Abstract

Due to incompleteness of input data inherent to Limited Angle Tomography (LAT), specific additional constraints are usually employed to suppress image artifacts. In this work we demonstrate a new two-stage regularization strategy, named Generalized Total Variation Iterative Constraint (GTVIC), dedicated to semi-piecewise-constant objects. It has been successfully applied as a supplementary module for two different reconstruction algorithms: an X-ray type solver and a diffraction-wise solver. Numerical tests performed on a detailed phantom of a biological cell under conical illumination pattern show significant reduction of axial blurring in the reconstructed refractive index distribution after GTVIC is added. Analogous results were obtained with experimental data.

© 2016 Optical Society of America

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References

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  1. T. E. Gureyev and K. A. Nugent, “Rapid quantitative phase imaging using the transport of intensity equation,” Opt. Commun. 133(1-6), 339–346 (1997).
    [Crossref]
  2. C. J. Mann, P. R. Bingham, V. C. Paquit, and K. W. Tobin, “Quantitative phase imaging by three-wavelength digital holography,” Opt. Express 16(13), 9753–9764 (2008).
    [Crossref] [PubMed]
  3. B. Rappaz, B. Breton, E. Shaffer, and G. Turcatti, “Digital holographic microscopy: a quantitative label-free microscopy technique for phenotypic screening,” Comb. Chem. High Throughput Screen. 17(1), 80–88 (2014).
    [Crossref] [PubMed]
  4. G. Popescu, “Quantitative phase imaging of nanoscale cell structure and dynamics,” Methods Cell Biol. 90, 87–115 (2008).
    [Crossref] [PubMed]
  5. H. Ding, Z. Wang, X. Liang, S. A. Boppart, K. Tangella, and G. Popescu, “Measuring the scattering parameters of tissues from quantitative phase imaging of thin slices,” Opt. Lett. 36(12), 2281–2283 (2011).
    [Crossref] [PubMed]
  6. K. Kim, H. Yoon, M. Diez-Silva, M. Dao, R. R. Dasari, and Y. Park, “High-resolution three-dimensional imaging of red blood cells parasitized by Plasmodium falciparum and in situ hemozoin crystals using optical diffraction tomography,” J. Biomed. Opt. 19(1), 011005 (2013).
    [Crossref] [PubMed]
  7. J. Kostencka, T. Kozacki, A. Kuś, M. Dudek, M. Kujawińska, and B. Kemper, “Holographic method for capillary induced aberration compensation for 3D tomographic measurements of living cells,” Proc. SPIE 8792, 879204 (2013).
    [Crossref]
  8. J. Kostencka, T. Kozacki, A. Kuś, and M. Kujawińska, “Accurate approach to capillary-supported optical diffraction tomography,” Opt. Express 23(6), 7908–7923 (2015).
    [Crossref] [PubMed]
  9. M. Kujawińska, W. Krauze, A. Kus, J. Kostencka, T. Kozacki, B. Kemper, and M. Dudek, “Problems and solutions in 3-D analysis of phase biological objects by optical diffraction tomography,” Int. J. Optomechatronics 8(4), 357–372 (2014).
    [Crossref]
  10. A. Kus, W. Krauze, and M. Kujawinska, “Active limited-angle tomographic phase microscope,” J. Biomed. Opt. 20(11), 111216 (2015).
    [Crossref] [PubMed]
  11. A. Kuś, W. Krauze, and M. Kujawińska, “Limited-angle, holographic tomography with optically controlled projection generation,” Proc. SPIE 9330, 933007 (2015).
    [Crossref]
  12. A. Kuś, W. Krauze, M. Kujawińska, and M. Filipiak, “Limited-angle hybrid diffraction tomography for biological samples,” Proc. SPIE 9132, 91320O (2014).
  13. E. Y. Sidky, C.-M. Kao, and X. Pan, “Accurate image reconstruction from few-views and limited-angle data in divergent-beam CT,” J. Opt. Soc. Am. 25, 1772–1782 (2009).
  14. Y. Cotte, F. Toy, P. Jourdain, N. Pavillon, D. Boss, P. Magistretti, P. Marquet, and C. Depeursinge, “Marker-free phase nanoscopy,” Nat. Photonics 7(2), 113–117 (2013).
    [Crossref]
  15. S. Vertu, I. Yamada, J.-J. Delaunay, and O. Haeberlé, “Tomographic observation of transparent objects under coherent illumination and reconstruction by filtered backprojection and Fourier diffraction theorem,” Proc. SPIE 6861, 686103 (2008).
    [Crossref]
  16. T. Sato, S. J. Norton, M. Linzer, O. Ikeda, and M. Hirama, “Tomographic image reconstruction from limited projections using iterative revisions in image and transform spaces,” Appl. Opt. 20(3), 395–399 (1981).
    [Crossref] [PubMed]
  17. D. Wang, H. Qiao, X. Song, Y. Fan, and D. Li, “Fluorescence molecular tomography using a two-step three-dimensional shape-based reconstruction with graphics processing unit acceleration,” Appl. Opt. 51(36), 8731–8744 (2012).
    [Crossref] [PubMed]
  18. T. Humphries, A. Saad, A. Celler, G. Hamarneh, T. Möller, and M. Trummer, “Segmentation-based regularization of dynamic SPECT reconstruction,” in Nuclear Science Symposium Conference Record, (IEEE, 2009), 2849–2852.
  19. D. Hyde, E. L. Miller, D. H. Brooks, and V. Ntziachristos, “Data specific spatially varying regularization for multimodal fluorescence molecular tomography,” IEEE Trans. Med. Imaging 29(2), 365–374 (2010).
    [Crossref] [PubMed]
  20. X. Jin, L. Li, Z. Chen, L. Zhang, and Y. Xing, “Anisotropic total variation for limited-angle CT reconstruction,” in Nuclear Science Symposium Conference Record, (IEEE, 2010), 2232–2238.
    [Crossref]
  21. W. Krauze, A. Kuś, and M. Kujawinska, “Limited-angle hybrid optical diffraction tomography system with total-variation-minimization-based reconstruction,” Opt. Eng. 54(5), 054104 (2015).
    [Crossref]
  22. W. Krauze, P. Makowski, and M. Kujawińska, “Total variation iterative constraint algorithm for limited-angle tomographic reconstruction of non-piecewise-constant structures,” Proc. SPIE 9526, 95260Y (2015).
  23. A. Chambolle and T. Pock, “A first-order primal-dual algorithm for convex problems with applications to imaging,” J. Math. Imaging Vis. 40(1), 120–145 (2011).
    [Crossref]
  24. N. Otsu, “A threshold selection method from gray-level histograms,” Automatica 11, 23–27 (1975).
  25. A. H. Andersen and A. C. Kak, “Simultaneous algebraic reconstruction technique (SART): a superior implementation of the art algorithm,” Ultrason. Imaging 6(1), 81–94 (1984).
    [Crossref] [PubMed]
  26. A. C. Kak and M. Slaney, Principles of Computerized Tomographic Imaging (Society of Industrial and Applied Mathematics, 2001).
  27. W. van Aarle, W. J. Palenstijn, J. De Beenhouwer, T. Altantzis, S. Bals, K. J. Batenburg, and J. Sijbers, “The ASTRA Toolbox: A platform for advanced algorithm development in electron tomography,” Ultramicroscopy 157, 35–47 (2015).
    [Crossref] [PubMed]
  28. Y. Sung, W. Choi, C. Fang-Yen, K. Badizadegan, R. R. Dasari, and M. S. Feld, “Optical diffraction tomography for high resolution live cell imaging,” Opt. Express 17(1), 266–277 (2009).
    [Crossref] [PubMed]
  29. K. Kim, K. S. Kim, H. Park, J. C. Ye, and Y. Park, “Real-time visualization of 3-D dynamic microscopic objects using optical diffraction tomography,” Opt. Express 21(26), 32269–32278 (2013).
    [Crossref] [PubMed]
  30. B. P. Medoff, W. R. Brody, M. Nassi, and A. Macovski, “Iterative convolution backprojection algorithms for image reconstruction from limited data,” J. Opt. Soc. Am. 73(11), 1493–1500 (1983).
    [Crossref]
  31. Y. Kim, H. Shim, K. Kim, H. Park, S. Jang, and Y. Park, “Profiling individual human red blood cells using common-path diffraction optical tomography,” Sci. Rep. 4, 6659 (2014).
    [Crossref] [PubMed]
  32. B. Kemper, S. Kosmeier, P. Langehanenberg, G. von Bally, I. Bredebusch, W. Domschke, and J. Schnekenburger, “Integral refractive index determination of living suspension cells by multifocus digital holographic phase contrast microscopy,” J. Biomed. Opt. 12(5), 054009 (2007).
    [Crossref] [PubMed]
  33. B. Kemper, L. Schmidt, S. Przibilla, C. Rommel, A. Vollmer, S. Ketelhut, J. Schnekenburger, and G. von Bally, “Influence of sample preparation and identification of subcelluar structures in quantitative holographic phase contrast microscopy,” Proc. SPIE 7715, 771504 (2010).
    [Crossref]
  34. C. Fang-Yen, W. Choi, Y. Sung, C. J. Holbrow, R. R. Dasari, and M. S. Feld, “Video-rate tomographic phase microscopy,” J. Biomed. Opt. 16(1), 011005 (2011).
    [Crossref] [PubMed]
  35. Z. Wang and A. C. Bovik, “A universal image quality index,” IEEE Signal Process. Lett. 9(3), 81–84 (2002).
    [Crossref]
  36. P. C. Hansen, Discrete Inverse Problems: Insight and Algorithms (Society of Industrial and Applied Mathematics, 2010).

