Abstract

Despite recent advances, high performance single-shot 3D microscopy remains an elusive task. By introducing designed diffractive optical elements (DOEs), one is capable of converting a microscope into a 3D “kaleidoscope,” in which case the snapshot image consists of an array of tiles and each tile focuses on different depths. However, the acquired multifocal microscopic (MFM) image suffers from multiple sources of degradation, which prevents MFM from further applications. We propose a unifying computational framework which simplifies the imaging system and achieves 3D reconstruction via computation. Our optical configuration omits optical elements for correcting chromatic aberrations and redesigns the multifocal grating to enlarge the tracking area. Our proposed setup features only one single grating in addition to a regular microscope. The aberration correction, along with Poisson and background denoising, are incorporated in our deconvolution-based fully-automated algorithm, which requires no empirical parameter-tuning. In experiments, we achieve spatial resolutions of 0.35um (lateral) and 0.5um (axial), which are comparable to the resolution that can be achieved with confocal deconvolution microscopy. We demonstrate a 3D video of moving bacteria recorded at 25 frames per second using our proposed computational multifocal microscopy technique.

© 2018 Optical Society of America under the terms of the OSA Open Access Publishing Agreement

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  1. P. M. Blanchard and A. H. Greenaway, “Simultaneous multiplane imaging with a distorted diffraction grating,” Appl. Opt. 38, 6692–6699 (1999).
    [Crossref]
  2. S. Abrahamsson, R. Ilic, J. Wisniewski, B. Mehl, L. Yu, L. Chen, M. Davanco, L. Oudjedi, J.-B. Fiche, B. Hajj, X. Jin, J. Pulupa, C. Cho, M. Mir, M. E. Beheiry, X. Darzacq, M. Nollmann, M. Dahan, C. Wu, T. Lionnet, J. A. Liddle, and C. I. Bargmann, “Multifocus microscopy with precise color multi-phase diffractive optics applied in functional neuronal imaging,” Biomed. Opt. Express 7, 855–869 (2016).
    [Crossref] [PubMed]
  3. L. Oudjedi, J.-B. Fiche, S. Abrahamsson, L. Mazenq, A. Lecestre, P.-F. Calmon, A. Cerf, and M. Nöllmann, “Astigmatic multifocus microscopy enables deep 3d super-resolved imaging,” Biomed. Opt. Express 7, 2163–2173 (2016).
    [Crossref] [PubMed]
  4. S. Abrahamsson, B. H. J. Chen, S. Stallinga, A. Y. Katsov, J. Wisniewski, G. Mizuguchi, P. Soule, F. Mueller, C. D. Darzacq, X. Darzacq, C. Wu, C. I. Bargmann, D. A. Agard, M. Dahan, and M. G. L. Gustafsson, “Fast multicolor 3d imaging using aberration-corrected multifocus microscopy,” Nat. methods 10, 60–63 (2013).
    [Crossref]
  5. R. Prevedel, Y.-G. Yoon, M. Hoffmann, N. Pak, G. Wetzstein, S. Kato, T. Schrödel, R. Raskar, M. Zimmer, E. S. Boyden, and A. Vaziri, “Simultaneous whole-animal 3d imaging of neuronal activity using light-field microscopy,” Nat. methods 11, 727–730 (2014).
    [Crossref] [PubMed]
  6. N. C. Pégard, H.-Y. Liu, N. Antipa, M. Gerlock, H. Adesnik, and L. Waller, “Compressive light-field microscopy for 3d neural activity recording,” Optica 3, 517–524 (2016).
    [Crossref]
  7. J.K. Adams, V. Boominathan, B.W. Avants, D.G. Vercosa, F. Ye, R.G. Baraniuk, J.T. Robinson, and A. Veeraraghavan, “Single-frame 3d fluorescence microscopy with ultraminiature lensless flatscope,” Sci. Adv. 3, 1701548 (2017).
    [Crossref] [PubMed]
  8. A. F. Coskun, I. Sencan, T.-W. Su, and A. Ozcan, “Lensless wide-field fluorescent imaging on a chip using compressive decoding of sparse objects,” Opt. Express 18, 10510–10523 (2010).
    [Crossref] [PubMed]
  9. N. Antipa, G. Kuo, R. Heckel, B. Mildenhall, E. Bostan, R. Ng, and L. Waller, “Diffusercam: lensless single-exposure 3d imaging,” Optica 5, 1–9 (2018).
    [Crossref]
  10. J. N. Mait, “Understanding diffractive optic design in the scalar domain,” J. Opt. Soc. Am. A 12, 2145–2158 (1995).
    [Crossref]
  11. G. Pedrini and S. Schedin, “Short coherence digital holography for 3d microscopy,” Optik-International J. for Light. Electron Opt. 112, 427–432 (2001).
    [Crossref]
  12. B. W. Schilling, T.-C. Poon, G. Indebetouw, B. Storrie, K. Shinoda, Y. Suzuki, and M. H. Wu, “Three-dimensional holographic fluorescence microscopy,” Opt. Lett. 22, 1506–1508 (1997).
    [Crossref]
  13. Z. Wang, D. Ryu, K. He, O. Cossairt, and A. K. Katsaggelos, “4d tracking of biological samples using lens-free on-chip in-line holography,” in Digital Holography and Three-Dimensional Imaging, (Optical Society of America, 2017), pp. Tu2A–4.
  14. L. Tian, J. Wang, and L. Waller, “3d differential phase-contrast microscopy with computational illumination using an led array,” Opt. letters 39, 1326–1329 (2014).
    [Crossref]
  15. L. Tian and L. Waller, “3d intensity and phase imaging from light field measurements in an led array microscope,” optica 2, 104–111 (2015).
    [Crossref]
  16. S. Chowdhury, W. J. Eldridge, A. Wax, and J. A. Izatt, “Structured illumination microscopy for dual-modality 3d sub-diffraction resolution fluorescence and refractive-index reconstruction,” Biomed. Opt. Express 8, 5776–5793 (2017).
    [Crossref]
  17. J. Rosen and G. Brooker, “Digital spatially incoherent fresnel holography,” Opt. letters 32, 912–914 (2007).
    [Crossref]
  18. J. Rosen and G. Brooker, “Non-scanning motionless fluorescence three-dimensional holographic microscopy,” Nat. Photonics 2, 190 (2008).
    [Crossref]
  19. O. Cossairt, K. He, R. Shang, N. Matsuda, M. Sharma, X. Huang, A. Katsaggelos, L. Spinoulas, and S. Yoo, “Compressive reconstruction for 3d incoherent holographic microscopy,” in Image Processing (ICIP), 2016 IEEE International Conference on, (IEEE, 2016), pp. 958–962.
  20. D. Ryu, Z. Wang, K. He, G. Zheng, R. Horstmeyer, and O. Cossairt, “Subsampled phase retrieval for temporal resolution enhancement in lensless on-chip holographic video,” Biomed. optics express 8, 1981–1995 (2017).
    [Crossref]
  21. Z. Wang, Q. Dai, D. Ryu, K. He, R. Horstmeyer, A. Katsaggelos, and O. S. Cossairt, “Dictionary-based phase retrieval for space-time super resolution using lens-free on-chip holographic video,” in Computational Optical Sensing and Imaging, (Optical Society of America, 2017), pp. CTu2B–3.
  22. H. Y. Liu, J. Zhong, and L. Waller, “Multiplexed phase-space imaging for 3d fluorescence microscopy,” Opt. Express 25, 14986–14995 (2017).
    [Crossref] [PubMed]
  23. Z. Wang, L. Spinoulas, K. He, L. Tian, O. Cossairt, A. K. Katsaggelos, and H. Chen, “Compressive holographic video,” Opt. Express 25, 250–262 (2017).
    [Crossref] [PubMed]
  24. M. Broxton, L. Grosenick, S. Yang, N. Cohen, A. Andalman, K. Deisseroth, and M. Levoy, “Wave optics theory and 3-d deconvolution for the light field microscope,” Opt. Express 21, 25418–25439 (2013).
    [Crossref] [PubMed]
  25. P. J. Greeb, “On the use of em algorithm for penalized likelihood estimation,” J. Royal Stat. Soc. B 52, 443–452 (1990).
  26. N. Dey, L. Blanc-Feraud, C. Zimmer, P. Roux, Z. Kam, J. C. Olivo-Marin, and J. Zerubia, “Richardson-lucy algorithm with total variation regularization for 3d confocal microscope deconvolution,” Microsc. Res. Tech. 4, 260–266 (2006).
    [Crossref]
  27. M. Laasmaa, M. Vendelin, and P. Peterson, “Application of regularized richardson-lucy algorithm for deconvolution of confocal microscopy images,” J. Microsc 2, 124–140 (2011).
    [Crossref]
  28. K. He, X. Huang, X. Wang, S. Yoo, P. Ruiz, I. Gdor, N. J. Ferrier, N. Scherer, M. Hereld, A. K. Katsaggelos, and O. Cossairt, “Design and simulation of a snapshot multi-focal interferometric microscope,” Opt. Express 26, 27381–27402 (2018).
    [Crossref]
  29. S. Hugelier, J. J. De Rooi, R. Bernex, S. Duwé, O. Devos, M. Sliwa, P. Dedecker, P. H. Eilers, and C. Ruckebusch, “Sparse deconvolution of high-density super-resolution images,” Sci. reports 6, 21413 (2016).
  30. S. Hugelier, P. Eilers, O. Devos, and C. Ruckebusch, “Improved superresolution microscopy imaging by sparse deconvolution with an interframe penalty,” J. Chemom. 31, e2847 (2017).
    [Crossref]
  31. A. Szameit, Y. Shechtman, E. Osherovich, E. Bullkich, P. Sidorenko, H. Dana, S. Steiner, E. B. Kley, S. Gazit, T. Cohen-Hyams, and et al., “Sparsity-based single-shot subwavelength coherent diffractive imaging,” Nat. materials 11, 455 (2012).
    [Crossref] [PubMed]
  32. O. Solomon, M. Mutzafi, M. Segev, and Y. C. Eldar, “Sparsity-based super-resolution microscopy from correlation information,” Opt. Express 26, 18238–18269 (2018).
    [Crossref] [PubMed]

