Abstract

Three-dimensional fluorescence microscopy based on Nyquist sampling of focal planes faces harsh trade-offs between acquisition time, light exposure, and signal-to-noise. We propose a 3D compressed sensing approach that uses temporal modulation of the excitation intensity during axial stage sweeping and can be adapted to fluorescence microscopes without hardware modification. We describe implementations on a lattice light sheet microscope and an epifluorescence microscope, and show that images of beads and biological samples can be reconstructed with a 5-10 fold reduction of light exposure and acquisition time. Our scheme opens a new door towards faster and less damaging 3D fluorescence microscopy.

© 2017 Optical Society of America

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References

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  1. P. Keller, A. Schmidt, J. Wittbrodt, and E. Stelzer, “Reconstruction of zebrafish early embryonic development by scanned light sheet microscopy,” Science 322, 5904 (2008).
    [Crossref]
  2. T. A. Planchon, L. Gao, D. E. Milkie, M. W. Davidson, J. A. Galbraith, C. G. Galbraith, and E. Betzig, “Rapid three-dimensional isotropic imaging of living cells using Bessel beam plane illumination,” Nat. Methods 8, 417–423 (2011).
    [Crossref] [PubMed]
  3. M. Weber, M. Mickoleit, and J. Huisken, “Light sheet microscopy,” in “Methods in Cell Biology” (Elsevier, 2014), pp. 193–215.
    [Crossref]
  4. R. Baraniuk, “Compressive sensing,” IEEE Signal Processing Mag. 24, 118–121 (2007)
    [Crossref]
  5. D. Donoho, “Compressed sensing,” IEEE Trans. Inf. Theory 52, 1289–1306 (2006).
    [Crossref]
  6. E. Candes and M. Wakin, “An introduction to compressive sampling,” IEEE Signal Processing Mag. 25, 21–30 (2008).
    [Crossref]
  7. Y. C. Eldar and G. Kutyniok, Compressed Sensing: Theory and Applications (Cambridge University, 2012).
    [Crossref]
  8. M. Elad, Sparse and Redundant Representations (Springer, 2010).
    [Crossref]
  9. J. Bobin, J.-L. Starck, and R. Ottensamer, “Compressed sensing in astronomy,” IEEE J. Sel. Top. Signal Process 2, 718–726 (2008).
    [Crossref]
  10. M. Lustig, D. Donoho, J. Santos, and J. Pauly, “Compressed sensing MRI,” IEEE Signal Processing Mag. 25, 72–82 (2008).
    [Crossref]
  11. J. Hunt, T. Driscoll, A. Mrozack, G. Lipworth, M. Reynolds, D. Brady, and D. R. Smith, “Metamaterial apertures for computational imaging,” Science 310, 399 (2013).
  12. J. Shin, B. T. Bosworth, and M. A. Foster, “Compressive fluorescence imaging using a multi-core fiber and spatially dependent scattering,” Opt Lett 109, 42 (2017).
  13. L. Gao, J. Liang, C. Li, and L. V. Wang, “Single-shot compressed ultrafast photography at one hundred billion frames per second,” Nature 516, 74–77 (2014).
    [Crossref] [PubMed]
  14. J. Liang, C. Ma, L. Zhu, Y. Chen, L. Gao, and L. V. Wang, “Single-shot real-time video recording of a photonic Mach cone induced by a scattered light pulse,” Sci Adv 3, e1601814 (2017).
    [Crossref] [PubMed]
  15. E. McLeod and A. Ozcan, “Unconventional methods of imaging: computational microscopy and compact implementations,” Rep. Prog. Phys. 79, 076001 (2016).
    [Crossref] [PubMed]
  16. M. M. Marim, E. D. Angelini, and J.-C. Olivo-Marin, “A compressed sensing approach for biological microscopic image processing,” in “2009 IEEE International Symposium on Biomedical Imaging: From Nano to Macro,” (IEEE, 2009), pp. 1374–1377.
  17. P. Ye, J. L. Paredes, Y. Wu, C. Chen, G. R. Arce, and D. W. Prather, “Compressive confocal microscopy: 3d reconstruction algorithms,” in “SPIE MOEMS-MEMS: Micro-and Nanofabrication,” (International Society for Optics and Photonics, 2009), pp. 72100G.
  18. Y. Wu, P. Ye, I. O. Mirza, G. R. Arce, and D. W. Prather, “Experimental demonstration of an optical-sectioning compressive sensing microscope (CSM),” Opt. Express 18, 24565–24578 (2010).
    [Crossref] [PubMed]
  19. V. Studer, J. Bobin, M. Chahid, H. S. Mousavi, E. Candes, and M. Dahan, “Compressive fluorescence microscopy for biological and hyperspectral imaging,” Proc. Natl. Acad. Sci. U. S. A. 109, E1679–E1687 (2012).
    [Crossref] [PubMed]
  20. S. Schwartz, A. Wong, and D. A. Clausi, “Compressive fluorescence microscopy using saliency-guided sparse reconstruction ensemble fusion,” Opt. Express 20, 17281–17296 (2012).
    [Crossref] [PubMed]
  21. L. Zhu, W. Zhang, D. Elnatan, and B. Huang, “Faster STORM using compressed sensing,” Nat. Methods 9, 721–723 (2012).
    [Crossref] [PubMed]
  22. N. Pavillon and N. I. Smith, “Compressed sensing laser scanning microscopy,” Opt. Express 24, 30038 (2016).
    [Crossref]
  23. E. J. Candès, Y. C. Eldar, D. Needell, and P. Randall, “Compressed sensing with coherent and redundant dictionaries,” Appl. Comput. Harmon Anal. 31, 59–73 (2011).
    [Crossref]
  24. T. Tao and E. Candès, “Decoding by linear programming,” arXiv preprint arXiv:math/0502327 (2004).
  25. M. Raginsky, R. M. Willett, Z. T. Harmany, and R. F. Marcia, “Compressed sensing performance bounds under Poisson noise,” IEEE Trans. Signal Process 58, 3990–4002 (2010).
    [Crossref]
  26. E. Candes, J. Romberg, and T. Tao, “Robust uncertainty principles: exact signal reconstruction from highly incomplete frequency information,” IEEE Trans. Inf. Theory 52, 489–509 (2006).
    [Crossref]
  27. Z. T. Harmany, R. F. Marcia, and R. M. Willett, “This is SPIRAL-TAP: Sparse Poisson intensity reconstruction algorithms–theory and practice,” IEEE Trans. Signal Process 21, 1084–1096 (2012).
  28. S. Becker, J. Bobin, and E. Candès, “NESTA: A fast and accurate first-order method for sparse recovery,” arXiv preprint arXiv:0904.3367 (2009).
  29. R. Baraniuk, M. A. Davenport, M. F. Duarte, and C. Hegde, An Introduction to Compressive Sensing (OpenStax CNX, 2011).
  30. C. Bilen, Y. Wang, and I. Selesnick, “Compressed sensing for moving imagery in medical imaging,” arXiv preprint arXiv:1203.5772 (2012).
  31. B.-C. Chen, W. R. Legant, K. Wang, L. Shao, D. E. Milkie, M. W. Davidson, C. Janetopoulos, X. S. Wu, J. A. Hammer, Z. Liu, B. P. English, Y. Mimori-Kiyosue, D. P. Romero, A. T. Ritter, J. Lippincott-Schwartz, L. Fritz-Laylin, R. D. Mullins, D. M. Mitchell, J. N. Bembenek, A.-C. Reymann, R. Bohme, S. W. Grill, J. T. Wang, G. Seydoux, U. S. Tulu, D. P. Kiehart, and E. Betzig, “Lattice light-sheet microscopy: Imaging molecules to embryos at high spatiotemporal resolution,” Science 346, 1257998 (2014).
    [Crossref] [PubMed]
  32. A. D. Edelstein, M. A. Tsuchida, N. Amodaj, H. Pinkard, R. D. Vale, and N. Stuurman, “Advanced methods of microscope control using micro-Manager software,” J. Biol. Methods 1, 10 (2014).
    [Crossref]
  33. J.-Y. Tinevez, J. Dragavon, L. Baba-Aissa, P. Roux, E. Perret, A. Canivet, V. Galy, and S. Shorte, “A quantitative method for measuring phototoxicity of a live cell imaging microscope,” in “Methods in Enzymology” (Elsevier, 2012), pp. 291–309.
    [Crossref]
  34. D. S. Smith, J. C. Gore, T. E. Yankeelov, and E. B. Welch, “Real-time compressive sensing MRI reconstruction using GPU computing and split Bregman methods,” Int. J. Biomed. Imaging 2012, 1–6 (2012).
    [Crossref]
  35. B. E. Nett, J. Tang, and G.-H. Chen, “GPU implementation of prior image constrained compressed sensing (PICCS),” Proc. SPIE 7622, 762239 (2010).
    [Crossref]
  36. M. Mordechay and Y. Y. Schechner, “Matrix optimization for Poisson compressed sensing,” in “2014 IEEE Global Conference on Signal and Information Processing (GlobalSIP)” (IEEE, 2014), pp. 684–688.
  37. J. D. Hunter, “Matplotlib: A 2d graphics environment,” Comput. Sci. Eng. 9, 90–95 (2007).
    [Crossref]

2017 (2)

J. Shin, B. T. Bosworth, and M. A. Foster, “Compressive fluorescence imaging using a multi-core fiber and spatially dependent scattering,” Opt Lett 109, 42 (2017).