2015 (6)

J. Kostencka, T. Kozacki, A. Kuś, and M. Kujawińska, “Accurate approach to capillary-supported optical diffraction tomography,” Opt. Express 23(6), 7908–7923 (2015).
[Crossref] [PubMed]

A. Kus, W. Krauze, and M. Kujawinska, “Active limited-angle tomographic phase microscope,” J. Biomed. Opt. 20(11), 111216 (2015).
[Crossref] [PubMed]

A. Kuś, W. Krauze, and M. Kujawińska, “Limited-angle, holographic tomography with optically controlled projection generation,” Proc. SPIE 9330, 933007 (2015).
[Crossref]

W. Krauze, A. Kuś, and M. Kujawinska, “Limited-angle hybrid optical diffraction tomography system with total-variation-minimization-based reconstruction,” Opt. Eng. 54(5), 054104 (2015).
[Crossref]

W. Krauze, P. Makowski, and M. Kujawińska, “Total variation iterative constraint algorithm for limited-angle tomographic reconstruction of non-piecewise-constant structures,” Proc. SPIE 9526, 95260Y (2015).

W. van Aarle, W. J. Palenstijn, J. De Beenhouwer, T. Altantzis, S. Bals, K. J. Batenburg, and J. Sijbers, “The ASTRA Toolbox: A platform for advanced algorithm development in electron tomography,” Ultramicroscopy 157, 35–47 (2015).
[Crossref] [PubMed]

2014 (4)

Y. Kim, H. Shim, K. Kim, H. Park, S. Jang, and Y. Park, “Profiling individual human red blood cells using common-path diffraction optical tomography,” Sci. Rep. 4, 6659 (2014).
[Crossref] [PubMed]

A. Kuś, W. Krauze, M. Kujawińska, and M. Filipiak, “Limited-angle hybrid diffraction tomography for biological samples,” Proc. SPIE 9132, 91320O (2014).

M. Kujawińska, W. Krauze, A. Kus, J. Kostencka, T. Kozacki, B. Kemper, and M. Dudek, “Problems and solutions in 3-D analysis of phase biological objects by optical diffraction tomography,” Int. J. Optomechatronics 8(4), 357–372 (2014).
[Crossref]

B. Rappaz, B. Breton, E. Shaffer, and G. Turcatti, “Digital holographic microscopy: a quantitative label-free microscopy technique for phenotypic screening,” Comb. Chem. High Throughput Screen. 17(1), 80–88 (2014).
[Crossref] [PubMed]

2013 (4)

K. Kim, H. Yoon, M. Diez-Silva, M. Dao, R. R. Dasari, and Y. Park, “High-resolution three-dimensional imaging of red blood cells parasitized by Plasmodium falciparum and in situ hemozoin crystals using optical diffraction tomography,” J. Biomed. Opt. 19(1), 011005 (2013).
[Crossref] [PubMed]

J. Kostencka, T. Kozacki, A. Kuś, M. Dudek, M. Kujawińska, and B. Kemper, “Holographic method for capillary induced aberration compensation for 3D tomographic measurements of living cells,” Proc. SPIE 8792, 879204 (2013).
[Crossref]

Y. Cotte, F. Toy, P. Jourdain, N. Pavillon, D. Boss, P. Magistretti, P. Marquet, and C. Depeursinge, “Marker-free phase nanoscopy,” Nat. Photonics 7(2), 113–117 (2013).
[Crossref]

K. Kim, K. S. Kim, H. Park, J. C. Ye, and Y. Park, “Real-time visualization of 3-D dynamic microscopic objects using optical diffraction tomography,” Opt. Express 21(26), 32269–32278 (2013).
[Crossref] [PubMed]

2012 (1)

2011 (3)

C. Fang-Yen, W. Choi, Y. Sung, C. J. Holbrow, R. R. Dasari, and M. S. Feld, “Video-rate tomographic phase microscopy,” J. Biomed. Opt. 16(1), 011005 (2011).
[Crossref] [PubMed]

H. Ding, Z. Wang, X. Liang, S. A. Boppart, K. Tangella, and G. Popescu, “Measuring the scattering parameters of tissues from quantitative phase imaging of thin slices,” Opt. Lett. 36(12), 2281–2283 (2011).
[Crossref] [PubMed]

A. Chambolle and T. Pock, “A first-order primal-dual algorithm for convex problems with applications to imaging,” J. Math. Imaging Vis. 40(1), 120–145 (2011).
[Crossref]

2010 (2)

B. Kemper, L. Schmidt, S. Przibilla, C. Rommel, A. Vollmer, S. Ketelhut, J. Schnekenburger, and G. von Bally, “Influence of sample preparation and identification of subcelluar structures in quantitative holographic phase contrast microscopy,” Proc. SPIE 7715, 771504 (2010).
[Crossref]

D. Hyde, E. L. Miller, D. H. Brooks, and V. Ntziachristos, “Data specific spatially varying regularization for multimodal fluorescence molecular tomography,” IEEE Trans. Med. Imaging 29(2), 365–374 (2010).
[Crossref] [PubMed]

2009 (2)

E. Y. Sidky, C.-M. Kao, and X. Pan, “Accurate image reconstruction from few-views and limited-angle data in divergent-beam CT,” J. Opt. Soc. Am. 25, 1772–1782 (2009).