2018 (3)

2017 (6)

Z. Wang, L. Spinoulas, K. He, L. Tian, O. Cossairt, A. K. Katsaggelos, and H. Chen, “Compressive holographic video,” Opt. Express 25, 250–262 (2017).
[Crossref] [PubMed]

H. Y. Liu, J. Zhong, and L. Waller, “Multiplexed phase-space imaging for 3d fluorescence microscopy,” Opt. Express 25, 14986–14995 (2017).
[Crossref] [PubMed]

S. Chowdhury, W. J. Eldridge, A. Wax, and J. A. Izatt, “Structured illumination microscopy for dual-modality 3d sub-diffraction resolution fluorescence and refractive-index reconstruction,” Biomed. Opt. Express 8, 5776–5793 (2017).
[Crossref]

J.K. Adams, V. Boominathan, B.W. Avants, D.G. Vercosa, F. Ye, R.G. Baraniuk, J.T. Robinson, and A. Veeraraghavan, “Single-frame 3d fluorescence microscopy with ultraminiature lensless flatscope,” Sci. Adv. 3, 1701548 (2017).
[Crossref] [PubMed]

D. Ryu, Z. Wang, K. He, G. Zheng, R. Horstmeyer, and O. Cossairt, “Subsampled phase retrieval for temporal resolution enhancement in lensless on-chip holographic video,” Biomed. optics express 8, 1981–1995 (2017).
[Crossref]

S. Hugelier, P. Eilers, O. Devos, and C. Ruckebusch, “Improved superresolution microscopy imaging by sparse deconvolution with an interframe penalty,” J. Chemom. 31, e2847 (2017).
[Crossref]

2016 (4)

2015 (1)

2014 (2)

L. Tian, J. Wang, and L. Waller, “3d differential phase-contrast microscopy with computational illumination using an led array,” Opt. letters 39, 1326–1329 (2014).
[Crossref]

R. Prevedel, Y.-G. Yoon, M. Hoffmann, N. Pak, G. Wetzstein, S. Kato, T. Schrödel, R. Raskar, M. Zimmer, E. S. Boyden, and A. Vaziri, “Simultaneous whole-animal 3d imaging of neuronal activity using light-field microscopy,” Nat. methods 11, 727–730 (2014).
[Crossref] [PubMed]

2013 (2)

S. Abrahamsson, B. H. J. Chen, S. Stallinga, A. Y. Katsov, J. Wisniewski, G. Mizuguchi, P. Soule, F. Mueller, C. D. Darzacq, X. Darzacq, C. Wu, C. I. Bargmann, D. A. Agard, M. Dahan, and M. G. L. Gustafsson, “Fast multicolor 3d imaging using aberration-corrected multifocus microscopy,” Nat. methods 10, 60–63 (2013).
[Crossref]

M. Broxton, L. Grosenick, S. Yang, N. Cohen, A. Andalman, K. Deisseroth, and M. Levoy, “Wave optics theory and 3-d deconvolution for the light field microscope,” Opt. Express 21, 25418–25439 (2013).
[Crossref] [PubMed]

2012 (1)

A. Szameit, Y. Shechtman, E. Osherovich, E. Bullkich, P. Sidorenko, H. Dana, S. Steiner, E. B. Kley, S. Gazit, T. Cohen-Hyams, and et al., “Sparsity-based single-shot subwavelength coherent diffractive imaging,” Nat. materials 11, 455 (2012).
[Crossref] [PubMed]

2011 (1)

M. Laasmaa, M. Vendelin, and P. Peterson, “Application of regularized richardson-lucy algorithm for deconvolution of confocal microscopy images,” J. Microsc 2, 124–140 (2011).
[Crossref]

2010 (1)

2008 (1)

J. Rosen and G. Brooker, “Non-scanning motionless fluorescence three-dimensional holographic microscopy,” Nat. Photonics 2, 190 (2008).
[Crossref]

2007 (1)

J. Rosen and G. Brooker, “Digital spatially incoherent fresnel holography,” Opt. letters 32, 912–914 (2007).
[Crossref]

2006 (1)

N. Dey, L. Blanc-Feraud, C. Zimmer, P. Roux, Z. Kam, J. C. Olivo-Marin, and J. Zerubia, “Richardson-lucy algorithm with total variation regularization for 3d confocal microscope deconvolution,” Microsc. Res. Tech. 4, 260–266 (2006).
[Crossref]

2001 (1)

G. Pedrini and S. Schedin, “Short coherence digital holography for 3d microscopy,” Optik-International J. for Light. Electron Opt. 112, 427–432 (2001).
[Crossref]

1999 (1)

1997 (1)

1995 (1)

1990 (1)

P. J. Greeb, “On the use of em algorithm for penalized likelihood estimation,” J. Royal Stat. Soc. B 52, 443–452 (1990).

Abrahamsson, S.

Adams, J.K.

J.K. Adams, V. Boominathan, B.W. Avants, D.G. Vercosa, F. Ye, R.G. Baraniuk, J.T. Robinson, and A. Veeraraghavan, “Single-frame 3d fluorescence microscopy with ultraminiature lensless flatscope,” Sci. Adv. 3, 1701548 (2017).
[Crossref] [PubMed]

Adesnik, H.

Agard, D. A.

S. Abrahamsson, B. H. J. Chen, S. Stallinga, A. Y. Katsov, J. Wisniewski, G. Mizuguchi, P. Soule, F. Mueller, C. D. Darzacq, X. Darzacq, C. Wu, C. I. Bargmann, D. A. Agard, M. Dahan, and M. G. L. Gustafsson, “Fast multicolor 3d imaging using aberration-corrected multifocus microscopy,” Nat. methods 10, 60–63 (2013).
[Crossref]

Andalman, A.

Antipa, N.

Avants, B.W.

J.K. Adams, V. Boominathan, B.W. Avants, D.G. Vercosa, F. Ye, R.G. Baraniuk, J.T. Robinson, and A. Veeraraghavan, “Single-frame 3d fluorescence microscopy with ultraminiature lensless flatscope,” Sci. Adv. 3, 1701548 (2017).
[Crossref] [PubMed]

Baraniuk, R.G.

J.K. Adams, V. Boominathan, B.W. Avants, D.G. Vercosa, F. Ye, R.G. Baraniuk, J.T. Robinson, and A. Veeraraghavan, “Single-frame 3d fluorescence microscopy with ultraminiature lensless flatscope,” Sci. Adv. 3, 1701548 (2017).
[Crossref] [PubMed]

Bargmann, C. I.

S. Abrahamsson, R. Ilic, J. Wisniewski, B. Mehl, L. Yu, L. Chen, M. Davanco, L. Oudjedi, J.-B. Fiche, B. Hajj, X. Jin, J. Pulupa, C. Cho, M. Mir, M. E. Beheiry, X. Darzacq, M. Nollmann, M. Dahan, C. Wu, T. Lionnet, J. A. Liddle, and C. I. Bargmann, “Multifocus microscopy with precise color multi-phase diffractive optics applied in functional neuronal imaging,” Biomed. Opt. Express 7, 855–869 (2016).
[Crossref] [PubMed]

S. Abrahamsson, B. H. J. Chen, S. Stallinga, A. Y. Katsov, J. Wisniewski, G. Mizuguchi, P. Soule, F. Mueller, C. D. Darzacq, X. Darzacq, C. Wu, C. I. Bargmann, D. A. Agard, M. Dahan, and M. G. L. Gustafsson, “Fast multicolor 3d imaging using aberration-corrected multifocus microscopy,” Nat. methods 10, 60–63 (2013).
[Crossref]

Beheiry, M. E.