J. Liang, C. Ma, L. Zhu, Y. Chen, L. Gao, and L. V. Wang, “Single-shot real-time video recording of a photonic Mach cone induced by a scattered light pulse,” Sci Adv 3, e1601814 (2017).
[Crossref] [PubMed]

2016 (2)

E. McLeod and A. Ozcan, “Unconventional methods of imaging: computational microscopy and compact implementations,” Rep. Prog. Phys. 79, 076001 (2016).
[Crossref] [PubMed]

N. Pavillon and N. I. Smith, “Compressed sensing laser scanning microscopy,” Opt. Express 24, 30038 (2016).
[Crossref]

2014 (3)

L. Gao, J. Liang, C. Li, and L. V. Wang, “Single-shot compressed ultrafast photography at one hundred billion frames per second,” Nature 516, 74–77 (2014).
[Crossref] [PubMed]

B.-C. Chen, W. R. Legant, K. Wang, L. Shao, D. E. Milkie, M. W. Davidson, C. Janetopoulos, X. S. Wu, J. A. Hammer, Z. Liu, B. P. English, Y. Mimori-Kiyosue, D. P. Romero, A. T. Ritter, J. Lippincott-Schwartz, L. Fritz-Laylin, R. D. Mullins, D. M. Mitchell, J. N. Bembenek, A.-C. Reymann, R. Bohme, S. W. Grill, J. T. Wang, G. Seydoux, U. S. Tulu, D. P. Kiehart, and E. Betzig, “Lattice light-sheet microscopy: Imaging molecules to embryos at high spatiotemporal resolution,” Science 346, 1257998 (2014).
[Crossref] [PubMed]

A. D. Edelstein, M. A. Tsuchida, N. Amodaj, H. Pinkard, R. D. Vale, and N. Stuurman, “Advanced methods of microscope control using micro-Manager software,” J. Biol. Methods 1, 10 (2014).
[Crossref]

2013 (1)

J. Hunt, T. Driscoll, A. Mrozack, G. Lipworth, M. Reynolds, D. Brady, and D. R. Smith, “Metamaterial apertures for computational imaging,” Science 310, 399 (2013).

2012 (5)

V. Studer, J. Bobin, M. Chahid, H. S. Mousavi, E. Candes, and M. Dahan, “Compressive fluorescence microscopy for biological and hyperspectral imaging,” Proc. Natl. Acad. Sci. U. S. A. 109, E1679–E1687 (2012).
[Crossref] [PubMed]

S. Schwartz, A. Wong, and D. A. Clausi, “Compressive fluorescence microscopy using saliency-guided sparse reconstruction ensemble fusion,” Opt. Express 20, 17281–17296 (2012).
[Crossref] [PubMed]

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

D. S. Smith, J. C. Gore, T. E. Yankeelov, and E. B. Welch, “Real-time compressive sensing MRI reconstruction using GPU computing and split Bregman methods,” Int. J. Biomed. Imaging 2012, 1–6 (2012).
[Crossref]

Z. T. Harmany, R. F. Marcia, and R. M. Willett, “This is SPIRAL-TAP: Sparse Poisson intensity reconstruction algorithms–theory and practice,” IEEE Trans. Signal Process 21, 1084–1096 (2012).

2011 (2)

E. J. Candès, Y. C. Eldar, D. Needell, and P. Randall, “Compressed sensing with coherent and redundant dictionaries,” Appl. Comput. Harmon Anal. 31, 59–73 (2011).
[Crossref]

T. A. Planchon, L. Gao, D. E. Milkie, M. W. Davidson, J. A. Galbraith, C. G. Galbraith, and E. Betzig, “Rapid three-dimensional isotropic imaging of living cells using Bessel beam plane illumination,” Nat. Methods 8, 417–423 (2011).
[Crossref] [PubMed]

2010 (3)

M. Raginsky, R. M. Willett, Z. T. Harmany, and R. F. Marcia, “Compressed sensing performance bounds under Poisson noise,” IEEE Trans. Signal Process 58, 3990–4002 (2010).
[Crossref]

Y. Wu, P. Ye, I. O. Mirza, G. R. Arce, and D. W. Prather, “Experimental demonstration of an optical-sectioning compressive sensing microscope (CSM),” Opt. Express 18, 24565–24578 (2010).
[Crossref] [PubMed]

B. E. Nett, J. Tang, and G.-H. Chen, “GPU implementation of prior image constrained compressed sensing (PICCS),” Proc. SPIE 7622, 762239 (2010).
[Crossref]

2008 (4)

E. Candes and M. Wakin, “An introduction to compressive sampling,” IEEE Signal Processing Mag. 25, 21–30 (2008).
[Crossref]

J. Bobin, J.-L. Starck, and R. Ottensamer, “Compressed sensing in astronomy,” IEEE J. Sel. Top. Signal Process 2, 718–726 (2008).
[Crossref]

M. Lustig, D. Donoho, J. Santos, and J. Pauly, “Compressed sensing MRI,” IEEE Signal Processing Mag. 25, 72–82 (2008).
[Crossref]

P. Keller, A. Schmidt, J. Wittbrodt, and E. Stelzer, “Reconstruction of zebrafish early embryonic development by scanned light sheet microscopy,” Science 322, 5904 (2008).
[Crossref]

2007 (2)

R. Baraniuk, “Compressive sensing,” IEEE Signal Processing Mag. 24, 118–121 (2007)
[Crossref]

J. D. Hunter, “Matplotlib: A 2d graphics environment,” Comput. Sci. Eng. 9, 90–95 (2007).
[Crossref]

2006 (2)

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

E. Candes, J. Romberg, and T. Tao, “Robust uncertainty principles: exact signal reconstruction from highly incomplete frequency information,” IEEE Trans. Inf. Theory 52, 489–509 (2006).
[Crossref]

Amodaj, N.

A. D. Edelstein, M. A. Tsuchida, N. Amodaj, H. Pinkard, R. D. Vale, and N. Stuurman, “Advanced methods of microscope control using micro-Manager software,” J. Biol. Methods 1, 10 (2014).
[Crossref]

Angelini, E. D.

M. M. Marim, E. D. Angelini, and J.-C. Olivo-Marin, “A compressed sensing approach for biological microscopic image processing,” in “2009 IEEE International Symposium on Biomedical Imaging: From Nano to Macro,” (IEEE, 2009), pp. 1374–1377.

Arce, G. R.

Y. Wu, P. Ye, I. O. Mirza, G. R. Arce, and D. W. Prather, “Experimental demonstration of an optical-sectioning compressive sensing microscope (CSM),” Opt. Express 18, 24565–24578 (2010).
[Crossref] [PubMed]

P. Ye, J. L. Paredes, Y. Wu, C. Chen, G. R. Arce, and D. W. Prather, “Compressive confocal microscopy: 3d reconstruction algorithms,” in “SPIE MOEMS-MEMS: Micro-and Nanofabrication,” (International Society for Optics and Photonics, 2009), pp. 72100G.

Baba-Aissa, L.

J.-Y. Tinevez, J. Dragavon, L. Baba-Aissa, P. Roux, E. Perret, A. Canivet, V. Galy, and S. Shorte, “A quantitative method for measuring phototoxicity of a live cell imaging microscope,” in “Methods in Enzymology” (Elsevier, 2012), pp. 291–309.
[Crossref]

Baraniuk, R.

R. Baraniuk, “Compressive sensing,” IEEE Signal Processing Mag. 24, 118–121 (2007)
[Crossref]

R. Baraniuk, M. A. Davenport, M. F. Duarte, and C. Hegde, An Introduction to Compressive Sensing (OpenStax CNX, 2011).

Becker, S.

S. Becker, J. Bobin, and E. Candès, “NESTA: A fast and accurate first-order method for sparse recovery,” arXiv preprint arXiv:0904.3367 (2009).

Bembenek, J. N.

B.-C. Chen, W. R. Legant, K. Wang, L. Shao, D. E. Milkie, M. W. Davidson, C. Janetopoulos, X. S. Wu, J. A. Hammer, Z. Liu, B. P. English, Y. Mimori-Kiyosue, D. P. Romero, A. T. Ritter, J. Lippincott-Schwartz, L. Fritz-Laylin, R. D. Mullins, D. M. Mitchell, J. N. Bembenek, A.-C. Reymann, R. Bohme, S. W. Grill, J. T. Wang, G. Seydoux, U. S. Tulu, D. P. Kiehart, and E. Betzig, “Lattice light-sheet microscopy: Imaging molecules to embryos at high spatiotemporal resolution,” Science 346, 1257998 (2014).
[Crossref] [PubMed]

Betzig, E.

B.-C. Chen, W. R. Legant, K. Wang, L. Shao, D. E. Milkie, M. W. Davidson, C. Janetopoulos, X. S. Wu, J. A. Hammer, Z. Liu, B. P. English, Y. Mimori-Kiyosue, D. P. Romero, A. T. Ritter, J. Lippincott-Schwartz, L. Fritz-Laylin, R. D. Mullins, D. M. Mitchell, J. N. Bembenek, A.-C. Reymann, R. Bohme, S. W. Grill, J. T. Wang, G. Seydoux, U. S. Tulu, D. P. Kiehart, and E. Betzig, “Lattice light-sheet microscopy: Imaging molecules to embryos at high spatiotemporal resolution,” Science 346, 1257998 (2014).
[Crossref] [PubMed]

T. A. Planchon, L. Gao, D. E. Milkie, M. W. Davidson, J. A. Galbraith, C. G. Galbraith, and E. Betzig, “Rapid three-dimensional isotropic imaging of living cells using Bessel beam plane illumination,” Nat. Methods 8, 417–423 (2011).
[Crossref] [PubMed]

Bilen, C.

C. Bilen, Y. Wang, and I. Selesnick, “Compressed sensing for moving imagery in medical imaging,” arXiv preprint arXiv:1203.5772 (2012).

Bobin, J.

V. Studer, J. Bobin, M. Chahid, H. S. Mousavi, E. Candes, and M. Dahan, “Compressive fluorescence microscopy for biological and hyperspectral imaging,” Proc. Natl. Acad. Sci. U. S. A. 109, E1679–E1687 (2012).
[Crossref] [PubMed]

J. Bobin, J.-L. Starck, and R. Ottensamer, “Compressed sensing in astronomy,” IEEE J. Sel. Top. Signal Process 2, 718–726 (2008).
[Crossref]

S. Becker, J. Bobin, and E. Candès, “NESTA: A fast and accurate first-order method for sparse recovery,” arXiv preprint arXiv:0904.3367 (2009).

Bohme, R.

B.-C. Chen, W. R. Legant, K. Wang, L. Shao, D. E. Milkie, M. W. Davidson, C. Janetopoulos, X. S. Wu, J. A. Hammer, Z. Liu, B. P. English, Y. Mimori-Kiyosue, D. P. Romero, A. T. Ritter, J. Lippincott-Schwartz, L. Fritz-Laylin, R. D. Mullins, D. M. Mitchell, J. N. Bembenek, A.-C. Reymann, R. Bohme, S. W. Grill, J. T. Wang, G. Seydoux, U. S. Tulu, D. P. Kiehart, and E. Betzig, “Lattice light-sheet microscopy: Imaging molecules to embryos at high spatiotemporal resolution,” Science 346, 1257998 (2014).
[Crossref] [PubMed]

Bosworth, B. T.