Y. Sung, W. Choi, C. Fang-Yen, K. Badizadegan, R. R. Dasari, and M. S. Feld, “Optical diffraction tomography for high resolution live cell imaging,” Opt. Express 17(1), 266–277 (2009).
[Crossref] [PubMed]

2008 (3)

S. Vertu, I. Yamada, J.-J. Delaunay, and O. Haeberlé, “Tomographic observation of transparent objects under coherent illumination and reconstruction by filtered backprojection and Fourier diffraction theorem,” Proc. SPIE 6861, 686103 (2008).
[Crossref]

G. Popescu, “Quantitative phase imaging of nanoscale cell structure and dynamics,” Methods Cell Biol. 90, 87–115 (2008).
[Crossref] [PubMed]

C. J. Mann, P. R. Bingham, V. C. Paquit, and K. W. Tobin, “Quantitative phase imaging by three-wavelength digital holography,” Opt. Express 16(13), 9753–9764 (2008).
[Crossref] [PubMed]

2007 (1)

B. Kemper, S. Kosmeier, P. Langehanenberg, G. von Bally, I. Bredebusch, W. Domschke, and J. Schnekenburger, “Integral refractive index determination of living suspension cells by multifocus digital holographic phase contrast microscopy,” J. Biomed. Opt. 12(5), 054009 (2007).
[Crossref] [PubMed]

2002 (1)

Z. Wang and A. C. Bovik, “A universal image quality index,” IEEE Signal Process. Lett. 9(3), 81–84 (2002).
[Crossref]

1997 (1)

T. E. Gureyev and K. A. Nugent, “Rapid quantitative phase imaging using the transport of intensity equation,” Opt. Commun. 133(1-6), 339–346 (1997).
[Crossref]

1984 (1)

A. H. Andersen and A. C. Kak, “Simultaneous algebraic reconstruction technique (SART): a superior implementation of the art algorithm,” Ultrason. Imaging 6(1), 81–94 (1984).
[Crossref] [PubMed]

1983 (1)

1981 (1)

1975 (1)

N. Otsu, “A threshold selection method from gray-level histograms,” Automatica 11, 23–27 (1975).

Altantzis, T.

W. van Aarle, W. J. Palenstijn, J. De Beenhouwer, T. Altantzis, S. Bals, K. J. Batenburg, and J. Sijbers, “The ASTRA Toolbox: A platform for advanced algorithm development in electron tomography,” Ultramicroscopy 157, 35–47 (2015).
[Crossref] [PubMed]

Andersen, A. H.

A. H. Andersen and A. C. Kak, “Simultaneous algebraic reconstruction technique (SART): a superior implementation of the art algorithm,” Ultrason. Imaging 6(1), 81–94 (1984).
[Crossref] [PubMed]

Badizadegan, K.

Bals, S.

W. van Aarle, W. J. Palenstijn, J. De Beenhouwer, T. Altantzis, S. Bals, K. J. Batenburg, and J. Sijbers, “The ASTRA Toolbox: A platform for advanced algorithm development in electron tomography,” Ultramicroscopy 157, 35–47 (2015).
[Crossref] [PubMed]

Batenburg, K. J.

W. van Aarle, W. J. Palenstijn, J. De Beenhouwer, T. Altantzis, S. Bals, K. J. Batenburg, and J. Sijbers, “The ASTRA Toolbox: A platform for advanced algorithm development in electron tomography,” Ultramicroscopy 157, 35–47 (2015).
[Crossref] [PubMed]

Bingham, P. R.

Boppart, S. A.

Boss, D.

Y. Cotte, F. Toy, P. Jourdain, N. Pavillon, D. Boss, P. Magistretti, P. Marquet, and C. Depeursinge, “Marker-free phase nanoscopy,” Nat. Photonics 7(2), 113–117 (2013).
[Crossref]

Bovik, A. C.

Z. Wang and A. C. Bovik, “A universal image quality index,” IEEE Signal Process. Lett. 9(3), 81–84 (2002).
[Crossref]

Bredebusch, I.

B. Kemper, S. Kosmeier, P. Langehanenberg, G. von Bally, I. Bredebusch, W. Domschke, and J. Schnekenburger, “Integral refractive index determination of living suspension cells by multifocus digital holographic phase contrast microscopy,” J. Biomed. Opt. 12(5), 054009 (2007).
[Crossref] [PubMed]

Breton, B.

B. Rappaz, B. Breton, E. Shaffer, and G. Turcatti, “Digital holographic microscopy: a quantitative label-free microscopy technique for phenotypic screening,” Comb. Chem. High Throughput Screen. 17(1), 80–88 (2014).
[Crossref] [PubMed]

Brody, W. R.

Brooks, D. H.

D. Hyde, E. L. Miller, D. H. Brooks, and V. Ntziachristos, “Data specific spatially varying regularization for multimodal fluorescence molecular tomography,” IEEE Trans. Med. Imaging 29(2), 365–374 (2010).
[Crossref] [PubMed]

Celler, A.

T. Humphries, A. Saad, A. Celler, G. Hamarneh, T. Möller, and M. Trummer, “Segmentation-based regularization of dynamic SPECT reconstruction,” in Nuclear Science Symposium Conference Record, (IEEE, 2009), 2849–2852.

Chambolle, A.

A. Chambolle and T. Pock, “A first-order primal-dual algorithm for convex problems with applications to imaging,” J. Math. Imaging Vis. 40(1), 120–145 (2011).
[Crossref]

Chen, Z.

X. Jin, L. Li, Z. Chen, L. Zhang, and Y. Xing, “Anisotropic total variation for limited-angle CT reconstruction,” in Nuclear Science Symposium Conference Record, (IEEE, 2010), 2232–2238.
[Crossref]

Choi, W.

C. Fang-Yen, W. Choi, Y. Sung, C. J. Holbrow, R. R. Dasari, and M. S. Feld, “Video-rate tomographic phase microscopy,” J. Biomed. Opt. 16(1), 011005 (2011).
[Crossref] [PubMed]

Y. Sung, W. Choi, C. Fang-Yen, K. Badizadegan, R. R. Dasari, and M. S. Feld, “Optical diffraction tomography for high resolution live cell imaging,” Opt. Express 17(1), 266–277 (2009).
[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,” Nat. Photonics 7(2), 113–117 (2013).
[Crossref]

Dao, M.

K. Kim, H. Yoon, M. Diez-Silva, M. Dao, R. R. Dasari, and Y. Park, “High-resolution three-dimensional imaging of red blood cells parasitized by Plasmodium falciparum and in situ hemozoin crystals using optical diffraction tomography,” J. Biomed. Opt. 19(1), 011005 (2013).
[Crossref] [PubMed]

Dasari, R. R.

K. Kim, H. Yoon, M. Diez-Silva, M. Dao, R. R. Dasari, and Y. Park, “High-resolution three-dimensional imaging of red blood cells parasitized by Plasmodium falciparum and in situ hemozoin crystals using optical diffraction tomography,” J. Biomed. Opt. 19(1), 011005 (2013).
[Crossref] [PubMed]

C. Fang-Yen, W. Choi, Y. Sung, C. J. Holbrow, R. R. Dasari, and M. S. Feld, “Video-rate tomographic phase microscopy,” J. Biomed. Opt. 16(1), 011005 (2011).
[Crossref] [PubMed]

Y. Sung, W. Choi, C. Fang-Yen, K. Badizadegan, R. R. Dasari, and M. S. Feld, “Optical diffraction tomography for high resolution live cell imaging,” Opt. Express 17(1), 266–277 (2009).
[Crossref] [PubMed]

De Beenhouwer, J.

W. van Aarle, W. J. Palenstijn, J. De Beenhouwer, T. Altantzis, S. Bals, K. J. Batenburg, and J. Sijbers, “The ASTRA Toolbox: A platform for advanced algorithm development in electron tomography,” Ultramicroscopy 157, 35–47 (2015).
[Crossref] [PubMed]

Delaunay, J.-J.

S. Vertu, I. Yamada, J.-J. Delaunay, and O. Haeberlé, “Tomographic observation of transparent objects under coherent illumination and reconstruction by filtered backprojection and Fourier diffraction theorem,” Proc. SPIE 6861, 686103 (2008).
[Crossref]

Depeursinge, C.

Y. Cotte, F. Toy, P. Jourdain, N. Pavillon, D. Boss, P. Magistretti, P. Marquet, and C. Depeursinge, “Marker-free phase nanoscopy,” Nat. Photonics 7(2), 113–117 (2013).
[Crossref]

Diez-Silva, M.

K. Kim, H. Yoon, M. Diez-Silva, M. Dao, R. R. Dasari, and Y. Park, “High-resolution three-dimensional imaging of red blood cells parasitized by Plasmodium falciparum and in situ hemozoin crystals using optical diffraction tomography,” J. Biomed. Opt. 19(1), 011005 (2013).
[Crossref] [PubMed]

Ding, H.

