Abstract

New microscopes are needed to help realize the full potential of 3D organoid culture studies. In order to image large volumes of 3D organoid cultures while preserving the ability to catch every single cell, we propose a new imaging platform based on lensfree microscopy. We have built a lensfree diffractive tomography setup performing multi-angle acquisitions of 3D organoid culture embedded in Matrigel and developed a dedicated 3D holographic reconstruction algorithm based on the Fourier diffraction theorem. With this new imaging platform, we have been able to reconstruct a 3D volume as large as 21.5 mm3 of a 3D organoid culture of prostatic RWPE1 cells showing the ability of these cells to assemble in 3D intricate cellular network at the mesoscopic scale. Importantly, comparisons with 2D images show that it is possible to resolve single cells isolated from the main cellular structure with our lensfree diffractive tomography setup.

© 2016 Optical Society of America

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References

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  1. N. Scherf and J. Huisken, “The smart and gentle microscope,” Nature Biotechnol. 33(8), 815–818 (2015).
    [Crossref]
  2. S. Vinjimore Kesavan, F. Momey, O. Cioni, B. David-Watine, N. Dubrulle, S. Shorte, E. Sulpice, D. Freida, B. Chalmond, J. M. Dinten, X. Gidrol, and C. Allier, “High-throughput monitoring of major cell functions by means of lensfree video microscopy,” Sci. Rep. 4, 5942 (2014).
    [PubMed]
  3. I. Pushkarsky, Y. Liu, W. Weaver, T.-W. Su, O. Mudanyali, A. Ozcan, and D. Di Carlo, “Automated single-cell motility analysis on a chip using lensfree microscopy,” Sci. Rep. 4, 4717 (2014).
    [PubMed]
  4. G. Zheng, S. A. Lee, Y. Antebi, M. B. Elowitz, and C. Yang, “The ePetri dish, an on-chip cell imaging platform based on subpixel perspective sweeping microscopy (SPSM),” Proc. Natl. Acad. Sci. U.S.A. 108(18), 16889–16894. (2011).
    [Crossref] [PubMed]
  5. M. E. Dolega, C. Allier, S. V. Kesavan, S. Gerbaud, F. Kermarrec, P. Marcoux, J.-M. Dinten, X. Gidrol, and N. Picollet-D’hahan, “Label-free analysis of prostate acini-like 3D structures by lensfree imaging,” Biosens. Bioelectron. 49, 176–183, (2013).
    [Crossref] [PubMed]
  6. S. O. Isikman, W. Bishara, S. Mavandadi, F. W. Yu, S. Feng, R. Lau, and A. Ozcan, “Lens-free optical tomographic microscope with a large imaging volume on a chip,” Proc. Natl. Acad. Sci. U.S.A. 108(18), 7296–7301. (2011).
    [Crossref] [PubMed]
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2015 (1)

N. Scherf and J. Huisken, “The smart and gentle microscope,” Nature Biotechnol. 33(8), 815–818 (2015).
[Crossref]

2014 (2)

S. Vinjimore Kesavan, F. Momey, O. Cioni, B. David-Watine, N. Dubrulle, S. Shorte, E. Sulpice, D. Freida, B. Chalmond, J. M. Dinten, X. Gidrol, and C. Allier, “High-throughput monitoring of major cell functions by means of lensfree video microscopy,” Sci. Rep. 4, 5942 (2014).
[PubMed]

I. Pushkarsky, Y. Liu, W. Weaver, T.-W. Su, O. Mudanyali, A. Ozcan, and D. Di Carlo, “Automated single-cell motility analysis on a chip using lensfree microscopy,” Sci. Rep. 4, 4717 (2014).
[PubMed]

2013 (2)

M. E. Dolega, C. Allier, S. V. Kesavan, S. Gerbaud, F. Kermarrec, P. Marcoux, J.-M. Dinten, X. Gidrol, and N. Picollet-D’hahan, “Label-free analysis of prostate acini-like 3D structures by lensfree imaging,” Biosens. Bioelectron. 49, 176–183, (2013).
[Crossref] [PubMed]