J. Shin, B. T. Bosworth, and M. A. Foster, “Compressive fluorescence imaging using a multi-core fiber and spatially dependent scattering,” Opt Lett 109, 42 (2017).

Brady, D.

J. Hunt, T. Driscoll, A. Mrozack, G. Lipworth, M. Reynolds, D. Brady, and D. R. Smith, “Metamaterial apertures for computational imaging,” Science 310, 399 (2013).

Candes, E.

V. Studer, J. Bobin, M. Chahid, H. S. Mousavi, E. Candes, and M. Dahan, “Compressive fluorescence microscopy for biological and hyperspectral imaging,” Proc. Natl. Acad. Sci. U. S. A. 109, E1679–E1687 (2012).
[Crossref] [PubMed]

E. Candes and M. Wakin, “An introduction to compressive sampling,” IEEE Signal Processing Mag. 25, 21–30 (2008).
[Crossref]

E. Candes, J. Romberg, and T. Tao, “Robust uncertainty principles: exact signal reconstruction from highly incomplete frequency information,” IEEE Trans. Inf. Theory 52, 489–509 (2006).
[Crossref]

Candès, E.

T. Tao and E. Candès, “Decoding by linear programming,” arXiv preprint arXiv:math/0502327 (2004).

S. Becker, J. Bobin, and E. Candès, “NESTA: A fast and accurate first-order method for sparse recovery,” arXiv preprint arXiv:0904.3367 (2009).

Candès, E. J.

E. J. Candès, Y. C. Eldar, D. Needell, and P. Randall, “Compressed sensing with coherent and redundant dictionaries,” Appl. Comput. Harmon Anal. 31, 59–73 (2011).
[Crossref]

Canivet, A.

J.-Y. Tinevez, J. Dragavon, L. Baba-Aissa, P. Roux, E. Perret, A. Canivet, V. Galy, and S. Shorte, “A quantitative method for measuring phototoxicity of a live cell imaging microscope,” in “Methods in Enzymology” (Elsevier, 2012), pp. 291–309.
[Crossref]

Chahid, M.

V. Studer, J. Bobin, M. Chahid, H. S. Mousavi, E. Candes, and M. Dahan, “Compressive fluorescence microscopy for biological and hyperspectral imaging,” Proc. Natl. Acad. Sci. U. S. A. 109, E1679–E1687 (2012).
[Crossref] [PubMed]

Chen, B.-C.

B.-C. Chen, W. R. Legant, K. Wang, L. Shao, D. E. Milkie, M. W. Davidson, C. Janetopoulos, X. S. Wu, J. A. Hammer, Z. Liu, B. P. English, Y. Mimori-Kiyosue, D. P. Romero, A. T. Ritter, J. Lippincott-Schwartz, L. Fritz-Laylin, R. D. Mullins, D. M. Mitchell, J. N. Bembenek, A.-C. Reymann, R. Bohme, S. W. Grill, J. T. Wang, G. Seydoux, U. S. Tulu, D. P. Kiehart, and E. Betzig, “Lattice light-sheet microscopy: Imaging molecules to embryos at high spatiotemporal resolution,” Science 346, 1257998 (2014).
[Crossref] [PubMed]

Chen, C.

P. Ye, J. L. Paredes, Y. Wu, C. Chen, G. R. Arce, and D. W. Prather, “Compressive confocal microscopy: 3d reconstruction algorithms,” in “SPIE MOEMS-MEMS: Micro-and Nanofabrication,” (International Society for Optics and Photonics, 2009), pp. 72100G.

Chen, G.-H.

B. E. Nett, J. Tang, and G.-H. Chen, “GPU implementation of prior image constrained compressed sensing (PICCS),” Proc. SPIE 7622, 762239 (2010).
[Crossref]

Chen, Y.

J. Liang, C. Ma, L. Zhu, Y. Chen, L. Gao, and L. V. Wang, “Single-shot real-time video recording of a photonic Mach cone induced by a scattered light pulse,” Sci Adv 3, e1601814 (2017).
[Crossref] [PubMed]

Clausi, D. A.

Dahan, M.

V. Studer, J. Bobin, M. Chahid, H. S. Mousavi, E. Candes, and M. Dahan, “Compressive fluorescence microscopy for biological and hyperspectral imaging,” Proc. Natl. Acad. Sci. U. S. A. 109, E1679–E1687 (2012).
[Crossref] [PubMed]

Davenport, M. A.

R. Baraniuk, M. A. Davenport, M. F. Duarte, and C. Hegde, An Introduction to Compressive Sensing (OpenStax CNX, 2011).

Davidson, M. W.

B.-C. Chen, W. R. Legant, K. Wang, L. Shao, D. E. Milkie, M. W. Davidson, C. Janetopoulos, X. S. Wu, J. A. Hammer, Z. Liu, B. P. English, Y. Mimori-Kiyosue, D. P. Romero, A. T. Ritter, J. Lippincott-Schwartz, L. Fritz-Laylin, R. D. Mullins, D. M. Mitchell, J. N. Bembenek, A.-C. Reymann, R. Bohme, S. W. Grill, J. T. Wang, G. Seydoux, U. S. Tulu, D. P. Kiehart, and E. Betzig, “Lattice light-sheet microscopy: Imaging molecules to embryos at high spatiotemporal resolution,” Science 346, 1257998 (2014).
[Crossref] [PubMed]

T. A. Planchon, L. Gao, D. E. Milkie, M. W. Davidson, J. A. Galbraith, C. G. Galbraith, and E. Betzig, “Rapid three-dimensional isotropic imaging of living cells using Bessel beam plane illumination,” Nat. Methods 8, 417–423 (2011).
[Crossref] [PubMed]

Donoho, D.

M. Lustig, D. Donoho, J. Santos, and J. Pauly, “Compressed sensing MRI,” IEEE Signal Processing Mag. 25, 72–82 (2008).
[Crossref]

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

Dragavon, J.

J.-Y. Tinevez, J. Dragavon, L. Baba-Aissa, P. Roux, E. Perret, A. Canivet, V. Galy, and S. Shorte, “A quantitative method for measuring phototoxicity of a live cell imaging microscope,” in “Methods in Enzymology” (Elsevier, 2012), pp. 291–309.
[Crossref]

Driscoll, T.

J. Hunt, T. Driscoll, A. Mrozack, G. Lipworth, M. Reynolds, D. Brady, and D. R. Smith, “Metamaterial apertures for computational imaging,” Science 310, 399 (2013).

Duarte, M. F.

R. Baraniuk, M. A. Davenport, M. F. Duarte, and C. Hegde, An Introduction to Compressive Sensing (OpenStax CNX, 2011).

Edelstein, A. D.

A. D. Edelstein, M. A. Tsuchida, N. Amodaj, H. Pinkard, R. D. Vale, and N. Stuurman, “Advanced methods of microscope control using micro-Manager software,” J. Biol. Methods 1, 10 (2014).
[Crossref]

Elad, M.

M. Elad, Sparse and Redundant Representations (Springer, 2010).
[Crossref]

Eldar, Y. C.

E. J. Candès, Y. C. Eldar, D. Needell, and P. Randall, “Compressed sensing with coherent and redundant dictionaries,” Appl. Comput. Harmon Anal. 31, 59–73 (2011).
[Crossref]

Y. C. Eldar and G. Kutyniok, Compressed Sensing: Theory and Applications (Cambridge University, 2012).
[Crossref]

Elnatan, D.

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

English, B. P.

B.-C. Chen, W. R. Legant, K. Wang, L. Shao, D. E. Milkie, M. W. Davidson, C. Janetopoulos, X. S. Wu, J. A. Hammer, Z. Liu, B. P. English, Y. Mimori-Kiyosue, D. P. Romero, A. T. Ritter, J. Lippincott-Schwartz, L. Fritz-Laylin, R. D. Mullins, D. M. Mitchell, J. N. Bembenek, A.-C. Reymann, R. Bohme, S. W. Grill, J. T. Wang, G. Seydoux, U. S. Tulu, D. P. Kiehart, and E. Betzig, “Lattice light-sheet microscopy: Imaging molecules to embryos at high spatiotemporal resolution,” Science 346, 1257998 (2014).
[Crossref] [PubMed]

Foster, M. A.

J. Shin, B. T. Bosworth, and M. A. Foster, “Compressive fluorescence imaging using a multi-core fiber and spatially dependent scattering,” Opt Lett 109, 42 (2017).

Fritz-Laylin, L.

B.-C. Chen, W. R. Legant, K. Wang, L. Shao, D. E. Milkie, M. W. Davidson, C. Janetopoulos, X. S. Wu, J. A. Hammer, Z. Liu, B. P. English, Y. Mimori-Kiyosue, D. P. Romero, A. T. Ritter, J. Lippincott-Schwartz, L. Fritz-Laylin, R. D. Mullins, D. M. Mitchell, J. N. Bembenek, A.-C. Reymann, R. Bohme, S. W. Grill, J. T. Wang, G. Seydoux, U. S. Tulu, D. P. Kiehart, and E. Betzig, “Lattice light-sheet microscopy: Imaging molecules to embryos at high spatiotemporal resolution,” Science 346, 1257998 (2014).
[Crossref] [PubMed]

Galbraith, C. G.

T. A. Planchon, L. Gao, D. E. Milkie, M. W. Davidson, J. A. Galbraith, C. G. Galbraith, and E. Betzig, “Rapid three-dimensional isotropic imaging of living cells using Bessel beam plane illumination,” Nat. Methods 8, 417–423 (2011).
[Crossref] [PubMed]

Galbraith, J. A.

T. A. Planchon, L. Gao, D. E. Milkie, M. W. Davidson, J. A. Galbraith, C. G. Galbraith, and E. Betzig, “Rapid three-dimensional isotropic imaging of living cells using Bessel beam plane illumination,” Nat. Methods 8, 417–423 (2011).
[Crossref] [PubMed]

Galy, V.

