Abstract

In this work we demonstrate large-scale high-sensitivity optical diffraction tomography (ODT) of zebrafish. We make this possible by three improvements. First, we obtain a large field of view while still maintaining a high resolution by using a high magnification over numerical aperture ratio digital holography set-up. With the inclusion of phase shifting we operate close to the optimum magnification over numerical aperture ratio. Second, we decrease the noise in the reconstructed images by implementing off-axis sample placement and numerical focus tracking in combination with the acquisition of a large number of projections. Although both techniques lead to an increase in sensitivity independently, we show that combining them is necessary in order to make optimal use of the potential gain offered by each respective method and obtain a refractive index (RI) sensitivity of 8105. Third, we optimize the optical clearing procedure to prevent scattering and refraction to occur. We demonstrate our technique by imaging a zebrafish larva over 13 mm 3 field of view with 4 micrometer resolution. Finally, we demonstrate a clinical application of our technique by imaging an entire adult cryoinjured zebrafish heart.

© 2019 Optical Society of America under the terms of the OSA Open Access Publishing Agreement

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References

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2018 (3)

M. M. Villone, P. Memmolo, F. Merola, M. Mugnano, L. Miccio, P. L. Maffettone, and P. Ferraro, “Full-angle tomographic phase microscopy of flowing quasi-spherical cells,” Lab Chip 18, 126–131 (2018).
[Crossref]

J. Bailleul, B. Simon, M. Debailleul, L. Foucault, N. Verrier, and O. Haeberlé, “Tomographic diffractive microscopy: Towards high-resolution 3D real-time data acquisition, image reconstruction and display of unlabeled samples,” Opt. Commun. 422, 28–37 (2018).
[Crossref]

W. Krauze, A. Kus, D. Sladowski, E. Skrzypek, and M. Kujawińska, “Reconstruction method for extended depth-of-field optical diffraction tomography,” Methods 136, 40–49 (2018).
[Crossref]

2017 (4)

Y. M. Bradford, S. Toro, S. Ramachandran, L. Ruzicka, D. G. Howe, A. Eagle, P. Kalita, R. Martin, S. A. T. Moxon, K. Schaper, and M. Westerfield, “Zebrafish models of human disease: Gaining insight into human disease at ZFIN,” ILAR Journal 58, 4–16 (2017).
[Crossref] [PubMed]

S.-L. Lai, R. Marín-Juez, P. L. Moura, C. Kuenne, J. K. H. Lai, A. T. Tsedeke, S. Guenther, M. Looso, and D. Y. Stainier, “Reciprocal analyses in zebrafish and medaka reveal that harnessing the immune response promotes cardiac regeneration,” eLife 6, e25605 (2017).
[Crossref]

J. van Rooij and J. Kalkman, “Sub-millimeter depth-resolved digital holography,” Appl. Opt. 56, 7286–7293 (2017).
[Crossref] [PubMed]

K. Kim, W. S. Park, S. Na, S. Kim, T. Kim, W. D. Heo, and Y. Park, “Correlative three-dimensional fluorescence and refractive index tomography: bridging the gap between molecular specificity and quantitative bioimaging,” Biomed. Opt. Express 8, 5688–5697 (2017).
[Crossref]

2016 (2)

K. Kim, J. Yoon, and Y. Park, “Large-scale optical diffraction tomography for inspection of optical plastic lenses,” Opt. Lett. 41, 934–937 (2016).
[Crossref] [PubMed]

M. Malek, H. Khelfa, P. Picart, D. Mounier, and C. Poilâne, “Microtomography imaging of an isolated plant fiber: a digital holographic approach,” Appl. Opt. 55, 111–121 (2016).
[Crossref]

2015 (2)

D. S. Richardson and J. W. Lichtman, “Clarifying tissue clearing,” Cell 162, 246–257 (2015).
[Crossref] [PubMed]

T. Correia, N. Lockwood, S. Kumar, J. Yin, M.-C. Ramel, N. Andrews, M. Katan, L. Bugeon, M. J. Dallman, J. McGinty, P. Frankel, P. M. W. French, and S. Arridge, “Accelerated optical projection tomography applied to in vivo imaging of zebrafish,” PLOS ONE 10, 1–17 (2015).
[Crossref]

2014 (3)

N. C. Pégard, M. L. Toth, M. Driscoll, and J. W. Fleischer, “Flow-scanning optical tomography,” Lab Chip 14, 4447–4450 (2014).
[Crossref] [PubMed]

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

J. Kostencka, T. Kozacki, M. Dudek, and M. Kujawińska, “Noise suppressed optical diffraction tomography with autofocus correction,” Opt. Express 22, 5731–5745 (2014).
[Crossref] [PubMed]

2012 (1)

J. M. González-Rosa and N. Mercader, “Cryoinjury as a myocardial infarction model for the study of cardiac regeneration in the zebrafish,” Nat. Protoc. 7, 782–788 (2012).
[Crossref] [PubMed]

2011 (2)

F. Chablais, J. Veit, G. Rainer, and A. Jaźwińska, “The zebrafish heart regenerates after cryoinjury-induced myocardial infarction,” BMC Dev. Biol. 11, 21 (2011).
[Crossref] [PubMed]

A. Bassi, L. Fieramonti, C. D’Andrea, M. C. Mione, and G. Valentini, “In vivo label-free three-dimensional imaging of zebrafish vasculature with optical projection tomography,” J. Biomed. Opt. 16(10), 100502 (2011).
[Crossref] [PubMed]

2009 (1)

2006 (1)

T. Alanentalo, A. Asayesh, H. Morrison, C. Lorén, D. Holmberg, J. Sharpe, and U. Ahlgren, “Tomographic molecular imaging and 3D quantification within adult mouse organs,” Nat. Methods 4, 31–33 (2006).
[Crossref] [PubMed]

1997 (1)

1994 (1)

Ahlgren, U.

T. Alanentalo, A. Asayesh, H. Morrison, C. Lorén, D. Holmberg, J. Sharpe, and U. Ahlgren, “Tomographic molecular imaging and 3D quantification within adult mouse organs,” Nat. Methods 4, 31–33 (2006).
[Crossref] [PubMed]

Alanentalo, T.

