Abstract

Single-molecule-localization-based super-resolution microscopic technologies, such as stochastic optical reconstruction microscopy (STORM), require lengthy runtimes. Compressed sensing (CS) can partially overcome this inherent disadvantage, but its effect on super-resolution reconstruction has not been thoroughly examined. In CS, measurement matrices play more important roles than reconstruction algorithms. Larger measurement matrices have better restricted isometry properties (RIPs). This paper proposes, analyzes, and compares uses of higher resolution cameras and interpolation to achieve better outcomes. Statistical results demonstrate that super-resolution reconstructions is significantly improved by interpolating low-resolution STORM raw images and using point-spread-function-based measurement matrices with better RIPs. The analysis of publically accessible experimental data confirms this conclusion.

© 2017 Optical Society of America

Full Article  |  PDF Article
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2015 (4)

T. Cheng, “Directional remote sensing,” Geodetski List 36, 251–262 (2015).

D. Sage, H. Kirshner, T. Pengo, N. Stuurman, J. Min, S. Manley, and M. Unser, “Quantitative evaluation of software packages for single-molecule localization microscopy,” Nat. Methods 12(8), 717–724 (2015).
[Crossref] [PubMed]

J. Huang, K. Gumpper, Y. Chi, M. Sun, and J. Ma, “Fast two-dimensional super-resolution image reconstruction algorithm for ultra-high emitter density,” Opt. Lett. 40(13), 2989–2992 (2015).
[Crossref] [PubMed]

S. Zhang, D. Chen, and H. Niu, “3D localization of high particle density images using sparse recovery,” Appl. Opt. 54(26), 7859–7864 (2015).
[Crossref] [PubMed]

2014 (4)

J. Min, S. J. Holden, L. Carlini, M. Unser, S. Manley, and J. C. Ye, “3D high-density localization microscopy using hybrid astigmatic/ biplane imaging and sparse image reconstruction,” Biomed. Opt. Express 5(11), 3935–3948 (2014).
[Crossref] [PubMed]

M. Ovesný, P. Křížek, Z. Švindrych, and G. M. Hagen, “High density 3D localization microscopy using sparse support recovery,” Opt. Express 22(25), 31263–31276 (2014).
[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(11), 2443–2449 (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] [PubMed]

2013 (1)

2012 (2)

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

L. Zhu, W. Zhang, D. Elnatan, and B. Huang, “Faster STORM using compressed sensing,” Nat. Methods 9(7), 721–723 (2012).
[Crossref] [PubMed]

2011 (5)

J. Y. Park, H. L. Yap, C. J. Rozell, and M. B. Wakin, “Concentration of measure for block diagonal matrices with applications to compressive signal processing,” IEEE Trans. Signal Process. 59(12), 5859–5875 (2011).
[Crossref]

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

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

D. T. Burnette, P. Sengupta, Y. Dai, J. Lippincott-Schwartz, and B. Kachar, “Bleaching/blinking assisted localization microscopy for superresolution imaging using standard fluorescent molecules,” Proc. Natl. Acad. Sci. U.S.A. 108(52), 21081–21086 (2011).
[Crossref] [PubMed]

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

2009 (1)

D. Wei and O. Milenkovic, “Subspace pursuit for compressive sensing signal reconstruction,” IEEE Trans. Inf. Theory 55(5), 2230–2249 (2009).
[Crossref]

2007 (2)

M. Elad, “Optimized projections for compressed sensing,” IEEE Trans. Signal Process. 55(12), 5695–5702 (2007).
[Crossref]

R. G. Baraniuk, “Compressive sensing [Lecture Notes],” IEEE Signal Process. Mag. 24(4), 118–121 (2007).
[Crossref]

2006 (5)

Y. Tsaig and D. L. Donoho, “Extensions of compressed sensing,” Signal Process. 86(3), 549–571 (2006).
[Crossref]

D. L. Donoho, “Compressed sensing,” IEEE Trans. Inf. Theory 52(4), 1289–1306 (2006).
[Crossref]

S. T. Hess, T. P. 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]

2005 (1)

M. Hofmann, C. Eggeling, S. Jakobs, and S. W. Hell, “Breaking the diffraction barrier in fluorescence microscopy at low light intensities by using reversibly photoswitchable proteins,” Proc. Natl. Acad. Sci. U.S.A. 102(49), 17565–17569 (2005).
[Crossref] [PubMed]

2002 (1)

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]

Babcock, H. P.