Y. Cotte, F. Toy, P. Jourdain, N. Pavillon, D. Boss, P. Magistretti, P. Marquet, and C. Depeursinge, “Marker-free phase nanoscopy,” Nature Photon. 7, 113–117 (2013).
[Crossref]

2012 (1)

S. O. Isikman, A. Greenbaum, W. Luo, A. Coskun, and A. Ozcan, “Giga-pixel lensfree holographic microscopy and tomography using color image sensors,” PLOS one 7(9), e45044 (2012).
[Crossref] [PubMed]

2011 (2)

S. O. Isikman, W. Bishara, S. Mavandadi, F. W. Yu, S. Feng, R. Lau, and A. Ozcan, “Lens-free optical tomographic microscope with a large imaging volume on a chip,” Proc. Natl. Acad. Sci. U.S.A. 108(18), 7296–7301. (2011).
[Crossref] [PubMed]

G. Zheng, S. A. Lee, Y. Antebi, M. B. Elowitz, and C. Yang, “The ePetri dish, an on-chip cell imaging platform based on subpixel perspective sweeping microscopy (SPSM),” Proc. Natl. Acad. Sci. U.S.A. 108(18), 16889–16894. (2011).
[Crossref] [PubMed]

2010 (1)

O. Haeberlé, K. Belkebir, H. Giovaninni, and A. Sentenac, “Tomographic diffractive microscopy: basics, techniques and perspectives,” J. Mod. Opt. 57(9), 686–699 (2010).
[Crossref]

2009 (1)

1982 (1)

1969 (1)

E. Wolf, “Three-Dimensional structure determination of semi-transparent objects from holographic data,” Opt. Commun. 1(14), 153–156 (1969).
[Crossref]

Allier, C.

S. Vinjimore Kesavan, F. Momey, O. Cioni, B. David-Watine, N. Dubrulle, S. Shorte, E. Sulpice, D. Freida, B. Chalmond, J. M. Dinten, X. Gidrol, and C. Allier, “High-throughput monitoring of major cell functions by means of lensfree video microscopy,” Sci. Rep. 4, 5942 (2014).
[PubMed]

M. E. Dolega, C. Allier, S. V. Kesavan, S. Gerbaud, F. Kermarrec, P. Marcoux, J.-M. Dinten, X. Gidrol, and N. Picollet-D’hahan, “Label-free analysis of prostate acini-like 3D structures by lensfree imaging,” Biosens. Bioelectron. 49, 176–183, (2013).
[Crossref] [PubMed]

Antebi, Y.

G. Zheng, S. A. Lee, Y. Antebi, M. B. Elowitz, and C. Yang, “The ePetri dish, an on-chip cell imaging platform based on subpixel perspective sweeping microscopy (SPSM),” Proc. Natl. Acad. Sci. U.S.A. 108(18), 16889–16894. (2011).
[Crossref] [PubMed]

Badizadegan, K.

Belkebir, K.

O. Haeberlé, K. Belkebir, H. Giovaninni, and A. Sentenac, “Tomographic diffractive microscopy: basics, techniques and perspectives,” J. Mod. Opt. 57(9), 686–699 (2010).
[Crossref]

Bishara, W.

S. O. Isikman, W. Bishara, S. Mavandadi, F. W. Yu, S. Feng, R. Lau, and A. Ozcan, “Lens-free optical tomographic microscope with a large imaging volume on a chip,” Proc. Natl. Acad. Sci. U.S.A. 108(18), 7296–7301. (2011).
[Crossref] [PubMed]

Boss, D.

Y. Cotte, F. Toy, P. Jourdain, N. Pavillon, D. Boss, P. Magistretti, P. Marquet, and C. Depeursinge, “Marker-free phase nanoscopy,” Nature Photon. 7, 113–117 (2013).
[Crossref]

Chalmond, B.

S. Vinjimore Kesavan, F. Momey, O. Cioni, B. David-Watine, N. Dubrulle, S. Shorte, E. Sulpice, D. Freida, B. Chalmond, J. M. Dinten, X. Gidrol, and C. Allier, “High-throughput monitoring of major cell functions by means of lensfree video microscopy,” Sci. Rep. 4, 5942 (2014).
[PubMed]

Choi, W.