T. Alanentalo, A. Asayesh, H. Morrison, C. Lorén, D. Holmberg, J. Sharpe, and U. Ahlgren, “Tomographic molecular imaging and 3D quantification within adult mouse organs,” Nat. Methods 4, 31–33 (2006).
[Crossref] [PubMed]

Andrews, N.

T. Correia, N. Lockwood, S. Kumar, J. Yin, M.-C. Ramel, N. Andrews, M. Katan, L. Bugeon, M. J. Dallman, J. McGinty, P. Frankel, P. M. W. French, and S. Arridge, “Accelerated optical projection tomography applied to in vivo imaging of zebrafish,” PLOS ONE 10, 1–17 (2015).
[Crossref]

Arridge, S.

T. Correia, N. Lockwood, S. Kumar, J. Yin, M.-C. Ramel, N. Andrews, M. Katan, L. Bugeon, M. J. Dallman, J. McGinty, P. Frankel, P. M. W. French, and S. Arridge, “Accelerated optical projection tomography applied to in vivo imaging of zebrafish,” PLOS ONE 10, 1–17 (2015).
[Crossref]

Asayesh, A.

T. Alanentalo, A. Asayesh, H. Morrison, C. Lorén, D. Holmberg, J. Sharpe, and U. Ahlgren, “Tomographic molecular imaging and 3D quantification within adult mouse organs,” Nat. Methods 4, 31–33 (2006).
[Crossref] [PubMed]

Badizadegan, K.

Bailleul, J.

J. Bailleul, B. Simon, M. Debailleul, L. Foucault, N. Verrier, and O. Haeberlé, “Tomographic diffractive microscopy: Towards high-resolution 3D real-time data acquisition, image reconstruction and display of unlabeled samples,” Opt. Commun. 422, 28–37 (2018).
[Crossref]

Bassi, A.

A. Bassi, L. Fieramonti, C. D’Andrea, M. C. Mione, and G. Valentini, “In vivo label-free three-dimensional imaging of zebrafish vasculature with optical projection tomography,” J. Biomed. Opt. 16(10), 100502 (2011).
[Crossref] [PubMed]

Belay, B.

B. Belay, J. T. Koivisto, K. Vuornos, T. Montonen, O. Koskela, M. Lehti-Polojärvi, S. Miettinen, M. Kellomäki, E. Figueiras, and J. Hyttinen, “Optical projection tomography imaging of single cells in 3D gellan gum hydrogel,” in EMBEC & NBC 2017, H. Eskola, O. Väisänen, J. Viik, and J. Hyttinen, eds. (Springer Singapore, 2018), pp. 996–999.
[Crossref]

Berger, S.

R. Bryson-Richardson, S. Berger, and P. Currie, “Chapter 6 - 72 hours,” in Atlas of Zebrafish Development, R. Bryson-Richardson, S. Berger, and P. Currie, eds. (Academic Press, San Diego, 2012), pp. 55–76.
[Crossref]

Bradford, Y. M.

Y. M. Bradford, S. Toro, S. Ramachandran, L. Ruzicka, D. G. Howe, A. Eagle, P. Kalita, R. Martin, S. A. T. Moxon, K. Schaper, and M. Westerfield, “Zebrafish models of human disease: Gaining insight into human disease at ZFIN,” ILAR Journal 58, 4–16 (2017).
[Crossref] [PubMed]

Bryson-Richardson, R.

R. Bryson-Richardson, S. Berger, and P. Currie, “Chapter 6 - 72 hours,” in Atlas of Zebrafish Development, R. Bryson-Richardson, S. Berger, and P. Currie, eds. (Academic Press, San Diego, 2012), pp. 55–76.
[Crossref]

Bugeon, L.

T. Correia, N. Lockwood, S. Kumar, J. Yin, M.-C. Ramel, N. Andrews, M. Katan, L. Bugeon, M. J. Dallman, J. McGinty, P. Frankel, P. M. W. French, and S. Arridge, “Accelerated optical projection tomography applied to in vivo imaging of zebrafish,” PLOS ONE 10, 1–17 (2015).
[Crossref]

Chablais, F.

F. Chablais, J. Veit, G. Rainer, and A. Jaźwińska, “The zebrafish heart regenerates after cryoinjury-induced myocardial infarction,” BMC Dev. Biol. 11, 21 (2011).
[Crossref] [PubMed]

Choi, W.

Correia, T.

T. Correia, N. Lockwood, S. Kumar, J. Yin, M.-C. Ramel, N. Andrews, M. Katan, L. Bugeon, M. J. Dallman, J. McGinty, P. Frankel, P. M. W. French, and S. Arridge, “Accelerated optical projection tomography applied to in vivo imaging of zebrafish,” PLOS ONE 10, 1–17 (2015).
[Crossref]

Currie, P.

R. Bryson-Richardson, S. Berger, and P. Currie, “Chapter 6 - 72 hours,” in Atlas of Zebrafish Development, R. Bryson-Richardson, S. Berger, and P. Currie, eds. (Academic Press, San Diego, 2012), pp. 55–76.
[Crossref]

D’Andrea, C.

A. Bassi, L. Fieramonti, C. D’Andrea, M. C. Mione, and G. Valentini, “In vivo label-free three-dimensional imaging of zebrafish vasculature with optical projection tomography,” J. Biomed. Opt. 16(10), 100502 (2011).
[Crossref] [PubMed]

Dallman, M. J.

T. Correia, N. Lockwood, S. Kumar, J. Yin, M.-C. Ramel, N. Andrews, M. Katan, L. Bugeon, M. J. Dallman, J. McGinty, P. Frankel, P. M. W. French, and S. Arridge, “Accelerated optical projection tomography applied to in vivo imaging of zebrafish,” PLOS ONE 10, 1–17 (2015).
[Crossref]

Dasari, R. R.

Debailleul, M.