J.-Y. Tinevez, J. Dragavon, L. Baba-Aissa, P. Roux, E. Perret, A. Canivet, V. Galy, and S. Shorte, “A quantitative method for measuring phototoxicity of a live cell imaging microscope,” in “Methods in Enzymology” (Elsevier, 2012), pp. 291–309.
[Crossref]

Gao, L.

J. Liang, C. Ma, L. Zhu, Y. Chen, L. Gao, and L. V. Wang, “Single-shot real-time video recording of a photonic Mach cone induced by a scattered light pulse,” Sci Adv 3, e1601814 (2017).
[Crossref] [PubMed]

L. Gao, J. Liang, C. Li, and L. V. Wang, “Single-shot compressed ultrafast photography at one hundred billion frames per second,” Nature 516, 74–77 (2014).
[Crossref] [PubMed]

T. A. Planchon, L. Gao, D. E. Milkie, M. W. Davidson, J. A. Galbraith, C. G. Galbraith, and E. Betzig, “Rapid three-dimensional isotropic imaging of living cells using Bessel beam plane illumination,” Nat. Methods 8, 417–423 (2011).
[Crossref] [PubMed]

Gore, J. C.

D. S. Smith, J. C. Gore, T. E. Yankeelov, and E. B. Welch, “Real-time compressive sensing MRI reconstruction using GPU computing and split Bregman methods,” Int. J. Biomed. Imaging 2012, 1–6 (2012).
[Crossref]

Grill, S. W.

B.-C. Chen, W. R. Legant, K. Wang, L. Shao, D. E. Milkie, M. W. Davidson, C. Janetopoulos, X. S. Wu, J. A. Hammer, Z. Liu, B. P. English, Y. Mimori-Kiyosue, D. P. Romero, A. T. Ritter, J. Lippincott-Schwartz, L. Fritz-Laylin, R. D. Mullins, D. M. Mitchell, J. N. Bembenek, A.-C. Reymann, R. Bohme, S. W. Grill, J. T. Wang, G. Seydoux, U. S. Tulu, D. P. Kiehart, and E. Betzig, “Lattice light-sheet microscopy: Imaging molecules to embryos at high spatiotemporal resolution,” Science 346, 1257998 (2014).
[Crossref] [PubMed]

Hammer, J. A.

B.-C. Chen, W. R. Legant, K. Wang, L. Shao, D. E. Milkie, M. W. Davidson, C. Janetopoulos, X. S. Wu, J. A. Hammer, Z. Liu, B. P. English, Y. Mimori-Kiyosue, D. P. Romero, A. T. Ritter, J. Lippincott-Schwartz, L. Fritz-Laylin, R. D. Mullins, D. M. Mitchell, J. N. Bembenek, A.-C. Reymann, R. Bohme, S. W. Grill, J. T. Wang, G. Seydoux, U. S. Tulu, D. P. Kiehart, and E. Betzig, “Lattice light-sheet microscopy: Imaging molecules to embryos at high spatiotemporal resolution,” Science 346, 1257998 (2014).
[Crossref] [PubMed]

Harmany, Z. T.

Z. T. Harmany, R. F. Marcia, and R. M. Willett, “This is SPIRAL-TAP: Sparse Poisson intensity reconstruction algorithms–theory and practice,” IEEE Trans. Signal Process 21, 1084–1096 (2012).

M. Raginsky, R. M. Willett, Z. T. Harmany, and R. F. Marcia, “Compressed sensing performance bounds under Poisson noise,” IEEE Trans. Signal Process 58, 3990–4002 (2010).
[Crossref]

Hegde, C.

R. Baraniuk, M. A. Davenport, M. F. Duarte, and C. Hegde, An Introduction to Compressive Sensing (OpenStax CNX, 2011).

Huang, B.

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

Huisken, J.

M. Weber, M. Mickoleit, and J. Huisken, “Light sheet microscopy,” in “Methods in Cell Biology” (Elsevier, 2014), pp. 193–215.
[Crossref]

Hunt, J.

J. Hunt, T. Driscoll, A. Mrozack, G. Lipworth, M. Reynolds, D. Brady, and D. R. Smith, “Metamaterial apertures for computational imaging,” Science 310, 399 (2013).

Hunter, J. D.

J. D. Hunter, “Matplotlib: A 2d graphics environment,” Comput. Sci. Eng. 9, 90–95 (2007).
[Crossref]

Janetopoulos, C.

B.-C. Chen, W. R. Legant, K. Wang, L. Shao, D. E. Milkie, M. W. Davidson, C. Janetopoulos, X. S. Wu, J. A. Hammer, Z. Liu, B. P. English, Y. Mimori-Kiyosue, D. P. Romero, A. T. Ritter, J. Lippincott-Schwartz, L. Fritz-Laylin, R. D. Mullins, D. M. Mitchell, J. N. Bembenek, A.-C. Reymann, R. Bohme, S. W. Grill, J. T. Wang, G. Seydoux, U. S. Tulu, D. P. Kiehart, and E. Betzig, “Lattice light-sheet microscopy: Imaging molecules to embryos at high spatiotemporal resolution,” Science 346, 1257998 (2014).
[Crossref] [PubMed]

Keller, P.

P. Keller, A. Schmidt, J. Wittbrodt, and E. Stelzer, “Reconstruction of zebrafish early embryonic development by scanned light sheet microscopy,” Science 322, 5904 (2008).
[Crossref]

Kiehart, D. P.

B.-C. Chen, W. R. Legant, K. Wang, L. Shao, D. E. Milkie, M. W. Davidson, C. Janetopoulos, X. S. Wu, J. A. Hammer, Z. Liu, B. P. English, Y. Mimori-Kiyosue, D. P. Romero, A. T. Ritter, J. Lippincott-Schwartz, L. Fritz-Laylin, R. D. Mullins, D. M. Mitchell, J. N. Bembenek, A.-C. Reymann, R. Bohme, S. W. Grill, J. T. Wang, G. Seydoux, U. S. Tulu, D. P. Kiehart, and E. Betzig, “Lattice light-sheet microscopy: Imaging molecules to embryos at high spatiotemporal resolution,” Science 346, 1257998 (2014).
[Crossref] [PubMed]

Kutyniok, G.

Y. C. Eldar and G. Kutyniok, Compressed Sensing: Theory and Applications (Cambridge University, 2012).
[Crossref]

Legant, W. R.

B.-C. Chen, W. R. Legant, K. Wang, L. Shao, D. E. Milkie, M. W. Davidson, C. Janetopoulos, X. S. Wu, J. A. Hammer, Z. Liu, B. P. English, Y. Mimori-Kiyosue, D. P. Romero, A. T. Ritter, J. Lippincott-Schwartz, L. Fritz-Laylin, R. D. Mullins, D. M. Mitchell, J. N. Bembenek, A.-C. Reymann, R. Bohme, S. W. Grill, J. T. Wang, G. Seydoux, U. S. Tulu, D. P. Kiehart, and E. Betzig, “Lattice light-sheet microscopy: Imaging molecules to embryos at high spatiotemporal resolution,” Science 346, 1257998 (2014).
[Crossref] [PubMed]

Li, C.

L. Gao, J. Liang, C. Li, and L. V. Wang, “Single-shot compressed ultrafast photography at one hundred billion frames per second,” Nature 516, 74–77 (2014).
[Crossref] [PubMed]

Liang, J.

J. Liang, C. Ma, L. Zhu, Y. Chen, L. Gao, and L. V. Wang, “Single-shot real-time video recording of a photonic Mach cone induced by a scattered light pulse,” Sci Adv 3, e1601814 (2017).
[Crossref] [PubMed]

L. Gao, J. Liang, C. Li, and L. V. Wang, “Single-shot compressed ultrafast photography at one hundred billion frames per second,” Nature 516, 74–77 (2014).
[Crossref] [PubMed]

Lippincott-Schwartz, J.

B.-C. Chen, W. R. Legant, K. Wang, L. Shao, D. E. Milkie, M. W. Davidson, C. Janetopoulos, X. S. Wu, J. A. Hammer, Z. Liu, B. P. English, Y. Mimori-Kiyosue, D. P. Romero, A. T. Ritter, J. Lippincott-Schwartz, L. Fritz-Laylin, R. D. Mullins, D. M. Mitchell, J. N. Bembenek, A.-C. Reymann, R. Bohme, S. W. Grill, J. T. Wang, G. Seydoux, U. S. Tulu, D. P. Kiehart, and E. Betzig, “Lattice light-sheet microscopy: Imaging molecules to embryos at high spatiotemporal resolution,” Science 346, 1257998 (2014).
[Crossref] [PubMed]

Lipworth, G.

J. Hunt, T. Driscoll, A. Mrozack, G. Lipworth, M. Reynolds, D. Brady, and D. R. Smith, “Metamaterial apertures for computational imaging,” Science 310, 399 (2013).

Liu, Z.

B.-C. Chen, W. R. Legant, K. Wang, L. Shao, D. E. Milkie, M. W. Davidson, C. Janetopoulos, X. S. Wu, J. A. Hammer, Z. Liu, B. P. English, Y. Mimori-Kiyosue, D. P. Romero, A. T. Ritter, J. Lippincott-Schwartz, L. Fritz-Laylin, R. D. Mullins, D. M. Mitchell, J. N. Bembenek, A.-C. Reymann, R. Bohme, S. W. Grill, J. T. Wang, G. Seydoux, U. S. Tulu, D. P. Kiehart, and E. Betzig, “Lattice light-sheet microscopy: Imaging molecules to embryos at high spatiotemporal resolution,” Science 346, 1257998 (2014).
[Crossref] [PubMed]

Lustig, M.

M. Lustig, D. Donoho, J. Santos, and J. Pauly, “Compressed sensing MRI,” IEEE Signal Processing Mag. 25, 72–82 (2008).
[Crossref]

Ma, C.

J. Liang, C. Ma, L. Zhu, Y. Chen, L. Gao, and L. V. Wang, “Single-shot real-time video recording of a photonic Mach cone induced by a scattered light pulse,” Sci Adv 3, e1601814 (2017).
[Crossref] [PubMed]

Marcia, R. F.

Z. T. Harmany, R. F. Marcia, and R. M. Willett, “This is SPIRAL-TAP: Sparse Poisson intensity reconstruction algorithms–theory and practice,” IEEE Trans. Signal Process 21, 1084–1096 (2012).