Cioni, O.

S. Vinjimore Kesavan, F. Momey, O. Cioni, B. David-Watine, N. Dubrulle, S. Shorte, E. Sulpice, D. Freida, B. Chalmond, J. M. Dinten, X. Gidrol, and C. Allier, “High-throughput monitoring of major cell functions by means of lensfree video microscopy,” Sci. Rep. 4, 5942 (2014).
[PubMed]

Coskun, A.

S. O. Isikman, A. Greenbaum, W. Luo, A. Coskun, and A. Ozcan, “Giga-pixel lensfree holographic microscopy and tomography using color image sensors,” PLOS one 7(9), e45044 (2012).
[Crossref] [PubMed]

Cotte, Y.

Y. Cotte, F. Toy, P. Jourdain, N. Pavillon, D. Boss, P. Magistretti, P. Marquet, and C. Depeursinge, “Marker-free phase nanoscopy,” Nature Photon. 7, 113–117 (2013).
[Crossref]

Dasari, R. R.

David-Watine, B.

S. Vinjimore Kesavan, F. Momey, O. Cioni, B. David-Watine, N. Dubrulle, S. Shorte, E. Sulpice, D. Freida, B. Chalmond, J. M. Dinten, X. Gidrol, and C. Allier, “High-throughput monitoring of major cell functions by means of lensfree video microscopy,” Sci. Rep. 4, 5942 (2014).
[PubMed]

Depeursinge, C.

Y. Cotte, F. Toy, P. Jourdain, N. Pavillon, D. Boss, P. Magistretti, P. Marquet, and C. Depeursinge, “Marker-free phase nanoscopy,” Nature Photon. 7, 113–117 (2013).
[Crossref]

Di Carlo, D.

I. Pushkarsky, Y. Liu, W. Weaver, T.-W. Su, O. Mudanyali, A. Ozcan, and D. Di Carlo, “Automated single-cell motility analysis on a chip using lensfree microscopy,” Sci. Rep. 4, 4717 (2014).
[PubMed]

Dinten, J. M.

S. Vinjimore Kesavan, F. Momey, O. Cioni, B. David-Watine, N. Dubrulle, S. Shorte, E. Sulpice, D. Freida, B. Chalmond, J. M. Dinten, X. Gidrol, and C. Allier, “High-throughput monitoring of major cell functions by means of lensfree video microscopy,” Sci. Rep. 4, 5942 (2014).
[PubMed]

Dinten, J.-M.

M. E. Dolega, C. Allier, S. V. Kesavan, S. Gerbaud, F. Kermarrec, P. Marcoux, J.-M. Dinten, X. Gidrol, and N. Picollet-D’hahan, “Label-free analysis of prostate acini-like 3D structures by lensfree imaging,” Biosens. Bioelectron. 49, 176–183, (2013).
[Crossref] [PubMed]

Dolega, M. E.

M. E. Dolega, C. Allier, S. V. Kesavan, S. Gerbaud, F. Kermarrec, P. Marcoux, J.-M. Dinten, X. Gidrol, and N. Picollet-D’hahan, “Label-free analysis of prostate acini-like 3D structures by lensfree imaging,” Biosens. Bioelectron. 49, 176–183, (2013).
[Crossref] [PubMed]

Dubrulle, N.

S. Vinjimore Kesavan, F. Momey, O. Cioni, B. David-Watine, N. Dubrulle, S. Shorte, E. Sulpice, D. Freida, B. Chalmond, J. M. Dinten, X. Gidrol, and C. Allier, “High-throughput monitoring of major cell functions by means of lensfree video microscopy,” Sci. Rep. 4, 5942 (2014).
[PubMed]

Elowitz, M. B.

G. Zheng, S. A. Lee, Y. Antebi, M. B. Elowitz, and C. Yang, “The ePetri dish, an on-chip cell imaging platform based on subpixel perspective sweeping microscopy (SPSM),” Proc. Natl. Acad. Sci. U.S.A. 108(18), 16889–16894. (2011).
[Crossref] [PubMed]

Fang-Yen, C.