Bernex, R.

S. Hugelier, J. J. De Rooi, R. Bernex, S. Duwé, O. Devos, M. Sliwa, P. Dedecker, P. H. Eilers, and C. Ruckebusch, “Sparse deconvolution of high-density super-resolution images,” Sci. reports 6, 21413 (2016).

Blanc-Feraud, L.

N. Dey, L. Blanc-Feraud, C. Zimmer, P. Roux, Z. Kam, J. C. Olivo-Marin, and J. Zerubia, “Richardson-lucy algorithm with total variation regularization for 3d confocal microscope deconvolution,” Microsc. Res. Tech. 4, 260–266 (2006).
[Crossref]

Blanchard, P. M.

Boominathan, V.

J.K. Adams, V. Boominathan, B.W. Avants, D.G. Vercosa, F. Ye, R.G. Baraniuk, J.T. Robinson, and A. Veeraraghavan, “Single-frame 3d fluorescence microscopy with ultraminiature lensless flatscope,” Sci. Adv. 3, 1701548 (2017).
[Crossref] [PubMed]

Bostan, E.

Boyden, E. S.

R. Prevedel, Y.-G. Yoon, M. Hoffmann, N. Pak, G. Wetzstein, S. Kato, T. Schrödel, R. Raskar, M. Zimmer, E. S. Boyden, and A. Vaziri, “Simultaneous whole-animal 3d imaging of neuronal activity using light-field microscopy,” Nat. methods 11, 727–730 (2014).
[Crossref] [PubMed]

Brooker, G.

J. Rosen and G. Brooker, “Non-scanning motionless fluorescence three-dimensional holographic microscopy,” Nat. Photonics 2, 190 (2008).
[Crossref]

J. Rosen and G. Brooker, “Digital spatially incoherent fresnel holography,” Opt. letters 32, 912–914 (2007).
[Crossref]

Broxton, M.

Bullkich, E.

A. Szameit, Y. Shechtman, E. Osherovich, E. Bullkich, P. Sidorenko, H. Dana, S. Steiner, E. B. Kley, S. Gazit, T. Cohen-Hyams, and et al., “Sparsity-based single-shot subwavelength coherent diffractive imaging,” Nat. materials 11, 455 (2012).
[Crossref] [PubMed]

Calmon, P.-F.

Cerf, A.

Chen, B. H. J.

S. Abrahamsson, B. H. J. Chen, S. Stallinga, A. Y. Katsov, J. Wisniewski, G. Mizuguchi, P. Soule, F. Mueller, C. D. Darzacq, X. Darzacq, C. Wu, C. I. Bargmann, D. A. Agard, M. Dahan, and M. G. L. Gustafsson, “Fast multicolor 3d imaging using aberration-corrected multifocus microscopy,” Nat. methods 10, 60–63 (2013).
[Crossref]

Chen, H.

Chen, L.

Cho, C.

Chowdhury, S.

Cohen, N.

Cohen-Hyams, T.

A. Szameit, Y. Shechtman, E. Osherovich, E. Bullkich, P. Sidorenko, H. Dana, S. Steiner, E. B. Kley, S. Gazit, T. Cohen-Hyams, and et al., “Sparsity-based single-shot subwavelength coherent diffractive imaging,” Nat. materials 11, 455 (2012).
[Crossref] [PubMed]

Coskun, A. F.

Cossairt, O.

K. He, X. Huang, X. Wang, S. Yoo, P. Ruiz, I. Gdor, N. J. Ferrier, N. Scherer, M. Hereld, A. K. Katsaggelos, and O. Cossairt, “Design and simulation of a snapshot multi-focal interferometric microscope,” Opt. Express 26, 27381–27402 (2018).
[Crossref]

Z. Wang, L. Spinoulas, K. He, L. Tian, O. Cossairt, A. K. Katsaggelos, and H. Chen, “Compressive holographic video,” Opt. Express 25, 250–262 (2017).
[Crossref] [PubMed]

D. Ryu, Z. Wang, K. He, G. Zheng, R. Horstmeyer, and O. Cossairt, “Subsampled phase retrieval for temporal resolution enhancement in lensless on-chip holographic video,” Biomed. optics express 8, 1981–1995 (2017).
[Crossref]

Z. Wang, D. Ryu, K. He, O. Cossairt, and A. K. Katsaggelos, “4d tracking of biological samples using lens-free on-chip in-line holography,” in Digital Holography and Three-Dimensional Imaging, (Optical Society of America, 2017), pp. Tu2A–4.

O. Cossairt, K. He, R. Shang, N. Matsuda, M. Sharma, X. Huang, A. Katsaggelos, L. Spinoulas, and S. Yoo, “Compressive reconstruction for 3d incoherent holographic microscopy,” in Image Processing (ICIP), 2016 IEEE International Conference on, (IEEE, 2016), pp. 958–962.

Cossairt, O. S.

Z. Wang, Q. Dai, D. Ryu, K. He, R. Horstmeyer, A. Katsaggelos, and O. S. Cossairt, “Dictionary-based phase retrieval for space-time super resolution using lens-free on-chip holographic video,” in Computational Optical Sensing and Imaging, (Optical Society of America, 2017), pp. CTu2B–3.

Dahan, M.

S. Abrahamsson, R. Ilic, J. Wisniewski, B. Mehl, L. Yu, L. Chen, M. Davanco, L. Oudjedi, J.-B. Fiche, B. Hajj, X. Jin, J. Pulupa, C. Cho, M. Mir, M. E. Beheiry, X. Darzacq, M. Nollmann, M. Dahan, C. Wu, T. Lionnet, J. A. Liddle, and C. I. Bargmann, “Multifocus microscopy with precise color multi-phase diffractive optics applied in functional neuronal imaging,” Biomed. Opt. Express 7, 855–869 (2016).
[Crossref] [PubMed]

S. Abrahamsson, B. H. J. Chen, S. Stallinga, A. Y. Katsov, J. Wisniewski, G. Mizuguchi, P. Soule, F. Mueller, C. D. Darzacq, X. Darzacq, C. Wu, C. I. Bargmann, D. A. Agard, M. Dahan, and M. G. L. Gustafsson, “Fast multicolor 3d imaging using aberration-corrected multifocus microscopy,” Nat. methods 10, 60–63 (2013).
[Crossref]

Dai, Q.

Z. Wang, Q. Dai, D. Ryu, K. He, R. Horstmeyer, A. Katsaggelos, and O. S. Cossairt, “Dictionary-based phase retrieval for space-time super resolution using lens-free on-chip holographic video,” in Computational Optical Sensing and Imaging, (Optical Society of America, 2017), pp. CTu2B–3.

Dana, H.

A. Szameit, Y. Shechtman, E. Osherovich, E. Bullkich, P. Sidorenko, H. Dana, S. Steiner, E. B. Kley, S. Gazit, T. Cohen-Hyams, and et al., “Sparsity-based single-shot subwavelength coherent diffractive imaging,” Nat. materials 11, 455 (2012).
[Crossref] [PubMed]

Darzacq, C. D.

S. Abrahamsson, B. H. J. Chen, S. Stallinga, A. Y. Katsov, J. Wisniewski, G. Mizuguchi, P. Soule, F. Mueller, C. D. Darzacq, X. Darzacq, C. Wu, C. I. Bargmann, D. A. Agard, M. Dahan, and M. G. L. Gustafsson, “Fast multicolor 3d imaging using aberration-corrected multifocus microscopy,” Nat. methods 10, 60–63 (2013).
[Crossref]

Darzacq, X.

S. Abrahamsson, R. Ilic, J. Wisniewski, B. Mehl, L. Yu, L. Chen, M. Davanco, L. Oudjedi, J.-B. Fiche, B. Hajj, X. Jin, J. Pulupa, C. Cho, M. Mir, M. E. Beheiry, X. Darzacq, M. Nollmann, M. Dahan, C. Wu, T. Lionnet, J. A. Liddle, and C. I. Bargmann, “Multifocus microscopy with precise color multi-phase diffractive optics applied in functional neuronal imaging,” Biomed. Opt. Express 7, 855–869 (2016).
[Crossref] [PubMed]

S. Abrahamsson, B. H. J. Chen, S. Stallinga, A. Y. Katsov, J. Wisniewski, G. Mizuguchi, P. Soule, F. Mueller, C. D. Darzacq, X. Darzacq, C. Wu, C. I. Bargmann, D. A. Agard, M. Dahan, and M. G. L. Gustafsson, “Fast multicolor 3d imaging using aberration-corrected multifocus microscopy,” Nat. methods 10, 60–63 (2013).
[Crossref]

Davanco, M.

De Rooi, J. J.