M. Raginsky, R. M. Willett, Z. T. Harmany, and R. F. Marcia, “Compressed sensing performance bounds under Poisson noise,” IEEE Trans. Signal Process 58, 3990–4002 (2010).
[Crossref]

Marim, M. M.

M. M. Marim, E. D. Angelini, and J.-C. Olivo-Marin, “A compressed sensing approach for biological microscopic image processing,” in “2009 IEEE International Symposium on Biomedical Imaging: From Nano to Macro,” (IEEE, 2009), pp. 1374–1377.

McLeod, E.

E. McLeod and A. Ozcan, “Unconventional methods of imaging: computational microscopy and compact implementations,” Rep. Prog. Phys. 79, 076001 (2016).
[Crossref] [PubMed]

Mickoleit, M.

M. Weber, M. Mickoleit, and J. Huisken, “Light sheet microscopy,” in “Methods in Cell Biology” (Elsevier, 2014), pp. 193–215.
[Crossref]

Milkie, D. E.

B.-C. Chen, W. R. Legant, K. Wang, L. Shao, D. E. Milkie, M. W. Davidson, C. Janetopoulos, X. S. Wu, J. A. Hammer, Z. Liu, B. P. English, Y. Mimori-Kiyosue, D. P. Romero, A. T. Ritter, J. Lippincott-Schwartz, L. Fritz-Laylin, R. D. Mullins, D. M. Mitchell, J. N. Bembenek, A.-C. Reymann, R. Bohme, S. W. Grill, J. T. Wang, G. Seydoux, U. S. Tulu, D. P. Kiehart, and E. Betzig, “Lattice light-sheet microscopy: Imaging molecules to embryos at high spatiotemporal resolution,” Science 346, 1257998 (2014).
[Crossref] [PubMed]

T. A. Planchon, L. Gao, D. E. Milkie, M. W. Davidson, J. A. Galbraith, C. G. Galbraith, and E. Betzig, “Rapid three-dimensional isotropic imaging of living cells using Bessel beam plane illumination,” Nat. Methods 8, 417–423 (2011).
[Crossref] [PubMed]

Mimori-Kiyosue, Y.

B.-C. Chen, W. R. Legant, K. Wang, L. Shao, D. E. Milkie, M. W. Davidson, C. Janetopoulos, X. S. Wu, J. A. Hammer, Z. Liu, B. P. English, Y. Mimori-Kiyosue, D. P. Romero, A. T. Ritter, J. Lippincott-Schwartz, L. Fritz-Laylin, R. D. Mullins, D. M. Mitchell, J. N. Bembenek, A.-C. Reymann, R. Bohme, S. W. Grill, J. T. Wang, G. Seydoux, U. S. Tulu, D. P. Kiehart, and E. Betzig, “Lattice light-sheet microscopy: Imaging molecules to embryos at high spatiotemporal resolution,” Science 346, 1257998 (2014).
[Crossref] [PubMed]

Mirza, I. O.

Mitchell, D. M.

B.-C. Chen, W. R. Legant, K. Wang, L. Shao, D. E. Milkie, M. W. Davidson, C. Janetopoulos, X. S. Wu, J. A. Hammer, Z. Liu, B. P. English, Y. Mimori-Kiyosue, D. P. Romero, A. T. Ritter, J. Lippincott-Schwartz, L. Fritz-Laylin, R. D. Mullins, D. M. Mitchell, J. N. Bembenek, A.-C. Reymann, R. Bohme, S. W. Grill, J. T. Wang, G. Seydoux, U. S. Tulu, D. P. Kiehart, and E. Betzig, “Lattice light-sheet microscopy: Imaging molecules to embryos at high spatiotemporal resolution,” Science 346, 1257998 (2014).
[Crossref] [PubMed]

Mordechay, M.

M. Mordechay and Y. Y. Schechner, “Matrix optimization for Poisson compressed sensing,” in “2014 IEEE Global Conference on Signal and Information Processing (GlobalSIP)” (IEEE, 2014), pp. 684–688.

Mousavi, H. S.

V. Studer, J. Bobin, M. Chahid, H. S. Mousavi, E. Candes, and M. Dahan, “Compressive fluorescence microscopy for biological and hyperspectral imaging,” Proc. Natl. Acad. Sci. U. S. A. 109, E1679–E1687 (2012).
[Crossref] [PubMed]

Mrozack, A.

J. Hunt, T. Driscoll, A. Mrozack, G. Lipworth, M. Reynolds, D. Brady, and D. R. Smith, “Metamaterial apertures for computational imaging,” Science 310, 399 (2013).

Mullins, R. D.

B.-C. Chen, W. R. Legant, K. Wang, L. Shao, D. E. Milkie, M. W. Davidson, C. Janetopoulos, X. S. Wu, J. A. Hammer, Z. Liu, B. P. English, Y. Mimori-Kiyosue, D. P. Romero, A. T. Ritter, J. Lippincott-Schwartz, L. Fritz-Laylin, R. D. Mullins, D. M. Mitchell, J. N. Bembenek, A.-C. Reymann, R. Bohme, S. W. Grill, J. T. Wang, G. Seydoux, U. S. Tulu, D. P. Kiehart, and E. Betzig, “Lattice light-sheet microscopy: Imaging molecules to embryos at high spatiotemporal resolution,” Science 346, 1257998 (2014).
[Crossref] [PubMed]

Needell, D.

E. J. Candès, Y. C. Eldar, D. Needell, and P. Randall, “Compressed sensing with coherent and redundant dictionaries,” Appl. Comput. Harmon Anal. 31, 59–73 (2011).
[Crossref]

Nett, B. E.

B. E. Nett, J. Tang, and G.-H. Chen, “GPU implementation of prior image constrained compressed sensing (PICCS),” Proc. SPIE 7622, 762239 (2010).
[Crossref]

Olivo-Marin, J.-C.

M. M. Marim, E. D. Angelini, and J.-C. Olivo-Marin, “A compressed sensing approach for biological microscopic image processing,” in “2009 IEEE International Symposium on Biomedical Imaging: From Nano to Macro,” (IEEE, 2009), pp. 1374–1377.

Ottensamer, R.

J. Bobin, J.-L. Starck, and R. Ottensamer, “Compressed sensing in astronomy,” IEEE J. Sel. Top. Signal Process 2, 718–726 (2008).
[Crossref]

Ozcan, A.

E. McLeod and A. Ozcan, “Unconventional methods of imaging: computational microscopy and compact implementations,” Rep. Prog. Phys. 79, 076001 (2016).
[Crossref] [PubMed]

Paredes, J. L.

P. Ye, J. L. Paredes, Y. Wu, C. Chen, G. R. Arce, and D. W. Prather, “Compressive confocal microscopy: 3d reconstruction algorithms,” in “SPIE MOEMS-MEMS: Micro-and Nanofabrication,” (International Society for Optics and Photonics, 2009), pp. 72100G.

Pauly, J.

M. Lustig, D. Donoho, J. Santos, and J. Pauly, “Compressed sensing MRI,” IEEE Signal Processing Mag. 25, 72–82 (2008).
[Crossref]

Pavillon, N.

Perret, E.

J.-Y. Tinevez, J. Dragavon, L. Baba-Aissa, P. Roux, E. Perret, A. Canivet, V. Galy, and S. Shorte, “A quantitative method for measuring phototoxicity of a live cell imaging microscope,” in “Methods in Enzymology” (Elsevier, 2012), pp. 291–309.
[Crossref]

Pinkard, H.

A. D. Edelstein, M. A. Tsuchida, N. Amodaj, H. Pinkard, R. D. Vale, and N. Stuurman, “Advanced methods of microscope control using micro-Manager software,” J. Biol. Methods 1, 10 (2014).
[Crossref]

Planchon, T. A.

T. A. Planchon, L. Gao, D. E. Milkie, M. W. Davidson, J. A. Galbraith, C. G. Galbraith, and E. Betzig, “Rapid three-dimensional isotropic imaging of living cells using Bessel beam plane illumination,” Nat. Methods 8, 417–423 (2011).
[Crossref] [PubMed]

Prather, D. W.

Y. Wu, P. Ye, I. O. Mirza, G. R. Arce, and D. W. Prather, “Experimental demonstration of an optical-sectioning compressive sensing microscope (CSM),” Opt. Express 18, 24565–24578 (2010).
[Crossref] [PubMed]

P. Ye, J. L. Paredes, Y. Wu, C. Chen, G. R. Arce, and D. W. Prather, “Compressive confocal microscopy: 3d reconstruction algorithms,” in “SPIE MOEMS-MEMS: Micro-and Nanofabrication,” (International Society for Optics and Photonics, 2009), pp. 72100G.

Raginsky, M.

M. Raginsky, R. M. Willett, Z. T. Harmany, and R. F. Marcia, “Compressed sensing performance bounds under Poisson noise,” IEEE Trans. Signal Process 58, 3990–4002 (2010).
[Crossref]

Randall, P.

E. J. Candès, Y. C. Eldar, D. Needell, and P. Randall, “Compressed sensing with coherent and redundant dictionaries,” Appl. Comput. Harmon Anal. 31, 59–73 (2011).
[Crossref]

Reymann, A.-C.

B.-C. Chen, W. R. Legant, K. Wang, L. Shao, D. E. Milkie, M. W. Davidson, C. Janetopoulos, X. S. Wu, J. A. Hammer, Z. Liu, B. P. English, Y. Mimori-Kiyosue, D. P. Romero, A. T. Ritter, J. Lippincott-Schwartz, L. Fritz-Laylin, R. D. Mullins, D. M. Mitchell, J. N. Bembenek, A.-C. Reymann, R. Bohme, S. W. Grill, J. T. Wang, G. Seydoux, U. S. Tulu, D. P. Kiehart, and E. Betzig, “Lattice light-sheet microscopy: Imaging molecules to embryos at high spatiotemporal resolution,” Science 346, 1257998 (2014).
[Crossref] [PubMed]

Reynolds, M.

J. Hunt, T. Driscoll, A. Mrozack, G. Lipworth, M. Reynolds, D. Brady, and D. R. Smith, “Metamaterial apertures for computational imaging,” Science 310, 399 (2013).

Ritter, A. T.