J. Bailleul, B. Simon, M. Debailleul, L. Foucault, N. Verrier, and O. Haeberlé, “Tomographic diffractive microscopy: Towards high-resolution 3D real-time data acquisition, image reconstruction and display of unlabeled samples,” Opt. Commun. 422, 28–37 (2018).
[Crossref]

Driscoll, M.

N. C. Pégard, M. L. Toth, M. Driscoll, and J. W. Fleischer, “Flow-scanning optical tomography,” Lab Chip 14, 4447–4450 (2014).
[Crossref] [PubMed]

Dudek, M.

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

J. Kostencka, T. Kozacki, M. Dudek, and M. Kujawińska, “Noise suppressed optical diffraction tomography with autofocus correction,” Opt. Express 22, 5731–5745 (2014).
[Crossref] [PubMed]

Eagle, A.

Y. M. Bradford, S. Toro, S. Ramachandran, L. Ruzicka, D. G. Howe, A. Eagle, P. Kalita, R. Martin, S. A. T. Moxon, K. Schaper, and M. Westerfield, “Zebrafish models of human disease: Gaining insight into human disease at ZFIN,” ILAR Journal 58, 4–16 (2017).
[Crossref] [PubMed]

Fang-Yen, C.

Feld, M. S.

Ferraro, P.

M. M. Villone, P. Memmolo, F. Merola, M. Mugnano, L. Miccio, P. L. Maffettone, and P. Ferraro, “Full-angle tomographic phase microscopy of flowing quasi-spherical cells,” Lab Chip 18, 126–131 (2018).
[Crossref]

Fieramonti, L.

A. Bassi, L. Fieramonti, C. D’Andrea, M. C. Mione, and G. Valentini, “In vivo label-free three-dimensional imaging of zebrafish vasculature with optical projection tomography,” J. Biomed. Opt. 16(10), 100502 (2011).
[Crossref] [PubMed]

Figueiras, E.

B. Belay, J. T. Koivisto, K. Vuornos, T. Montonen, O. Koskela, M. Lehti-Polojärvi, S. Miettinen, M. Kellomäki, E. Figueiras, and J. Hyttinen, “Optical projection tomography imaging of single cells in 3D gellan gum hydrogel,” in EMBEC & NBC 2017, H. Eskola, O. Väisänen, J. Viik, and J. Hyttinen, eds. (Springer Singapore, 2018), pp. 996–999.
[Crossref]

Fleischer, J. W.

N. C. Pégard, M. L. Toth, M. Driscoll, and J. W. Fleischer, “Flow-scanning optical tomography,” Lab Chip 14, 4447–4450 (2014).
[Crossref] [PubMed]

Foucault, L.

J. Bailleul, B. Simon, M. Debailleul, L. Foucault, N. Verrier, and O. Haeberlé, “Tomographic diffractive microscopy: Towards high-resolution 3D real-time data acquisition, image reconstruction and display of unlabeled samples,” Opt. Commun. 422, 28–37 (2018).
[Crossref]

Frankel, P.

T. Correia, N. Lockwood, S. Kumar, J. Yin, M.-C. Ramel, N. Andrews, M. Katan, L. Bugeon, M. J. Dallman, J. McGinty, P. Frankel, P. M. W. French, and S. Arridge, “Accelerated optical projection tomography applied to in vivo imaging of zebrafish,” PLOS ONE 10, 1–17 (2015).
[Crossref]

French, P. M. W.

T. Correia, N. Lockwood, S. Kumar, J. Yin, M.-C. Ramel, N. Andrews, M. Katan, L. Bugeon, M. J. Dallman, J. McGinty, P. Frankel, P. M. W. French, and S. Arridge, “Accelerated optical projection tomography applied to in vivo imaging of zebrafish,” PLOS ONE 10, 1–17 (2015).
[Crossref]

Ghiglia, D. C.

González-Rosa, J. M.

J. M. González-Rosa and N. Mercader, “Cryoinjury as a myocardial infarction model for the study of cardiac regeneration in the zebrafish,” Nat. Protoc. 7, 782–788 (2012).
[Crossref] [PubMed]

Guenther, S.

S.-L. Lai, R. Marín-Juez, P. L. Moura, C. Kuenne, J. K. H. Lai, A. T. Tsedeke, S. Guenther, M. Looso, and D. Y. Stainier, “Reciprocal analyses in zebrafish and medaka reveal that harnessing the immune response promotes cardiac regeneration,” eLife 6, e25605 (2017).
[Crossref]

Haeberlé, O.

J. Bailleul, B. Simon, M. Debailleul, L. Foucault, N. Verrier, and O. Haeberlé, “Tomographic diffractive microscopy: Towards high-resolution 3D real-time data acquisition, image reconstruction and display of unlabeled samples,” Opt. Commun. 422, 28–37 (2018).
[Crossref]

Heo, W. D.

Holmberg, D.

T. Alanentalo, A. Asayesh, H. Morrison, C. Lorén, D. Holmberg, J. Sharpe, and U. Ahlgren, “Tomographic molecular imaging and 3D quantification within adult mouse organs,” Nat. Methods 4, 31–33 (2006).
[Crossref] [PubMed]

Howe, D. G.

Y. M. Bradford, S. Toro, S. Ramachandran, L. Ruzicka, D. G. Howe, A. Eagle, P. Kalita, R. Martin, S. A. T. Moxon, K. Schaper, and M. Westerfield, “Zebrafish models of human disease: Gaining insight into human disease at ZFIN,” ILAR Journal 58, 4–16 (2017).
[Crossref] [PubMed]

Hyttinen, J.

B. Belay, J. T. Koivisto, K. Vuornos, T. Montonen, O. Koskela, M. Lehti-Polojärvi, S. Miettinen, M. Kellomäki, E. Figueiras, and J. Hyttinen, “Optical projection tomography imaging of single cells in 3D gellan gum hydrogel,” in EMBEC & NBC 2017, H. Eskola, O. Väisänen, J. Viik, and J. Hyttinen, eds. (Springer Singapore, 2018), pp. 996–999.
[Crossref]

Jazwinska, A.

