Abstract

Data acquisition and processing is a critical issue for high-speed applications, especially in three-dimensional live cell imaging and analysis. This paper focuses on sparse-data sample rotation tomographic reconstruction and analysis with several noise-reduction techniques. For the sample rotation experiments, a live Candida rugosa sample is used and controlled by holographic optical tweezers, and the transmitted complex wavefronts of the sample are recorded with digital holographic microscopy. Three different cases of sample rotation tomography were reconstructed for dense angle with a step rotation at every 2°, and for sparse angles with step rotation at every 5° and 10°. The three cases of tomographic reconstruction performance are analyzed with consideration for data processing using four noise-reduction techniques. The experimental results demonstrate potential capability in retaining the tomographic image quality, even at the sparse angle reconstructions, with the help of noise-reduction techniques.

© 2021 Optical Society of America

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References

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2020 (3)

Y. Deng, C. H. Huang, B. Vinoth, D. Chu, X. J. Lai, and C. J. Cheng, “A compact synthetic aperture digital holographic microscope with mechanical movement-free beam scanning and optimized active aberration compensation for isotropic resolution enhancement,” Opt. Laser Eng. 134, 106251 (2020).
[Crossref]

B. Vinoth, A. Vijayakumar, M. Rai, J. Rosen, C. J. Cheng, O. V. Minin, and I. V. Minin, “Binary square axicon with chiral focusing properties for optical trapping,” Opt. Eng. 59, 041204 (2020).
[Crossref]

S. Montresor, M. Tahon, A. Laurent, and P. Picart, “Computational de-noising based on deep learning for phase data in digital holographic interferometry,” APL Photon. 5, 030802 (2020).
[Crossref]

2019 (3)

2018 (1)

B. Vinoth, X. J. Lai, Y. C. Lin, and C. J. Cheng, “Integrated dual-tomography for refractive index analysis of free-floating single living cell with isotropic superresolution,” Sci. Rep. 8, 5943 (2018).
[Crossref]

2017 (8)

2016 (5)

P. Y. Liu, L. K. Chin, W. Ser, H. F. Chen, C. M. Hsieh, C. H. Lee, K. B. Sung, T. C. Ayi, P. H. Yap, B. Liedberg, K. Wang, T. Bourouina, and Y. L. Wang, “Cell refractive index for cell biology and disease diagnosis: past, present and future,” Lab Chip 16, 634–644 (2016).
[Crossref]

X. Ma, W. Xiao, and F. Pan, “Accuracy improvement in digital holographic microtomography by multiple numerical reconstructions,” Opt. Laser Eng. 86, 338–344 (2016).
[Crossref]

A. V. Belashov, N. V. Petrov, and I. V. Semenova, “Accuracy of image-plane holographic tomography with filtered backprojection: random and systematic errors,” Appl. Opt. 55, 81–88 (2016).
[Crossref]

J. Kostencka, T. Kozacki, A. Kus, B. Kemper, and M. Kujawinska, “Holographic tomography with scanning of illumination: space-domain reconstruction for spatially invariant accuracy,” Biomed. Opt. Express 7, 4086–4101 (2016).
[Crossref]

S. Montresor and P. Picart, “Quantitative appraisal for noise reduction in digital holographic phase imaging,” Opt. Express 24, 14322–14343 (2016).
[Crossref]

2015 (4)

2014 (3)

T. Kim, R. Zhou, M. Mir, S. D. Babacan, P. S. Carney, L. L. Goddard, and G. Popescu, “White-light diffraction tomography of unlabelled live cells,” Nat. Photonics 8, 256 (2014).
[Crossref]

M. Kujawinska, 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. Optomechatron. 8, 357–372 (2014).
[Crossref]

Y. C. Lin and C. J. Cheng, “Sectional imaging of spatially refractive index distribution using coaxial rotation digital holographic microtomography,” J. Opt. 16, 065401 (2014).
[Crossref]

2011 (1)

S. Vertu, J. Flügge, J. J. Delaunay, and O. Haeberlé, “Improved and isotropic resolution in tomographic diffractive microscopy combining sample and illumination rotation,” Central Eur. J. Phys. 9, 969–974 (2011).
[Crossref]

2007 (2)

S. S. Kou and C. J. R. Sheppard, “Imaging in digital holographic microscopy,” Opt. Express 15, 13640–13648 (2007).
[Crossref]

W. Choi, C. F. Yen, K. Badizadegan, S. Oh, N. Lue, R. R. Dasari, and M. S. Feld, “Tomographic phase microscopy,” Nat. Methods 4, 717–719 (2007).
[Crossref]

2006 (1)

2005 (1)

I. Selesnick, R. G. Baraniuk, and N. G. Kingsbury, “The dual-tree complex wavelet transform,” IEEE Signal Process. Mag. 22(6), 123–151 (2005).
[Crossref]

2004 (1)

2003 (1)

V. Bingelyte, J. Leach, J. Courtial, and M. J. Padgett, “Optically controlled three-dimensional rotation of microscopic objects,” Appl. Phys. Lett. 82, 829–831 (2003).
[Crossref]

2000 (1)

1994 (1)

B. Beauvoit, H. Liu, K. Kang, P. D. Kaplan, M. Miwa, and B. Chance, “Characterization of absorption and scattering properties for various yeast strains by time-resolved spectroscopy,” Cell Biophy. 23, 91–109 (1994).
[Crossref]

1987 (1)

A. Ashkin and J. M. Dziedzic, “Optical trapping and manipulation of viruses and bacteria,” Science 235, 1517–1520 (1987).
[Crossref]

1969 (1)

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

Ashkin, A.