Baraniuk, R. G.

R. G. Baraniuk, “Compressive sensing [Lecture Notes],” IEEE Signal Process. Mag. 24(4), 118–121 (2007).
[Crossref]

Bates, M.

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]

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]

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]

Burnette, D. T.

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

D. T. Burnette, P. Sengupta, Y. Dai, J. Lippincott-Schwartz, and B. Kachar, “Bleaching/blinking assisted localization microscopy for superresolution imaging using standard fluorescent molecules,” Proc. Natl. Acad. Sci. U.S.A. 108(52), 21081–21086 (2011).
[Crossref] [PubMed]

Cao, Y.

Carlini, L.

J. Min, S. J. Holden, L. Carlini, M. Unser, S. Manley, and J. C. Ye, “3D high-density localization microscopy using hybrid astigmatic/ biplane imaging and sparse image reconstruction,” Biomed. Opt. Express 5(11), 3935–3948 (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] [PubMed]

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(11), 2443–2449 (2014).
[Crossref] [PubMed]

Chen, D.

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(11), 2443–2449 (2014).
[Crossref] [PubMed]

Cheng, T.

T. Cheng, “Directional remote sensing,” Geodetski List 36, 251–262 (2015).

Chi, Y.

J. Huang, K. Gumpper, Y. Chi, M. Sun, and J. Ma, “Fast two-dimensional super-resolution image reconstruction algorithm for ultra-high emitter density,” Opt. Lett. 40(13), 2989–2992 (2015).
[Crossref] [PubMed]

J. Huang, M. Sun, and Y. Chi, “Super-resolution image reconstruction for high-density 3D single-molecule microscopy,” in IEEE International Symposium on Biomedical Imaging, (IEEE, 2016), 241–244.
[Crossref]

Cox, S.

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

Cremer, C.

Dai, Y.

D. T. Burnette, P. Sengupta, Y. Dai, J. Lippincott-Schwartz, and B. Kachar, “Bleaching/blinking assisted localization microscopy for superresolution imaging using standard fluorescent molecules,” Proc. Natl. Acad. Sci. U.S.A. 108(52), 21081–21086 (2011).
[Crossref] [PubMed]

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]

Ding, J.

Donoho, D. L.

Y. Tsaig and D. L. Donoho, “Extensions of compressed sensing,” Signal Process. 86(3), 549–571 (2006).
[Crossref]

D. L. Donoho, “Compressed sensing,” IEEE Trans. Inf. Theory 52(4), 1289–1306 (2006).
[Crossref]

Eggeling, C.

M. Hofmann, C. Eggeling, S. Jakobs, and S. W. Hell, “Breaking the diffraction barrier in fluorescence microscopy at low light intensities by using reversibly photoswitchable proteins,” Proc. Natl. Acad. Sci. U.S.A. 102(49), 17565–17569 (2005).
[Crossref] [PubMed]

Elad, M.

M. Elad, “Optimized projections for compressed sensing,” IEEE Trans. Signal Process. 55(12), 5695–5702 (2007).
[Crossref]

Elnatan, D.

L. Zhu, W. Zhang, D. Elnatan, and B. Huang, “Faster STORM using compressed sensing,” Nat. Methods 9(7), 721–723 (2012).
[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(11), 4258–4272 (2006).
[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(11), 2443–2449 (2014).
[Crossref] [PubMed]

Gumpper, K.

Hagen, G. M.

Heintzmann, R.

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

R. Heintzmann, T. M. Jovin, and C. Cremer, “Saturated patterned excitation microscopy--a concept for optical resolution improvement,” J. Opt. Soc. Am. A 19(8), 1599–1609 (2002).
[Crossref] [PubMed]

Hell, S. W.

M. Hofmann, C. Eggeling, S. Jakobs, and S. W. Hell, “Breaking the diffraction barrier in fluorescence microscopy at low light intensities by using reversibly photoswitchable proteins,” Proc. Natl. Acad. Sci. U.S.A. 102(49), 17565–17569 (2005).
[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. Girirajan, and M. D. Mason, “Ultra-high resolution imaging by fluorescence photoactivation localization microscopy,” Biophys. J. 91(11), 4258–4272 (2006).
[Crossref] [PubMed]

Hofmann, M.