F. Chablais, J. Veit, G. Rainer, and A. Jaźwińska, “The zebrafish heart regenerates after cryoinjury-induced myocardial infarction,” BMC Dev. Biol. 11, 21 (2011).
[Crossref] [PubMed]

Kalita, P.

Y. M. Bradford, S. Toro, S. Ramachandran, L. Ruzicka, D. G. Howe, A. Eagle, P. Kalita, R. Martin, S. A. T. Moxon, K. Schaper, and M. Westerfield, “Zebrafish models of human disease: Gaining insight into human disease at ZFIN,” ILAR Journal 58, 4–16 (2017).
[Crossref] [PubMed]

Kalkman, J.

Katan, M.

T. Correia, N. Lockwood, S. Kumar, J. Yin, M.-C. Ramel, N. Andrews, M. Katan, L. Bugeon, M. J. Dallman, J. McGinty, P. Frankel, P. M. W. French, and S. Arridge, “Accelerated optical projection tomography applied to in vivo imaging of zebrafish,” PLOS ONE 10, 1–17 (2015).
[Crossref]

Kellomäki, M.

B. Belay, J. T. Koivisto, K. Vuornos, T. Montonen, O. Koskela, M. Lehti-Polojärvi, S. Miettinen, M. Kellomäki, E. Figueiras, and J. Hyttinen, “Optical projection tomography imaging of single cells in 3D gellan gum hydrogel,” in EMBEC & NBC 2017, H. Eskola, O. Väisänen, J. Viik, and J. Hyttinen, eds. (Springer Singapore, 2018), pp. 996–999.
[Crossref]

Kemper, B.

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

Khelfa, H.

M. Malek, H. Khelfa, P. Picart, D. Mounier, and C. Poilâne, “Microtomography imaging of an isolated plant fiber: a digital holographic approach,” Appl. Opt. 55, 111–121 (2016).
[Crossref]

Kim, K.

Kim, S.

Kim, T.

Koivisto, J. T.

B. Belay, J. T. Koivisto, K. Vuornos, T. Montonen, O. Koskela, M. Lehti-Polojärvi, S. Miettinen, M. Kellomäki, E. Figueiras, and J. Hyttinen, “Optical projection tomography imaging of single cells in 3D gellan gum hydrogel,” in EMBEC & NBC 2017, H. Eskola, O. Väisänen, J. Viik, and J. Hyttinen, eds. (Springer Singapore, 2018), pp. 996–999.
[Crossref]

Koskela, O.

B. Belay, J. T. Koivisto, K. Vuornos, T. Montonen, O. Koskela, M. Lehti-Polojärvi, S. Miettinen, M. Kellomäki, E. Figueiras, and J. Hyttinen, “Optical projection tomography imaging of single cells in 3D gellan gum hydrogel,” in EMBEC & NBC 2017, H. Eskola, O. Väisänen, J. Viik, and J. Hyttinen, eds. (Springer Singapore, 2018), pp. 996–999.
[Crossref]

Kostencka, J.

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

J. Kostencka, T. Kozacki, M. Dudek, and M. Kujawińska, “Noise suppressed optical diffraction tomography with autofocus correction,” Opt. Express 22, 5731–5745 (2014).
[Crossref] [PubMed]

Kozacki, T.

J. Kostencka, T. Kozacki, M. Dudek, and M. Kujawińska, “Noise suppressed optical diffraction tomography with autofocus correction,” Opt. Express 22, 5731–5745 (2014).
[Crossref] [PubMed]

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

Krauze, W.

W. Krauze, A. Kus, D. Sladowski, E. Skrzypek, and M. Kujawińska, “Reconstruction method for extended depth-of-field optical diffraction tomography,” Methods 136, 40–49 (2018).
[Crossref]

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

Kroon, D.-J.

D.-J. Kroon, Region growing algorithm (m-file) (MathWorks, Accessed 2 Dec. 2019).

Kuenne, C.

S.-L. Lai, R. Marín-Juez, P. L. Moura, C. Kuenne, J. K. H. Lai, A. T. Tsedeke, S. Guenther, M. Looso, and D. Y. Stainier, “Reciprocal analyses in zebrafish and medaka reveal that harnessing the immune response promotes cardiac regeneration,” eLife 6, e25605 (2017).
[Crossref]

Kujawinska, M.

W. Krauze, A. Kus, D. Sladowski, E. Skrzypek, and M. Kujawińska, “Reconstruction method for extended depth-of-field optical diffraction tomography,” Methods 136, 40–49 (2018).
[Crossref]

J. Kostencka, T. Kozacki, M. Dudek, and M. Kujawińska, “Noise suppressed optical diffraction tomography with autofocus correction,” Opt. Express 22, 5731–5745 (2014).
[Crossref] [PubMed]

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

Kumar, S.

T. Correia, N. Lockwood, S. Kumar, J. Yin, M.-C. Ramel, N. Andrews, M. Katan, L. Bugeon, M. J. Dallman, J. McGinty, P. Frankel, P. M. W. French, and S. Arridge, “Accelerated optical projection tomography applied to in vivo imaging of zebrafish,” PLOS ONE 10, 1–17 (2015).
[Crossref]

Kus, A.

W. Krauze, A. Kus, D. Sladowski, E. Skrzypek, and M. Kujawińska, “Reconstruction method for extended depth-of-field optical diffraction tomography,” Methods 136, 40–49 (2018).
[Crossref]

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

Lai, J. K. H.

S.-L. Lai, R. Marín-Juez, P. L. Moura, C. Kuenne, J. K. H. Lai, A. T. Tsedeke, S. Guenther, M. Looso, and D. Y. Stainier, “Reciprocal analyses in zebrafish and medaka reveal that harnessing the immune response promotes cardiac regeneration,” eLife 6, e25605 (2017).
[Crossref]

Lai, S.-L.

S.-L. Lai, R. Marín-Juez, P. L. Moura, C. Kuenne, J. K. H. Lai, A. T. Tsedeke, S. Guenther, M. Looso, and D. Y. Stainier, “Reciprocal analyses in zebrafish and medaka reveal that harnessing the immune response promotes cardiac regeneration,” eLife 6, e25605 (2017).
[Crossref]

Lehti-Polojärvi, M.