B.-C. Chen, W. R. Legant, K. Wang, L. Shao, D. E. Milkie, M. W. Davidson, C. Janetopoulos, X. S. Wu, J. A. Hammer, Z. Liu, B. P. English, Y. Mimori-Kiyosue, D. P. Romero, A. T. Ritter, J. Lippincott-Schwartz, L. Fritz-Laylin, R. D. Mullins, D. M. Mitchell, J. N. Bembenek, A.-C. Reymann, R. Bohme, S. W. Grill, J. T. Wang, G. Seydoux, U. S. Tulu, D. P. Kiehart, and E. Betzig, “Lattice light-sheet microscopy: Imaging molecules to embryos at high spatiotemporal resolution,” Science 346, 1257998 (2014).
[Crossref] [PubMed]

Romberg, J.

E. Candes, J. Romberg, and T. Tao, “Robust uncertainty principles: exact signal reconstruction from highly incomplete frequency information,” IEEE Trans. Inf. Theory 52, 489–509 (2006).
[Crossref]

Romero, D. P.

B.-C. Chen, W. R. Legant, K. Wang, L. Shao, D. E. Milkie, M. W. Davidson, C. Janetopoulos, X. S. Wu, J. A. Hammer, Z. Liu, B. P. English, Y. Mimori-Kiyosue, D. P. Romero, A. T. Ritter, J. Lippincott-Schwartz, L. Fritz-Laylin, R. D. Mullins, D. M. Mitchell, J. N. Bembenek, A.-C. Reymann, R. Bohme, S. W. Grill, J. T. Wang, G. Seydoux, U. S. Tulu, D. P. Kiehart, and E. Betzig, “Lattice light-sheet microscopy: Imaging molecules to embryos at high spatiotemporal resolution,” Science 346, 1257998 (2014).
[Crossref] [PubMed]

Roux, P.

J.-Y. Tinevez, J. Dragavon, L. Baba-Aissa, P. Roux, E. Perret, A. Canivet, V. Galy, and S. Shorte, “A quantitative method for measuring phototoxicity of a live cell imaging microscope,” in “Methods in Enzymology” (Elsevier, 2012), pp. 291–309.
[Crossref]

Santos, J.

M. Lustig, D. Donoho, J. Santos, and J. Pauly, “Compressed sensing MRI,” IEEE Signal Processing Mag. 25, 72–82 (2008).
[Crossref]

Schechner, Y. Y.

M. Mordechay and Y. Y. Schechner, “Matrix optimization for Poisson compressed sensing,” in “2014 IEEE Global Conference on Signal and Information Processing (GlobalSIP)” (IEEE, 2014), pp. 684–688.

Schmidt, A.

P. Keller, A. Schmidt, J. Wittbrodt, and E. Stelzer, “Reconstruction of zebrafish early embryonic development by scanned light sheet microscopy,” Science 322, 5904 (2008).
[Crossref]

Schwartz, S.

Selesnick, I.

C. Bilen, Y. Wang, and I. Selesnick, “Compressed sensing for moving imagery in medical imaging,” arXiv preprint arXiv:1203.5772 (2012).

Seydoux, G.

B.-C. Chen, W. R. Legant, K. Wang, L. Shao, D. E. Milkie, M. W. Davidson, C. Janetopoulos, X. S. Wu, J. A. Hammer, Z. Liu, B. P. English, Y. Mimori-Kiyosue, D. P. Romero, A. T. Ritter, J. Lippincott-Schwartz, L. Fritz-Laylin, R. D. Mullins, D. M. Mitchell, J. N. Bembenek, A.-C. Reymann, R. Bohme, S. W. Grill, J. T. Wang, G. Seydoux, U. S. Tulu, D. P. Kiehart, and E. Betzig, “Lattice light-sheet microscopy: Imaging molecules to embryos at high spatiotemporal resolution,” Science 346, 1257998 (2014).
[Crossref] [PubMed]

Shao, L.

B.-C. Chen, W. R. Legant, K. Wang, L. Shao, D. E. Milkie, M. W. Davidson, C. Janetopoulos, X. S. Wu, J. A. Hammer, Z. Liu, B. P. English, Y. Mimori-Kiyosue, D. P. Romero, A. T. Ritter, J. Lippincott-Schwartz, L. Fritz-Laylin, R. D. Mullins, D. M. Mitchell, J. N. Bembenek, A.-C. Reymann, R. Bohme, S. W. Grill, J. T. Wang, G. Seydoux, U. S. Tulu, D. P. Kiehart, and E. Betzig, “Lattice light-sheet microscopy: Imaging molecules to embryos at high spatiotemporal resolution,” Science 346, 1257998 (2014).
[Crossref] [PubMed]

Shin, J.

J. Shin, B. T. Bosworth, and M. A. Foster, “Compressive fluorescence imaging using a multi-core fiber and spatially dependent scattering,” Opt Lett 109, 42 (2017).

Shorte, S.

J.-Y. Tinevez, J. Dragavon, L. Baba-Aissa, P. Roux, E. Perret, A. Canivet, V. Galy, and S. Shorte, “A quantitative method for measuring phototoxicity of a live cell imaging microscope,” in “Methods in Enzymology” (Elsevier, 2012), pp. 291–309.
[Crossref]

Smith, D. R.

J. Hunt, T. Driscoll, A. Mrozack, G. Lipworth, M. Reynolds, D. Brady, and D. R. Smith, “Metamaterial apertures for computational imaging,” Science 310, 399 (2013).

Smith, D. S.

D. S. Smith, J. C. Gore, T. E. Yankeelov, and E. B. Welch, “Real-time compressive sensing MRI reconstruction using GPU computing and split Bregman methods,” Int. J. Biomed. Imaging 2012, 1–6 (2012).
[Crossref]

Smith, N. I.

Starck, J.-L.

J. Bobin, J.-L. Starck, and R. Ottensamer, “Compressed sensing in astronomy,” IEEE J. Sel. Top. Signal Process 2, 718–726 (2008).
[Crossref]

Stelzer, E.

P. Keller, A. Schmidt, J. Wittbrodt, and E. Stelzer, “Reconstruction of zebrafish early embryonic development by scanned light sheet microscopy,” Science 322, 5904 (2008).
[Crossref]

Studer, V.

V. Studer, J. Bobin, M. Chahid, H. S. Mousavi, E. Candes, and M. Dahan, “Compressive fluorescence microscopy for biological and hyperspectral imaging,” Proc. Natl. Acad. Sci. U. S. A. 109, E1679–E1687 (2012).
[Crossref] [PubMed]

Stuurman, N.

A. D. Edelstein, M. A. Tsuchida, N. Amodaj, H. Pinkard, R. D. Vale, and N. Stuurman, “Advanced methods of microscope control using micro-Manager software,” J. Biol. Methods 1, 10 (2014).
[Crossref]

Tang, J.

B. E. Nett, J. Tang, and G.-H. Chen, “GPU implementation of prior image constrained compressed sensing (PICCS),” Proc. SPIE 7622, 762239 (2010).
[Crossref]

Tao, T.

E. Candes, J. Romberg, and T. Tao, “Robust uncertainty principles: exact signal reconstruction from highly incomplete frequency information,” IEEE Trans. Inf. Theory 52, 489–509 (2006).
[Crossref]

T. Tao and E. Candès, “Decoding by linear programming,” arXiv preprint arXiv:math/0502327 (2004).

Tinevez, J.-Y.

J.-Y. Tinevez, J. Dragavon, L. Baba-Aissa, P. Roux, E. Perret, A. Canivet, V. Galy, and S. Shorte, “A quantitative method for measuring phototoxicity of a live cell imaging microscope,” in “Methods in Enzymology” (Elsevier, 2012), pp. 291–309.
[Crossref]

Tsuchida, M. A.

A. D. Edelstein, M. A. Tsuchida, N. Amodaj, H. Pinkard, R. D. Vale, and N. Stuurman, “Advanced methods of microscope control using micro-Manager software,” J. Biol. Methods 1, 10 (2014).
[Crossref]

Tulu, U. S.

B.-C. Chen, W. R. Legant, K. Wang, L. Shao, D. E. Milkie, M. W. Davidson, C. Janetopoulos, X. S. Wu, J. A. Hammer, Z. Liu, B. P. English, Y. Mimori-Kiyosue, D. P. Romero, A. T. Ritter, J. Lippincott-Schwartz, L. Fritz-Laylin, R. D. Mullins, D. M. Mitchell, J. N. Bembenek, A.-C. Reymann, R. Bohme, S. W. Grill, J. T. Wang, G. Seydoux, U. S. Tulu, D. P. Kiehart, and E. Betzig, “Lattice light-sheet microscopy: Imaging molecules to embryos at high spatiotemporal resolution,” Science 346, 1257998 (2014).
[Crossref] [PubMed]

Vale, R. D.

A. D. Edelstein, M. A. Tsuchida, N. Amodaj, H. Pinkard, R. D. Vale, and N. Stuurman, “Advanced methods of microscope control using micro-Manager software,” J. Biol. Methods 1, 10 (2014).
[Crossref]

Wakin, M.

E. Candes and M. Wakin, “An introduction to compressive sampling,” IEEE Signal Processing Mag. 25, 21–30 (2008).
[Crossref]

Wang, J. T.

B.-C. Chen, W. R. Legant, K. Wang, L. Shao, D. E. Milkie, M. W. Davidson, C. Janetopoulos, X. S. Wu, J. A. Hammer, Z. Liu, B. P. English, Y. Mimori-Kiyosue, D. P. Romero, A. T. Ritter, J. Lippincott-Schwartz, L. Fritz-Laylin, R. D. Mullins, D. M. Mitchell, J. N. Bembenek, A.-C. Reymann, R. Bohme, S. W. Grill, J. T. Wang, G. Seydoux, U. S. Tulu, D. P. Kiehart, and E. Betzig, “Lattice light-sheet microscopy: Imaging molecules to embryos at high spatiotemporal resolution,” Science 346, 1257998 (2014).
[Crossref] [PubMed]

Wang, K.