A. Ashkin and J. M. Dziedzic, “Optical trapping and manipulation of viruses and bacteria,” Science 235, 1517–1520 (1987).
[Crossref]

Ayi, T. C.

P. Y. Liu, L. K. Chin, W. Ser, H. F. Chen, C. M. Hsieh, C. H. Lee, K. B. Sung, T. C. Ayi, P. H. Yap, B. Liedberg, K. Wang, T. Bourouina, and Y. L. Wang, “Cell refractive index for cell biology and disease diagnosis: past, present and future,” Lab Chip 16, 634–644 (2016).
[Crossref]

Babacan, S. D.

T. Kim, R. Zhou, M. Mir, S. D. Babacan, P. S. Carney, L. L. Goddard, and G. Popescu, “White-light diffraction tomography of unlabelled live cells,” Nat. Photonics 8, 256 (2014).
[Crossref]

Badizadegan, K.

W. Choi, C. F. Yen, K. Badizadegan, S. Oh, N. Lue, R. R. Dasari, and M. S. Feld, “Tomographic phase microscopy,” Nat. Methods 4, 717–719 (2007).
[Crossref]

Bailleul, J.

Baraniuk, R. G.

I. Selesnick, R. G. Baraniuk, and N. G. Kingsbury, “The dual-tree complex wavelet transform,” IEEE Signal Process. Mag. 22(6), 123–151 (2005).
[Crossref]

Barbastathis, G.

Beauvoit, B.

B. Beauvoit, H. Liu, K. Kang, P. D. Kaplan, M. Miwa, and B. Chance, “Characterization of absorption and scattering properties for various yeast strains by time-resolved spectroscopy,” Cell Biophy. 23, 91–109 (1994).
[Crossref]

Belashov, A. V.

Bengio, Y.

Y. LeCun, Y. Bengio, and G. Hinton, “Deep learning,” Nature 521, 436–444 (2015).
[Crossref]

Bingelyte, V.

V. Bingelyte, J. Leach, J. Courtial, and M. J. Padgett, “Optically controlled three-dimensional rotation of microscopic objects,” Appl. Phys. Lett. 82, 829–831 (2003).
[Crossref]

Bourouina, T.

P. Y. Liu, L. K. Chin, W. Ser, H. F. Chen, C. M. Hsieh, C. H. Lee, K. B. Sung, T. C. Ayi, P. H. Yap, B. Liedberg, K. Wang, T. Bourouina, and Y. L. Wang, “Cell refractive index for cell biology and disease diagnosis: past, present and future,” Lab Chip 16, 634–644 (2016).
[Crossref]

Carney, P. S.

T. Kim, R. Zhou, M. Mir, S. D. Babacan, P. S. Carney, L. L. Goddard, and G. Popescu, “White-light diffraction tomography of unlabelled live cells,” Nat. Photonics 8, 256 (2014).
[Crossref]

Chance, B.

B. Beauvoit, H. Liu, K. Kang, P. D. Kaplan, M. Miwa, and B. Chance, “Characterization of absorption and scattering properties for various yeast strains by time-resolved spectroscopy,” Cell Biophy. 23, 91–109 (1994).
[Crossref]

Charrière, F.

Chen, H. C.

Chen, H. F.

P. Y. Liu, L. K. Chin, W. Ser, H. F. Chen, C. M. Hsieh, C. H. Lee, K. B. Sung, T. C. Ayi, P. H. Yap, B. Liedberg, K. Wang, T. Bourouina, and Y. L. Wang, “Cell refractive index for cell biology and disease diagnosis: past, present and future,” Lab Chip 16, 634–644 (2016).
[Crossref]

Chen, Y.

K. Zhang, W. Zuo, Y. Chen, D. Meng, and L. Zhang, “Beyond a Gaussian denoiser: residual learning of deep CNN for image de-noising,” IEEE Trans. Image Process. 26, 3142–3155 (2017).
[Crossref]

Cheng, C. J.