S. Hugelier, J. J. De Rooi, R. Bernex, S. Duwé, O. Devos, M. Sliwa, P. Dedecker, P. H. Eilers, and C. Ruckebusch, “Sparse deconvolution of high-density super-resolution images,” Sci. reports 6, 21413 (2016).

Dedecker, P.

S. Hugelier, J. J. De Rooi, R. Bernex, S. Duwé, O. Devos, M. Sliwa, P. Dedecker, P. H. Eilers, and C. Ruckebusch, “Sparse deconvolution of high-density super-resolution images,” Sci. reports 6, 21413 (2016).

Deisseroth, K.

Devos, O.

S. Hugelier, P. Eilers, O. Devos, and C. Ruckebusch, “Improved superresolution microscopy imaging by sparse deconvolution with an interframe penalty,” J. Chemom. 31, e2847 (2017).
[Crossref]

S. Hugelier, J. J. De Rooi, R. Bernex, S. Duwé, O. Devos, M. Sliwa, P. Dedecker, P. H. Eilers, and C. Ruckebusch, “Sparse deconvolution of high-density super-resolution images,” Sci. reports 6, 21413 (2016).

Dey, N.

N. Dey, L. Blanc-Feraud, C. Zimmer, P. Roux, Z. Kam, J. C. Olivo-Marin, and J. Zerubia, “Richardson-lucy algorithm with total variation regularization for 3d confocal microscope deconvolution,” Microsc. Res. Tech. 4, 260–266 (2006).
[Crossref]

Duwé, S.

S. Hugelier, J. J. De Rooi, R. Bernex, S. Duwé, O. Devos, M. Sliwa, P. Dedecker, P. H. Eilers, and C. Ruckebusch, “Sparse deconvolution of high-density super-resolution images,” Sci. reports 6, 21413 (2016).

Eilers, P.

S. Hugelier, P. Eilers, O. Devos, and C. Ruckebusch, “Improved superresolution microscopy imaging by sparse deconvolution with an interframe penalty,” J. Chemom. 31, e2847 (2017).
[Crossref]

Eilers, P. H.

S. Hugelier, J. J. De Rooi, R. Bernex, S. Duwé, O. Devos, M. Sliwa, P. Dedecker, P. H. Eilers, and C. Ruckebusch, “Sparse deconvolution of high-density super-resolution images,” Sci. reports 6, 21413 (2016).

Eldar, Y. C.

Eldridge, W. J.

Ferrier, N. J.

Fiche, J.-B.

Gazit, S.

A. Szameit, Y. Shechtman, E. Osherovich, E. Bullkich, P. Sidorenko, H. Dana, S. Steiner, E. B. Kley, S. Gazit, T. Cohen-Hyams, and et al., “Sparsity-based single-shot subwavelength coherent diffractive imaging,” Nat. materials 11, 455 (2012).
[Crossref] [PubMed]

Gdor, I.

Gerlock, M.

Greeb, P. J.

P. J. Greeb, “On the use of em algorithm for penalized likelihood estimation,” J. Royal Stat. Soc. B 52, 443–452 (1990).

Greenaway, A. H.

Grosenick, L.

Gustafsson, M. G. L.

S. Abrahamsson, B. H. J. Chen, S. Stallinga, A. Y. Katsov, J. Wisniewski, G. Mizuguchi, P. Soule, F. Mueller, C. D. Darzacq, X. Darzacq, C. Wu, C. I. Bargmann, D. A. Agard, M. Dahan, and M. G. L. Gustafsson, “Fast multicolor 3d imaging using aberration-corrected multifocus microscopy,” Nat. methods 10, 60–63 (2013).
[Crossref]

Hajj, B.

He, K.

K. He, X. Huang, X. Wang, S. Yoo, P. Ruiz, I. Gdor, N. J. Ferrier, N. Scherer, M. Hereld, A. K. Katsaggelos, and O. Cossairt, “Design and simulation of a snapshot multi-focal interferometric microscope,” Opt. Express 26, 27381–27402 (2018).
[Crossref]

Z. Wang, L. Spinoulas, K. He, L. Tian, O. Cossairt, A. K. Katsaggelos, and H. Chen, “Compressive holographic video,” Opt. Express 25, 250–262 (2017).
[Crossref] [PubMed]

D. Ryu, Z. Wang, K. He, G. Zheng, R. Horstmeyer, and O. Cossairt, “Subsampled phase retrieval for temporal resolution enhancement in lensless on-chip holographic video,” Biomed. optics express 8, 1981–1995 (2017).
[Crossref]

Z. Wang, Q. Dai, D. Ryu, K. He, R. Horstmeyer, A. Katsaggelos, and O. S. Cossairt, “Dictionary-based phase retrieval for space-time super resolution using lens-free on-chip holographic video,” in Computational Optical Sensing and Imaging, (Optical Society of America, 2017), pp. CTu2B–3.

O. Cossairt, K. He, R. Shang, N. Matsuda, M. Sharma, X. Huang, A. Katsaggelos, L. Spinoulas, and S. Yoo, “Compressive reconstruction for 3d incoherent holographic microscopy,” in Image Processing (ICIP), 2016 IEEE International Conference on, (IEEE, 2016), pp. 958–962.

Z. Wang, D. Ryu, K. He, O. Cossairt, and A. K. Katsaggelos, “4d tracking of biological samples using lens-free on-chip in-line holography,” in Digital Holography and Three-Dimensional Imaging, (Optical Society of America, 2017), pp. Tu2A–4.

Heckel, R.

Hereld, M.

Hoffmann, M.

R. Prevedel, Y.-G. Yoon, M. Hoffmann, N. Pak, G. Wetzstein, S. Kato, T. Schrödel, R. Raskar, M. Zimmer, E. S. Boyden, and A. Vaziri, “Simultaneous whole-animal 3d imaging of neuronal activity using light-field microscopy,” Nat. methods 11, 727–730 (2014).
[Crossref] [PubMed]

Horstmeyer, R.

D. Ryu, Z. Wang, K. He, G. Zheng, R. Horstmeyer, and O. Cossairt, “Subsampled phase retrieval for temporal resolution enhancement in lensless on-chip holographic video,” Biomed. optics express 8, 1981–1995 (2017).
[Crossref]

Z. Wang, Q. Dai, D. Ryu, K. He, R. Horstmeyer, A. Katsaggelos, and O. S. Cossairt, “Dictionary-based phase retrieval for space-time super resolution using lens-free on-chip holographic video,” in Computational Optical Sensing and Imaging, (Optical Society of America, 2017), pp. CTu2B–3.

Huang, X.

K. He, X. Huang, X. Wang, S. Yoo, P. Ruiz, I. Gdor, N. J. Ferrier, N. Scherer, M. Hereld, A. K. Katsaggelos, and O. Cossairt, “Design and simulation of a snapshot multi-focal interferometric microscope,” Opt. Express 26, 27381–27402 (2018).
[Crossref]

O. Cossairt, K. He, R. Shang, N. Matsuda, M. Sharma, X. Huang, A. Katsaggelos, L. Spinoulas, and S. Yoo, “Compressive reconstruction for 3d incoherent holographic microscopy,” in Image Processing (ICIP), 2016 IEEE International Conference on, (IEEE, 2016), pp. 958–962.

Hugelier, S.

S. Hugelier, P. Eilers, O. Devos, and C. Ruckebusch, “Improved superresolution microscopy imaging by sparse deconvolution with an interframe penalty,” J. Chemom. 31, e2847 (2017).
[Crossref]

S. Hugelier, J. J. De Rooi, R. Bernex, S. Duwé, O. Devos, M. Sliwa, P. Dedecker, P. H. Eilers, and C. Ruckebusch, “Sparse deconvolution of high-density super-resolution images,” Sci. reports 6, 21413 (2016).

Ilic, R.

Indebetouw, G.

Izatt, J. A.

Jin, X.

Kam, Z.

N. Dey, L. Blanc-Feraud, C. Zimmer, P. Roux, Z. Kam, J. C. Olivo-Marin, and J. Zerubia, “Richardson-lucy algorithm with total variation regularization for 3d confocal microscope deconvolution,” Microsc. Res. Tech. 4, 260–266 (2006).
[Crossref]

Kato, S.

R. Prevedel, Y.-G. Yoon, M. Hoffmann, N. Pak, G. Wetzstein, S. Kato, T. Schrödel, R. Raskar, M. Zimmer, E. S. Boyden, and A. Vaziri, “Simultaneous whole-animal 3d imaging of neuronal activity using light-field microscopy,” Nat. methods 11, 727–730 (2014).
[Crossref] [PubMed]

Katsaggelos, A.

Z. Wang, Q. Dai, D. Ryu, K. He, R. Horstmeyer, A. Katsaggelos, and O. S. Cossairt, “Dictionary-based phase retrieval for space-time super resolution using lens-free on-chip holographic video,” in Computational Optical Sensing and Imaging, (Optical Society of America, 2017), pp. CTu2B–3.