Domschke, W.

B. Kemper, S. Kosmeier, P. Langehanenberg, G. von Bally, I. Bredebusch, W. Domschke, and J. Schnekenburger, “Integral refractive index determination of living suspension cells by multifocus digital holographic phase contrast microscopy,” J. Biomed. Opt. 12(5), 054009 (2007).
[Crossref] [PubMed]

Dudek, M.

M. Kujawińska, W. Krauze, A. Kus, J. Kostencka, T. Kozacki, B. Kemper, and M. Dudek, “Problems and solutions in 3-D analysis of phase biological objects by optical diffraction tomography,” Int. J. Optomechatronics 8(4), 357–372 (2014).
[Crossref]

J. Kostencka, T. Kozacki, A. Kuś, M. Dudek, M. Kujawińska, and B. Kemper, “Holographic method for capillary induced aberration compensation for 3D tomographic measurements of living cells,” Proc. SPIE 8792, 879204 (2013).
[Crossref]

Fan, Y.

Fang-Yen, C.

C. Fang-Yen, W. Choi, Y. Sung, C. J. Holbrow, R. R. Dasari, and M. S. Feld, “Video-rate tomographic phase microscopy,” J. Biomed. Opt. 16(1), 011005 (2011).
[Crossref] [PubMed]

Y. Sung, W. Choi, C. Fang-Yen, K. Badizadegan, R. R. Dasari, and M. S. Feld, “Optical diffraction tomography for high resolution live cell imaging,” Opt. Express 17(1), 266–277 (2009).
[Crossref] [PubMed]

Feld, M. S.

C. Fang-Yen, W. Choi, Y. Sung, C. J. Holbrow, R. R. Dasari, and M. S. Feld, “Video-rate tomographic phase microscopy,” J. Biomed. Opt. 16(1), 011005 (2011).
[Crossref] [PubMed]

Y. Sung, W. Choi, C. Fang-Yen, K. Badizadegan, R. R. Dasari, and M. S. Feld, “Optical diffraction tomography for high resolution live cell imaging,” Opt. Express 17(1), 266–277 (2009).
[Crossref] [PubMed]

Filipiak, M.

A. Kuś, W. Krauze, M. Kujawińska, and M. Filipiak, “Limited-angle hybrid diffraction tomography for biological samples,” Proc. SPIE 9132, 91320O (2014).

Gureyev, T. E.

T. E. Gureyev and K. A. Nugent, “Rapid quantitative phase imaging using the transport of intensity equation,” Opt. Commun. 133(1-6), 339–346 (1997).
[Crossref]

Haeberlé, O.

S. Vertu, I. Yamada, J.-J. Delaunay, and O. Haeberlé, “Tomographic observation of transparent objects under coherent illumination and reconstruction by filtered backprojection and Fourier diffraction theorem,” Proc. SPIE 6861, 686103 (2008).
[Crossref]

Hamarneh, G.

T. Humphries, A. Saad, A. Celler, G. Hamarneh, T. Möller, and M. Trummer, “Segmentation-based regularization of dynamic SPECT reconstruction,” in Nuclear Science Symposium Conference Record, (IEEE, 2009), 2849–2852.

Hirama, M.

Holbrow, C. J.

C. Fang-Yen, W. Choi, Y. Sung, C. J. Holbrow, R. R. Dasari, and M. S. Feld, “Video-rate tomographic phase microscopy,” J. Biomed. Opt. 16(1), 011005 (2011).
[Crossref] [PubMed]

Humphries, T.

T. Humphries, A. Saad, A. Celler, G. Hamarneh, T. Möller, and M. Trummer, “Segmentation-based regularization of dynamic SPECT reconstruction,” in Nuclear Science Symposium Conference Record, (IEEE, 2009), 2849–2852.

Hyde, D.

D. Hyde, E. L. Miller, D. H. Brooks, and V. Ntziachristos, “Data specific spatially varying regularization for multimodal fluorescence molecular tomography,” IEEE Trans. Med. Imaging 29(2), 365–374 (2010).
[Crossref] [PubMed]

Ikeda, O.

Jang, S.

Y. Kim, H. Shim, K. Kim, H. Park, S. Jang, and Y. Park, “Profiling individual human red blood cells using common-path diffraction optical tomography,” Sci. Rep. 4, 6659 (2014).
[Crossref] [PubMed]

Jin, X.

X. Jin, L. Li, Z. Chen, L. Zhang, and Y. Xing, “Anisotropic total variation for limited-angle CT reconstruction,” in Nuclear Science Symposium Conference Record, (IEEE, 2010), 2232–2238.
[Crossref]

Jourdain, P.

Y. Cotte, F. Toy, P. Jourdain, N. Pavillon, D. Boss, P. Magistretti, P. Marquet, and C. Depeursinge, “Marker-free phase nanoscopy,” Nat. Photonics 7(2), 113–117 (2013).
[Crossref]

Kak, A. C.

A. H. Andersen and A. C. Kak, “Simultaneous algebraic reconstruction technique (SART): a superior implementation of the art algorithm,” Ultrason. Imaging 6(1), 81–94 (1984).
[Crossref] [PubMed]

Kao, C.-M.

E. Y. Sidky, C.-M. Kao, and X. Pan, “Accurate image reconstruction from few-views and limited-angle data in divergent-beam CT,” J. Opt. Soc. Am. 25, 1772–1782 (2009).

Kemper, B.

M. Kujawińska, W. Krauze, A. Kus, J. Kostencka, T. Kozacki, B. Kemper, and M. Dudek, “Problems and solutions in 3-D analysis of phase biological objects by optical diffraction tomography,” Int. J. Optomechatronics 8(4), 357–372 (2014).
[Crossref]

J. Kostencka, T. Kozacki, A. Kuś, M. Dudek, M. Kujawińska, and B. Kemper, “Holographic method for capillary induced aberration compensation for 3D tomographic measurements of living cells,” Proc. SPIE 8792, 879204 (2013).
[Crossref]

B. Kemper, L. Schmidt, S. Przibilla, C. Rommel, A. Vollmer, S. Ketelhut, J. Schnekenburger, and G. von Bally, “Influence of sample preparation and identification of subcelluar structures in quantitative holographic phase contrast microscopy,” Proc. SPIE 7715, 771504 (2010).
[Crossref]

B. Kemper, S. Kosmeier, P. Langehanenberg, G. von Bally, I. Bredebusch, W. Domschke, and J. Schnekenburger, “Integral refractive index determination of living suspension cells by multifocus digital holographic phase contrast microscopy,” J. Biomed. Opt. 12(5), 054009 (2007).
[Crossref] [PubMed]

Ketelhut, S.

B. Kemper, L. Schmidt, S. Przibilla, C. Rommel, A. Vollmer, S. Ketelhut, J. Schnekenburger, and G. von Bally, “Influence of sample preparation and identification of subcelluar structures in quantitative holographic phase contrast microscopy,” Proc. SPIE 7715, 771504 (2010).
[Crossref]

Kim, K.

Y. Kim, H. Shim, K. Kim, H. Park, S. Jang, and Y. Park, “Profiling individual human red blood cells using common-path diffraction optical tomography,” Sci. Rep. 4, 6659 (2014).
[Crossref] [PubMed]

K. Kim, H. Yoon, M. Diez-Silva, M. Dao, R. R. Dasari, and Y. Park, “High-resolution three-dimensional imaging of red blood cells parasitized by Plasmodium falciparum and in situ hemozoin crystals using optical diffraction tomography,” J. Biomed. Opt. 19(1), 011005 (2013).
[Crossref] [PubMed]

K. Kim, K. S. Kim, H. Park, J. C. Ye, and Y. Park, “Real-time visualization of 3-D dynamic microscopic objects using optical diffraction tomography,” Opt. Express 21(26), 32269–32278 (2013).
[Crossref] [PubMed]

Kim, K. S.