B. Vinoth, A. Vijayakumar, M. Rai, J. Rosen, C. J. Cheng, O. V. Minin, and I. V. Minin, “Binary square axicon with chiral focusing properties for optical trapping,” Opt. Eng. 59, 041204 (2020).
[Crossref]

Y. Deng, C. H. Huang, B. Vinoth, D. Chu, X. J. Lai, and C. J. Cheng, “A compact synthetic aperture digital holographic microscope with mechanical movement-free beam scanning and optimized active aberration compensation for isotropic resolution enhancement,” Opt. Laser Eng. 134, 106251 (2020).
[Crossref]

B. Vinoth, H. Y. Tu, X. J. Lai, and C. J. Cheng, “Adaptive wavefront correction structured illumination holographic tomography,” Sci. Rep. 9, 10489 (2019).
[Crossref]

B. Vinoth, X. J. Lai, Y. C. Lin, and C. J. Cheng, “Integrated dual-tomography for refractive index analysis of free-floating single living cell with isotropic superresolution,” Sci. Rep. 8, 5943 (2018).
[Crossref]

Y. C. Lin, H. C. Chen, H. Y. Tu, C. Y. Liu, and C. J. Cheng, “Optically driven full-angle sample rotation for tomographic imaging in digital holographic microscopy,” Opt. Lett. 42, 1321–1324 (2017).
[Crossref]

A. Vijayakumar, B. Vinoth, I. V. Minin, J. Rosen, O. V. Minin, and C. J. Cheng, “Experimental demonstration of square Fresnel zone plate with chiral side lobes,” Appl. Opt. 56, F128–F133 (2017).
[Crossref]

X. J. Lai, H. Y. Tu, C. H. Wu, Y. C. Lin, and C. J. Cheng, “Resolution enhancement of spectrum normalization in synthetic aperture digital holographic microscopy,” Appl. Opt. 54, A51–A58 (2015).
[Crossref]

Y. C. Lin and C. J. Cheng, “Sectional imaging of spatially refractive index distribution using coaxial rotation digital holographic microtomography,” J. Opt. 16, 065401 (2014).
[Crossref]

Chin, L. K.

P. Y. Liu, L. K. Chin, W. Ser, H. F. Chen, C. M. Hsieh, C. H. Lee, K. B. Sung, T. C. Ayi, P. H. Yap, B. Liedberg, K. Wang, T. Bourouina, and Y. L. Wang, “Cell refractive index for cell biology and disease diagnosis: past, present and future,” Lab Chip 16, 634–644 (2016).
[Crossref]

Choi, W.

W. Choi, C. F. Yen, K. Badizadegan, S. Oh, N. Lue, R. R. Dasari, and M. S. Feld, “Tomographic phase microscopy,” Nat. Methods 4, 717–719 (2007).
[Crossref]

Chowdhury, S.

Chu, D.

Y. Deng, C. H. Huang, B. Vinoth, D. Chu, X. J. Lai, and C. J. Cheng, “A compact synthetic aperture digital holographic microscope with mechanical movement-free beam scanning and optimized active aberration compensation for isotropic resolution enhancement,” Opt. Laser Eng. 134, 106251 (2020).
[Crossref]

Colomb, T.

Courtial, J.

V. Bingelyte, J. Leach, J. Courtial, and M. J. Padgett, “Optically controlled three-dimensional rotation of microscopic objects,” Appl. Phys. Lett. 82, 829–831 (2003).
[Crossref]

Dasari, R. R.

W. Choi, C. F. Yen, K. Badizadegan, S. Oh, N. Lue, R. R. Dasari, and M. S. Feld, “Tomographic phase microscopy,” Nat. Methods 4, 717–719 (2007).
[Crossref]

Debaileul, M.

Delaunay, J. J.

S. Vertu, J. Flügge, J. J. Delaunay, and O. Haeberlé, “Improved and isotropic resolution in tomographic diffractive microscopy combining sample and illumination rotation,” Central Eur. J. Phys. 9, 969–974 (2011).
[Crossref]

Deng, Y.

Y. Deng, C. H. Huang, B. Vinoth, D. Chu, X. J. Lai, and C. J. Cheng, “A compact synthetic aperture digital holographic microscope with mechanical movement-free beam scanning and optimized active aberration compensation for isotropic resolution enhancement,” Opt. Laser Eng. 134, 106251 (2020).
[Crossref]

Depeursinge, C.

Dudek, M.

M. Kujawinska, 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. Optomechatron. 8, 357–372 (2014).
[Crossref]

Dziedzic, J. M.

A. Ashkin and J. M. Dziedzic, “Optical trapping and manipulation of viruses and bacteria,” Science 235, 1517–1520 (1987).
[Crossref]

Ecoffet, C.

Egiazarian, K.

V. Katkovnik and K. Egiazarian, “Sparse phase imaging based on complex domain nonlocal BM3D techniques,” Digit. Signal Process. 63, 72–85 (2017).
[Crossref]

Eldridge, W. J.

Feld, M. S.

W. Choi, C. F. Yen, K. Badizadegan, S. Oh, N. Lue, R. R. Dasari, and M. S. Feld, “Tomographic phase microscopy,” Nat. Methods 4, 717–719 (2007).
[Crossref]

Flügge, J.

S. Vertu, J. Flügge, J. J. Delaunay, and O. Haeberlé, “Improved and isotropic resolution in tomographic diffractive microscopy combining sample and illumination rotation,” Central Eur. J. Phys. 9, 969–974 (2011).
[Crossref]

Gilboa, B.