B. Belay, J. T. Koivisto, K. Vuornos, T. Montonen, O. Koskela, M. Lehti-Polojärvi, S. Miettinen, M. Kellomäki, E. Figueiras, and J. Hyttinen, “Optical projection tomography imaging of single cells in 3D gellan gum hydrogel,” in EMBEC & NBC 2017, H. Eskola, O. Väisänen, J. Viik, and J. Hyttinen, eds. (Springer Singapore, 2018), pp. 996–999.
[Crossref]

Lichtman, J. W.

D. S. Richardson and J. W. Lichtman, “Clarifying tissue clearing,” Cell 162, 246–257 (2015).
[Crossref] [PubMed]

Limaye, A.

A. Limaye, “Drishti: a volume exploration and presentation tool,” Proc. SPIE 8506, Developments in X-Ray Tomography VIII, 85060X (2012).
[Crossref]

Lockwood, N.

T. Correia, N. Lockwood, S. Kumar, J. Yin, M.-C. Ramel, N. Andrews, M. Katan, L. Bugeon, M. J. Dallman, J. McGinty, P. Frankel, P. M. W. French, and S. Arridge, “Accelerated optical projection tomography applied to in vivo imaging of zebrafish,” PLOS ONE 10, 1–17 (2015).
[Crossref]

Looso, M.

S.-L. Lai, R. Marín-Juez, P. L. Moura, C. Kuenne, J. K. H. Lai, A. T. Tsedeke, S. Guenther, M. Looso, and D. Y. Stainier, “Reciprocal analyses in zebrafish and medaka reveal that harnessing the immune response promotes cardiac regeneration,” eLife 6, e25605 (2017).
[Crossref]

Lorén, C.

T. Alanentalo, A. Asayesh, H. Morrison, C. Lorén, D. Holmberg, J. Sharpe, and U. Ahlgren, “Tomographic molecular imaging and 3D quantification within adult mouse organs,” Nat. Methods 4, 31–33 (2006).
[Crossref] [PubMed]

Maffettone, P. L.

M. M. Villone, P. Memmolo, F. Merola, M. Mugnano, L. Miccio, P. L. Maffettone, and P. Ferraro, “Full-angle tomographic phase microscopy of flowing quasi-spherical cells,” Lab Chip 18, 126–131 (2018).
[Crossref]

Malek, M.

M. Malek, H. Khelfa, P. Picart, D. Mounier, and C. Poilâne, “Microtomography imaging of an isolated plant fiber: a digital holographic approach,” Appl. Opt. 55, 111–121 (2016).
[Crossref]

Marín-Juez, R.

S.-L. Lai, R. Marín-Juez, P. L. Moura, C. Kuenne, J. K. H. Lai, A. T. Tsedeke, S. Guenther, M. Looso, and D. Y. Stainier, “Reciprocal analyses in zebrafish and medaka reveal that harnessing the immune response promotes cardiac regeneration,” eLife 6, e25605 (2017).
[Crossref]

Martin, R.

Y. M. Bradford, S. Toro, S. Ramachandran, L. Ruzicka, D. G. Howe, A. Eagle, P. Kalita, R. Martin, S. A. T. Moxon, K. Schaper, and M. Westerfield, “Zebrafish models of human disease: Gaining insight into human disease at ZFIN,” ILAR Journal 58, 4–16 (2017).
[Crossref] [PubMed]

McGinty, J.

T. Correia, N. Lockwood, S. Kumar, J. Yin, M.-C. Ramel, N. Andrews, M. Katan, L. Bugeon, M. J. Dallman, J. McGinty, P. Frankel, P. M. W. French, and S. Arridge, “Accelerated optical projection tomography applied to in vivo imaging of zebrafish,” PLOS ONE 10, 1–17 (2015).
[Crossref]

Memmolo, P.

M. M. Villone, P. Memmolo, F. Merola, M. Mugnano, L. Miccio, P. L. Maffettone, and P. Ferraro, “Full-angle tomographic phase microscopy of flowing quasi-spherical cells,” Lab Chip 18, 126–131 (2018).
[Crossref]

Mercader, N.

J. M. González-Rosa and N. Mercader, “Cryoinjury as a myocardial infarction model for the study of cardiac regeneration in the zebrafish,” Nat. Protoc. 7, 782–788 (2012).
[Crossref] [PubMed]

Merola, F.

M. M. Villone, P. Memmolo, F. Merola, M. Mugnano, L. Miccio, P. L. Maffettone, and P. Ferraro, “Full-angle tomographic phase microscopy of flowing quasi-spherical cells,” Lab Chip 18, 126–131 (2018).
[Crossref]

Miccio, L.

M. M. Villone, P. Memmolo, F. Merola, M. Mugnano, L. Miccio, P. L. Maffettone, and P. Ferraro, “Full-angle tomographic phase microscopy of flowing quasi-spherical cells,” Lab Chip 18, 126–131 (2018).
[Crossref]

Miettinen, S.

B. Belay, J. T. Koivisto, K. Vuornos, T. Montonen, O. Koskela, M. Lehti-Polojärvi, S. Miettinen, M. Kellomäki, E. Figueiras, and J. Hyttinen, “Optical projection tomography imaging of single cells in 3D gellan gum hydrogel,” in EMBEC & NBC 2017, H. Eskola, O. Väisänen, J. Viik, and J. Hyttinen, eds. (Springer Singapore, 2018), pp. 996–999.
[Crossref]

Mione, M. C.

A. Bassi, L. Fieramonti, C. D’Andrea, M. C. Mione, and G. Valentini, “In vivo label-free three-dimensional imaging of zebrafish vasculature with optical projection tomography,” J. Biomed. Opt. 16(10), 100502 (2011).
[Crossref] [PubMed]

Montonen, T.

B. Belay, J. T. Koivisto, K. Vuornos, T. Montonen, O. Koskela, M. Lehti-Polojärvi, S. Miettinen, M. Kellomäki, E. Figueiras, and J. Hyttinen, “Optical projection tomography imaging of single cells in 3D gellan gum hydrogel,” in EMBEC & NBC 2017, H. Eskola, O. Väisänen, J. Viik, and J. Hyttinen, eds. (Springer Singapore, 2018), pp. 996–999.
[Crossref]

Morrison, H.