Kim, Y.

Y. Kim, H. Shim, K. Kim, H. Park, S. Jang, and Y. Park, “Profiling individual human red blood cells using common-path diffraction optical tomography,” Sci. Rep. 4, 6659 (2014).
[Crossref] [PubMed]

Kosmeier, S.

B. Kemper, S. Kosmeier, P. Langehanenberg, G. von Bally, I. Bredebusch, W. Domschke, and J. Schnekenburger, “Integral refractive index determination of living suspension cells by multifocus digital holographic phase contrast microscopy,” J. Biomed. Opt. 12(5), 054009 (2007).
[Crossref] [PubMed]

Kostencka, J.

J. Kostencka, T. Kozacki, A. Kuś, and M. Kujawińska, “Accurate approach to capillary-supported optical diffraction tomography,” Opt. Express 23(6), 7908–7923 (2015).
[Crossref] [PubMed]

M. Kujawińska, W. Krauze, A. Kus, J. Kostencka, T. Kozacki, B. Kemper, and M. Dudek, “Problems and solutions in 3-D analysis of phase biological objects by optical diffraction tomography,” Int. J. Optomechatronics 8(4), 357–372 (2014).
[Crossref]

J. Kostencka, T. Kozacki, A. Kuś, M. Dudek, M. Kujawińska, and B. Kemper, “Holographic method for capillary induced aberration compensation for 3D tomographic measurements of living cells,” Proc. SPIE 8792, 879204 (2013).
[Crossref]

Kozacki, T.

J. Kostencka, T. Kozacki, A. Kuś, and M. Kujawińska, “Accurate approach to capillary-supported optical diffraction tomography,” Opt. Express 23(6), 7908–7923 (2015).
[Crossref] [PubMed]

M. Kujawińska, W. Krauze, A. Kus, J. Kostencka, T. Kozacki, B. Kemper, and M. Dudek, “Problems and solutions in 3-D analysis of phase biological objects by optical diffraction tomography,” Int. J. Optomechatronics 8(4), 357–372 (2014).
[Crossref]

J. Kostencka, T. Kozacki, A. Kuś, M. Dudek, M. Kujawińska, and B. Kemper, “Holographic method for capillary induced aberration compensation for 3D tomographic measurements of living cells,” Proc. SPIE 8792, 879204 (2013).
[Crossref]

Krauze, W.

A. Kus, W. Krauze, and M. Kujawinska, “Active limited-angle tomographic phase microscope,” J. Biomed. Opt. 20(11), 111216 (2015).
[Crossref] [PubMed]

A. Kuś, W. Krauze, and M. Kujawińska, “Limited-angle, holographic tomography with optically controlled projection generation,” Proc. SPIE 9330, 933007 (2015).
[Crossref]

W. Krauze, A. Kuś, and M. Kujawinska, “Limited-angle hybrid optical diffraction tomography system with total-variation-minimization-based reconstruction,” Opt. Eng. 54(5), 054104 (2015).
[Crossref]

W. Krauze, P. Makowski, and M. Kujawińska, “Total variation iterative constraint algorithm for limited-angle tomographic reconstruction of non-piecewise-constant structures,” Proc. SPIE 9526, 95260Y (2015).

A. Kuś, W. Krauze, M. Kujawińska, and M. Filipiak, “Limited-angle hybrid diffraction tomography for biological samples,” Proc. SPIE 9132, 91320O (2014).

M. Kujawińska, W. Krauze, A. Kus, J. Kostencka, T. Kozacki, B. Kemper, and M. Dudek, “Problems and solutions in 3-D analysis of phase biological objects by optical diffraction tomography,” Int. J. Optomechatronics 8(4), 357–372 (2014).
[Crossref]

Kujawinska, M.

A. Kuś, W. Krauze, and M. Kujawińska, “Limited-angle, holographic tomography with optically controlled projection generation,” Proc. SPIE 9330, 933007 (2015).
[Crossref]

A. Kus, W. Krauze, and M. Kujawinska, “Active limited-angle tomographic phase microscope,” J. Biomed. Opt. 20(11), 111216 (2015).
[Crossref] [PubMed]

W. Krauze, A. Kuś, and M. Kujawinska, “Limited-angle hybrid optical diffraction tomography system with total-variation-minimization-based reconstruction,” Opt. Eng. 54(5), 054104 (2015).
[Crossref]

W. Krauze, P. Makowski, and M. Kujawińska, “Total variation iterative constraint algorithm for limited-angle tomographic reconstruction of non-piecewise-constant structures,” Proc. SPIE 9526, 95260Y (2015).

J. Kostencka, T. Kozacki, A. Kuś, and M. Kujawińska, “Accurate approach to capillary-supported optical diffraction tomography,” Opt. Express 23(6), 7908–7923 (2015).
[Crossref] [PubMed]

A. Kuś, W. Krauze, M. Kujawińska, and M. Filipiak, “Limited-angle hybrid diffraction tomography for biological samples,” Proc. SPIE 9132, 91320O (2014).

M. Kujawińska, W. Krauze, A. Kus, J. Kostencka, T. Kozacki, B. Kemper, and M. Dudek, “Problems and solutions in 3-D analysis of phase biological objects by optical diffraction tomography,” Int. J. Optomechatronics 8(4), 357–372 (2014).
[Crossref]

J. Kostencka, T. Kozacki, A. Kuś, M. Dudek, M. Kujawińska, and B. Kemper, “Holographic method for capillary induced aberration compensation for 3D tomographic measurements of living cells,” Proc. SPIE 8792, 879204 (2013).
[Crossref]

Kus, A.

A. Kus, W. Krauze, and M. Kujawinska, “Active limited-angle tomographic phase microscope,” J. Biomed. Opt. 20(11), 111216 (2015).
[Crossref] [PubMed]

A. Kuś, W. Krauze, and M. Kujawińska, “Limited-angle, holographic tomography with optically controlled projection generation,” Proc. SPIE 9330, 933007 (2015).
[Crossref]

W. Krauze, A. Kuś, and M. Kujawinska, “Limited-angle hybrid optical diffraction tomography system with total-variation-minimization-based reconstruction,” Opt. Eng. 54(5), 054104 (2015).
[Crossref]

J. Kostencka, T. Kozacki, A. Kuś, and M. Kujawińska, “Accurate approach to capillary-supported optical diffraction tomography,” Opt. Express 23(6), 7908–7923 (2015).
[Crossref] [PubMed]

A. Kuś, W. Krauze, M. Kujawińska, and M. Filipiak, “Limited-angle hybrid diffraction tomography for biological samples,” Proc. SPIE 9132, 91320O (2014).

M. Kujawińska, W. Krauze, A. Kus, J. Kostencka, T. Kozacki, B. Kemper, and M. Dudek, “Problems and solutions in 3-D analysis of phase biological objects by optical diffraction tomography,” Int. J. Optomechatronics 8(4), 357–372 (2014).
[Crossref]

J. Kostencka, T. Kozacki, A. Kuś, M. Dudek, M. Kujawińska, and B. Kemper, “Holographic method for capillary induced aberration compensation for 3D tomographic measurements of living cells,” Proc. SPIE 8792, 879204 (2013).
[Crossref]

Langehanenberg, P.

B. Kemper, S. Kosmeier, P. Langehanenberg, G. von Bally, I. Bredebusch, W. Domschke, and J. Schnekenburger, “Integral refractive index determination of living suspension cells by multifocus digital holographic phase contrast microscopy,” J. Biomed. Opt. 12(5), 054009 (2007).
[Crossref] [PubMed]

Li, D.

Li, L.

X. Jin, L. Li, Z. Chen, L. Zhang, and Y. Xing, “Anisotropic total variation for limited-angle CT reconstruction,” in Nuclear Science Symposium Conference Record, (IEEE, 2010), 2232–2238.
[Crossref]

Liang, X.

Linzer, M.

Macovski, A.