Goddard, L. L.

T. Kim, R. Zhou, M. Mir, S. D. Babacan, P. S. Carney, L. L. Goddard, and G. Popescu, “White-light diffraction tomography of unlabelled live cells,” Nat. Photonics 8, 256 (2014).
[Crossref]

Habaza, M.

Haeberle, O.

Haeberlé, O.

S. Vertu, J. Flügge, J. J. Delaunay, and O. Haeberlé, “Improved and isotropic resolution in tomographic diffractive microscopy combining sample and illumination rotation,” Central Eur. J. Phys. 9, 969–974 (2011).
[Crossref]

Heger, T. J.

Hinton, G.

Y. LeCun, Y. Bengio, and G. Hinton, “Deep learning,” Nature 521, 436–444 (2015).
[Crossref]

Houkal, M.

Hsieh, C. M.

P. Y. Liu, L. K. Chin, W. Ser, H. F. Chen, C. M. Hsieh, C. H. Lee, K. B. Sung, T. C. Ayi, P. H. Yap, B. Liedberg, K. Wang, T. Bourouina, and Y. L. Wang, “Cell refractive index for cell biology and disease diagnosis: past, present and future,” Lab Chip 16, 634–644 (2016).
[Crossref]

Huang, C. H.

Y. Deng, C. H. Huang, B. Vinoth, D. Chu, X. J. Lai, and C. J. Cheng, “A compact synthetic aperture digital holographic microscope with mechanical movement-free beam scanning and optimized active aberration compensation for isotropic resolution enhancement,” Opt. Laser Eng. 134, 106251 (2020).
[Crossref]

Izatt, J.

Kak, A. C.

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

Kang, K.

B. Beauvoit, H. Liu, K. Kang, P. D. Kaplan, M. Miwa, and B. Chance, “Characterization of absorption and scattering properties for various yeast strains by time-resolved spectroscopy,” Cell Biophy. 23, 91–109 (1994).
[Crossref]

Kaplan, P. D.

B. Beauvoit, H. Liu, K. Kang, P. D. Kaplan, M. Miwa, and B. Chance, “Characterization of absorption and scattering properties for various yeast strains by time-resolved spectroscopy,” Cell Biophy. 23, 91–109 (1994).
[Crossref]

Katkovnik, V.

V. Katkovnik and K. Egiazarian, “Sparse phase imaging based on complex domain nonlocal BM3D techniques,” Digit. Signal Process. 63, 72–85 (2017).
[Crossref]

Kemao, Q.

Kemper, B.

J. Kostencka, T. Kozacki, A. Kus, B. Kemper, and M. Kujawinska, “Holographic tomography with scanning of illumination: space-domain reconstruction for spatially invariant accuracy,” Biomed. Opt. Express 7, 4086–4101 (2016).
[Crossref]

M. Kujawinska, 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. Optomechatron. 8, 357–372 (2014).
[Crossref]

Kim, K.

K. Kim and Y. Park, “Tomographic active optical trapping of arbitrarily shaped objects by exploiting 3D refractive index maps,” Nat. Commun. 8, 15340 (2017).
[Crossref]

Kim, M. K.

Kim, T.

T. Kim, R. Zhou, M. Mir, S. D. Babacan, P. S. Carney, L. L. Goddard, and G. Popescu, “White-light diffraction tomography of unlabelled live cells,” Nat. Photonics 8, 256 (2014).
[Crossref]

Kingsbury, N. G.

I. Selesnick, R. G. Baraniuk, and N. G. Kingsbury, “The dual-tree complex wavelet transform,” IEEE Signal Process. Mag. 22(6), 123–151 (2005).
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Kostencka, J.

Kou, S. S.

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M. Kujawinska, 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. Optomechatron. 8, 357–372 (2014).
[Crossref]

Kujawinska, M.

Kus, A.

Lai, X. J.

Y. Deng, C. H. Huang, B. Vinoth, D. Chu, X. J. Lai, and C. J. Cheng, “A compact synthetic aperture digital holographic microscope with mechanical movement-free beam scanning and optimized active aberration compensation for isotropic resolution enhancement,” Opt. Laser Eng. 134, 106251 (2020).
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B. Vinoth, H. Y. Tu, X. J. Lai, and C. J. Cheng, “Adaptive wavefront correction structured illumination holographic tomography,” Sci. Rep. 9, 10489 (2019).
[Crossref]