T. Alanentalo, A. Asayesh, H. Morrison, C. Lorén, D. Holmberg, J. Sharpe, and U. Ahlgren, “Tomographic molecular imaging and 3D quantification within adult mouse organs,” Nat. Methods 4, 31–33 (2006).
[Crossref] [PubMed]

Mounier, D.

M. Malek, H. Khelfa, P. Picart, D. Mounier, and C. Poilâne, “Microtomography imaging of an isolated plant fiber: a digital holographic approach,” Appl. Opt. 55, 111–121 (2016).
[Crossref]

Moura, P. L.

S.-L. Lai, R. Marín-Juez, P. L. Moura, C. Kuenne, J. K. H. Lai, A. T. Tsedeke, S. Guenther, M. Looso, and D. Y. Stainier, “Reciprocal analyses in zebrafish and medaka reveal that harnessing the immune response promotes cardiac regeneration,” eLife 6, e25605 (2017).
[Crossref]

Moxon, S. A. T.

Y. M. Bradford, S. Toro, S. Ramachandran, L. Ruzicka, D. G. Howe, A. Eagle, P. Kalita, R. Martin, S. A. T. Moxon, K. Schaper, and M. Westerfield, “Zebrafish models of human disease: Gaining insight into human disease at ZFIN,” ILAR Journal 58, 4–16 (2017).
[Crossref] [PubMed]

Mugnano, M.

M. M. Villone, P. Memmolo, F. Merola, M. Mugnano, L. Miccio, P. L. Maffettone, and P. Ferraro, “Full-angle tomographic phase microscopy of flowing quasi-spherical cells,” Lab Chip 18, 126–131 (2018).
[Crossref]

Na, S.

Park, W. S.

Park, Y.

Pégard, N. C.

N. C. Pégard, M. L. Toth, M. Driscoll, and J. W. Fleischer, “Flow-scanning optical tomography,” Lab Chip 14, 4447–4450 (2014).
[Crossref] [PubMed]

Picart, P.

M. Malek, H. Khelfa, P. Picart, D. Mounier, and C. Poilâne, “Microtomography imaging of an isolated plant fiber: a digital holographic approach,” Appl. Opt. 55, 111–121 (2016).
[Crossref]

Poilâne, C.

M. Malek, H. Khelfa, P. Picart, D. Mounier, and C. Poilâne, “Microtomography imaging of an isolated plant fiber: a digital holographic approach,” Appl. Opt. 55, 111–121 (2016).
[Crossref]

Rainer, G.

F. Chablais, J. Veit, G. Rainer, and A. Jaźwińska, “The zebrafish heart regenerates after cryoinjury-induced myocardial infarction,” BMC Dev. Biol. 11, 21 (2011).
[Crossref] [PubMed]

Ramachandran, S.

Y. M. Bradford, S. Toro, S. Ramachandran, L. Ruzicka, D. G. Howe, A. Eagle, P. Kalita, R. Martin, S. A. T. Moxon, K. Schaper, and M. Westerfield, “Zebrafish models of human disease: Gaining insight into human disease at ZFIN,” ILAR Journal 58, 4–16 (2017).
[Crossref] [PubMed]

Ramel, M.-C.

T. Correia, N. Lockwood, S. Kumar, J. Yin, M.-C. Ramel, N. Andrews, M. Katan, L. Bugeon, M. J. Dallman, J. McGinty, P. Frankel, P. M. W. French, and S. Arridge, “Accelerated optical projection tomography applied to in vivo imaging of zebrafish,” PLOS ONE 10, 1–17 (2015).
[Crossref]

Richardson, D. S.

D. S. Richardson and J. W. Lichtman, “Clarifying tissue clearing,” Cell 162, 246–257 (2015).
[Crossref] [PubMed]

Romero, L. A.

Ruzicka, L.

Y. M. Bradford, S. Toro, S. Ramachandran, L. Ruzicka, D. G. Howe, A. Eagle, P. Kalita, R. Martin, S. A. T. Moxon, K. Schaper, and M. Westerfield, “Zebrafish models of human disease: Gaining insight into human disease at ZFIN,” ILAR Journal 58, 4–16 (2017).
[Crossref] [PubMed]

Schaper, K.

Y. M. Bradford, S. Toro, S. Ramachandran, L. Ruzicka, D. G. Howe, A. Eagle, P. Kalita, R. Martin, S. A. T. Moxon, K. Schaper, and M. Westerfield, “Zebrafish models of human disease: Gaining insight into human disease at ZFIN,” ILAR Journal 58, 4–16 (2017).
[Crossref] [PubMed]

Sharpe, J.

T. Alanentalo, A. Asayesh, H. Morrison, C. Lorén, D. Holmberg, J. Sharpe, and U. Ahlgren, “Tomographic molecular imaging and 3D quantification within adult mouse organs,” Nat. Methods 4, 31–33 (2006).
[Crossref] [PubMed]

J. Sharpe, Optical Projection Tomography(Springer Berlin Heidelberg, 2009), pp. 199–224.

Simon, B.

J. Bailleul, B. Simon, M. Debailleul, L. Foucault, N. Verrier, and O. Haeberlé, “Tomographic diffractive microscopy: Towards high-resolution 3D real-time data acquisition, image reconstruction and display of unlabeled samples,” Opt. Commun. 422, 28–37 (2018).
[Crossref]

Skrzypek, E.

W. Krauze, A. Kus, D. Sladowski, E. Skrzypek, and M. Kujawińska, “Reconstruction method for extended depth-of-field optical diffraction tomography,” Methods 136, 40–49 (2018).
[Crossref]

Sladowski, D.

W. Krauze, A. Kus, D. Sladowski, E. Skrzypek, and M. Kujawińska, “Reconstruction method for extended depth-of-field optical diffraction tomography,” Methods 136, 40–49 (2018).
[Crossref]

Stainier, D. Y.