M. Hofmann, C. Eggeling, S. Jakobs, and S. W. Hell, “Breaking the diffraction barrier in fluorescence microscopy at low light intensities by using reversibly photoswitchable proteins,” Proc. Natl. Acad. Sci. U.S.A. 102(49), 17565–17569 (2005).
[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]

Holden, S. J.

Huang, B.

L. Zhu, W. Zhang, D. Elnatan, and B. Huang, “Faster STORM using compressed sensing,” Nat. Methods 9(7), 721–723 (2012).
[Crossref] [PubMed]

Huang, J.

J. Huang, K. Gumpper, Y. Chi, M. Sun, and J. Ma, “Fast two-dimensional super-resolution image reconstruction algorithm for ultra-high emitter density,” Opt. Lett. 40(13), 2989–2992 (2015).
[Crossref] [PubMed]

J. Huang, M. Sun, and Y. Chi, “Super-resolution image reconstruction for high-density 3D single-molecule microscopy,” in IEEE International Symposium on Biomedical Imaging, (IEEE, 2016), 241–244.
[Crossref]

Huang, Z.-L.

Jakobs, S.

M. Hofmann, C. Eggeling, S. Jakobs, and S. W. Hell, “Breaking the diffraction barrier in fluorescence microscopy at low light intensities by using reversibly photoswitchable proteins,” Proc. Natl. Acad. Sci. U.S.A. 102(49), 17565–17569 (2005).
[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(11), 2443–2449 (2014).
[Crossref] [PubMed]

Jones, G. E.

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

Jovanovic-Talisman, T.

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

Jovin, T. M.

Kachar, B.

D. T. Burnette, P. Sengupta, Y. Dai, J. Lippincott-Schwartz, and B. Kachar, “Bleaching/blinking assisted localization microscopy for superresolution imaging using standard fluorescent molecules,” Proc. Natl. Acad. Sci. U.S.A. 108(52), 21081–21086 (2011).
[Crossref] [PubMed]

Kapanidis, A. N.

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

Kirshner, H.

D. Sage, H. Kirshner, T. Pengo, N. Stuurman, J. Min, S. Manley, and M. Unser, “Quantitative evaluation of software packages for single-molecule localization microscopy,” Nat. Methods 12(8), 717–724 (2015).
[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] [PubMed]

Krížek, P.

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.

D. T. Burnette, P. Sengupta, Y. Dai, J. Lippincott-Schwartz, and B. Kachar, “Bleaching/blinking assisted localization microscopy for superresolution imaging using standard fluorescent molecules,” Proc. Natl. Acad. Sci. U.S.A. 108(52), 21081–21086 (2011).
[Crossref] [PubMed]

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

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]

Liu, X.

Liu, Y.

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(11), 2443–2449 (2014).
[Crossref] [PubMed]

Ma, J.

Manley, S.

D. Sage, H. Kirshner, T. Pengo, N. Stuurman, J. Min, S. Manley, and M. Unser, “Quantitative evaluation of software packages for single-molecule localization microscopy,” Nat. Methods 12(8), 717–724 (2015).
[Crossref] [PubMed]

J. Min, S. J. Holden, L. Carlini, M. Unser, S. Manley, and J. C. Ye, “3D high-density localization microscopy using hybrid astigmatic/ biplane imaging and sparse image reconstruction,” Biomed. Opt. Express 5(11), 3935–3948 (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] [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(11), 4258–4272 (2006).
[Crossref] [PubMed]

Milenkovic, O.

D. Wei and O. Milenkovic, “Subspace pursuit for compressive sensing signal reconstruction,” IEEE Trans. Inf. Theory 55(5), 2230–2249 (2009).
[Crossref]

Min, J.