Magistretti, P.

Y. Cotte, F. Toy, P. Jourdain, N. Pavillon, D. Boss, P. Magistretti, P. Marquet, and C. Depeursinge, “Marker-free phase nanoscopy,” Nat. Photonics 7(2), 113–117 (2013).
[Crossref]

Makowski, P.

W. Krauze, P. Makowski, and M. Kujawińska, “Total variation iterative constraint algorithm for limited-angle tomographic reconstruction of non-piecewise-constant structures,” Proc. SPIE 9526, 95260Y (2015).

Mann, C. J.

Marquet, P.

Y. Cotte, F. Toy, P. Jourdain, N. Pavillon, D. Boss, P. Magistretti, P. Marquet, and C. Depeursinge, “Marker-free phase nanoscopy,” Nat. Photonics 7(2), 113–117 (2013).
[Crossref]

Medoff, B. P.

Miller, E. L.

D. Hyde, E. L. Miller, D. H. Brooks, and V. Ntziachristos, “Data specific spatially varying regularization for multimodal fluorescence molecular tomography,” IEEE Trans. Med. Imaging 29(2), 365–374 (2010).
[Crossref] [PubMed]

Möller, T.

T. Humphries, A. Saad, A. Celler, G. Hamarneh, T. Möller, and M. Trummer, “Segmentation-based regularization of dynamic SPECT reconstruction,” in Nuclear Science Symposium Conference Record, (IEEE, 2009), 2849–2852.

Nassi, M.

Norton, S. J.

Ntziachristos, V.

D. Hyde, E. L. Miller, D. H. Brooks, and V. Ntziachristos, “Data specific spatially varying regularization for multimodal fluorescence molecular tomography,” IEEE Trans. Med. Imaging 29(2), 365–374 (2010).
[Crossref] [PubMed]

Nugent, K. A.

T. E. Gureyev and K. A. Nugent, “Rapid quantitative phase imaging using the transport of intensity equation,” Opt. Commun. 133(1-6), 339–346 (1997).
[Crossref]

Otsu, N.

N. Otsu, “A threshold selection method from gray-level histograms,” Automatica 11, 23–27 (1975).

Palenstijn, W. J.

W. van Aarle, W. J. Palenstijn, J. De Beenhouwer, T. Altantzis, S. Bals, K. J. Batenburg, and J. Sijbers, “The ASTRA Toolbox: A platform for advanced algorithm development in electron tomography,” Ultramicroscopy 157, 35–47 (2015).
[Crossref] [PubMed]

Pan, X.

E. Y. Sidky, C.-M. Kao, and X. Pan, “Accurate image reconstruction from few-views and limited-angle data in divergent-beam CT,” J. Opt. Soc. Am. 25, 1772–1782 (2009).

Paquit, V. C.

Park, H.

Y. Kim, H. Shim, K. Kim, H. Park, S. Jang, and Y. Park, “Profiling individual human red blood cells using common-path diffraction optical tomography,” Sci. Rep. 4, 6659 (2014).
[Crossref] [PubMed]

K. Kim, K. S. Kim, H. Park, J. C. Ye, and Y. Park, “Real-time visualization of 3-D dynamic microscopic objects using optical diffraction tomography,” Opt. Express 21(26), 32269–32278 (2013).
[Crossref] [PubMed]

Park, Y.

Y. Kim, H. Shim, K. Kim, H. Park, S. Jang, and Y. Park, “Profiling individual human red blood cells using common-path diffraction optical tomography,” Sci. Rep. 4, 6659 (2014).
[Crossref] [PubMed]

K. Kim, H. Yoon, M. Diez-Silva, M. Dao, R. R. Dasari, and Y. Park, “High-resolution three-dimensional imaging of red blood cells parasitized by Plasmodium falciparum and in situ hemozoin crystals using optical diffraction tomography,” J. Biomed. Opt. 19(1), 011005 (2013).
[Crossref] [PubMed]

K. Kim, K. S. Kim, H. Park, J. C. Ye, and Y. Park, “Real-time visualization of 3-D dynamic microscopic objects using optical diffraction tomography,” Opt. Express 21(26), 32269–32278 (2013).
[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,” Nat. Photonics 7(2), 113–117 (2013).
[Crossref]

Pock, T.

A. Chambolle and T. Pock, “A first-order primal-dual algorithm for convex problems with applications to imaging,” J. Math. Imaging Vis. 40(1), 120–145 (2011).
[Crossref]

Popescu, G.

Przibilla, S.

B. Kemper, L. Schmidt, S. Przibilla, C. Rommel, A. Vollmer, S. Ketelhut, J. Schnekenburger, and G. von Bally, “Influence of sample preparation and identification of subcelluar structures in quantitative holographic phase contrast microscopy,” Proc. SPIE 7715, 771504 (2010).
[Crossref]

Qiao, H.

Rappaz, B.

B. Rappaz, B. Breton, E. Shaffer, and G. Turcatti, “Digital holographic microscopy: a quantitative label-free microscopy technique for phenotypic screening,” Comb. Chem. High Throughput Screen. 17(1), 80–88 (2014).
[Crossref] [PubMed]

Rommel, C.

B. Kemper, L. Schmidt, S. Przibilla, C. Rommel, A. Vollmer, S. Ketelhut, J. Schnekenburger, and G. von Bally, “Influence of sample preparation and identification of subcelluar structures in quantitative holographic phase contrast microscopy,” Proc. SPIE 7715, 771504 (2010).
[Crossref]

Saad, A.

T. Humphries, A. Saad, A. Celler, G. Hamarneh, T. Möller, and M. Trummer, “Segmentation-based regularization of dynamic SPECT reconstruction,” in Nuclear Science Symposium Conference Record, (IEEE, 2009), 2849–2852.

Sato, T.

Schmidt, L.

B. Kemper, L. Schmidt, S. Przibilla, C. Rommel, A. Vollmer, S. Ketelhut, J. Schnekenburger, and G. von Bally, “Influence of sample preparation and identification of subcelluar structures in quantitative holographic phase contrast microscopy,” Proc. SPIE 7715, 771504 (2010).
[Crossref]

Schnekenburger, J.

B. Kemper, L. Schmidt, S. Przibilla, C. Rommel, A. Vollmer, S. Ketelhut, J. Schnekenburger, and G. von Bally, “Influence of sample preparation and identification of subcelluar structures in quantitative holographic phase contrast microscopy,” Proc. SPIE 7715, 771504 (2010).
[Crossref]

B. Kemper, S. Kosmeier, P. Langehanenberg, G. von Bally, I. Bredebusch, W. Domschke, and J. Schnekenburger, “Integral refractive index determination of living suspension cells by multifocus digital holographic phase contrast microscopy,” J. Biomed. Opt. 12(5), 054009 (2007).
[Crossref] [PubMed]

Shaffer, E.

B. Rappaz, B. Breton, E. Shaffer, and G. Turcatti, “Digital holographic microscopy: a quantitative label-free microscopy technique for phenotypic screening,” Comb. Chem. High Throughput Screen. 17(1), 80–88 (2014).
[Crossref] [PubMed]

Shim, H.

Y. Kim, H. Shim, K. Kim, H. Park, S. Jang, and Y. Park, “Profiling individual human red blood cells using common-path diffraction optical tomography,” Sci. Rep. 4, 6659 (2014).
[Crossref] [PubMed]

Sidky, E. Y.

E. Y. Sidky, C.-M. Kao, and X. Pan, “Accurate image reconstruction from few-views and limited-angle data in divergent-beam CT,” J. Opt. Soc. Am. 25, 1772–1782 (2009).

Sijbers, J.

W. van Aarle, W. J. Palenstijn, J. De Beenhouwer, T. Altantzis, S. Bals, K. J. Batenburg, and J. Sijbers, “The ASTRA Toolbox: A platform for advanced algorithm development in electron tomography,” Ultramicroscopy 157, 35–47 (2015).
[Crossref] [PubMed]

Song, X.