Feld, M. S.

Feng, S.

S. O. Isikman, W. Bishara, S. Mavandadi, F. W. Yu, S. Feng, R. Lau, and A. Ozcan, “Lens-free optical tomographic microscope with a large imaging volume on a chip,” Proc. Natl. Acad. Sci. U.S.A. 108(18), 7296–7301. (2011).
[Crossref] [PubMed]

Fienup, J. R.

Freida, D.

S. Vinjimore Kesavan, F. Momey, O. Cioni, B. David-Watine, N. Dubrulle, S. Shorte, E. Sulpice, D. Freida, B. Chalmond, J. M. Dinten, X. Gidrol, and C. Allier, “High-throughput monitoring of major cell functions by means of lensfree video microscopy,” Sci. Rep. 4, 5942 (2014).
[PubMed]

Gerbaud, S.

M. E. Dolega, C. Allier, S. V. Kesavan, S. Gerbaud, F. Kermarrec, P. Marcoux, J.-M. Dinten, X. Gidrol, and N. Picollet-D’hahan, “Label-free analysis of prostate acini-like 3D structures by lensfree imaging,” Biosens. Bioelectron. 49, 176–183, (2013).
[Crossref] [PubMed]

Gidrol, X.

S. Vinjimore Kesavan, F. Momey, O. Cioni, B. David-Watine, N. Dubrulle, S. Shorte, E. Sulpice, D. Freida, B. Chalmond, J. M. Dinten, X. Gidrol, and C. Allier, “High-throughput monitoring of major cell functions by means of lensfree video microscopy,” Sci. Rep. 4, 5942 (2014).
[PubMed]

M. E. Dolega, C. Allier, S. V. Kesavan, S. Gerbaud, F. Kermarrec, P. Marcoux, J.-M. Dinten, X. Gidrol, and N. Picollet-D’hahan, “Label-free analysis of prostate acini-like 3D structures by lensfree imaging,” Biosens. Bioelectron. 49, 176–183, (2013).
[Crossref] [PubMed]

Giovaninni, H.

O. Haeberlé, K. Belkebir, H. Giovaninni, and A. Sentenac, “Tomographic diffractive microscopy: basics, techniques and perspectives,” J. Mod. Opt. 57(9), 686–699 (2010).
[Crossref]

Greenbaum, A.

S. O. Isikman, A. Greenbaum, W. Luo, A. Coskun, and A. Ozcan, “Giga-pixel lensfree holographic microscopy and tomography using color image sensors,” PLOS one 7(9), e45044 (2012).
[Crossref] [PubMed]

Haeberlé, O.

O. Haeberlé, K. Belkebir, H. Giovaninni, and A. Sentenac, “Tomographic diffractive microscopy: basics, techniques and perspectives,” J. Mod. Opt. 57(9), 686–699 (2010).
[Crossref]

Huisken, J.

N. Scherf and J. Huisken, “The smart and gentle microscope,” Nature Biotechnol. 33(8), 815–818 (2015).
[Crossref]

Isikman, S. O.

S. O. Isikman, A. Greenbaum, W. Luo, A. Coskun, and A. Ozcan, “Giga-pixel lensfree holographic microscopy and tomography using color image sensors,” PLOS one 7(9), e45044 (2012).
[Crossref] [PubMed]

S. O. Isikman, W. Bishara, S. Mavandadi, F. W. Yu, S. Feng, R. Lau, and A. Ozcan, “Lens-free optical tomographic microscope with a large imaging volume on a chip,” Proc. Natl. Acad. Sci. U.S.A. 108(18), 7296–7301. (2011).
[Crossref] [PubMed]

Jourdain, P.

Y. Cotte, F. Toy, P. Jourdain, N. Pavillon, D. Boss, P. Magistretti, P. Marquet, and C. Depeursinge, “Marker-free phase nanoscopy,” Nature Photon. 7, 113–117 (2013).
[Crossref]

Kak, A.

A. Kak and M. Slaney, Principles of Computerized Tomographic Imaging (IEEE Press, 1988).

Kermarrec, F.