O. Cossairt, K. He, R. Shang, N. Matsuda, M. Sharma, X. Huang, A. Katsaggelos, L. Spinoulas, and S. Yoo, “Compressive reconstruction for 3d incoherent holographic microscopy,” in Image Processing (ICIP), 2016 IEEE International Conference on, (IEEE, 2016), pp. 958–962.

Katsaggelos, A. K.

Katsov, A. Y.

S. Abrahamsson, B. H. J. Chen, S. Stallinga, A. Y. Katsov, J. Wisniewski, G. Mizuguchi, P. Soule, F. Mueller, C. D. Darzacq, X. Darzacq, C. Wu, C. I. Bargmann, D. A. Agard, M. Dahan, and M. G. L. Gustafsson, “Fast multicolor 3d imaging using aberration-corrected multifocus microscopy,” Nat. methods 10, 60–63 (2013).
[Crossref]

Kley, E. B.

A. Szameit, Y. Shechtman, E. Osherovich, E. Bullkich, P. Sidorenko, H. Dana, S. Steiner, E. B. Kley, S. Gazit, T. Cohen-Hyams, and et al., “Sparsity-based single-shot subwavelength coherent diffractive imaging,” Nat. materials 11, 455 (2012).
[Crossref] [PubMed]

Kuo, G.

Laasmaa, M.

M. Laasmaa, M. Vendelin, and P. Peterson, “Application of regularized richardson-lucy algorithm for deconvolution of confocal microscopy images,” J. Microsc 2, 124–140 (2011).
[Crossref]

Lecestre, A.

Levoy, M.

Liddle, J. A.

Lionnet, T.

Liu, H. Y.

Liu, H.-Y.

Mait, J. N.

Matsuda, N.

O. Cossairt, K. He, R. Shang, N. Matsuda, M. Sharma, X. Huang, A. Katsaggelos, L. Spinoulas, and S. Yoo, “Compressive reconstruction for 3d incoherent holographic microscopy,” in Image Processing (ICIP), 2016 IEEE International Conference on, (IEEE, 2016), pp. 958–962.

Mazenq, L.

Mehl, B.

Mildenhall, B.

Mir, M.

Mizuguchi, G.

S. Abrahamsson, B. H. J. Chen, S. Stallinga, A. Y. Katsov, J. Wisniewski, G. Mizuguchi, P. Soule, F. Mueller, C. D. Darzacq, X. Darzacq, C. Wu, C. I. Bargmann, D. A. Agard, M. Dahan, and M. G. L. Gustafsson, “Fast multicolor 3d imaging using aberration-corrected multifocus microscopy,” Nat. methods 10, 60–63 (2013).
[Crossref]

Mueller, F.

S. Abrahamsson, B. H. J. Chen, S. Stallinga, A. Y. Katsov, J. Wisniewski, G. Mizuguchi, P. Soule, F. Mueller, C. D. Darzacq, X. Darzacq, C. Wu, C. I. Bargmann, D. A. Agard, M. Dahan, and M. G. L. Gustafsson, “Fast multicolor 3d imaging using aberration-corrected multifocus microscopy,” Nat. methods 10, 60–63 (2013).
[Crossref]

Mutzafi, M.

Ng, R.

Nollmann, M.

Nöllmann, M.

Olivo-Marin, J. C.

N. Dey, L. Blanc-Feraud, C. Zimmer, P. Roux, Z. Kam, J. C. Olivo-Marin, and J. Zerubia, “Richardson-lucy algorithm with total variation regularization for 3d confocal microscope deconvolution,” Microsc. Res. Tech. 4, 260–266 (2006).
[Crossref]

Osherovich, E.

A. Szameit, Y. Shechtman, E. Osherovich, E. Bullkich, P. Sidorenko, H. Dana, S. Steiner, E. B. Kley, S. Gazit, T. Cohen-Hyams, and et al., “Sparsity-based single-shot subwavelength coherent diffractive imaging,” Nat. materials 11, 455 (2012).
[Crossref] [PubMed]

Oudjedi, L.

Ozcan, A.

Pak, N.

R. Prevedel, Y.-G. Yoon, M. Hoffmann, N. Pak, G. Wetzstein, S. Kato, T. Schrödel, R. Raskar, M. Zimmer, E. S. Boyden, and A. Vaziri, “Simultaneous whole-animal 3d imaging of neuronal activity using light-field microscopy,” Nat. methods 11, 727–730 (2014).
[Crossref] [PubMed]

Pedrini, G.

G. Pedrini and S. Schedin, “Short coherence digital holography for 3d microscopy,” Optik-International J. for Light. Electron Opt. 112, 427–432 (2001).
[Crossref]

Pégard, N. C.

Peterson, P.

M. Laasmaa, M. Vendelin, and P. Peterson, “Application of regularized richardson-lucy algorithm for deconvolution of confocal microscopy images,” J. Microsc 2, 124–140 (2011).
[Crossref]

Poon, T.-C.

Prevedel, R.

R. Prevedel, Y.-G. Yoon, M. Hoffmann, N. Pak, G. Wetzstein, S. Kato, T. Schrödel, R. Raskar, M. Zimmer, E. S. Boyden, and A. Vaziri, “Simultaneous whole-animal 3d imaging of neuronal activity using light-field microscopy,” Nat. methods 11, 727–730 (2014).
[Crossref] [PubMed]

Pulupa, J.

Raskar, R.

R. Prevedel, Y.-G. Yoon, M. Hoffmann, N. Pak, G. Wetzstein, S. Kato, T. Schrödel, R. Raskar, M. Zimmer, E. S. Boyden, and A. Vaziri, “Simultaneous whole-animal 3d imaging of neuronal activity using light-field microscopy,” Nat. methods 11, 727–730 (2014).
[Crossref] [PubMed]

Robinson, J.T.

J.K. Adams, V. Boominathan, B.W. Avants, D.G. Vercosa, F. Ye, R.G. Baraniuk, J.T. Robinson, and A. Veeraraghavan, “Single-frame 3d fluorescence microscopy with ultraminiature lensless flatscope,” Sci. Adv. 3, 1701548 (2017).
[Crossref] [PubMed]

Rosen, J.

J. Rosen and G. Brooker, “Non-scanning motionless fluorescence three-dimensional holographic microscopy,” Nat. Photonics 2, 190 (2008).
[Crossref]

J. Rosen and G. Brooker, “Digital spatially incoherent fresnel holography,” Opt. letters 32, 912–914 (2007).
[Crossref]

Roux, P.

N. Dey, L. Blanc-Feraud, C. Zimmer, P. Roux, Z. Kam, J. C. Olivo-Marin, and J. Zerubia, “Richardson-lucy algorithm with total variation regularization for 3d confocal microscope deconvolution,” Microsc. Res. Tech. 4, 260–266 (2006).
[Crossref]

Ruckebusch, C.

S. Hugelier, P. Eilers, O. Devos, and C. Ruckebusch, “Improved superresolution microscopy imaging by sparse deconvolution with an interframe penalty,” J. Chemom. 31, e2847 (2017).
[Crossref]

S. Hugelier, J. J. De Rooi, R. Bernex, S. Duwé, O. Devos, M. Sliwa, P. Dedecker, P. H. Eilers, and C. Ruckebusch, “Sparse deconvolution of high-density super-resolution images,” Sci. reports 6, 21413 (2016).

Ruiz, P.

Ryu, D.

D. Ryu, Z. Wang, K. He, G. Zheng, R. Horstmeyer, and O. Cossairt, “Subsampled phase retrieval for temporal resolution enhancement in lensless on-chip holographic video,” Biomed. optics express 8, 1981–1995 (2017).
[Crossref]

Z. Wang, Q. Dai, D. Ryu, K. He, R. Horstmeyer, A. Katsaggelos, and O. S. Cossairt, “Dictionary-based phase retrieval for space-time super resolution using lens-free on-chip holographic video,” in Computational Optical Sensing and Imaging, (Optical Society of America, 2017), pp. CTu2B–3.

Z. Wang, D. Ryu, K. He, O. Cossairt, and A. K. Katsaggelos, “4d tracking of biological samples using lens-free on-chip in-line holography,” in Digital Holography and Three-Dimensional Imaging, (Optical Society of America, 2017), pp. Tu2A–4.

Schedin, S.

G. Pedrini and S. Schedin, “Short coherence digital holography for 3d microscopy,” Optik-International J. for Light. Electron Opt. 112, 427–432 (2001).
[Crossref]

Scherer, N.

Schilling, B. W.

Schrödel, T.

