Abstract

Lens-free microscopy multispectral acquisitions are processed with an inverse problem approach: a multispectral total variation criterion is defined and minimized with the conjugate gradients method. Reconstruction results show that the method is efficient to recover the phase image of densely packed cells.

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

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References

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  1. A. Greenbaum, W. Luo, T.-W. Su, Z. Göröcs, L. Xue, S. O. Isikman, A. F. Coskun, O. Mudanyali, and A. Ozcan, “Imaging without lenses: achievements and remaining challenges of wide-field on-chip microscopy,” Nat. Methods 9, 889 (2012).
    [Crossref] [PubMed]
  2. C. Allier, S. Morel, R. Vincent, L. Ghenim, F. Navarro, M. Menneteau, T. Bordy, L. Hervé, O. Cioni, X. Gidrol, and et al., “Imaging of dense cell cultures by multiwavelength lens-free video microscopy,” Cytom. Part A 91, 433–442 (2017).
    [Crossref]
  3. J. R. Fienup, “Phase retrieval algorithms: a comparison,” Appl. Opt. 21, 2758–2769 (1982).
    [Crossref]
  4. T. Latychevskaia and H.-W. Fink, “Solution to the twin image problem in holography,” Phys. Rev. Lett. 98, 233901 (2007).
    [Crossref]
  5. Y. Rivenson, Y. Wu, H. Wang, Y. Zhang, A. Feizi, and A. Ozcan, “Sparsity-based multi-height phase recovery in holographic microscopy,” Sci. Rep. 6, 37862 (2016).
    [Crossref]
  6. L. Allen and M. Oxley, “Phase retrieval from series of images obtained by defocus variation,” Opt. Commun. 199, 65–75 (2001).
    [Crossref]
  7. A. Greenbaum and A. Ozcan, “Maskless imaging of dense samples using pixel super-resolution based multi-height lensfree on-chip microscopy,” Opt. Express 20, 3129–3143 (2012).
    [Crossref] [PubMed]
  8. M. Sanz, J. A. Picazo-Bueno, J. García, and V. Micó, “Improved quantitative phase imaging in lensless microscopy by single-shot multi-wavelength illumination using a fast convergence algorithm,” Opt. Express 23, 21352–21365 (2015).
    [Crossref] [PubMed]
  9. J. W. Goodman, Introduction to Fourier Optics (Roberts and Company Publishers, 2005).
  10. Y. Zhang, H. Wang, Y. Wu, M. Tamamitsu, and A. Ozcan, “Edge sparsity criterion for robust holographic autofocusing,” Opt. Lett. 42, 3824–3827 (2017).
    [Crossref]
  11. M. R. Hestenes and E. Stiefel, Methods of conjugate gradients for solving linear systems, vol. 49 (NBSWashington, DC, 1952).
  12. S. Grilli, P. Ferraro, S. De Nicola, A. Finizio, G. Pierattini, and R. Meucci, “Whole optical wavefields reconstruction by digital holography,” Opt. Express 9, 294–302 (2001).
    [Crossref] [PubMed]
  13. D. Claus, D. Iliescu, and P. Bryanston-Cross, “Quantitative space-bandwidth product analysis in digital holography,” Appl. Opt. 50, H116–H127 (2011).
    [Crossref]
  14. A. Ozcan and E. McLeod, “Lensless imaging and sensing,” Annu. Rev. Biomed. Eng. 18, 77–102 (2016).
    [Crossref]

2017 (2)

C. Allier, S. Morel, R. Vincent, L. Ghenim, F. Navarro, M. Menneteau, T. Bordy, L. Hervé, O. Cioni, X. Gidrol, and et al., “Imaging of dense cell cultures by multiwavelength lens-free video microscopy,” Cytom. Part A 91, 433–442 (2017).
[Crossref]

Y. Zhang, H. Wang, Y. Wu, M. Tamamitsu, and A. Ozcan, “Edge sparsity criterion for robust holographic autofocusing,” Opt. Lett. 42, 3824–3827 (2017).
[Crossref]