M. E. Dolega, C. Allier, S. V. Kesavan, S. Gerbaud, F. Kermarrec, P. Marcoux, J.-M. Dinten, X. Gidrol, and N. Picollet-D’hahan, “Label-free analysis of prostate acini-like 3D structures by lensfree imaging,” Biosens. Bioelectron. 49, 176–183, (2013).
[Crossref] [PubMed]

Kesavan, S. V.

M. E. Dolega, C. Allier, S. V. Kesavan, S. Gerbaud, F. Kermarrec, P. Marcoux, J.-M. Dinten, X. Gidrol, and N. Picollet-D’hahan, “Label-free analysis of prostate acini-like 3D structures by lensfree imaging,” Biosens. Bioelectron. 49, 176–183, (2013).
[Crossref] [PubMed]

Lau, R.

S. O. Isikman, W. Bishara, S. Mavandadi, F. W. Yu, S. Feng, R. Lau, and A. Ozcan, “Lens-free optical tomographic microscope with a large imaging volume on a chip,” Proc. Natl. Acad. Sci. U.S.A. 108(18), 7296–7301. (2011).
[Crossref] [PubMed]

Lee, S. A.

G. Zheng, S. A. Lee, Y. Antebi, M. B. Elowitz, and C. Yang, “The ePetri dish, an on-chip cell imaging platform based on subpixel perspective sweeping microscopy (SPSM),” Proc. Natl. Acad. Sci. U.S.A. 108(18), 16889–16894. (2011).
[Crossref] [PubMed]

Liu, Y.

I. Pushkarsky, Y. Liu, W. Weaver, T.-W. Su, O. Mudanyali, A. Ozcan, and D. Di Carlo, “Automated single-cell motility analysis on a chip using lensfree microscopy,” Sci. Rep. 4, 4717 (2014).
[PubMed]

Luo, W.

S. O. Isikman, A. Greenbaum, W. Luo, A. Coskun, and A. Ozcan, “Giga-pixel lensfree holographic microscopy and tomography using color image sensors,” PLOS one 7(9), e45044 (2012).
[Crossref] [PubMed]

Magistretti, P.

Y. Cotte, F. Toy, P. Jourdain, N. Pavillon, D. Boss, P. Magistretti, P. Marquet, and C. Depeursinge, “Marker-free phase nanoscopy,” Nature Photon. 7, 113–117 (2013).
[Crossref]

Marcoux, P.

M. E. Dolega, C. Allier, S. V. Kesavan, S. Gerbaud, F. Kermarrec, P. Marcoux, J.-M. Dinten, X. Gidrol, and N. Picollet-D’hahan, “Label-free analysis of prostate acini-like 3D structures by lensfree imaging,” Biosens. Bioelectron. 49, 176–183, (2013).
[Crossref] [PubMed]

Marquet, P.

Y. Cotte, F. Toy, P. Jourdain, N. Pavillon, D. Boss, P. Magistretti, P. Marquet, and C. Depeursinge, “Marker-free phase nanoscopy,” Nature Photon. 7, 113–117 (2013).
[Crossref]

Mavandadi, S.

S. O. Isikman, W. Bishara, S. Mavandadi, F. W. Yu, S. Feng, R. Lau, and A. Ozcan, “Lens-free optical tomographic microscope with a large imaging volume on a chip,” Proc. Natl. Acad. Sci. U.S.A. 108(18), 7296–7301. (2011).
[Crossref] [PubMed]

Momey, F.

S. Vinjimore Kesavan, F. Momey, O. Cioni, B. David-Watine, N. Dubrulle, S. Shorte, E. Sulpice, D. Freida, B. Chalmond, J. M. Dinten, X. Gidrol, and C. Allier, “High-throughput monitoring of major cell functions by means of lensfree video microscopy,” Sci. Rep. 4, 5942 (2014).
[PubMed]

Mudanyali, O.

I. Pushkarsky, Y. Liu, W. Weaver, T.-W. Su, O. Mudanyali, A. Ozcan, and D. Di Carlo, “Automated single-cell motility analysis on a chip using lensfree microscopy,” Sci. Rep. 4, 4717 (2014).
[PubMed]

Ozcan, A.