R. Prevedel, Y.-G. Yoon, M. Hoffmann, N. Pak, G. Wetzstein, S. Kato, T. Schrödel, R. Raskar, M. Zimmer, E. S. Boyden, and A. Vaziri, “Simultaneous whole-animal 3d imaging of neuronal activity using light-field microscopy,” Nat. methods 11, 727–730 (2014).
[Crossref] [PubMed]

Segev, M.

Sencan, I.

Shang, R.

O. Cossairt, K. He, R. Shang, N. Matsuda, M. Sharma, X. Huang, A. Katsaggelos, L. Spinoulas, and S. Yoo, “Compressive reconstruction for 3d incoherent holographic microscopy,” in Image Processing (ICIP), 2016 IEEE International Conference on, (IEEE, 2016), pp. 958–962.

Sharma, M.

O. Cossairt, K. He, R. Shang, N. Matsuda, M. Sharma, X. Huang, A. Katsaggelos, L. Spinoulas, and S. Yoo, “Compressive reconstruction for 3d incoherent holographic microscopy,” in Image Processing (ICIP), 2016 IEEE International Conference on, (IEEE, 2016), pp. 958–962.

Shechtman, Y.

A. Szameit, Y. Shechtman, E. Osherovich, E. Bullkich, P. Sidorenko, H. Dana, S. Steiner, E. B. Kley, S. Gazit, T. Cohen-Hyams, and et al., “Sparsity-based single-shot subwavelength coherent diffractive imaging,” Nat. materials 11, 455 (2012).
[Crossref] [PubMed]

Shinoda, K.

Sidorenko, P.

A. Szameit, Y. Shechtman, E. Osherovich, E. Bullkich, P. Sidorenko, H. Dana, S. Steiner, E. B. Kley, S. Gazit, T. Cohen-Hyams, and et al., “Sparsity-based single-shot subwavelength coherent diffractive imaging,” Nat. materials 11, 455 (2012).
[Crossref] [PubMed]

Sliwa, M.

S. Hugelier, J. J. De Rooi, R. Bernex, S. Duwé, O. Devos, M. Sliwa, P. Dedecker, P. H. Eilers, and C. Ruckebusch, “Sparse deconvolution of high-density super-resolution images,” Sci. reports 6, 21413 (2016).

Solomon, O.

Soule, P.

S. Abrahamsson, B. H. J. Chen, S. Stallinga, A. Y. Katsov, J. Wisniewski, G. Mizuguchi, P. Soule, F. Mueller, C. D. Darzacq, X. Darzacq, C. Wu, C. I. Bargmann, D. A. Agard, M. Dahan, and M. G. L. Gustafsson, “Fast multicolor 3d imaging using aberration-corrected multifocus microscopy,” Nat. methods 10, 60–63 (2013).
[Crossref]

Spinoulas, L.

Z. Wang, L. Spinoulas, K. He, L. Tian, O. Cossairt, A. K. Katsaggelos, and H. Chen, “Compressive holographic video,” Opt. Express 25, 250–262 (2017).
[Crossref] [PubMed]

O. Cossairt, K. He, R. Shang, N. Matsuda, M. Sharma, X. Huang, A. Katsaggelos, L. Spinoulas, and S. Yoo, “Compressive reconstruction for 3d incoherent holographic microscopy,” in Image Processing (ICIP), 2016 IEEE International Conference on, (IEEE, 2016), pp. 958–962.

Stallinga, S.

S. Abrahamsson, B. H. J. Chen, S. Stallinga, A. Y. Katsov, J. Wisniewski, G. Mizuguchi, P. Soule, F. Mueller, C. D. Darzacq, X. Darzacq, C. Wu, C. I. Bargmann, D. A. Agard, M. Dahan, and M. G. L. Gustafsson, “Fast multicolor 3d imaging using aberration-corrected multifocus microscopy,” Nat. methods 10, 60–63 (2013).
[Crossref]

Steiner, S.

A. Szameit, Y. Shechtman, E. Osherovich, E. Bullkich, P. Sidorenko, H. Dana, S. Steiner, E. B. Kley, S. Gazit, T. Cohen-Hyams, and et al., “Sparsity-based single-shot subwavelength coherent diffractive imaging,” Nat. materials 11, 455 (2012).
[Crossref] [PubMed]

Storrie, B.

Su, T.-W.

Suzuki, Y.

Szameit, A.

A. Szameit, Y. Shechtman, E. Osherovich, E. Bullkich, P. Sidorenko, H. Dana, S. Steiner, E. B. Kley, S. Gazit, T. Cohen-Hyams, and et al., “Sparsity-based single-shot subwavelength coherent diffractive imaging,” Nat. materials 11, 455 (2012).
[Crossref] [PubMed]

Tian, L.

Vaziri, A.

R. Prevedel, Y.-G. Yoon, M. Hoffmann, N. Pak, G. Wetzstein, S. Kato, T. Schrödel, R. Raskar, M. Zimmer, E. S. Boyden, and A. Vaziri, “Simultaneous whole-animal 3d imaging of neuronal activity using light-field microscopy,” Nat. methods 11, 727–730 (2014).
[Crossref] [PubMed]

Veeraraghavan, A.

J.K. Adams, V. Boominathan, B.W. Avants, D.G. Vercosa, F. Ye, R.G. Baraniuk, J.T. Robinson, and A. Veeraraghavan, “Single-frame 3d fluorescence microscopy with ultraminiature lensless flatscope,” Sci. Adv. 3, 1701548 (2017).
[Crossref] [PubMed]

Vendelin, M.

M. Laasmaa, M. Vendelin, and P. Peterson, “Application of regularized richardson-lucy algorithm for deconvolution of confocal microscopy images,” J. Microsc 2, 124–140 (2011).
[Crossref]

Vercosa, D.G.

J.K. Adams, V. Boominathan, B.W. Avants, D.G. Vercosa, F. Ye, R.G. Baraniuk, J.T. Robinson, and A. Veeraraghavan, “Single-frame 3d fluorescence microscopy with ultraminiature lensless flatscope,” Sci. Adv. 3, 1701548 (2017).
[Crossref] [PubMed]

Waller, L.

Wang, J.

L. Tian, J. Wang, and L. Waller, “3d differential phase-contrast microscopy with computational illumination using an led array,” Opt. letters 39, 1326–1329 (2014).
[Crossref]

Wang, X.

Wang, Z.

Z. Wang, L. Spinoulas, K. He, L. Tian, O. Cossairt, A. K. Katsaggelos, and H. Chen, “Compressive holographic video,” Opt. Express 25, 250–262 (2017).
[Crossref] [PubMed]

D. Ryu, Z. Wang, K. He, G. Zheng, R. Horstmeyer, and O. Cossairt, “Subsampled phase retrieval for temporal resolution enhancement in lensless on-chip holographic video,” Biomed. optics express 8, 1981–1995 (2017).
[Crossref]

Z. Wang, D. Ryu, K. He, O. Cossairt, and A. K. Katsaggelos, “4d tracking of biological samples using lens-free on-chip in-line holography,” in Digital Holography and Three-Dimensional Imaging, (Optical Society of America, 2017), pp. Tu2A–4.

Z. Wang, Q. Dai, D. Ryu, K. He, R. Horstmeyer, A. Katsaggelos, and O. S. Cossairt, “Dictionary-based phase retrieval for space-time super resolution using lens-free on-chip holographic video,” in Computational Optical Sensing and Imaging, (Optical Society of America, 2017), pp. CTu2B–3.

Wax, A.

Wetzstein, G.

R. Prevedel, Y.-G. Yoon, M. Hoffmann, N. Pak, G. Wetzstein, S. Kato, T. Schrödel, R. Raskar, M. Zimmer, E. S. Boyden, and A. Vaziri, “Simultaneous whole-animal 3d imaging of neuronal activity using light-field microscopy,” Nat. methods 11, 727–730 (2014).
[Crossref] [PubMed]

Wisniewski, J.

S. Abrahamsson, R. Ilic, J. Wisniewski, B. Mehl, L. Yu, L. Chen, M. Davanco, L. Oudjedi, J.-B. Fiche, B. Hajj, X. Jin, J. Pulupa, C. Cho, M. Mir, M. E. Beheiry, X. Darzacq, M. Nollmann, M. Dahan, C. Wu, T. Lionnet, J. A. Liddle, and C. I. Bargmann, “Multifocus microscopy with precise color multi-phase diffractive optics applied in functional neuronal imaging,” Biomed. Opt. Express 7, 855–869 (2016).
[Crossref] [PubMed]

S. Abrahamsson, B. H. J. Chen, S. Stallinga, A. Y. Katsov, J. Wisniewski, G. Mizuguchi, P. Soule, F. Mueller, C. D. Darzacq, X. Darzacq, C. Wu, C. I. Bargmann, D. A. Agard, M. Dahan, and M. G. L. Gustafsson, “Fast multicolor 3d imaging using aberration-corrected multifocus microscopy,” Nat. methods 10, 60–63 (2013).
[Crossref]

Wu, C.