Sung, Y.

C. Fang-Yen, W. Choi, Y. Sung, C. J. Holbrow, R. R. Dasari, and M. S. Feld, “Video-rate tomographic phase microscopy,” J. Biomed. Opt. 16(1), 011005 (2011).
[Crossref] [PubMed]

Y. Sung, W. Choi, C. Fang-Yen, K. Badizadegan, R. R. Dasari, and M. S. Feld, “Optical diffraction tomography for high resolution live cell imaging,” Opt. Express 17(1), 266–277 (2009).
[Crossref] [PubMed]

Tangella, K.

Tobin, K. W.

Toy, F.

Y. Cotte, F. Toy, P. Jourdain, N. Pavillon, D. Boss, P. Magistretti, P. Marquet, and C. Depeursinge, “Marker-free phase nanoscopy,” Nat. Photonics 7(2), 113–117 (2013).
[Crossref]

Trummer, M.

T. Humphries, A. Saad, A. Celler, G. Hamarneh, T. Möller, and M. Trummer, “Segmentation-based regularization of dynamic SPECT reconstruction,” in Nuclear Science Symposium Conference Record, (IEEE, 2009), 2849–2852.

Turcatti, G.

B. Rappaz, B. Breton, E. Shaffer, and G. Turcatti, “Digital holographic microscopy: a quantitative label-free microscopy technique for phenotypic screening,” Comb. Chem. High Throughput Screen. 17(1), 80–88 (2014).
[Crossref] [PubMed]

van Aarle, W.

W. van Aarle, W. J. Palenstijn, J. De Beenhouwer, T. Altantzis, S. Bals, K. J. Batenburg, and J. Sijbers, “The ASTRA Toolbox: A platform for advanced algorithm development in electron tomography,” Ultramicroscopy 157, 35–47 (2015).
[Crossref] [PubMed]

Vertu, S.

S. Vertu, I. Yamada, J.-J. Delaunay, and O. Haeberlé, “Tomographic observation of transparent objects under coherent illumination and reconstruction by filtered backprojection and Fourier diffraction theorem,” Proc. SPIE 6861, 686103 (2008).
[Crossref]

Vollmer, A.

B. Kemper, L. Schmidt, S. Przibilla, C. Rommel, A. Vollmer, S. Ketelhut, J. Schnekenburger, and G. von Bally, “Influence of sample preparation and identification of subcelluar structures in quantitative holographic phase contrast microscopy,” Proc. SPIE 7715, 771504 (2010).
[Crossref]

von Bally, G.

B. Kemper, L. Schmidt, S. Przibilla, C. Rommel, A. Vollmer, S. Ketelhut, J. Schnekenburger, and G. von Bally, “Influence of sample preparation and identification of subcelluar structures in quantitative holographic phase contrast microscopy,” Proc. SPIE 7715, 771504 (2010).
[Crossref]

B. Kemper, S. Kosmeier, P. Langehanenberg, G. von Bally, I. Bredebusch, W. Domschke, and J. Schnekenburger, “Integral refractive index determination of living suspension cells by multifocus digital holographic phase contrast microscopy,” J. Biomed. Opt. 12(5), 054009 (2007).
[Crossref] [PubMed]

Wang, D.

Wang, Z.

Xing, Y.

X. Jin, L. Li, Z. Chen, L. Zhang, and Y. Xing, “Anisotropic total variation for limited-angle CT reconstruction,” in Nuclear Science Symposium Conference Record, (IEEE, 2010), 2232–2238.
[Crossref]

Yamada, I.

S. Vertu, I. Yamada, J.-J. Delaunay, and O. Haeberlé, “Tomographic observation of transparent objects under coherent illumination and reconstruction by filtered backprojection and Fourier diffraction theorem,” Proc. SPIE 6861, 686103 (2008).
[Crossref]

Ye, J. C.

Yoon, H.

K. Kim, H. Yoon, M. Diez-Silva, M. Dao, R. R. Dasari, and Y. Park, “High-resolution three-dimensional imaging of red blood cells parasitized by Plasmodium falciparum and in situ hemozoin crystals using optical diffraction tomography,” J. Biomed. Opt. 19(1), 011005 (2013).
[Crossref] [PubMed]

Zhang, L.

X. Jin, L. Li, Z. Chen, L. Zhang, and Y. Xing, “Anisotropic total variation for limited-angle CT reconstruction,” in Nuclear Science Symposium Conference Record, (IEEE, 2010), 2232–2238.
[Crossref]

Appl. Opt. (2)

Automatica (1)

N. Otsu, “A threshold selection method from gray-level histograms,” Automatica 11, 23–27 (1975).

Comb. Chem. High Throughput Screen. (1)

B. Rappaz, B. Breton, E. Shaffer, and G. Turcatti, “Digital holographic microscopy: a quantitative label-free microscopy technique for phenotypic screening,” Comb. Chem. High Throughput Screen. 17(1), 80–88 (2014).
[Crossref] [PubMed]

IEEE Signal Process. Lett. (1)

Z. Wang and A. C. Bovik, “A universal image quality index,” IEEE Signal Process. Lett. 9(3), 81–84 (2002).
[Crossref]

IEEE Trans. Med. Imaging (1)

D. Hyde, E. L. Miller, D. H. Brooks, and V. Ntziachristos, “Data specific spatially varying regularization for multimodal fluorescence molecular tomography,” IEEE Trans. Med. Imaging 29(2), 365–374 (2010).
[Crossref] [PubMed]

Int. J. Optomechatronics (1)

M. Kujawińska, W. Krauze, A. Kus, J. Kostencka, T. Kozacki, B. Kemper, and M. Dudek, “Problems and solutions in 3-D analysis of phase biological objects by optical diffraction tomography,” Int. J. Optomechatronics 8(4), 357–372 (2014).
[Crossref]

J. Biomed. Opt. (4)

A. Kus, W. Krauze, and M. Kujawinska, “Active limited-angle tomographic phase microscope,” J. Biomed. Opt. 20(11), 111216 (2015).
[Crossref] [PubMed]

K. Kim, H. Yoon, M. Diez-Silva, M. Dao, R. R. Dasari, and Y. Park, “High-resolution three-dimensional imaging of red blood cells parasitized by Plasmodium falciparum and in situ hemozoin crystals using optical diffraction tomography,” J. Biomed. Opt. 19(1), 011005 (2013).
[Crossref] [PubMed]

C. Fang-Yen, W. Choi, Y. Sung, C. J. Holbrow, R. R. Dasari, and M. S. Feld, “Video-rate tomographic phase microscopy,” J. Biomed. Opt. 16(1), 011005 (2011).
[Crossref] [PubMed]

B. Kemper, S. Kosmeier, P. Langehanenberg, G. von Bally, I. Bredebusch, W. Domschke, and J. Schnekenburger, “Integral refractive index determination of living suspension cells by multifocus digital holographic phase contrast microscopy,” J. Biomed. Opt. 12(5), 054009 (2007).
[Crossref] [PubMed]

J. Math. Imaging Vis. (1)

A. Chambolle and T. Pock, “A first-order primal-dual algorithm for convex problems with applications to imaging,” J. Math. Imaging Vis. 40(1), 120–145 (2011).
[Crossref]

J. Opt. Soc. Am. (2)

B. P. Medoff, W. R. Brody, M. Nassi, and A. Macovski, “Iterative convolution backprojection algorithms for image reconstruction from limited data,” J. Opt. Soc. Am. 73(11), 1493–1500 (1983).
[Crossref]

E. Y. Sidky, C.-M. Kao, and X. Pan, “Accurate image reconstruction from few-views and limited-angle data in divergent-beam CT,” J. Opt. Soc. Am. 25, 1772–1782 (2009).