I. Pushkarsky, Y. Liu, W. Weaver, T.-W. Su, O. Mudanyali, A. Ozcan, and D. Di Carlo, “Automated single-cell motility analysis on a chip using lensfree microscopy,” Sci. Rep. 4, 4717 (2014).
[PubMed]

S. O. Isikman, A. Greenbaum, W. Luo, A. Coskun, and A. Ozcan, “Giga-pixel lensfree holographic microscopy and tomography using color image sensors,” PLOS one 7(9), e45044 (2012).
[Crossref] [PubMed]

S. O. Isikman, W. Bishara, S. Mavandadi, F. W. Yu, S. Feng, R. Lau, and A. Ozcan, “Lens-free optical tomographic microscope with a large imaging volume on a chip,” Proc. Natl. Acad. Sci. U.S.A. 108(18), 7296–7301. (2011).
[Crossref] [PubMed]

Pavillon, N.

Y. Cotte, F. Toy, P. Jourdain, N. Pavillon, D. Boss, P. Magistretti, P. Marquet, and C. Depeursinge, “Marker-free phase nanoscopy,” Nature Photon. 7, 113–117 (2013).
[Crossref]

Picollet-D’hahan, N.

M. E. Dolega, C. Allier, S. V. Kesavan, S. Gerbaud, F. Kermarrec, P. Marcoux, J.-M. Dinten, X. Gidrol, and N. Picollet-D’hahan, “Label-free analysis of prostate acini-like 3D structures by lensfree imaging,” Biosens. Bioelectron. 49, 176–183, (2013).
[Crossref] [PubMed]

Pushkarsky, I.

I. Pushkarsky, Y. Liu, W. Weaver, T.-W. Su, O. Mudanyali, A. Ozcan, and D. Di Carlo, “Automated single-cell motility analysis on a chip using lensfree microscopy,” Sci. Rep. 4, 4717 (2014).
[PubMed]

Scherf, N.

N. Scherf and J. Huisken, “The smart and gentle microscope,” Nature Biotechnol. 33(8), 815–818 (2015).
[Crossref]

Sentenac, A.

O. Haeberlé, K. Belkebir, H. Giovaninni, and A. Sentenac, “Tomographic diffractive microscopy: basics, techniques and perspectives,” J. Mod. Opt. 57(9), 686–699 (2010).
[Crossref]

Shorte, S.

S. Vinjimore Kesavan, F. Momey, O. Cioni, B. David-Watine, N. Dubrulle, S. Shorte, E. Sulpice, D. Freida, B. Chalmond, J. M. Dinten, X. Gidrol, and C. Allier, “High-throughput monitoring of major cell functions by means of lensfree video microscopy,” Sci. Rep. 4, 5942 (2014).
[PubMed]

Slaney, M.

A. Kak and M. Slaney, Principles of Computerized Tomographic Imaging (IEEE Press, 1988).

Su, T.-W.

I. Pushkarsky, Y. Liu, W. Weaver, T.-W. Su, O. Mudanyali, A. Ozcan, and D. Di Carlo, “Automated single-cell motility analysis on a chip using lensfree microscopy,” Sci. Rep. 4, 4717 (2014).
[PubMed]

Sulpice, E.

S. Vinjimore Kesavan, F. Momey, O. Cioni, B. David-Watine, N. Dubrulle, S. Shorte, E. Sulpice, D. Freida, B. Chalmond, J. M. Dinten, X. Gidrol, and C. Allier, “High-throughput monitoring of major cell functions by means of lensfree video microscopy,” Sci. Rep. 4, 5942 (2014).
[PubMed]

Sung, Y.

Toy, F.

Y. Cotte, F. Toy, P. Jourdain, N. Pavillon, D. Boss, P. Magistretti, P. Marquet, and C. Depeursinge, “Marker-free phase nanoscopy,” Nature Photon. 7, 113–117 (2013).
[Crossref]

Vinjimore Kesavan, S.