B. Vinoth, X. J. Lai, Y. C. Lin, and C. J. Cheng, “Integrated dual-tomography for refractive index analysis of free-floating single living cell with isotropic superresolution,” Sci. Rep. 8, 5943 (2018).
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X. J. Lai, H. Y. Tu, C. H. Wu, Y. C. Lin, and C. J. Cheng, “Resolution enhancement of spectrum normalization in synthetic aperture digital holographic microscopy,” Appl. Opt. 54, A51–A58 (2015).
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Y. LeCun, Y. Bengio, and G. Hinton, “Deep learning,” Nature 521, 436–444 (2015).
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P. Y. Liu, L. K. Chin, W. Ser, H. F. Chen, C. M. Hsieh, C. H. Lee, K. B. Sung, T. C. Ayi, P. H. Yap, B. Liedberg, K. Wang, T. Bourouina, and Y. L. Wang, “Cell refractive index for cell biology and disease diagnosis: past, present and future,” Lab Chip 16, 634–644 (2016).
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B. Vinoth, X. J. Lai, Y. C. Lin, and C. J. Cheng, “Integrated dual-tomography for refractive index analysis of free-floating single living cell with isotropic superresolution,” Sci. Rep. 8, 5943 (2018).
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Y. C. Lin and C. J. Cheng, “Sectional imaging of spatially refractive index distribution using coaxial rotation digital holographic microtomography,” J. Opt. 16, 065401 (2014).
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B. Simon, M. Debaileul, M. Houkal, C. Ecoffet, J. Bailleul, J. Lambert, A. Spangenberg, H. Liu, O. Soppera, and O. Haeberle, “Tomographic diffractive microscopy with isotropic resolution,” Optica 4, 460–463 (2017).
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X. Ma, W. Xiao, and F. Pan, “Accuracy improvement in digital holographic microtomography by multiple numerical reconstructions,” Opt. Laser Eng. 86, 338–344 (2016).
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Meng, D.

K. Zhang, W. Zuo, Y. Chen, D. Meng, and L. Zhang, “Beyond a Gaussian denoiser: residual learning of deep CNN for image de-noising,” IEEE Trans. Image Process. 26, 3142–3155 (2017).
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B. Vinoth, A. Vijayakumar, M. Rai, J. Rosen, C. J. Cheng, O. V. Minin, and I. V. Minin, “Binary square axicon with chiral focusing properties for optical trapping,” Opt. Eng. 59, 041204 (2020).
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Minin, O. V.

B. Vinoth, A. Vijayakumar, M. Rai, J. Rosen, C. J. Cheng, O. V. Minin, and I. V. Minin, “Binary square axicon with chiral focusing properties for optical trapping,” Opt. Eng. 59, 041204 (2020).
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A. Vijayakumar, B. Vinoth, I. V. Minin, J. Rosen, O. V. Minin, and C. J. Cheng, “Experimental demonstration of square Fresnel zone plate with chiral side lobes,” Appl. Opt. 56, F128–F133 (2017).
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T. Kim, R. Zhou, M. Mir, S. D. Babacan, P. S. Carney, L. L. Goddard, and G. Popescu, “White-light diffraction tomography of unlabelled live cells,” Nat. Photonics 8, 256 (2014).
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Miwa, M.

B. Beauvoit, H. Liu, K. Kang, P. D. Kaplan, M. Miwa, and B. Chance, “Characterization of absorption and scattering properties for various yeast strains by time-resolved spectroscopy,” Cell Biophy. 23, 91–109 (1994).
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S. Montresor, M. Tahon, A. Laurent, and P. Picart, “Computational de-noising based on deep learning for phase data in digital holographic interferometry,” APL Photon. 5, 030802 (2020).
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S. Montresor and P. Picart, “Quantitative appraisal for noise reduction in digital holographic phase imaging,” Opt. Express 24, 14322–14343 (2016).
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Oh, S.

W. Choi, C. F. Yen, K. Badizadegan, S. Oh, N. Lue, R. R. Dasari, and M. S. Feld, “Tomographic phase microscopy,” Nat. Methods 4, 717–719 (2007).
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Ozcan, A.

Padgett, M. J.

V. Bingelyte, J. Leach, J. Courtial, and M. J. Padgett, “Optically controlled three-dimensional rotation of microscopic objects,” Appl. Phys. Lett. 82, 829–831 (2003).
[Crossref]

Pan, F.

X. Ma, W. Xiao, and F. Pan, “Accuracy improvement in digital holographic microtomography by multiple numerical reconstructions,” Opt. Laser Eng. 86, 338–344 (2016).
[Crossref]

Park, Y.

K. Kim and Y. Park, “Tomographic active optical trapping of arbitrarily shaped objects by exploiting 3D refractive index maps,” Nat. Commun. 8, 15340 (2017).
[Crossref]

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Petrov, N. V.

Picart, P.

S. Montresor, M. Tahon, A. Laurent, and P. Picart, “Computational de-noising based on deep learning for phase data in digital holographic interferometry,” APL Photon. 5, 030802 (2020).
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S. Montresor and P. Picart, “Quantitative appraisal for noise reduction in digital holographic phase imaging,” Opt. Express 24, 14322–14343 (2016).
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P. Picart, New Techniques in Digital Holography (ISTE-Wiley, 2015).

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T. Kim, R. Zhou, M. Mir, S. D. Babacan, P. S. Carney, L. L. Goddard, and G. Popescu, “White-light diffraction tomography of unlabelled live cells,” Nat. Photonics 8, 256 (2014).
[Crossref]

Rai, M.