S. Abrahamsson, R. Ilic, J. Wisniewski, B. Mehl, L. Yu, L. Chen, M. Davanco, L. Oudjedi, J.-B. Fiche, B. Hajj, X. Jin, J. Pulupa, C. Cho, M. Mir, M. E. Beheiry, X. Darzacq, M. Nollmann, M. Dahan, C. Wu, T. Lionnet, J. A. Liddle, and C. I. Bargmann, “Multifocus microscopy with precise color multi-phase diffractive optics applied in functional neuronal imaging,” Biomed. Opt. Express 7, 855–869 (2016).
[Crossref] [PubMed]

S. Abrahamsson, B. H. J. Chen, S. Stallinga, A. Y. Katsov, J. Wisniewski, G. Mizuguchi, P. Soule, F. Mueller, C. D. Darzacq, X. Darzacq, C. Wu, C. I. Bargmann, D. A. Agard, M. Dahan, and M. G. L. Gustafsson, “Fast multicolor 3d imaging using aberration-corrected multifocus microscopy,” Nat. methods 10, 60–63 (2013).
[Crossref]

Wu, M. H.

Yang, S.

Ye, F.

J.K. Adams, V. Boominathan, B.W. Avants, D.G. Vercosa, F. Ye, R.G. Baraniuk, J.T. Robinson, and A. Veeraraghavan, “Single-frame 3d fluorescence microscopy with ultraminiature lensless flatscope,” Sci. Adv. 3, 1701548 (2017).
[Crossref] [PubMed]

Yoo, S.

K. He, X. Huang, X. Wang, S. Yoo, P. Ruiz, I. Gdor, N. J. Ferrier, N. Scherer, M. Hereld, A. K. Katsaggelos, and O. Cossairt, “Design and simulation of a snapshot multi-focal interferometric microscope,” Opt. Express 26, 27381–27402 (2018).
[Crossref]

O. Cossairt, K. He, R. Shang, N. Matsuda, M. Sharma, X. Huang, A. Katsaggelos, L. Spinoulas, and S. Yoo, “Compressive reconstruction for 3d incoherent holographic microscopy,” in Image Processing (ICIP), 2016 IEEE International Conference on, (IEEE, 2016), pp. 958–962.

Yoon, Y.-G.

R. Prevedel, Y.-G. Yoon, M. Hoffmann, N. Pak, G. Wetzstein, S. Kato, T. Schrödel, R. Raskar, M. Zimmer, E. S. Boyden, and A. Vaziri, “Simultaneous whole-animal 3d imaging of neuronal activity using light-field microscopy,” Nat. methods 11, 727–730 (2014).
[Crossref] [PubMed]

Yu, L.

Zerubia, J.

N. Dey, L. Blanc-Feraud, C. Zimmer, P. Roux, Z. Kam, J. C. Olivo-Marin, and J. Zerubia, “Richardson-lucy algorithm with total variation regularization for 3d confocal microscope deconvolution,” Microsc. Res. Tech. 4, 260–266 (2006).
[Crossref]

Zheng, G.

D. Ryu, Z. Wang, K. He, G. Zheng, R. Horstmeyer, and O. Cossairt, “Subsampled phase retrieval for temporal resolution enhancement in lensless on-chip holographic video,” Biomed. optics express 8, 1981–1995 (2017).
[Crossref]

Zhong, J.

Zimmer, C.

N. Dey, L. Blanc-Feraud, C. Zimmer, P. Roux, Z. Kam, J. C. Olivo-Marin, and J. Zerubia, “Richardson-lucy algorithm with total variation regularization for 3d confocal microscope deconvolution,” Microsc. Res. Tech. 4, 260–266 (2006).
[Crossref]

Zimmer, M.

R. Prevedel, Y.-G. Yoon, M. Hoffmann, N. Pak, G. Wetzstein, S. Kato, T. Schrödel, R. Raskar, M. Zimmer, E. S. Boyden, and A. Vaziri, “Simultaneous whole-animal 3d imaging of neuronal activity using light-field microscopy,” Nat. methods 11, 727–730 (2014).
[Crossref] [PubMed]

Appl. Opt. (1)

Biomed. Opt. Express (3)

Biomed. optics express (1)

D. Ryu, Z. Wang, K. He, G. Zheng, R. Horstmeyer, and O. Cossairt, “Subsampled phase retrieval for temporal resolution enhancement in lensless on-chip holographic video,” Biomed. optics express 8, 1981–1995 (2017).
[Crossref]

J. Chemom. (1)

S. Hugelier, P. Eilers, O. Devos, and C. Ruckebusch, “Improved superresolution microscopy imaging by sparse deconvolution with an interframe penalty,” J. Chemom. 31, e2847 (2017).
[Crossref]

J. Microsc (1)

M. Laasmaa, M. Vendelin, and P. Peterson, “Application of regularized richardson-lucy algorithm for deconvolution of confocal microscopy images,” J. Microsc 2, 124–140 (2011).
[Crossref]

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

J. Royal Stat. Soc. B (1)

P. J. Greeb, “On the use of em algorithm for penalized likelihood estimation,” J. Royal Stat. Soc. B 52, 443–452 (1990).

Microsc. Res. Tech. (1)

N. Dey, L. Blanc-Feraud, C. Zimmer, P. Roux, Z. Kam, J. C. Olivo-Marin, and J. Zerubia, “Richardson-lucy algorithm with total variation regularization for 3d confocal microscope deconvolution,” Microsc. Res. Tech. 4, 260–266 (2006).
[Crossref]

Nat. materials (1)

A. Szameit, Y. Shechtman, E. Osherovich, E. Bullkich, P. Sidorenko, H. Dana, S. Steiner, E. B. Kley, S. Gazit, T. Cohen-Hyams, and et al., “Sparsity-based single-shot subwavelength coherent diffractive imaging,” Nat. materials 11, 455 (2012).
[Crossref] [PubMed]

Nat. methods (2)

S. Abrahamsson, B. H. J. Chen, S. Stallinga, A. Y. Katsov, J. Wisniewski, G. Mizuguchi, P. Soule, F. Mueller, C. D. Darzacq, X. Darzacq, C. Wu, C. I. Bargmann, D. A. Agard, M. Dahan, and M. G. L. Gustafsson, “Fast multicolor 3d imaging using aberration-corrected multifocus microscopy,” Nat. methods 10, 60–63 (2013).
[Crossref]

R. Prevedel, Y.-G. Yoon, M. Hoffmann, N. Pak, G. Wetzstein, S. Kato, T. Schrödel, R. Raskar, M. Zimmer, E. S. Boyden, and A. Vaziri, “Simultaneous whole-animal 3d imaging of neuronal activity using light-field microscopy,” Nat. methods 11, 727–730 (2014).
[Crossref] [PubMed]

Nat. Photonics (1)

J. Rosen and G. Brooker, “Non-scanning motionless fluorescence three-dimensional holographic microscopy,” Nat. Photonics 2, 190 (2008).
[Crossref]

Opt. Express (6)

Opt. Lett. (1)

Opt. letters (2)

L. Tian, J. Wang, and L. Waller, “3d differential phase-contrast microscopy with computational illumination using an led array,” Opt. letters 39, 1326–1329 (2014).
[Crossref]

J. Rosen and G. Brooker, “Digital spatially incoherent fresnel holography,” Opt. letters 32, 912–914 (2007).
[Crossref]

optica (1)

Optik-International J. for Light. Electron Opt. (1)

G. Pedrini and S. Schedin, “Short coherence digital holography for 3d microscopy,” Optik-International J. for Light. Electron Opt. 112, 427–432 (2001).
[Crossref]

Sci. Adv. (1)

J.K. Adams, V. Boominathan, B.W. Avants, D.G. Vercosa, F. Ye, R.G. Baraniuk, J.T. Robinson, and A. Veeraraghavan, “Single-frame 3d fluorescence microscopy with ultraminiature lensless flatscope,” Sci. Adv. 3, 1701548 (2017).
[Crossref] [PubMed]

Sci. reports (1)

S. Hugelier, J. J. De Rooi, R. Bernex, S. Duwé, O. Devos, M. Sliwa, P. Dedecker, P. H. Eilers, and C. Ruckebusch, “Sparse deconvolution of high-density super-resolution images,” Sci. reports 6, 21413 (2016).

Other (3)

Z. Wang, Q. Dai, D. Ryu, K. He, R. Horstmeyer, A. Katsaggelos, and O. S. Cossairt, “Dictionary-based phase retrieval for space-time super resolution using lens-free on-chip holographic video,” in Computational Optical Sensing and Imaging, (Optical Society of America, 2017), pp. CTu2B–3.

Z. Wang, D. Ryu, K. He, O. Cossairt, and A. K. Katsaggelos, “4d tracking of biological samples using lens-free on-chip in-line holography,” in Digital Holography and Three-Dimensional Imaging, (Optical Society of America, 2017), pp. Tu2A–4.