S.-L. Lai, R. Marín-Juez, P. L. Moura, C. Kuenne, J. K. H. Lai, A. T. Tsedeke, S. Guenther, M. Looso, and D. Y. Stainier, “Reciprocal analyses in zebrafish and medaka reveal that harnessing the immune response promotes cardiac regeneration,” eLife 6, e25605 (2017).
[Crossref]

Sung, Y.

Toro, S.

Y. M. Bradford, S. Toro, S. Ramachandran, L. Ruzicka, D. G. Howe, A. Eagle, P. Kalita, R. Martin, S. A. T. Moxon, K. Schaper, and M. Westerfield, “Zebrafish models of human disease: Gaining insight into human disease at ZFIN,” ILAR Journal 58, 4–16 (2017).
[Crossref] [PubMed]

Toth, M. L.

N. C. Pégard, M. L. Toth, M. Driscoll, and J. W. Fleischer, “Flow-scanning optical tomography,” Lab Chip 14, 4447–4450 (2014).
[Crossref] [PubMed]

Tsedeke, A. T.

S.-L. Lai, R. Marín-Juez, P. L. Moura, C. Kuenne, J. K. H. Lai, A. T. Tsedeke, S. Guenther, M. Looso, and D. Y. Stainier, “Reciprocal analyses in zebrafish and medaka reveal that harnessing the immune response promotes cardiac regeneration,” eLife 6, e25605 (2017).
[Crossref]

Valentini, G.

A. Bassi, L. Fieramonti, C. D’Andrea, M. C. Mione, and G. Valentini, “In vivo label-free three-dimensional imaging of zebrafish vasculature with optical projection tomography,” J. Biomed. Opt. 16(10), 100502 (2011).
[Crossref] [PubMed]

van Rooij, J.

Veit, J.

F. Chablais, J. Veit, G. Rainer, and A. Jaźwińska, “The zebrafish heart regenerates after cryoinjury-induced myocardial infarction,” BMC Dev. Biol. 11, 21 (2011).
[Crossref] [PubMed]

Verrier, N.

J. Bailleul, B. Simon, M. Debailleul, L. Foucault, N. Verrier, and O. Haeberlé, “Tomographic diffractive microscopy: Towards high-resolution 3D real-time data acquisition, image reconstruction and display of unlabeled samples,” Opt. Commun. 422, 28–37 (2018).
[Crossref]

Villone, M. M.

M. M. Villone, P. Memmolo, F. Merola, M. Mugnano, L. Miccio, P. L. Maffettone, and P. Ferraro, “Full-angle tomographic phase microscopy of flowing quasi-spherical cells,” Lab Chip 18, 126–131 (2018).
[Crossref]

Vuornos, K.

B. Belay, J. T. Koivisto, K. Vuornos, T. Montonen, O. Koskela, M. Lehti-Polojärvi, S. Miettinen, M. Kellomäki, E. Figueiras, and J. Hyttinen, “Optical projection tomography imaging of single cells in 3D gellan gum hydrogel,” in EMBEC & NBC 2017, H. Eskola, O. Väisänen, J. Viik, and J. Hyttinen, eds. (Springer Singapore, 2018), pp. 996–999.
[Crossref]

Westerfield, M.

Y. M. Bradford, S. Toro, S. Ramachandran, L. Ruzicka, D. G. Howe, A. Eagle, P. Kalita, R. Martin, S. A. T. Moxon, K. Schaper, and M. Westerfield, “Zebrafish models of human disease: Gaining insight into human disease at ZFIN,” ILAR Journal 58, 4–16 (2017).
[Crossref] [PubMed]

Yamaguchi, I.

Yin, J.

T. Correia, N. Lockwood, S. Kumar, J. Yin, M.-C. Ramel, N. Andrews, M. Katan, L. Bugeon, M. J. Dallman, J. McGinty, P. Frankel, P. M. W. French, and S. Arridge, “Accelerated optical projection tomography applied to in vivo imaging of zebrafish,” PLOS ONE 10, 1–17 (2015).
[Crossref]

Yoon, J.

Zhang, T.

Appl. Opt. (2)

M. Malek, H. Khelfa, P. Picart, D. Mounier, and C. Poilâne, “Microtomography imaging of an isolated plant fiber: a digital holographic approach,” Appl. Opt. 55, 111–121 (2016).
[Crossref]

J. van Rooij and J. Kalkman, “Sub-millimeter depth-resolved digital holography,” Appl. Opt. 56, 7286–7293 (2017).
[Crossref] [PubMed]

Biomed. Opt. Express (1)

BMC Dev. Biol. (1)

F. Chablais, J. Veit, G. Rainer, and A. Jaźwińska, “The zebrafish heart regenerates after cryoinjury-induced myocardial infarction,” BMC Dev. Biol. 11, 21 (2011).
[Crossref] [PubMed]

Cell (1)

D. S. Richardson and J. W. Lichtman, “Clarifying tissue clearing,” Cell 162, 246–257 (2015).
[Crossref] [PubMed]

eLife (1)

S.-L. Lai, R. Marín-Juez, P. L. Moura, C. Kuenne, J. K. H. Lai, A. T. Tsedeke, S. Guenther, M. Looso, and D. Y. Stainier, “Reciprocal analyses in zebrafish and medaka reveal that harnessing the immune response promotes cardiac regeneration,” eLife 6, e25605 (2017).
[Crossref]

ILAR Journal (1)

Y. M. Bradford, S. Toro, S. Ramachandran, L. Ruzicka, D. G. Howe, A. Eagle, P. Kalita, R. Martin, S. A. T. Moxon, K. Schaper, and M. Westerfield, “Zebrafish models of human disease: Gaining insight into human disease at ZFIN,” ILAR Journal 58, 4–16 (2017).
[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 3D analysis of phase biological objects by optical diffraction tomography,” Int. J. Optomechatronics 8, 357–372 (2014).
[Crossref]