Methods Cell Biol. (1)

G. Popescu, “Quantitative phase imaging of nanoscale cell structure and dynamics,” Methods Cell Biol. 90, 87–115 (2008).
[Crossref] [PubMed]

Nat. Photonics (1)

Y. Cotte, F. Toy, P. Jourdain, N. Pavillon, D. Boss, P. Magistretti, P. Marquet, and C. Depeursinge, “Marker-free phase nanoscopy,” Nat. Photonics 7(2), 113–117 (2013).
[Crossref]

Opt. Commun. (1)

T. E. Gureyev and K. A. Nugent, “Rapid quantitative phase imaging using the transport of intensity equation,” Opt. Commun. 133(1-6), 339–346 (1997).
[Crossref]

Opt. Eng. (1)

W. Krauze, A. Kuś, and M. Kujawinska, “Limited-angle hybrid optical diffraction tomography system with total-variation-minimization-based reconstruction,” Opt. Eng. 54(5), 054104 (2015).
[Crossref]

Opt. Express (4)

Opt. Lett. (1)

Proc. SPIE (6)

A. Kuś, W. Krauze, and M. Kujawińska, “Limited-angle, holographic tomography with optically controlled projection generation,” Proc. SPIE 9330, 933007 (2015).
[Crossref]

A. Kuś, W. Krauze, M. Kujawińska, and M. Filipiak, “Limited-angle hybrid diffraction tomography for biological samples,” Proc. SPIE 9132, 91320O (2014).

S. Vertu, I. Yamada, J.-J. Delaunay, and O. Haeberlé, “Tomographic observation of transparent objects under coherent illumination and reconstruction by filtered backprojection and Fourier diffraction theorem,” Proc. SPIE 6861, 686103 (2008).
[Crossref]

J. Kostencka, T. Kozacki, A. Kuś, M. Dudek, M. Kujawińska, and B. Kemper, “Holographic method for capillary induced aberration compensation for 3D tomographic measurements of living cells,” Proc. SPIE 8792, 879204 (2013).
[Crossref]

W. Krauze, P. Makowski, and M. Kujawińska, “Total variation iterative constraint algorithm for limited-angle tomographic reconstruction of non-piecewise-constant structures,” Proc. SPIE 9526, 95260Y (2015).

B. Kemper, L. Schmidt, S. Przibilla, C. Rommel, A. Vollmer, S. Ketelhut, J. Schnekenburger, and G. von Bally, “Influence of sample preparation and identification of subcelluar structures in quantitative holographic phase contrast microscopy,” Proc. SPIE 7715, 771504 (2010).
[Crossref]

Sci. Rep. (1)

Y. Kim, H. Shim, K. Kim, H. Park, S. Jang, and Y. Park, “Profiling individual human red blood cells using common-path diffraction optical tomography,” Sci. Rep. 4, 6659 (2014).
[Crossref] [PubMed]

Ultramicroscopy (1)

W. van Aarle, W. J. Palenstijn, J. De Beenhouwer, T. Altantzis, S. Bals, K. J. Batenburg, and J. Sijbers, “The ASTRA Toolbox: A platform for advanced algorithm development in electron tomography,” Ultramicroscopy 157, 35–47 (2015).
[Crossref] [PubMed]

Ultrason. Imaging (1)

A. H. Andersen and A. C. Kak, “Simultaneous algebraic reconstruction technique (SART): a superior implementation of the art algorithm,” Ultrason. Imaging 6(1), 81–94 (1984).
[Crossref] [PubMed]

Other (4)

A. C. Kak and M. Slaney, Principles of Computerized Tomographic Imaging (Society of Industrial and Applied Mathematics, 2001).

P. C. Hansen, Discrete Inverse Problems: Insight and Algorithms (Society of Industrial and Applied Mathematics, 2010).

X. Jin, L. Li, Z. Chen, L. Zhang, and Y. Xing, “Anisotropic total variation for limited-angle CT reconstruction,” in Nuclear Science Symposium Conference Record, (IEEE, 2010), 2232–2238.
[Crossref]

T. Humphries, A. Saad, A. Celler, G. Hamarneh, T. Möller, and M. Trummer, “Segmentation-based regularization of dynamic SPECT reconstruction,” in Nuclear Science Symposium Conference Record, (IEEE, 2009), 2849–2852.

Supplementary Material (3)

NameDescription
» Visualization 1: AVI (11515 KB)      Comparison of y-z cross-sections of reconstructions calculated with and without GTVIC support
» Visualization 2: AVI (5988 KB)      Comparison of x-z cross-sections of reconstructions calculated with and without GTVIC support
» Visualization 3: AVI (2981 KB)      Comparison of x-y cross-sections of reconstructions calculated with and without GTVIC support

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Figures (8)

Fig. 1
Fig. 1 Flow diagram of GTVIC strategy. M1: module 1, where 3D mask is generated; M2: module 2, where an arbitrary solver for LAT is utilized.
Fig. 2
Fig. 2 (a) Refractive index distribution of a synthetic phantom model of a Paramecium cell; the cell structure includes cytoplasm, a nucleus and a vacuole. (b) Schematic of the conical projection geometry used for synthetic sinogram generation (α = 45°).
Fig. 3
Fig. 3 Biological cell phantom reconstructions by GDRA solver (straight line propagation model, unwrapped phase projections). Left: GDRA algorithm with 180 auxiliary projection planes. Right: same GDRA algorithm supplemented by the GTVIC strategy; (a) cross-sections of the refractive index images (immersion subtracted), cropped to 0.75 of original output size; (b) reconstruction quality progress curves: Quality Index in XZ plane inside the phantom (circles) and RMS in full cube (triangles); (c) quality index for 3 sets of cross-section planes, rotated in ± 90° range around X, Y, Z axes respectively.
Fig. 4
Fig. 4 Biological cell phantom reconstructions by the diffraction-wise FTRA solver (Rytov approximation, amplitude-phase projections). Left: FTRA acting alone. Right: FTRA supplemented by GTVIC strategy. (a) reconstruction quality progress curves: Quality Index in XZ plane inside the phantom (circles) and RMS in full cube (triangles); (b) cross-sections of the reconstructed RI images, cropped to 0.75 of original output size; (c) quality index for 3 sets of cross-section planes, rotated in ± 90° range around X, Y, Z axes respectively.
Fig. 5
Fig. 5 Two comparisons of one-dimensional cross-sections of the reconstructions presented in Figs. 3 and 4. The cross-sections are parallel to Z axis and run through the center of the vacuole. Figure 5(a) presents comparison between phantom data and two reconstructions: one calculated with GDRA and GTVIC strategy (shown in Fig. 3(d)), and one calculated with GDRA only (Fig. 3(a)). Figure 5(b) presents analogical comparison, but with FTRA-based reconstructions (Figs. 4(d) and 4(a)).
Fig. 6
Fig. 6 Fourier-based reconstruction in Rytov approximation from complex projections with equalized amplitude patterns.
Fig. 7
Fig. 7 Quality of reconstructions by FTRA( + GTVIC) solver fed by different projection subsets of the original sinogram (360 views in conical pattern). In (a) the adaptive RI masks for GTVIC were calculated from the full sinogram and in (b) from corresponding limited subset of projections (realistic scenario); the dotted curves correspond to an alternative projection subset chosen from the same full sinogram in a pattern shifted azimuthally by 1°.
Fig. 8
Fig. 8 Experimental reconstruction of a C2C12 muscle cell by means of the iterative Fourier Transform solver; (a)-(b) K-space representation of input data (180 projections), (c)-(f) reconstruction by means of FTRA with Non-Negativity Constraint (50 iterations in 4 minuses), (g)-(j) reconstruction by means of FTRA with NNC + GTVIC (GTVIC mask generation and 5 FTRA + GTVIC iterations in 11 minutes). Animations with all Y-Z, X-Z, and X-Y cross-sections are presented in Visualization 1, Visualization 2 and Visualization 3, respectively.

Equations (2)

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min AxB 2 +λ x TV
QI= 4 σ xy x ¯ y ¯ ( σ x 2 + σ y 2 )( x ¯ 2 + y ¯ 2 )

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