2016 (2)

A. Ozcan and E. McLeod, “Lensless imaging and sensing,” Annu. Rev. Biomed. Eng. 18, 77–102 (2016).
[Crossref]

Y. Rivenson, Y. Wu, H. Wang, Y. Zhang, A. Feizi, and A. Ozcan, “Sparsity-based multi-height phase recovery in holographic microscopy,” Sci. Rep. 6, 37862 (2016).
[Crossref]

2015 (1)

2012 (2)

A. Greenbaum and A. Ozcan, “Maskless imaging of dense samples using pixel super-resolution based multi-height lensfree on-chip microscopy,” Opt. Express 20, 3129–3143 (2012).
[Crossref] [PubMed]

A. Greenbaum, W. Luo, T.-W. Su, Z. Göröcs, L. Xue, S. O. Isikman, A. F. Coskun, O. Mudanyali, and A. Ozcan, “Imaging without lenses: achievements and remaining challenges of wide-field on-chip microscopy,” Nat. Methods 9, 889 (2012).
[Crossref] [PubMed]

2011 (1)

2007 (1)

T. Latychevskaia and H.-W. Fink, “Solution to the twin image problem in holography,” Phys. Rev. Lett. 98, 233901 (2007).
[Crossref]

2001 (2)

1982 (1)

Allen, L.

L. Allen and M. Oxley, “Phase retrieval from series of images obtained by defocus variation,” Opt. Commun. 199, 65–75 (2001).
[Crossref]

Allier, C.

C. Allier, S. Morel, R. Vincent, L. Ghenim, F. Navarro, M. Menneteau, T. Bordy, L. Hervé, O. Cioni, X. Gidrol, and et al., “Imaging of dense cell cultures by multiwavelength lens-free video microscopy,” Cytom. Part A 91, 433–442 (2017).
[Crossref]

Bordy, T.

C. Allier, S. Morel, R. Vincent, L. Ghenim, F. Navarro, M. Menneteau, T. Bordy, L. Hervé, O. Cioni, X. Gidrol, and et al., “Imaging of dense cell cultures by multiwavelength lens-free video microscopy,” Cytom. Part A 91, 433–442 (2017).
[Crossref]

Bryanston-Cross, P.

Cioni, O.

C. Allier, S. Morel, R. Vincent, L. Ghenim, F. Navarro, M. Menneteau, T. Bordy, L. Hervé, O. Cioni, X. Gidrol, and et al., “Imaging of dense cell cultures by multiwavelength lens-free video microscopy,” Cytom. Part A 91, 433–442 (2017).
[Crossref]

Claus, D.

Coskun, A. F.

A. Greenbaum, W. Luo, T.-W. Su, Z. Göröcs, L. Xue, S. O. Isikman, A. F. Coskun, O. Mudanyali, and A. Ozcan, “Imaging without lenses: achievements and remaining challenges of wide-field on-chip microscopy,” Nat. Methods 9, 889 (2012).
[Crossref] [PubMed]

De Nicola, S.

Feizi, A.

Y. Rivenson, Y. Wu, H. Wang, Y. Zhang, A. Feizi, and A. Ozcan, “Sparsity-based multi-height phase recovery in holographic microscopy,” Sci. Rep. 6, 37862 (2016).
[Crossref]

Ferraro, P.

Fienup, J. R.

Finizio, A.

Fink, H.-W.

T. Latychevskaia and H.-W. Fink, “Solution to the twin image problem in holography,” Phys. Rev. Lett. 98, 233901 (2007).
[Crossref]

García, J.

Ghenim, L.

C. Allier, S. Morel, R. Vincent, L. Ghenim, F. Navarro, M. Menneteau, T. Bordy, L. Hervé, O. Cioni, X. Gidrol, and et al., “Imaging of dense cell cultures by multiwavelength lens-free video microscopy,” Cytom. Part A 91, 433–442 (2017).
[Crossref]

Gidrol, X.