D. Sage, H. Kirshner, T. Pengo, N. Stuurman, J. Min, S. Manley, and M. Unser, “Quantitative evaluation of software packages for single-molecule localization microscopy,” Nat. Methods 12(8), 717–724 (2015).
[Crossref] [PubMed]

J. Min, S. J. Holden, L. Carlini, M. Unser, S. Manley, and J. C. Ye, “3D high-density localization microscopy using hybrid astigmatic/ biplane imaging and sparse image reconstruction,” Biomed. Opt. Express 5(11), 3935–3948 (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] [PubMed]

Moffitt, J. R.

Monypenny, J.

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

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]

Niu, H.

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]

Ovesný, M.

Park, J. Y.

J. Y. Park, H. L. Yap, C. J. Rozell, and M. B. Wakin, “Concentration of measure for block diagonal matrices with applications to compressive signal processing,” IEEE Trans. Signal Process. 59(12), 5859–5875 (2011).
[Crossref]

Patterson, G. H.

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

Pengo, T.

D. Sage, H. Kirshner, T. Pengo, N. Stuurman, J. Min, S. Manley, and M. Unser, “Quantitative evaluation of software packages for single-molecule localization microscopy,” Nat. Methods 12(8), 717–724 (2015).
[Crossref] [PubMed]

Quan, T.

Rosten, E.

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

Rozell, C. J.

J. Y. Park, H. L. Yap, C. J. Rozell, and M. B. Wakin, “Concentration of measure for block diagonal matrices with applications to compressive signal processing,” IEEE Trans. Signal Process. 59(12), 5859–5875 (2011).
[Crossref]

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]

Sage, D.

D. Sage, H. Kirshner, T. Pengo, N. Stuurman, J. Min, S. Manley, and M. Unser, “Quantitative evaluation of software packages for single-molecule localization microscopy,” Nat. Methods 12(8), 717–724 (2015).
[Crossref] [PubMed]

Sengupta, P.

D. T. Burnette, P. Sengupta, Y. Dai, J. Lippincott-Schwartz, and B. Kachar, “Bleaching/blinking assisted localization microscopy for superresolution imaging using standard fluorescent molecules,” Proc. Natl. Acad. Sci. U.S.A. 108(52), 21081–21086 (2011).
[Crossref] [PubMed]

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(11), 2443–2449 (2014).
[Crossref] [PubMed]

Sougrat, R.

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

Stuurman, N.

D. Sage, H. Kirshner, T. Pengo, N. Stuurman, J. Min, S. Manley, and M. Unser, “Quantitative evaluation of software packages for single-molecule localization microscopy,” Nat. Methods 12(8), 717–724 (2015).
[Crossref] [PubMed]

Sun, M.

J. Huang, K. Gumpper, Y. Chi, M. Sun, and J. Ma, “Fast two-dimensional super-resolution image reconstruction algorithm for ultra-high emitter density,” Opt. Lett. 40(13), 2989–2992 (2015).
[Crossref] [PubMed]

J. Huang, M. Sun, and Y. Chi, “Super-resolution image reconstruction for high-density 3D single-molecule microscopy,” in IEEE International Symposium on Biomedical Imaging, (IEEE, 2016), 241–244.
[Crossref]

Švindrych, Z.

Tsaig, Y.

Y. Tsaig and D. L. Donoho, “Extensions of compressed sensing,” Signal Process. 86(3), 549–571 (2006).
[Crossref]

Unser, M.

D. Sage, H. Kirshner, T. Pengo, N. Stuurman, J. Min, S. Manley, and M. Unser, “Quantitative evaluation of software packages for single-molecule localization microscopy,” Nat. Methods 12(8), 717–724 (2015).
[Crossref] [PubMed]

J. Min, S. J. Holden, L. Carlini, M. Unser, S. Manley, and J. C. Ye, “3D high-density localization microscopy using hybrid astigmatic/ biplane imaging and sparse image reconstruction,” Biomed. Opt. Express 5(11), 3935–3948 (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] [PubMed]

Uphoff, S.

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

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]

Wakin, M. B.

J. Y. Park, H. L. Yap, C. J. Rozell, and M. B. Wakin, “Concentration of measure for block diagonal matrices with applications to compressive signal processing,” IEEE Trans. Signal Process. 59(12), 5859–5875 (2011).
[Crossref]

Wei, D.

D. Wei and O. Milenkovic, “Subspace pursuit for compressive sensing signal reconstruction,” IEEE Trans. Inf. Theory 55(5), 2230–2249 (2009).
[Crossref]

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(11), 2443–2449 (2014).
[Crossref] [PubMed]

Yap, H. L.