S. Vinjimore Kesavan, F. Momey, O. Cioni, B. David-Watine, N. Dubrulle, S. Shorte, E. Sulpice, D. Freida, B. Chalmond, J. M. Dinten, X. Gidrol, and C. Allier, “High-throughput monitoring of major cell functions by means of lensfree video microscopy,” Sci. Rep. 4, 5942 (2014).
[PubMed]

Weaver, W.

I. Pushkarsky, Y. Liu, W. Weaver, T.-W. Su, O. Mudanyali, A. Ozcan, and D. Di Carlo, “Automated single-cell motility analysis on a chip using lensfree microscopy,” Sci. Rep. 4, 4717 (2014).
[PubMed]

Wolf, E.

E. Wolf, “Three-Dimensional structure determination of semi-transparent objects from holographic data,” Opt. Commun. 1(14), 153–156 (1969).
[Crossref]

Yang, C.

G. Zheng, S. A. Lee, Y. Antebi, M. B. Elowitz, and C. Yang, “The ePetri dish, an on-chip cell imaging platform based on subpixel perspective sweeping microscopy (SPSM),” Proc. Natl. Acad. Sci. U.S.A. 108(18), 16889–16894. (2011).
[Crossref] [PubMed]

Yu, F. W.

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Supplementary Material (8)

NameDescription
» Visualization 1: AVI (4403 KB)      Full reconstructed volume (3D view flyover)
» Visualization 2: AVI (2308 KB)      3D view of the full reconstructed volume (3D view flyover)
» Visualization 3: AVI (7959 KB)      Crop 1 of the reconstructed volume (3D view flyover)
» Visualization 4: AVI (3226 KB)      ROI1 of the crop 1 (3D view flyover)
» Visualization 5: AVI (2918 KB)      ROI2 of the crop 1 (3D view flyover)
» Visualization 6: AVI (6313 KB)      ROI1 of the crop 2 (3D view flyover)
» Visualization 7: AVI (8186 KB)      Crop 2 of the reconstructed volume (3D view flyover)
» Visualization 8: AVI (4742 KB)      ROI2 of the crop 2 (3D view flyover)

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Figures (10)