J. Biomed. Opt. (1)

A. Bassi, L. Fieramonti, C. D’Andrea, M. C. Mione, and G. Valentini, “In vivo label-free three-dimensional imaging of zebrafish vasculature with optical projection tomography,” J. Biomed. Opt. 16(10), 100502 (2011).
[Crossref] [PubMed]

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

Lab Chip (2)

M. M. Villone, P. Memmolo, F. Merola, M. Mugnano, L. Miccio, P. L. Maffettone, and P. Ferraro, “Full-angle tomographic phase microscopy of flowing quasi-spherical cells,” Lab Chip 18, 126–131 (2018).
[Crossref]

N. C. Pégard, M. L. Toth, M. Driscoll, and J. W. Fleischer, “Flow-scanning optical tomography,” Lab Chip 14, 4447–4450 (2014).
[Crossref] [PubMed]

Methods (1)

W. Krauze, A. Kus, D. Sladowski, E. Skrzypek, and M. Kujawińska, “Reconstruction method for extended depth-of-field optical diffraction tomography,” Methods 136, 40–49 (2018).
[Crossref]

Nat. Methods (1)

T. Alanentalo, A. Asayesh, H. Morrison, C. Lorén, D. Holmberg, J. Sharpe, and U. Ahlgren, “Tomographic molecular imaging and 3D quantification within adult mouse organs,” Nat. Methods 4, 31–33 (2006).
[Crossref] [PubMed]

Nat. Protoc. (1)

J. M. González-Rosa and N. Mercader, “Cryoinjury as a myocardial infarction model for the study of cardiac regeneration in the zebrafish,” Nat. Protoc. 7, 782–788 (2012).
[Crossref] [PubMed]

Opt. Commun. (1)

J. Bailleul, B. Simon, M. Debailleul, L. Foucault, N. Verrier, and O. Haeberlé, “Tomographic diffractive microscopy: Towards high-resolution 3D real-time data acquisition, image reconstruction and display of unlabeled samples,” Opt. Commun. 422, 28–37 (2018).
[Crossref]

Opt. Express (2)

Opt. Lett. (2)

PLOS ONE (1)

T. Correia, N. Lockwood, S. Kumar, J. Yin, M.-C. Ramel, N. Andrews, M. Katan, L. Bugeon, M. J. Dallman, J. McGinty, P. Frankel, P. M. W. French, and S. Arridge, “Accelerated optical projection tomography applied to in vivo imaging of zebrafish,” PLOS ONE 10, 1–17 (2015).
[Crossref]

Other (5)

B. Belay, J. T. Koivisto, K. Vuornos, T. Montonen, O. Koskela, M. Lehti-Polojärvi, S. Miettinen, M. Kellomäki, E. Figueiras, and J. Hyttinen, “Optical projection tomography imaging of single cells in 3D gellan gum hydrogel,” in EMBEC & NBC 2017, H. Eskola, O. Väisänen, J. Viik, and J. Hyttinen, eds. (Springer Singapore, 2018), pp. 996–999.
[Crossref]

J. Sharpe, Optical Projection Tomography(Springer Berlin Heidelberg, 2009), pp. 199–224.

R. Bryson-Richardson, S. Berger, and P. Currie, “Chapter 6 - 72 hours,” in Atlas of Zebrafish Development, R. Bryson-Richardson, S. Berger, and P. Currie, eds. (Academic Press, San Diego, 2012), pp. 55–76.
[Crossref]

D.-J. Kroon, Region growing algorithm (m-file) (MathWorks, Accessed 2 Dec. 2019).

A. Limaye, “Drishti: a volume exploration and presentation tool,” Proc. SPIE 8506, Developments in X-Ray Tomography VIII, 85060X (2012).
[Crossref]

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Figures (6)

Fig. 1
Fig. 1 Experimental setup for acquiring the digital holograms. HeNe: Helium Neon laser, BE: Beam expander, BS: Beam splitter, IML: Index matching liquid, S: Sample rotated around the z-axis, MO: Microscope objective, M: Mirror, TL: Tube lens, PZT: Mirror mounted on piezo stage, C: Camera.
Fig. 2
Fig. 2 (a) Reconstruction of a horizontal cross-section of the agar sample indicating the a point close to the center of rotation (green circle) and one 1 mm radially outward (red circle). (b) Noise levels at the center of rotation and 1.5 mm radially outward as a function of the number of projections (Np), with y = a N p 0.5 fitted to the off-axis data and the on-axis noise limit indicated by a constant. (c) Plot of the precision, defined as the inverse of the variance, of the same data and model as in (b), with y = a N p fitted to the off-axis data and the on-axis noise limit indicated by a constant. (d) Noise levels as a function of distance to the center for 1440 and 144 projections respectively (cross-section horizontally through the middle in (a)).
Fig. 3
Fig. 3 Flowchart that shows schematically the steps from acquisition of the phase shifted holograms to the final 3D reconstruction.
Fig. 4
Fig. 4 (a-c) Coronal, saggital, and axial cross-sections of ODT reconstructed refractive index contrast of an optically cleared 3 day old zebrafish larva. (d) Δ n distribution of agarose background in which the zebrafish sample is placed. From this the sensitivity in the reconstruction was calculated as the standard deviation of the distribution and yields σ = 8 10 5 .
Fig. 5
Fig. 5 A 3D visualization of a complete zebrafish larva (3 days old) based on RI differences is shown in (a) and for different cross-sections in (b-e). In (f), a logarithmic plot is shown of the RI distribution of the complete sample (zebrafish larva and agarose). Indicated are the estimated Δ n distributions of different types of tissue in the zebrafish larvae. The first two peaks in blue from the left are from the agarose and index matching liquid (BABB) contributions respectively.
Fig. 6
Fig. 6 Virtual cross-sections in the y-z plane (a), x-y plane (b) and the x-z plane (c) showing the Δ n distribution of a 1 year old zebrafish heart, damaged through cryoinjury. The regenerating tissue can be seen in the bounded region (red) in image (a) obtained through region growing segmentation. Features can be seen such as the injured area (IA), the ventricle (V), the bulbus (B) and the atrium (A).

Equations (2)

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0.61 λ N A M 4 ξ
M N A > 57 .