B. Vinoth, A. Vijayakumar, M. Rai, J. Rosen, C. J. Cheng, O. V. Minin, and I. V. Minin, “Binary square axicon with chiral focusing properties for optical trapping,” Opt. Eng. 59, 041204 (2020).
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Roichman, Y.

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B. Vinoth, A. Vijayakumar, M. Rai, J. Rosen, C. J. Cheng, O. V. Minin, and I. V. Minin, “Binary square axicon with chiral focusing properties for optical trapping,” Opt. Eng. 59, 041204 (2020).
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A. Vijayakumar, B. Vinoth, I. V. Minin, J. Rosen, O. V. Minin, and C. J. Cheng, “Experimental demonstration of square Fresnel zone plate with chiral side lobes,” Appl. Opt. 56, F128–F133 (2017).
[Crossref]

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I. Selesnick, R. G. Baraniuk, and N. G. Kingsbury, “The dual-tree complex wavelet transform,” IEEE Signal Process. Mag. 22(6), 123–151 (2005).
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Semenova, I. V.

Ser, W.

P. Y. Liu, L. K. Chin, W. Ser, H. F. Chen, C. M. Hsieh, C. H. Lee, K. B. Sung, T. C. Ayi, P. H. Yap, B. Liedberg, K. Wang, T. Bourouina, and Y. L. Wang, “Cell refractive index for cell biology and disease diagnosis: past, present and future,” Lab Chip 16, 634–644 (2016).
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Soppera, O.

Spangenberg, A.

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P. Y. Liu, L. K. Chin, W. Ser, H. F. Chen, C. M. Hsieh, C. H. Lee, K. B. Sung, T. C. Ayi, P. H. Yap, B. Liedberg, K. Wang, T. Bourouina, and Y. L. Wang, “Cell refractive index for cell biology and disease diagnosis: past, present and future,” Lab Chip 16, 634–644 (2016).
[Crossref]

Tahon, M.

S. Montresor, M. Tahon, A. Laurent, and P. Picart, “Computational de-noising based on deep learning for phase data in digital holographic interferometry,” APL Photon. 5, 030802 (2020).
[Crossref]

Tu, H. Y.

Vertu, S.

S. Vertu, J. Flügge, J. J. Delaunay, and O. Haeberlé, “Improved and isotropic resolution in tomographic diffractive microscopy combining sample and illumination rotation,” Central Eur. J. Phys. 9, 969–974 (2011).
[Crossref]

Vijayakumar, A.

B. Vinoth, A. Vijayakumar, M. Rai, J. Rosen, C. J. Cheng, O. V. Minin, and I. V. Minin, “Binary square axicon with chiral focusing properties for optical trapping,” Opt. Eng. 59, 041204 (2020).
[Crossref]

A. Vijayakumar, B. Vinoth, I. V. Minin, J. Rosen, O. V. Minin, and C. J. Cheng, “Experimental demonstration of square Fresnel zone plate with chiral side lobes,” Appl. Opt. 56, F128–F133 (2017).
[Crossref]

Vinoth, B.

B. Vinoth, A. Vijayakumar, M. Rai, J. Rosen, C. J. Cheng, O. V. Minin, and I. V. Minin, “Binary square axicon with chiral focusing properties for optical trapping,” Opt. Eng. 59, 041204 (2020).
[Crossref]

Y. Deng, C. H. Huang, B. Vinoth, D. Chu, X. J. Lai, and C. J. Cheng, “A compact synthetic aperture digital holographic microscope with mechanical movement-free beam scanning and optimized active aberration compensation for isotropic resolution enhancement,” Opt. Laser Eng. 134, 106251 (2020).
[Crossref]

B. Vinoth, H. Y. Tu, X. J. Lai, and C. J. Cheng, “Adaptive wavefront correction structured illumination holographic tomography,” Sci. Rep. 9, 10489 (2019).
[Crossref]

B. Vinoth, X. J. Lai, Y. C. Lin, and C. J. Cheng, “Integrated dual-tomography for refractive index analysis of free-floating single living cell with isotropic superresolution,” Sci. Rep. 8, 5943 (2018).
[Crossref]

A. Vijayakumar, B. Vinoth, I. V. Minin, J. Rosen, O. V. Minin, and C. J. Cheng, “Experimental demonstration of square Fresnel zone plate with chiral side lobes,” Appl. Opt. 56, F128–F133 (2017).
[Crossref]

Wang, K.

P. Y. Liu, L. K. Chin, W. Ser, H. F. Chen, C. M. Hsieh, C. H. Lee, K. B. Sung, T. C. Ayi, P. H. Yap, B. Liedberg, K. Wang, T. Bourouina, and Y. L. Wang, “Cell refractive index for cell biology and disease diagnosis: past, present and future,” Lab Chip 16, 634–644 (2016).
[Crossref]

Wang, Y. L.