B.-C. Chen, W. R. Legant, K. Wang, L. Shao, D. E. Milkie, M. W. Davidson, C. Janetopoulos, X. S. Wu, J. A. Hammer, Z. Liu, B. P. English, Y. Mimori-Kiyosue, D. P. Romero, A. T. Ritter, J. Lippincott-Schwartz, L. Fritz-Laylin, R. D. Mullins, D. M. Mitchell, J. N. Bembenek, A.-C. Reymann, R. Bohme, S. W. Grill, J. T. Wang, G. Seydoux, U. S. Tulu, D. P. Kiehart, and E. Betzig, “Lattice light-sheet microscopy: Imaging molecules to embryos at high spatiotemporal resolution,” Science 346, 1257998 (2014).
[Crossref] [PubMed]

Wang, L. V.

J. Liang, C. Ma, L. Zhu, Y. Chen, L. Gao, and L. V. Wang, “Single-shot real-time video recording of a photonic Mach cone induced by a scattered light pulse,” Sci Adv 3, e1601814 (2017).
[Crossref] [PubMed]

L. Gao, J. Liang, C. Li, and L. V. Wang, “Single-shot compressed ultrafast photography at one hundred billion frames per second,” Nature 516, 74–77 (2014).
[Crossref] [PubMed]

Wang, Y.

C. Bilen, Y. Wang, and I. Selesnick, “Compressed sensing for moving imagery in medical imaging,” arXiv preprint arXiv:1203.5772 (2012).

Weber, M.

M. Weber, M. Mickoleit, and J. Huisken, “Light sheet microscopy,” in “Methods in Cell Biology” (Elsevier, 2014), pp. 193–215.
[Crossref]

Welch, E. B.

D. S. Smith, J. C. Gore, T. E. Yankeelov, and E. B. Welch, “Real-time compressive sensing MRI reconstruction using GPU computing and split Bregman methods,” Int. J. Biomed. Imaging 2012, 1–6 (2012).
[Crossref]

Willett, R. M.

Z. T. Harmany, R. F. Marcia, and R. M. Willett, “This is SPIRAL-TAP: Sparse Poisson intensity reconstruction algorithms–theory and practice,” IEEE Trans. Signal Process 21, 1084–1096 (2012).

M. Raginsky, R. M. Willett, Z. T. Harmany, and R. F. Marcia, “Compressed sensing performance bounds under Poisson noise,” IEEE Trans. Signal Process 58, 3990–4002 (2010).
[Crossref]

Wittbrodt, J.

P. Keller, A. Schmidt, J. Wittbrodt, and E. Stelzer, “Reconstruction of zebrafish early embryonic development by scanned light sheet microscopy,” Science 322, 5904 (2008).
[Crossref]

Wong, A.

Wu, X. S.

B.-C. Chen, W. R. Legant, K. Wang, L. Shao, D. E. Milkie, M. W. Davidson, C. Janetopoulos, X. S. Wu, J. A. Hammer, Z. Liu, B. P. English, Y. Mimori-Kiyosue, D. P. Romero, A. T. Ritter, J. Lippincott-Schwartz, L. Fritz-Laylin, R. D. Mullins, D. M. Mitchell, J. N. Bembenek, A.-C. Reymann, R. Bohme, S. W. Grill, J. T. Wang, G. Seydoux, U. S. Tulu, D. P. Kiehart, and E. Betzig, “Lattice light-sheet microscopy: Imaging molecules to embryos at high spatiotemporal resolution,” Science 346, 1257998 (2014).
[Crossref] [PubMed]

Wu, Y.

Y. Wu, P. Ye, I. O. Mirza, G. R. Arce, and D. W. Prather, “Experimental demonstration of an optical-sectioning compressive sensing microscope (CSM),” Opt. Express 18, 24565–24578 (2010).
[Crossref] [PubMed]

P. Ye, J. L. Paredes, Y. Wu, C. Chen, G. R. Arce, and D. W. Prather, “Compressive confocal microscopy: 3d reconstruction algorithms,” in “SPIE MOEMS-MEMS: Micro-and Nanofabrication,” (International Society for Optics and Photonics, 2009), pp. 72100G.

Yankeelov, T. E.

D. S. Smith, J. C. Gore, T. E. Yankeelov, and E. B. Welch, “Real-time compressive sensing MRI reconstruction using GPU computing and split Bregman methods,” Int. J. Biomed. Imaging 2012, 1–6 (2012).
[Crossref]

Ye, P.

Y. Wu, P. Ye, I. O. Mirza, G. R. Arce, and D. W. Prather, “Experimental demonstration of an optical-sectioning compressive sensing microscope (CSM),” Opt. Express 18, 24565–24578 (2010).
[Crossref] [PubMed]

P. Ye, J. L. Paredes, Y. Wu, C. Chen, G. R. Arce, and D. W. Prather, “Compressive confocal microscopy: 3d reconstruction algorithms,” in “SPIE MOEMS-MEMS: Micro-and Nanofabrication,” (International Society for Optics and Photonics, 2009), pp. 72100G.

Zhang, W.

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

Zhu, L.

J. Liang, C. Ma, L. Zhu, Y. Chen, L. Gao, and L. V. Wang, “Single-shot real-time video recording of a photonic Mach cone induced by a scattered light pulse,” Sci Adv 3, e1601814 (2017).
[Crossref] [PubMed]

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

Appl. Comput. Harmon Anal. (1)

E. J. Candès, Y. C. Eldar, D. Needell, and P. Randall, “Compressed sensing with coherent and redundant dictionaries,” Appl. Comput. Harmon Anal. 31, 59–73 (2011).
[Crossref]

Comput. Sci. Eng. (1)

J. D. Hunter, “Matplotlib: A 2d graphics environment,” Comput. Sci. Eng. 9, 90–95 (2007).
[Crossref]

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

J. Bobin, J.-L. Starck, and R. Ottensamer, “Compressed sensing in astronomy,” IEEE J. Sel. Top. Signal Process 2, 718–726 (2008).
[Crossref]

IEEE Signal Processing Mag. (3)

M. Lustig, D. Donoho, J. Santos, and J. Pauly, “Compressed sensing MRI,” IEEE Signal Processing Mag. 25, 72–82 (2008).
[Crossref]

E. Candes and M. Wakin, “An introduction to compressive sampling,” IEEE Signal Processing Mag. 25, 21–30 (2008).
[Crossref]

R. Baraniuk, “Compressive sensing,” IEEE Signal Processing Mag. 24, 118–121 (2007)
[Crossref]

IEEE Trans. Inf. Theory (2)

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

E. Candes, J. Romberg, and T. Tao, “Robust uncertainty principles: exact signal reconstruction from highly incomplete frequency information,” IEEE Trans. Inf. Theory 52, 489–509 (2006).
[Crossref]

IEEE Trans. Signal Process (2)

Z. T. Harmany, R. F. Marcia, and R. M. Willett, “This is SPIRAL-TAP: Sparse Poisson intensity reconstruction algorithms–theory and practice,” IEEE Trans. Signal Process 21, 1084–1096 (2012).

M. Raginsky, R. M. Willett, Z. T. Harmany, and R. F. Marcia, “Compressed sensing performance bounds under Poisson noise,” IEEE Trans. Signal Process 58, 3990–4002 (2010).
[Crossref]

Int. J. Biomed. Imaging (1)

D. S. Smith, J. C. Gore, T. E. Yankeelov, and E. B. Welch, “Real-time compressive sensing MRI reconstruction using GPU computing and split Bregman methods,” Int. J. Biomed. Imaging 2012, 1–6 (2012).
[Crossref]

J. Biol. Methods (1)

A. D. Edelstein, M. A. Tsuchida, N. Amodaj, H. Pinkard, R. D. Vale, and N. Stuurman, “Advanced methods of microscope control using micro-Manager software,” J. Biol. Methods 1, 10 (2014).
[Crossref]

Nat. Methods (2)

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

T. A. Planchon, L. Gao, D. E. Milkie, M. W. Davidson, J. A. Galbraith, C. G. Galbraith, and E. Betzig, “Rapid three-dimensional isotropic imaging of living cells using Bessel beam plane illumination,” Nat. Methods 8, 417–423 (2011).
[Crossref] [PubMed]

Nature (1)

L. Gao, J. Liang, C. Li, and L. V. Wang, “Single-shot compressed ultrafast photography at one hundred billion frames per second,” Nature 516, 74–77 (2014).
[Crossref] [PubMed]

Opt Lett (1)

J. Shin, B. T. Bosworth, and M. A. Foster, “Compressive fluorescence imaging using a multi-core fiber and spatially dependent scattering,” Opt Lett 109, 42 (2017).

Opt. Express (3)

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

V. Studer, J. Bobin, M. Chahid, H. S. Mousavi, E. Candes, and M. Dahan, “Compressive fluorescence microscopy for biological and hyperspectral imaging,” Proc. Natl. Acad. Sci. U. S. A. 109, E1679–E1687 (2012).
[Crossref] [PubMed]

Proc. SPIE (1)

B. E. Nett, J. Tang, and G.-H. Chen, “GPU implementation of prior image constrained compressed sensing (PICCS),” Proc. SPIE 7622, 762239 (2010).
[Crossref]

Rep. Prog. Phys. (1)

E. McLeod and A. Ozcan, “Unconventional methods of imaging: computational microscopy and compact implementations,” Rep. Prog. Phys. 79, 076001 (2016).
[Crossref] [PubMed]

Sci Adv (1)

J. Liang, C. Ma, L. Zhu, Y. Chen, L. Gao, and L. V. Wang, “Single-shot real-time video recording of a photonic Mach cone induced by a scattered light pulse,” Sci Adv 3, e1601814 (2017).
[Crossref] [PubMed]

Science (3)

P. Keller, A. Schmidt, J. Wittbrodt, and E. Stelzer, “Reconstruction of zebrafish early embryonic development by scanned light sheet microscopy,” Science 322, 5904 (2008).
[Crossref]

J. Hunt, T. Driscoll, A. Mrozack, G. Lipworth, M. Reynolds, D. Brady, and D. R. Smith, “Metamaterial apertures for computational imaging,” Science 310, 399 (2013).