C. Allier, S. Morel, R. Vincent, L. Ghenim, F. Navarro, M. Menneteau, T. Bordy, L. Hervé, O. Cioni, X. Gidrol, and et al., “Imaging of dense cell cultures by multiwavelength lens-free video microscopy,” Cytom. Part A 91, 433–442 (2017).
[Crossref]

Goodman, J. W.

J. W. Goodman, Introduction to Fourier Optics (Roberts and Company Publishers, 2005).

Göröcs, Z.

A. Greenbaum, W. Luo, T.-W. Su, Z. Göröcs, L. Xue, S. O. Isikman, A. F. Coskun, O. Mudanyali, and A. Ozcan, “Imaging without lenses: achievements and remaining challenges of wide-field on-chip microscopy,” Nat. Methods 9, 889 (2012).
[Crossref] [PubMed]

Greenbaum, A.

A. Greenbaum, W. Luo, T.-W. Su, Z. Göröcs, L. Xue, S. O. Isikman, A. F. Coskun, O. Mudanyali, and A. Ozcan, “Imaging without lenses: achievements and remaining challenges of wide-field on-chip microscopy,” Nat. Methods 9, 889 (2012).
[Crossref] [PubMed]

A. Greenbaum and A. Ozcan, “Maskless imaging of dense samples using pixel super-resolution based multi-height lensfree on-chip microscopy,” Opt. Express 20, 3129–3143 (2012).
[Crossref] [PubMed]

Grilli, S.

Hervé, L.

C. Allier, S. Morel, R. Vincent, L. Ghenim, F. Navarro, M. Menneteau, T. Bordy, L. Hervé, O. Cioni, X. Gidrol, and et al., “Imaging of dense cell cultures by multiwavelength lens-free video microscopy,” Cytom. Part A 91, 433–442 (2017).
[Crossref]

Hestenes, M. R.

M. R. Hestenes and E. Stiefel, Methods of conjugate gradients for solving linear systems, vol. 49 (NBSWashington, DC, 1952).

Iliescu, D.

Isikman, S. O.

A. Greenbaum, W. Luo, T.-W. Su, Z. Göröcs, L. Xue, S. O. Isikman, A. F. Coskun, O. Mudanyali, and A. Ozcan, “Imaging without lenses: achievements and remaining challenges of wide-field on-chip microscopy,” Nat. Methods 9, 889 (2012).
[Crossref] [PubMed]

Latychevskaia, T.

T. Latychevskaia and H.-W. Fink, “Solution to the twin image problem in holography,” Phys. Rev. Lett. 98, 233901 (2007).
[Crossref]

Luo, W.

A. Greenbaum, W. Luo, T.-W. Su, Z. Göröcs, L. Xue, S. O. Isikman, A. F. Coskun, O. Mudanyali, and A. Ozcan, “Imaging without lenses: achievements and remaining challenges of wide-field on-chip microscopy,” Nat. Methods 9, 889 (2012).
[Crossref] [PubMed]

McLeod, E.

A. Ozcan and E. McLeod, “Lensless imaging and sensing,” Annu. Rev. Biomed. Eng. 18, 77–102 (2016).
[Crossref]

Menneteau, M.

C. Allier, S. Morel, R. Vincent, L. Ghenim, F. Navarro, M. Menneteau, T. Bordy, L. Hervé, O. Cioni, X. Gidrol, and et al., “Imaging of dense cell cultures by multiwavelength lens-free video microscopy,” Cytom. Part A 91, 433–442 (2017).
[Crossref]

Meucci, R.

Micó, V.

Morel, S.

C. Allier, S. Morel, R. Vincent, L. Ghenim, F. Navarro, M. Menneteau, T. Bordy, L. Hervé, O. Cioni, X. Gidrol, and et al., “Imaging of dense cell cultures by multiwavelength lens-free video microscopy,” Cytom. Part A 91, 433–442 (2017).
[Crossref]

Mudanyali, O.