O. Cossairt, K. He, R. Shang, N. Matsuda, M. Sharma, X. Huang, A. Katsaggelos, L. Spinoulas, and S. Yoo, “Compressive reconstruction for 3d incoherent holographic microscopy,” in Image Processing (ICIP), 2016 IEEE International Conference on, (IEEE, 2016), pp. 958–962.

Supplementary Material (2)

NameDescription
» Visualization 1       A 2D video raw data of moving bacteria recorded at 25 frames per second.
» Visualization 2       A 3D video of moving bacteria reconstructed using our CMFM techniques.

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Figures (12)

Fig. 1
Fig. 1 Single-DOE multifocal microscopy (MFM) setup (a) and computational 3D reconstruction pipeline (d-f). In (a), a conventional microscope is augmented by a 4f system. An MFG (b) is inserted at the Fourier plane of the 4 f system to produce an array of l × l differently focused tile images in a single exposure (c; l = 3). Note that our CMFM system discards CA corrective optics, significantly reducing the system complexity and cost compared to conventional MFM. We correct for CA computationally rather than optically. (d-f) The pipeline of proposed computational framework: by capturing a z-stack 3D PSFs (d), the algorithm can simultaneously recover the background noise b, the optimal regularizer parameter λ and a high resolution 3D image (f) from a single captured 2D MFM image (e).
Fig. 2
Fig. 2 A z-stack 3D PSFs of CMFM, measured from a 170nm fluorescent bead. Top row: CMFM lateral PSFs imaged under five different axial positions (columns). each PSF consists of one focused image (outlined by a green box) and eight out-of-focus version images of the bead. xy and xz PSFs (second and third rows) and corresponding OTFs (bottom two rows) of five differently focused tiles (columns). The focal shift property of CMFM can be observed from xz PSFs (third row), verifying that CMFM is capable of capturing a focal stack instantaneously. Although the central tile’s PSF CA-free (first column), the off-axis tiles’ PSFs suffer from directional CA (second to last columns) due to geometry. The lateral spatial frequencies that are lost by CA are shown in xy OTFs (fourth row).
Fig. 3
Fig. 3 CA blur vs defocus blur. An in-focus tile with CA blur (red) and a defocus blur (blue) are highlighted in (a), whose PSFs and OTFs are shown in (b). (c) plots a comparison of linecuts indicated by blue and magenta lines in (b). For reference, a linecut in CA-free central tile’s OTF (shown in first column and fourth row of Fig. 2) is also plotted (red). A reconstruction comparison is shown in the right panel. (d) Object image. (e) Observation image (for visualization purpose, each tile image is cropped). (f) Reconstruction using only in-focus PSF. (g) Reconstruction using all the PSFs.
Fig. 4
Fig. 4 (a) Conventional MFM design uses a large tile spacing. (b) We propose to use a smaller tile spacing, so as to achieve a small lateral FOV that can be tracked over a large area for MFM tracking applications.
Fig. 5
Fig. 5 Simulations showing the capability of the proposed MFM of achieving larger lateral tracking space than conventional MFM does. (a) The synthetic 3D ground truth of an ellipsoid (left) and its xz slice (right). The center of the ellipsoid is 35.8um away from the center of the detector in x direction. MFM measurements (e-f) and corresponding reconstructions (b-c) by different design methods. (d) 1D axial profile comparison between ground truth (red) and reconstructions (black and blue). It is clear that the ellipsoid is reconstructed poorly from conventional MFM method while our design provides a good reconstruction. Signal loss as a function of lateral position of the tracked object for conventional (g) and our designed MFM (h). Similar to vignetting effect, the signal falls off when approaching the edges. Our proposed design alleviates peripheral signal loss and achieves an enlarged lateral tracking area.
Fig. 6
Fig. 6 Two experimental snapshot MFM raw images. (a) Experiment 1: snapshot captured 2D MFM image of multiple static periplasms by using an MFG with 9 focal planes under exposure time of 0.5s. (b) Experiment 2: a frame from an MFM video of a moving bacterium captured at 25 fps by using an MFG with 25 focal planes. The raw MFM video is shown in Visualization 1.
Fig. 7
Fig. 7 Proposed computational 3D reconstruction of CMFM image in comparison with confocal deconvolution results. (a) Confocal raw data and (b) its deconvolution results. (c) CMFM raw data and (d) its computational reconstruction results. In (a), confocal scan is taken with a dual spinning disk confocal microscope (Model: CSU-W1) with the total acquisition time of 20s, while in (c), the CMFM raw data is captured in a single exposure of 0.5s. The lateral resolution of the proposed computational reconstruction is about 0.35um (second row of d) and the axial resolution is about 0.5um (fourth row of d), which are comparable with those achievable with confocal deconvolution microscopy (second and fourth rows of b).
Fig. 8
Fig. 8 Experimental 3D reconstructions of a movable bacterium. A raw MFM video (shown in Visualization 1) was captured at 25fps as the bacterial moves in 3D space. The computational 3D reconstruction was performed for each video frame. Five out of sixty frames reconstruction is shown in (a-e). (f) 3D trajectory of the bacterium by computing and tracking its center of mass for each frame reconstruction. The colorbar indicate the frame index over time. The complete 3D video reconstruction from the first frame to the last frame is shown in Visualization 2.
Fig. 9
Fig. 9 Simulations that demonstrate the capability of the joint RL-TV algorithm to simultaneously recover the 3D image, background noise and the optimal regularizer parameter for CMFM. Top left: a ground truth image. Top right: the standard RL deconvolution without TV regularizer (λ = 0). Bottom left: RL-TV deconvolution by using an incorrect background values (b = 10). Bottom right: joint RL-TV deconvolution can simultaneously recover a 3D image, background noise and the optimal regularizer parameter. The PSNRs for three methods are 34.2dB, 27.5dB, 40.2dB, and I-divergences are 204.3, 517, and 96.7, respectively.
Fig. 10
Fig. 10 The convergence analysis of the joint RL-TV algorithm for the simulated CMFM. (a) The reconstructed background noise value and (b) optimal regularizer parameter during the iteration of joint RL-TV deconvolution process. (c) PSNR and (d) I-divergence between the ground truth image and reconstructed image at each iteration of the deconvolution process.
Fig. 11
Fig. 11 The recovered background values (left) and optimal regularizer parameter λ (right) at each iteration of the joint RL-TV deconvolution process for the first experiment.
Fig. 12
Fig. 12 The recovered background values (left) and optimal regularizer parameter λ (right) for each video frame of a movable bacterium.

Tables (1)

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Algorithm 1 Joint regularized RL algorithm for MFM

Equations (20)

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g ( x , y ) = o z ( x , y ) h z ( x , y ) d z ,
g = [ H , , H N z ] [ o 1 , , o N z ] T = Ho
g = P { Ho + b } ,
p ( g | o , b ) = i = 1 M ( Ho + b ) i g i e ( Ho + b ) i g i ! ,
o * = arg max o 0 p ( g | o , b ) = arg max o 0 f ( o , b ) ,
f ( o , b ) = i = 1 M [ ( Ho + b ) i g i log ( Ho + b ) i ]
Φ ( o , b , λ ) = f ( o , b ) + λ TV ( o ) ,
{ o * , b * , λ * } = arg min o 0 , b , λ Φ ( o , b , λ ) .
Φ ( o k ; b k , λ k ) o j k = i = 1 M h i , j [ H T g H o k + b k ] j λ k d i v ( o j k | o j k | ) ,
o j k + 1 = [ H T g H o k + b k ] j o j k 1 λ k d i v ( o j k | o j k | ) , o j k + 1 0 ,
Φ ( b k ; o k + 1 , λ k ) b k = i = 1 M { 1 [ g H o k + 1 + b k ] i } .
b k + 1 = { 1 M i = 1 M [ g H o k + 1 + b k ] i } b k .
λ k + 1 = arg min λ j = 1 N Φ ( o k + 1 ; b k + 1 , λ ) o j k + 1 2 .
λ k + 1 = j = 1 N { 1 [ H T g H o k + 1 + b k + 1 ] j } d i v ( o j k + 1 | o j k + 1 | ) j = 1 N [ d i v ( o j k + 1 | o j k + 1 | ) ] 2 .
δ x = m f Δ λ d x ; δ y = n f Δ λ d y ,
δ z = Δ λ λ c f m , n ,
F O V x = L x l M ^ ; F O V y = L y l M ^ ,
F O V z = ( l 2 1 ) Δ z .
T x = L x ( l 1 ) s x M ^ ; T y = L y ( l 1 ) s y M ^ ,
P S N R = 10 log 10 ( MAX u 2 MSE ) , I u , v = i = 1 N [ u i ln u i v i ( u i v i ) ] ,

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