Fig. 1
Fig. 1 Left-hand side - Experimental bench dedicated to lensfree diffractive tomography. Right-hand side - Optical schema of the system. The semi-coherent incident plane wave Uinc passes through the sample volume. Each element of the volume diffracts the incident plane, behaving like secondary spherical sources, creating a diffracted wave Udif. The sensor records the intensity of their summation: Itot = |Utot|2 = |Uinc + Udif|2
Fig. 2
Fig. 2 Schema of three different acquisitions at the illumination angles φ j 1, φ j 2 and φ j 3, with (j1, j2, j3) ∈ ⟦1, N3, where N is the total number of acquisitions.
Fig. 3
Fig. 3 Illustration of the Fourier diffraction theorem with the notations of Fig. 2. The 3D frequency space of the object of interest f is mapped with the 2D Fourier transform of the projections U d i f j 1, U d i f j 2 and U d i f j 3. An example of a Fourier region which is actually filled by the algorithm is given in the medallion in the 3D frequency domain part of the figure with the parameters used in section 3 to reconstruct a given region of interest: a volume of 1.34 × 1.34 × 1.34 mm3 with a voxel size of 1.67 × 1.67 × 3.34 µm3 at λ = 520 nm with an illumination angle varying from −30° (blue) to 30° (green) with a step angle of 5°. The red cap corresponds to the region map with the normal illumination.
Fig. 4
Fig. 4 Illustration of the steps to get an approximation of U d i f j for a given j.
Fig. 5
Fig. 5 3D lensfree data of a culture of prostatic cells RWPE1 in Matrigel. 61 angles of view were acquired from −30° to 30° with an angular pitch of 1° around the x axis. The illumination wavelength is 520 nm. A region of interest (ROI) is extracted on each projection and centered by registration. This aims at performing a localized reconstruction to save computation from RAM overflows. The centering has to be taken into account in the algorithm (Eq. (5)).
Fig. 6
Fig. 6 Extraction of 9 ROIs of size 1.34 × 1.34 mm2 (800 × 800 pixels) for the piecewise 3D reconstruction of the 3D culture of prostatic cells RWPE1 presented on Fig. 5.
Fig. 7
Fig. 7 Piecewise 3D reconstruction (imaginary part of f) of a large volume (4 × 4 × 1.34 mm3) of the culture of prostatic cells RWPE1 from tomographic data presented on Fig. 5. (a) 3 sectional views - xy (center), xz (right) and yz (bottom) - are shown, each one focused at a given distance d = zs − z from the sensor. (b) 3D views of the reconstruction from different observation points (see Visualization 1 and Visualization 2). The dash red curves indicate the tilt of the network relative to the horizontal plane. The red arrows point out isolated objects that are not focused at the same altitude as the network.
Fig. 8
Fig. 8 ROI at the center of the piecewise 3D reconstruction of the volume of Fig. 7. (a) 3 sectional views - xy (center), xz (right) and yz (bottom) - and a 3D view of the ROI. (a) same representation rules on two specific organoids at the full resolution of the reconstruction (see Visualization 3, Visualization 4, and Visualization 5). These are pointed by arrows on the global view. The dashed-line indicates the network plane. The red arrow points toward a 33 × 38 × 42 µm3 object and the blue arrow toward a 16 × 17 × 40 µm3 object.
Fig. 9
Fig. 9 ROI at the to right corner of the piecewise 3D reconstruction of the volume of Fig. 7. (a) 3 sectional views - xy (center), xz (right) and yz (bottom) - and a 3D view of the ROI. (b) same representation rules on two specific organoids at the full resolution of the reconstruction (see Visualization 6, Visualization 7, and Visualization 8). These are pointed by arrows on the global view. The dashed-line indicates the network plane. The red arrow points toward a 12 × 43 × 96 µm3 object and the blue arrow toward a 80 × 80 × 100 µm3 object.
Fig. 10
Fig. 10 2D reconstruction from 2D lensfree data acquired on the 3D culture of prostatic cells RWPE1 presented on Fig. 5. Comparisons of two axial cut profiles respectively in x and y directions taken on both 2D and 3D reconstructions, and one cut profile in the z direction taken on the 3D reconstruction, for three biological objects: two cells, one identified on Fig. 8 (ROI 1 in red) and one identified on Fig. 9 (ROI 2 in blue) and one organoid identified on Fig. 9 (ROI 3 in green). The dashed and solid curves correspond respectively to the 2D and 3D reconstruction cut profiles.

Equations (12)

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U d i f ( r ) = 1 4 π O b j e c t f ( r ) U i n c ( r ) exp ( i k 0 r r ) r r d 3 r = 1 4 π ( f . U i n c ) * h
f ( r ) = k 0 2 ( ( n ( r ) n 0 ) 2 1 )
f ^ ( α j , β j , γ j ) = 4 i π w exp ( 2 i π w z s ) H z s { k 0 j ; λ 0 } U ^ d i f j ( u , v ; z s )
{ p 0 j = 0 q 0 j = sin φ j m 0 j = cos φ j
g ^ ( u ) = g ( x ) exp ( 2 i π u x ) d x
f = 3 D 1 [ S ( H z s j 2 D [ M 0 j U d i f j ] ) | { k 0 j | j = 1 N } ]
M 0 j ( x , y ) = exp ( 2 i π ( n 0 p 0 j λ 0 x + n 0 q 0 j λ 0 y ) )
U d i f j I ¯ t o t j exp ( i k 0 j r ) U i n c j
{ x 0 j = 0 y 0 j = z s tan φ j
f = 3 D 1 [ S ( H z s j D 0 j 2 D [ M 0 j U d i f R O I j ] ) | { k 0 j , x 0 j , y 0 j | j = 1 N j } ]
D 0 j ( u , v ) = exp ( 2 i π ( u x 0 j + v y 0 j ) )
M 0 j ( x , y ) = exp ( 2 i π ( n 0 p 0 j λ 0 ( x + x 0 j ) + n 0 q 0 j λ 0 ( y + y 0 j ) ) ) .

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