A. Greenbaum, W. Luo, T.-W. Su, Z. Göröcs, L. Xue, S. O. Isikman, A. F. Coskun, O. Mudanyali, and A. Ozcan, “Imaging without lenses: achievements and remaining challenges of wide-field on-chip microscopy,” Nat. Methods 9, 889 (2012).
[Crossref] [PubMed]

Navarro, F.

C. Allier, S. Morel, R. Vincent, L. Ghenim, F. Navarro, M. Menneteau, T. Bordy, L. Hervé, O. Cioni, X. Gidrol, and et al., “Imaging of dense cell cultures by multiwavelength lens-free video microscopy,” Cytom. Part A 91, 433–442 (2017).
[Crossref]

Oxley, M.

L. Allen and M. Oxley, “Phase retrieval from series of images obtained by defocus variation,” Opt. Commun. 199, 65–75 (2001).
[Crossref]

Ozcan, A.

Y. Zhang, H. Wang, Y. Wu, M. Tamamitsu, and A. Ozcan, “Edge sparsity criterion for robust holographic autofocusing,” Opt. Lett. 42, 3824–3827 (2017).
[Crossref]

Y. Rivenson, Y. Wu, H. Wang, Y. Zhang, A. Feizi, and A. Ozcan, “Sparsity-based multi-height phase recovery in holographic microscopy,” Sci. Rep. 6, 37862 (2016).
[Crossref]

A. Ozcan and E. McLeod, “Lensless imaging and sensing,” Annu. Rev. Biomed. Eng. 18, 77–102 (2016).
[Crossref]

A. Greenbaum, W. Luo, T.-W. Su, Z. Göröcs, L. Xue, S. O. Isikman, A. F. Coskun, O. Mudanyali, and A. Ozcan, “Imaging without lenses: achievements and remaining challenges of wide-field on-chip microscopy,” Nat. Methods 9, 889 (2012).
[Crossref] [PubMed]

A. Greenbaum and A. Ozcan, “Maskless imaging of dense samples using pixel super-resolution based multi-height lensfree on-chip microscopy,” Opt. Express 20, 3129–3143 (2012).
[Crossref] [PubMed]

Picazo-Bueno, J. A.

Pierattini, G.

Rivenson, Y.

Y. Rivenson, Y. Wu, H. Wang, Y. Zhang, A. Feizi, and A. Ozcan, “Sparsity-based multi-height phase recovery in holographic microscopy,” Sci. Rep. 6, 37862 (2016).
[Crossref]

Sanz, M.

Stiefel, E.

M. R. Hestenes and E. Stiefel, Methods of conjugate gradients for solving linear systems, vol. 49 (NBSWashington, DC, 1952).

Su, T.-W.

A. Greenbaum, W. Luo, T.-W. Su, Z. Göröcs, L. Xue, S. O. Isikman, A. F. Coskun, O. Mudanyali, and A. Ozcan, “Imaging without lenses: achievements and remaining challenges of wide-field on-chip microscopy,” Nat. Methods 9, 889 (2012).
[Crossref] [PubMed]

Tamamitsu, M.

Vincent, R.

C. Allier, S. Morel, R. Vincent, L. Ghenim, F. Navarro, M. Menneteau, T. Bordy, L. Hervé, O. Cioni, X. Gidrol, and et al., “Imaging of dense cell cultures by multiwavelength lens-free video microscopy,” Cytom. Part A 91, 433–442 (2017).
[Crossref]

Wang, H.

Y. Zhang, H. Wang, Y. Wu, M. Tamamitsu, and A. Ozcan, “Edge sparsity criterion for robust holographic autofocusing,” Opt. Lett. 42, 3824–3827 (2017).
[Crossref]

Y. Rivenson, Y. Wu, H. Wang, Y. Zhang, A. Feizi, and A. Ozcan, “Sparsity-based multi-height phase recovery in holographic microscopy,” Sci. Rep. 6, 37862 (2016).
[Crossref]

Wu, Y.