P. Y. Liu, L. K. Chin, W. Ser, H. F. Chen, C. M. Hsieh, C. H. Lee, K. B. Sung, T. C. Ayi, P. H. Yap, B. Liedberg, K. Wang, T. Bourouina, and Y. L. Wang, “Cell refractive index for cell biology and disease diagnosis: past, present and future,” Lab Chip 16, 634–644 (2016).
[Crossref]

Wax, A.

Wolf, E.

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

Wu, C. H.

Xiao, W.

X. Ma, W. Xiao, and F. Pan, “Accuracy improvement in digital holographic microtomography by multiple numerical reconstructions,” Opt. Laser Eng. 86, 338–344 (2016).
[Crossref]

Yap, P. H.

P. Y. Liu, L. K. Chin, W. Ser, H. F. Chen, C. M. Hsieh, C. H. Lee, K. B. Sung, T. C. Ayi, P. H. Yap, B. Liedberg, K. Wang, T. Bourouina, and Y. L. Wang, “Cell refractive index for cell biology and disease diagnosis: past, present and future,” Lab Chip 16, 634–644 (2016).
[Crossref]

Yen, C. F.

W. Choi, C. F. Yen, K. Badizadegan, S. Oh, N. Lue, R. R. Dasari, and M. S. Feld, “Tomographic phase microscopy,” Nat. Methods 4, 717–719 (2007).
[Crossref]

Zeng, T.

Zhang, K.

K. Zhang, W. Zuo, Y. Chen, D. Meng, and L. Zhang, “Beyond a Gaussian denoiser: residual learning of deep CNN for image de-noising,” IEEE Trans. Image Process. 26, 3142–3155 (2017).
[Crossref]

Zhang, L.

K. Zhang, W. Zuo, Y. Chen, D. Meng, and L. Zhang, “Beyond a Gaussian denoiser: residual learning of deep CNN for image de-noising,” IEEE Trans. Image Process. 26, 3142–3155 (2017).
[Crossref]

Zhou, R.

T. Kim, R. Zhou, M. Mir, S. D. Babacan, P. S. Carney, L. L. Goddard, and G. Popescu, “White-light diffraction tomography of unlabelled live cells,” Nat. Photonics 8, 256 (2014).
[Crossref]

Zuo, W.

K. Zhang, W. Zuo, Y. Chen, D. Meng, and L. Zhang, “Beyond a Gaussian denoiser: residual learning of deep CNN for image de-noising,” IEEE Trans. Image Process. 26, 3142–3155 (2017).
[Crossref]

APL Photon. (1)

S. Montresor, M. Tahon, A. Laurent, and P. Picart, “Computational de-noising based on deep learning for phase data in digital holographic interferometry,” APL Photon. 5, 030802 (2020).
[Crossref]

Appl. Opt. (6)

Appl. Phys. Lett. (1)

V. Bingelyte, J. Leach, J. Courtial, and M. J. Padgett, “Optically controlled three-dimensional rotation of microscopic objects,” Appl. Phys. Lett. 82, 829–831 (2003).
[Crossref]

Biomed. Opt. Express (1)

Cell Biophy. (1)

B. Beauvoit, H. Liu, K. Kang, P. D. Kaplan, M. Miwa, and B. Chance, “Characterization of absorption and scattering properties for various yeast strains by time-resolved spectroscopy,” Cell Biophy. 23, 91–109 (1994).
[Crossref]

Central Eur. J. Phys. (1)

S. Vertu, J. Flügge, J. J. Delaunay, and O. Haeberlé, “Improved and isotropic resolution in tomographic diffractive microscopy combining sample and illumination rotation,” Central Eur. J. Phys. 9, 969–974 (2011).
[Crossref]

Digit. Signal Process. (1)

V. Katkovnik and K. Egiazarian, “Sparse phase imaging based on complex domain nonlocal BM3D techniques,” Digit. Signal Process. 63, 72–85 (2017).
[Crossref]

IEEE Signal Process. Mag. (1)

I. Selesnick, R. G. Baraniuk, and N. G. Kingsbury, “The dual-tree complex wavelet transform,” IEEE Signal Process. Mag. 22(6), 123–151 (2005).
[Crossref]

IEEE Trans. Image Process. (1)

K. Zhang, W. Zuo, Y. Chen, D. Meng, and L. Zhang, “Beyond a Gaussian denoiser: residual learning of deep CNN for image de-noising,” IEEE Trans. Image Process. 26, 3142–3155 (2017).
[Crossref]

Int. J. Optomechatron. (1)

M. Kujawinska, 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. Optomechatron. 8, 357–372 (2014).
[Crossref]

J. Opt. (1)

Y. C. Lin and C. J. Cheng, “Sectional imaging of spatially refractive index distribution using coaxial rotation digital holographic microtomography,” J. Opt. 16, 065401 (2014).
[Crossref]

Lab Chip (1)

P. Y. Liu, L. K. Chin, W. Ser, H. F. Chen, C. M. Hsieh, C. H. Lee, K. B. Sung, T. C. Ayi, P. H. Yap, B. Liedberg, K. Wang, T. Bourouina, and Y. L. Wang, “Cell refractive index for cell biology and disease diagnosis: past, present and future,” Lab Chip 16, 634–644 (2016).
[Crossref]

