref] [PubMed]

M. K. Cheezum, W. F. Walker, and W. H. Guilford, “Quantitative comparison of algorithms for tracking single fluorescent particles,” Biophys. J. 81(4), 2378–2388 (2001).
[Crossref] [PubMed]

R. N. Ghosh and W. W. Webb, “Automated detection and tracking of individual and clustered cell surface low density lipoprotein receptor molecules,” Biophys. J. 66(5), 1301–1318 (1994).
[Crossref] [PubMed]

Biopolymers (1)

R. Henriques, C. Griffiths, E. Hesper Rego, and M. M. Mhlanga, “PALM and STORM: unlocking live-cell super-resolution,” Biopolymers 95(5), 322–331 (2011).
[Crossref] [PubMed]

IEEE Signal Process. Lett. (1)

M. H. Asghari and B. Jalali, “Discrete anamorphic transform for image compression,” IEEE Signal Process. Lett. 21(7), 829–833 (2014).
[Crossref]

IEEE Trans. Med. Imaging (1)

L. A. Shepp and Y. Vardi, “Maximum likelihood reconstruction for emission tomography,” IEEE Trans. Med. Imaging 1(2), 113–122 (1982).
[Crossref] [PubMed]

Int. J. Biomed. Imaging (1)

M. H. Asghari and B. Jalali, “Edge Detection in Digital Images Using Dispersive Phase Stretch Transform,” Int. J. Biomed. Imaging 2015, 687819 (2015).
[Crossref] [PubMed]

J. Lightwave Technol. (1)

J. Opt. Soc. Am. (1)

London, Edinburgh, Dublin Philos. Mag. J. Sci. (1)

L. Rayleigh, “On the theory of optical images, with special reference to the microscope,” London, Edinburgh, Dublin Philos. Mag. J. Sci. 42, 167–195 (1896).
[Crossref]

Nat. Methods (4)

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Figures (6)

Fig. 1
Fig. 1 Image of two PSFs separated by a distance of 1.5σ~300nm. Original image (blue line). Modified K-factor algorithm applied to the original image (black), and the PST method applied to the original image (red).

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Fig. 2
Fig. 2 Simulation results. (a) original image with additive shot noise (N = 5000) and background noise (Nb = 5). (b) The K-factor algorithm result. (c) PST result. (d)-(f) is the magnification of the yellow regions marked by 1 in (a)-(c) respectively. (g) is the PST phase kernel profile with parameters of W = 50, S = 5. (h) OTF of a single PSF for the raw data (black line) and for the PST processed image (red line).

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Fig. 3
Fig. 3 (a). Error in localization for an isolated emitter as a function of the SNR. (b). The minimal resolvable distance between two point sources as a function of SNR. Both simulations contain 1000 Monte-Carlo iterations. Gaussian fitting applied to the raw image is presented in the blue line. PST applied to the raw data and fitted using a PST processed Gaussian is presented in the red line.

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Fig. 4
Fig. 4 Individual dSTORM frame without processing (a). and after PST processing (b). Marked regions are examples where the difference can be clearly seen. (c), (e) and (g) are the magnification of the marked areas in (a).(d), (f) and (h) are is the magnification of the marked areas in (b). (i) compares the OTF of an isolated PSF taken from the raw image in (a) (black line), and the PST processed frame taken from (b) (red line).

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Fig. 5
Fig. 5 SR dSTORM reconstruction of imaging data from Alexa647 labeled microtubules sample without processing and using the PST method. Images in the upper row represent reconstructed image using 10,000 frames and those in the lower row represent reconstructed image using 2,500 frames. (a) and (d) Conventional dSTORM analysis. (b) and (e) PST processing applied on raw data coming from dSTORM regular analysis. The black and red lines in (c) presents the cross sections of the white dashed lines in (a) and (b) respectively.

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Fig. 6
Fig. 6 The number of PST frames required to generate the SR image as a function of correlation percentage with the 10,000 raw data images reconstruction.

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Equations (5)

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σ= 0.6×λ 2 N.A.
I PST (x,y)=∡〈 IFFT2{ K ˜ [ u,v ]⋅FFT2{ I(x,y) } } 〉
K ˜ [ u,v ]= e jφ(u,v)
φ(u,v)= φ polar (r)=S⋅ W⋅(1−r)⋅ tan −1 (W(1−r))− 1 2 ln( 1+ W 2 (1−r) 2 ) W⋅ tan −1 (W)− 1 2 ln( 1+ W 2 )
er r rms = 1 ^ L ∑ i=1 L [ ( x ^ i − x i ) 2 + ( y ^ i − y i ) 2 ]

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