Y. Zhang, H. Wang, Y. Wu, M. Tamamitsu, and A. Ozcan, “Edge sparsity criterion for robust holographic autofocusing,” Opt. Lett. 42, 3824–3827 (2017).
[Crossref]

Y. Rivenson, Y. Wu, H. Wang, Y. Zhang, A. Feizi, and A. Ozcan, “Sparsity-based multi-height phase recovery in holographic microscopy,” Sci. Rep. 6, 37862 (2016).
[Crossref]

Xue, L.

A. Greenbaum, W. Luo, T.-W. Su, Z. Göröcs, L. Xue, S. O. Isikman, A. F. Coskun, O. Mudanyali, and A. Ozcan, “Imaging without lenses: achievements and remaining challenges of wide-field on-chip microscopy,” Nat. Methods 9, 889 (2012).
[Crossref] [PubMed]

Zhang, Y.

Y. Zhang, H. Wang, Y. Wu, M. Tamamitsu, and A. Ozcan, “Edge sparsity criterion for robust holographic autofocusing,” Opt. Lett. 42, 3824–3827 (2017).
[Crossref]

Y. Rivenson, Y. Wu, H. Wang, Y. Zhang, A. Feizi, and A. Ozcan, “Sparsity-based multi-height phase recovery in holographic microscopy,” Sci. Rep. 6, 37862 (2016).
[Crossref]

Annu. Rev. Biomed. Eng. (1)

A. Ozcan and E. McLeod, “Lensless imaging and sensing,” Annu. Rev. Biomed. Eng. 18, 77–102 (2016).
[Crossref]

Appl. Opt. (2)

Cytom. Part A (1)

C. Allier, S. Morel, R. Vincent, L. Ghenim, F. Navarro, M. Menneteau, T. Bordy, L. Hervé, O. Cioni, X. Gidrol, and et al., “Imaging of dense cell cultures by multiwavelength lens-free video microscopy,” Cytom. Part A 91, 433–442 (2017).
[Crossref]

Nat. Methods (1)

A. Greenbaum, W. Luo, T.-W. Su, Z. Göröcs, L. Xue, S. O. Isikman, A. F. Coskun, O. Mudanyali, and A. Ozcan, “Imaging without lenses: achievements and remaining challenges of wide-field on-chip microscopy,” Nat. Methods 9, 889 (2012).
[Crossref] [PubMed]

Opt. Commun. (1)

L. Allen and M. Oxley, “Phase retrieval from series of images obtained by defocus variation,” Opt. Commun. 199, 65–75 (2001).
[Crossref]

Opt. Express (3)

Opt. Lett. (1)

Phys. Rev. Lett. (1)

T. Latychevskaia and H.-W. Fink, “Solution to the twin image problem in holography,” Phys. Rev. Lett. 98, 233901 (2007).
[Crossref]

Sci. Rep. (1)

Y. Rivenson, Y. Wu, H. Wang, Y. Zhang, A. Feizi, and A. Ozcan, “Sparsity-based multi-height phase recovery in holographic microscopy,” Sci. Rep. 6, 37862 (2016).
[Crossref]

Other (2)

J. W. Goodman, Introduction to Fourier Optics (Roberts and Company Publishers, 2005).

M. R. Hestenes and E. Stiefel, Methods of conjugate gradients for solving linear systems, vol. 49 (NBSWashington, DC, 1952).