J. Y. Park, H. L. Yap, C. J. Rozell, and M. B. Wakin, “Concentration of measure for block diagonal matrices with applications to compressive signal processing,” IEEE Trans. Signal Process. 59(12), 5859–5875 (2011).
[Crossref]

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]

J. Min, S. J. Holden, L. Carlini, M. Unser, S. Manley, and J. C. Ye, “3D high-density localization microscopy using hybrid astigmatic/ biplane imaging and sparse image reconstruction,” Biomed. Opt. Express 5(11), 3935–3948 (2014).
[Crossref] [PubMed]

Zeng, S.

Zhang, S.

Zhang, W.

L. Zhu, W. Zhang, D. Elnatan, and B. Huang, “Faster STORM using compressed sensing,” Nat. Methods 9(7), 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(11), 2443–2449 (2014).
[Crossref] [PubMed]

Zhu, H.

Zhu, L.

L. Zhu, W. Zhang, D. Elnatan, and B. Huang, “Faster STORM using compressed sensing,” Nat. Methods 9(7), 721–723 (2012).
[Crossref] [PubMed]

Zhuang, X.

H. P. Babcock, J. R. Moffitt, Y. Cao, and X. Zhuang, “Fast compressed sensing analysis for super-resolution imaging using L1-homotopy,” Opt. Express 21(23), 28583–28596 (2013).
[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. 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]

Appl. Opt. (1)

Biomed. Opt. Express (1)

Biophys. J. (3)

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

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(11), 2443–2449 (2014).
[Crossref] [PubMed]

Geodetski List (1)

T. Cheng, “Directional remote sensing,” Geodetski List 36, 251–262 (2015).

IEEE Signal Process. Mag. (1)

R. G. Baraniuk, “Compressive sensing [Lecture Notes],” IEEE Signal Process. Mag. 24(4), 118–121 (2007).
[Crossref]

IEEE Trans. Inf. Theory (2)

D. Wei and O. Milenkovic, “Subspace pursuit for compressive sensing signal reconstruction,” IEEE Trans. Inf. Theory 55(5), 2230–2249 (2009).
[Crossref]

D. L. Donoho, “Compressed sensing,” IEEE Trans. Inf. Theory 52(4), 1289–1306 (2006).
[Crossref]

IEEE Trans. Signal Process. (2)

M. Elad, “Optimized projections for compressed sensing,” IEEE Trans. Signal Process. 55(12), 5695–5702 (2007).
[Crossref]

J. Y. Park, H. L. Yap, C. J. Rozell, and M. B. Wakin, “Concentration of measure for block diagonal matrices with applications to compressive signal processing,” IEEE Trans. Signal Process. 59(12), 5859–5875 (2011).
[Crossref]

J. Opt. Soc. Am. A (1)

Nat. Methods (5)

L. Zhu, W. Zhang, D. Elnatan, and B. Huang, “Faster STORM using compressed sensing,” Nat. Methods 9(7), 721–723 (2012).
[Crossref] [PubMed]

D. Sage, H. Kirshner, T. Pengo, N. Stuurman, J. Min, S. Manley, and M. Unser, “Quantitative evaluation of software packages for single-molecule localization microscopy,” Nat. Methods 12(8), 717–724 (2015).
[Crossref] [PubMed]

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

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

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]

Opt. Express (3)

Opt. Lett. (1)

Proc. Natl. Acad. Sci. U.S.A. (2)

D. T. Burnette, P. Sengupta, Y. Dai, J. Lippincott-Schwartz, and B. Kachar, “Bleaching/blinking assisted localization microscopy for superresolution imaging using standard fluorescent molecules,” Proc. Natl. Acad. Sci. U.S.A. 108(52), 21081–21086 (2011).
[Crossref] [PubMed]

M. Hofmann, C. Eggeling, S. Jakobs, and S. W. Hell, “Breaking the diffraction barrier in fluorescence microscopy at low light intensities by using reversibly photoswitchable proteins,” Proc. Natl. Acad. Sci. U.S.A. 102(49), 17565–17569 (2005).
[Crossref] [PubMed]

Sci. Rep. (1)

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]

Science (1)

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]

Signal Process. (1)

Y. Tsaig and D. L. Donoho, “Extensions of compressed sensing,” Signal Process. 86(3), 549–571 (2006).
[Crossref]

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Y. Lifeng, L. Gang, and C. Liping, “Optimizing projection matrix for compressed sensing systems,” in International Conference on Information, Communications and Signal Processing, (IEEE 2011), 1–5.
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H. Rauhut, “Circulant and Toeplitz matrices in compressed sensing,” arXiv preprint arXiv:0902.4394 (2009).