B.-C. Chen, W. R. Legant, K. Wang, L. Shao, D. E. Milkie, M. W. Davidson, C. Janetopoulos, X. S. Wu, J. A. Hammer, Z. Liu, B. P. English, Y. Mimori-Kiyosue, D. P. Romero, A. T. Ritter, J. Lippincott-Schwartz, L. Fritz-Laylin, R. D. Mullins, D. M. Mitchell, J. N. Bembenek, A.-C. Reymann, R. Bohme, S. W. Grill, J. T. Wang, G. Seydoux, U. S. Tulu, D. P. Kiehart, and E. Betzig, “Lattice light-sheet microscopy: Imaging molecules to embryos at high spatiotemporal resolution,” Science 346, 1257998 (2014).
[Crossref] [PubMed]

Other (11)

J.-Y. Tinevez, J. Dragavon, L. Baba-Aissa, P. Roux, E. Perret, A. Canivet, V. Galy, and S. Shorte, “A quantitative method for measuring phototoxicity of a live cell imaging microscope,” in “Methods in Enzymology” (Elsevier, 2012), pp. 291–309.
[Crossref]

S. Becker, J. Bobin, and E. Candès, “NESTA: A fast and accurate first-order method for sparse recovery,” arXiv preprint arXiv:0904.3367 (2009).

R. Baraniuk, M. A. Davenport, M. F. Duarte, and C. Hegde, An Introduction to Compressive Sensing (OpenStax CNX, 2011).

C. Bilen, Y. Wang, and I. Selesnick, “Compressed sensing for moving imagery in medical imaging,” arXiv preprint arXiv:1203.5772 (2012).

M. Mordechay and Y. Y. Schechner, “Matrix optimization for Poisson compressed sensing,” in “2014 IEEE Global Conference on Signal and Information Processing (GlobalSIP)” (IEEE, 2014), pp. 684–688.

Y. C. Eldar and G. Kutyniok, Compressed Sensing: Theory and Applications (Cambridge University, 2012).
[Crossref]

M. Elad, Sparse and Redundant Representations (Springer, 2010).
[Crossref]

M. Weber, M. Mickoleit, and J. Huisken, “Light sheet microscopy,” in “Methods in Cell Biology” (Elsevier, 2014), pp. 193–215.
[Crossref]

M. M. Marim, E. D. Angelini, and J.-C. Olivo-Marin, “A compressed sensing approach for biological microscopic image processing,” in “2009 IEEE International Symposium on Biomedical Imaging: From Nano to Macro,” (IEEE, 2009), pp. 1374–1377.

P. Ye, J. L. Paredes, Y. Wu, C. Chen, G. R. Arce, and D. W. Prather, “Compressive confocal microscopy: 3d reconstruction algorithms,” in “SPIE MOEMS-MEMS: Micro-and Nanofabrication,” (International Society for Optics and Photonics, 2009), pp. 72100G.

T. Tao and E. Candès, “Decoding by linear programming,” arXiv preprint arXiv:math/0502327 (2004).

Supplementary Material (3)

NameDescription
» Visualization 1: AVI (3757 KB)      Supplementary movie 1: reconstruction of fluorescent beads acquired with a LLSM (movie along the y dimension)
» Visualization 2: AVI (1097 KB)      Supplementary movie 2: reconstruction of mESCs labeled with actin acquired with a LLSM (movie along the y dimension)
» Visualization 3: AVI (1029 KB)      Supplementary movie 3: reconstruction of fluorescent beads acquired with an epifluorescence microscope (movie along the y dimension)

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Figures (5)

Fig. 1
Fig. 1

Principle of the proposed 3D compressed imaging method compared to traditional 3D plane-by-plane imaging. (a) Plane-by-plane imaging: for each camera frame (green curve indicates if the shutter is open or closed), one plane of the sample (red curve indicates z position) is illuminated at a constant laser intensity (blue curve shows transmission percentage of the excitation light source). The process is repeated for each plane (N = 101 times) to acquire a z-stack. Finally, the full imaging sequence is repeated n times to acquire a 4D movie for a total of N * n frames. The blue and red dots represent the illumination intensity and stage position at each time point respectively. This imaging scheme can be represented as the application of a square diagonal measurement matrix A as shown in (b): for each camera frame (row), only one z plane is illuminated (column). (c) Axially compressed imaging: the stage continually sweeps through the entire axial range while the illumination is modulated to create a specific axial light pattern. In this scheme, multiple planes of the sample are illuminated during a single camera exposure frame. This process is repeated M = 10 < N times with different light patterns, thus performing an optomechanical implementation of a compressed measurement matrix, as shown in (d). Finally, the full imaging sequence is repeated n times to acquire a 4D dataset with a total of M*n (10*101) frames.

Fig. 2
Fig. 2

Simulations comparing the compressed sensing scheme with the traditional plane-by-plane scheme under various compression ratios and SNR. (a). Principle of the simulation: from a generated ground truth image (GT) and a specified SNR, (left) a noisy reference (NRSNR) is generated by adding Poisson and Gaussian noise to the ground truth. In parallel (right), the ground truth is compressed (along the z axis) with a compression ratio κ and an equivalent amount of noise is added at the same time as the compression (see main text for details). The compressed images are further decompressed ( image C S SNR κ ) and the mean square error (MSE) is computed with respect to the ground truth. (b). Examples of simulated images in the (x, z) plane. From top to bottom: (plane-by-plane) GT, (1:2) to (1:20) C S SNR κ image reconstructed at a SNR of 20 and with a compression ratio of 1:2 to 1:20. The blue arrows represent lines of low sparsity, high sparsity and medium sparsity (respectively x1, x2 and x3). (c). quality of the reconstruction (assessed by the MSE with respect to GT) for various SNR and compression-ratios. The dashed line is the MSE of the noisy reference NRSNR with respect to the ground truth GT. The dash-dotted line is the MSE of the noisy reference acquired with a ten times lower exposure time N R SNR 10 x. Inset: close-up of the low SNR region (SNR=1–10).

Fig. 3
Fig. 3

Compressed imaging reconstructions of fluorescent beads acquired with a lattice light sheet microscope. (a). Principle of a lattice light sheet microscope: two objectives at a 90°angle are used to observe the sample. The light sheet is generated through a spatial light modulator (SLM) and associated optics. The focus is adjusted by a coordinated move of the z piezo (that translates the observation objective) and of the z galvo (that translates the light sheet). Synchronization is achieved by a FPGA (Field-Programmable Gate Array). (b). Sample reconstructions (compressed) in the (x, z) plane from a 1:10 compressed acquisition and the corresponding acquisition in the plane-by-plane imaging scheme for two y positions (termed position 1 and position 2). (c). Compressed imaging sample reconstructions at increasing compression ratios (from 1:2 to 1:50) compared to the plane-by-plane scheme (top). For each reconstruction, a close-up of the PSF is displayed (PSF column) and the 2D frequency content of the PSF is displayed next to the PSF (FFT column). The PSF shown in red is the typical response of the LLSM whereas the shape of the yellow PSF is likely due to a defect in the bead. (d). Line profile across the two highlighted PSFs (in yellow and red, respectively left and right). top Close-up along the x axis, bottom close-up along the z axis. The colors correspond to different compression ratios and the dotted line to the plane-by-plane reference. Horizontal axis in µm. A field of view in the (x, z) plane is 50×20 µm (512×101 px). A full 3D reconstructions is provided in blue) Visualization 1.

Fig. 4
Fig. 4

Compressed imaging reconstruction of phalloidin-RFP-stained, fixed mouse embryonic stem cells (mESCs) acquired with a lattice light sheet microscope. (a). Example reconstruction from a 5 fold compression ratio (right) and the corresponding plane-by-plane reference acquisition (left) (1., top in the (x, y) plane and (2., middle) in the (x, z) plane. Dotted lines indicate the location of the line profiles presented in (panel 3., bottom) (left) profile along the x axis (yellow dotted line of panel 2.) for increasing compression ratios. (right) profile along the z axis (red dotted line of panel 3.) the curves are the average over 3 planes in the y dimension. (b). Maximum intensity projection in the (x, y) plane (1., left) and in the (x, z) plane (2., right) of the plane-by-plane stack (top) and reconstructed stack at increasing compression ratios (two bottom pictures). The orange dotted line shows the location of the line profile displayed in panel 3., bottom: line profile of the reconstruction at increasing compression ratios (dotted line) compare to the plane-by-plane reference (continuous line). A field of view in the (x, z) plane is 25×20 µm (256×101 px) and a field of view in the (x, y) plane is 25×25 µm (256×256 px). A full 3D reconstructions is provided in blue) Visualization 2.

Fig. 5
Fig. 5

Compressed imaging reconstructions of fluorescent beads acquired with an epifluorescence microscope. (a). Principle of the epifluorescence microscope: both the AOTF and the motorized stage in z are synchronized by hardware (Arduino). (b). Example reconstructions (compressed) in the (x, z) plane from a 1:10 compressed acquisition and the corresponding acquisition in the traditional imaging scheme (plane-by-plane) for two y positions (termed position 1 and position 2). (c). Sample reconstructions at increasing compression ratios (from 1:2 to 1:50) compared to the plane-by-plane imaging scheme (top). (d). x and z profiles of one selected PSF (highlighted in panel c) reconstructed from various compression ratios. The black dotted line represents the plane-by-plane reference. A full 3D reconstructions is provided in blue) Visualization 3.

Equations (9)

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F ( α ) = α 1 + λ A α Y 2 2
F ( α ) = α 1 + λ ( α )
z f ( t ) = E ( t Δ t ) × Δ z
F k p . b y p . ( x , y ) = L 0 × Δ t × ( I * P S F ) ( x , y , k Δ z ) for k = 1 N
F k c o m p ( x , y ) = L 0 × Δ t × 0 ( N 1 ) Δ z A k ( z ) × ( I * P S F ) ( x , y , z ) d z for k = 1 M < N
F k c o m p ( x , y ) = L 0 × Δ t × i = 1 i = N A k , i × ( I * P S F ) ( x , y , i Δ z ) for k = 1 M < N
z f ( t ) = N Δ z ( t Δ t E ( t Δ t ) )
F k c o m p ( x , y ) = L 0 ( k 1 ) Δ t k Δ t T ( t ) × ( I * P S F ) ( x , y , z f ( t ) ) d t = Δ t N Δ z L 0 0 ( N 1 ) Δ z T ( z ) × ( I * P S F ) ( x , y , z ) d z
F k c o m p ( x , y ) = L 0 × Δ t × 1 N i = 1 i = N T k , i × ( I * P S F ) ( x , y , i Δ z )

Metrics