Supplementary Material (1)

NameDescription
» Visualization 1       Phase images time-lapse of densily packed mammamial A549 cells. The original acquisition set consist of 1065 frames (1 frame per 5 minutes) of 3840x2748 images (pitch 1.67 µm) acquired with the Cytonote lensless tri-chromatique (RGB) microscope. The

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Figures (5)

Fig. 1
Fig. 1 Illustration showing that multispectral L1-norm is lower when high values of fields are colocalized. In the case of a), the high values are at various spatial positions whereas in b), the fields are colocalized. The L1-norm is lower for the second case as designed.
Fig. 2
Fig. 2 (a) Geometry of the system, (b) Picture of the Cytonote lens-free video microscope.
Fig. 3
Fig. 3 (a) Example of a full 3840 × 2748 pixels reconstruction (phase, i.e. mean angle of A0 over its 3 color-channels) of a A549 cells culture acquired on the system of Fig. 2(b). Zooms of the reconstructed phase from RGB channels measurements ((b) and (e)), from only red-channel measurements ((c) and (f)) and red-channel diffraction measurements ((d) and (g)). Images (b), (c) and (d) are 1000 × 1000 pixel zooms and images (e), (f) and (g) are 235 × 235 pixel zooms. This example is frame #465 of the entire reconstructed movie, which can be found in Visualization 1 of the supplementary material. The phase colorbar apply to phase subplots ((a), (b), (c), (e) and (f)).
Fig. 4
Fig. 4 Reconstruction of standard USAF 1951 phase target by using the MS-TV algorithm from a tri-chromatic acquisition. A gradual loss of contrast can be observed in group 7.
Fig. 5
Fig. 5 Reconstructions performed with the standard multispectral algorithms applied to the biological sample shown in section 4 and to the phase test target shown in Appendix B.

Equations (22)

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

A Z = A 0 * h Z
A Z λ ( r ) = d r A 0 λ ( r ) . h Z λ ( r r )
( φ Z ) = d r ε + λ ( | A 0 λ ( r ) x | + | A 0 λ ( r ) y | )
d r f ( r ) i j f i j
f x ( r i j ) k f i k , j . S x k
h ˜ Z λ ( μ ) = exp ( i π λ Z μ 2 )
φ Z ( unknown detector phase )
A Z = I Z . exp ( i . φ Z ) ( detector light field )
A 0 = A Z * h Z ( sample light field )
= d r ε + λ ( | A 0 λ ( r ) x | + | A 0 λ ( r ) y | ) ( criterion )
f ( a + h ) = f ( a ) + D a f ( h ) + o ( h )
f ( a + δ a ) f ( a ) = δ f ( δ a ) + o ( δ a )
δ = λ d r λ ( r ) . δ φ λ ( r )
δ = Re d r λ 1 e λ ( r ) ( A 0 λ ( r ) x δ A 0 λ ( r ) * x + A 0 λ ( r ) y δ A 0 λ ( r ) * y )
δ = Re d r λ ( x ( 1 e λ ( r ) A 0 λ ( r ) x ) + y ( 1 e λ ( r ) A 0 λ ( r ) y ) ) . δ A 0 λ ( r ) *
δ = + Re i d r λ ( x ( 1 e λ ( r ) A 0 λ ( r ) x ) + y ( 1 e λ ( r ) A 0 λ ( r ) y ) ) . ( ( A Z λ . δ φ Z ) * h Z λ ( r ) ) r *
δ = Im d r λ ( ( x ( 1 e λ ( r ) A 0 λ ( r ) x ) + y ( 1 e λ ( r ) A 0 λ ( r ) y ) ) * h Z λ ) . A Z λ ( r ) * . δ φ Z ( r )
λ ( r ) = Im ( ( ( x ( 1 e λ ( r ) A 0 λ ( r ) x ) + y ( 1 e λ ( r ) A 0 λ ( r ) y ) ) * h Z λ ) . A Z λ ( r ) * )
= d r 1 N λ λ | A 0 λ ( r ) A 0 ¯ ( r ) | 2
λ ( r ) = 2 Im ( ( A 0 ¯ * h Z λ ) . A Z λ ( r ) * )
φ ( A 0 ¯ * h Z λ ) = φ ( A Z λ ( r ) ) = φ Z λ ( r )
φ Z λ ( k ) ( r ) = φ ( A 0 ( k 1 ) ¯ * h Z λ )

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