J. Huang, M. Sun, and Y. Chi, “Super-resolution image reconstruction for high-density 3D single-molecule microscopy,” in IEEE International Symposium on Biomedical Imaging, (IEEE, 2016), 241–244.
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M. D. Pedro and P. Pahud, Vibration Mechanics (Springer Netherlands, 1991).

F. M. Sacerdoti, Digital Image Processing (Springer, 2016).

J. M. Duarte-Carvajalino and G. Sapiro, “Learning to sense sparse signals: Simultaneous sensing matrix and sparsifying dictionary optimization,” (DTIC Document, 2008).

M. Zhengle, W. Chen, and C. Ya, “Superresolution far-field fluorescence bio-imaging: breaking the diffraction barrier,” Chin. J. Lasers 9, 002 (2008).
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Biomedical Imaging Group, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, “Benchmarking of Single-Molecule Localization Microscopy Software,” ( http://bigwww.epfl.ch/smlm/ , 2015).

Z. Sun, “3D Tracking of Quantum Dots and Endosomes in DrosophilaMelanogaster (Leiden University, 2007), 1–36.

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Figures (3)

Fig. 1
Fig. 1 STORM image simulation analysis for LR, LI, HR, and HI based on CS and EPFL website data. The x axes represent molecule density and signal sparsity. (a) Comparison of measures of localization precision. (b) Comparison of recall rates. (c) Comparison of the JAC values. (d) Comparison of precision measures. (e) Comparison of SNRs. (f) Comparison of NSRs.
Fig. 2
Fig. 2 STORM image simulation analysis using CS to demonstrate its capability for identifying molecules efficiently at high densities. The scale bar in (e) is 200 nm. (a) The reconstructed result of an LR raw image. (b) The reconstructed result of an LI raw image. (c) The reconstructed result of an HR raw image. (d) The reconstructed result of an HI raw image. (e) True positions of six molecules. In (a)–(e), results were obtained after taking the logarithm of (f)–(j) based on real data. Thus, (f)–(j) correspond to (a)–(e). (k) A low-resolution raw image of STORM. The grid size of (a)–(j) equals 1/8 pixel of (k). (l) An interpolated low-resolution raw image of STORM. (m) A high-resolution raw image of STORM. (n) An interpolated high-resolution raw image of STORM.
Fig. 3
Fig. 3 Comparison of LR and LI based on experimental 2D high-density data (500 raw images) from the EPFL website. The yellow squares in (a) and (b) are 3200 × 3200 nm, and the scale bar in (c) indicates 2000 nm. (a) A reconstructed result of LR. (b) A reconstructed result of LI. (c) A frame of a raw STORM images. (d) Enlarged LR and LI images from the top areas marked by yellow squares in (a) and (b), respectively. (e) Enlarged LR and LI images from the middle areas marked by yellow squares in (a) and (b), respectively. (e) Enlarged LR and LI images from the bottom areas marked by yellow squares in (a) and (b), respectively. (g) Plots of photon-count profiles obtained by measurements made along the yellow lines in (f).

Tables (2)

Tables Icon

Table 1 Parameters of Three Measurement Matrices, Raw Images and Super-resolution Images

Tables Icon

Table 2 Simulation Analysis Results for LR and LI from Fig. 1

Equations (5)

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

min x 0 s . t . y = Φ x ,
min c T x 1 s . t . Φ x y 2 < ε y j a n d x i 0 ,
p = TP FP+TP , r = TP FN + TP , JAC = TP FN + FP + TP , and F1-score = 2 p r p + r .
S N R = 20 × log 10 ( x 2 x R x 2 )
N S R = y n o i y 2 y 2 .

Metrics