Nat. Commun. (1)

K. Kim and Y. Park, “Tomographic active optical trapping of arbitrarily shaped objects by exploiting 3D refractive index maps,” Nat. Commun. 8, 15340 (2017).
[Crossref]

Nat. Methods (1)

W. Choi, C. F. Yen, K. Badizadegan, S. Oh, N. Lue, R. R. Dasari, and M. S. Feld, “Tomographic phase microscopy,” Nat. Methods 4, 717–719 (2007).
[Crossref]

Nat. Photonics (1)

T. Kim, R. Zhou, M. Mir, S. D. Babacan, P. S. Carney, L. L. Goddard, and G. Popescu, “White-light diffraction tomography of unlabelled live cells,” Nat. Photonics 8, 256 (2014).
[Crossref]

Nature (1)

Y. LeCun, Y. Bengio, and G. Hinton, “Deep learning,” Nature 521, 436–444 (2015).
[Crossref]

Opt. Commun. (1)

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

Opt. Eng. (1)

B. Vinoth, A. Vijayakumar, M. Rai, J. Rosen, C. J. Cheng, O. V. Minin, and I. V. Minin, “Binary square axicon with chiral focusing properties for optical trapping,” Opt. Eng. 59, 041204 (2020).
[Crossref]

Opt. Express (5)

Opt. Laser Eng. (2)

Y. Deng, C. H. Huang, B. Vinoth, D. Chu, X. J. Lai, and C. J. Cheng, “A compact synthetic aperture digital holographic microscope with mechanical movement-free beam scanning and optimized active aberration compensation for isotropic resolution enhancement,” Opt. Laser Eng. 134, 106251 (2020).
[Crossref]

X. Ma, W. Xiao, and F. Pan, “Accuracy improvement in digital holographic microtomography by multiple numerical reconstructions,” Opt. Laser Eng. 86, 338–344 (2016).
[Crossref]

Opt. Lett. (2)

Optica (3)

Sci. Rep. (2)

B. Vinoth, X. J. Lai, Y. C. Lin, and C. J. Cheng, “Integrated dual-tomography for refractive index analysis of free-floating single living cell with isotropic superresolution,” Sci. Rep. 8, 5943 (2018).
[Crossref]

B. Vinoth, H. Y. Tu, X. J. Lai, and C. J. Cheng, “Adaptive wavefront correction structured illumination holographic tomography,” Sci. Rep. 9, 10489 (2019).
[Crossref]

Science (1)

A. Ashkin and J. M. Dziedzic, “Optical trapping and manipulation of viruses and bacteria,” Science 235, 1517–1520 (1987).
[Crossref]

Other (2)

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

P. Picart, New Techniques in Digital Holography (ISTE-Wiley, 2015).

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Figures (8)

Fig. 1.
Fig. 1. Experimental setup of sample rotation tomography. The green representation illustrates the holographic optical tweezers, and the red representation shows the digital holographic microscopy. HWP, half-wave plate; BS, beam splitter; M, mirror; L, lens; QWP, quarter-wave plate; SLM, spatial light modulator.
Fig. 2.
Fig. 2. Reconstructed phase results of live Candida rugosa orientation at different rotation angles. Scale bar: 2 µm.
Fig. 3.
Fig. 3. Different slice views of tomography results of Candida rugosa. (a) 2° step rotation; (b) 5°step rotation; (c) 10° step rotation. Scale bar: 2 µm, Color bar: refractive index values.
Fig. 4.
Fig. 4. Comparison of different slice views obtained after processing with the DTDWT. (a) Dense angle reconstruction with step rotation of 2°; (b) sparse angle reconstruction with step rotation of 5°; (c) sparse angle reconstruction with step rotation of 10°. Scale bar: 2 µm.
Fig. 5.
Fig. 5. Tomography reconstruction comparison of raw data and with BM3D. (a) Tomography reconstruction with 2° step rotation; (b) sparse angle tomography reconstruction with step rotation of 5°; (c) sparse angle tomography reconstruction with step rotation of 10°. Scale bar: 2 µm.
Fig. 6.
Fig. 6. Tomography slices comparison with and without WFT2F noise-reduction technique. (a) Dense angle reconstruction with 2° step rotation; (b) sparse angle reconstruction with step rotation of 5°; (c) sparse angle reconstruction with step rotation of 10°. Scale bar: 2 µm.
Fig. 7.
Fig. 7. Tomography slice comparison of raw data with and without the DL approach. (a) Dense angle reconstruction with 2° step rotation; (b) sparse angle reconstruction with step rotation of 5°; (c) sparse angle reconstruction with step rotation of 10°. Scale bar: 2 µm.
Fig. 8.
Fig. 8. Cross-sectional profile comparisons of different tomographic slices corresponding to (a) step rotation of 2°; (b) step rotation of 5°; and (c) step rotation of 10°.

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