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Large scale high sensitivity optical diffraction tomography of zebrafish. / van Rooij, Jos; Kalkman, Jeroen.

Proceedings of SPIE: Advances in Microscopic Imaging II. ed. / Emmanuel Beaurepaire; Francesco Saverio Pavone. Vol. 11076 SPIE, 2019. 110760U.

Research output: Chapter in Book/Report/Conference proceedingConference contributionScientificpeer-review

Harvard

van Rooij, J & Kalkman, J 2019, Large scale high sensitivity optical diffraction tomography of zebrafish. in E Beaurepaire & FS Pavone (eds), Proceedings of SPIE: Advances in Microscopic Imaging II. vol. 11076, 110760U, SPIE, Advances in Microscopic Imaging II 2019, Munich, Germany, 26/06/19. https://doi.org/10.1117/12.2526612

APA

van Rooij, J., & Kalkman, J. (2019). Large scale high sensitivity optical diffraction tomography of zebrafish. In E. Beaurepaire, & F. S. Pavone (Eds.), Proceedings of SPIE: Advances in Microscopic Imaging II (Vol. 11076). [110760U] SPIE. https://doi.org/10.1117/12.2526612

Vancouver

van Rooij J, Kalkman J. Large scale high sensitivity optical diffraction tomography of zebrafish. In Beaurepaire E, Pavone FS, editors, Proceedings of SPIE: Advances in Microscopic Imaging II. Vol. 11076. SPIE. 2019. 110760U https://doi.org/10.1117/12.2526612

Author

van Rooij, Jos ; Kalkman, Jeroen. / Large scale high sensitivity optical diffraction tomography of zebrafish. Proceedings of SPIE: Advances in Microscopic Imaging II. editor / Emmanuel Beaurepaire ; Francesco Saverio Pavone. Vol. 11076 SPIE, 2019.

BibTeX

@inproceedings{7e71f880b7dd42979fe6a20ef1fec1bd,
title = "Large scale high sensitivity optical diffraction tomography of zebrafish",
abstract = "In this work we demonstrate large scale high sensitivity optical diffraction tomography (ODT) of zebrafish. Compared to previous work the scale and sensitivity are enhanced by the following steps. First, we obtain a large field of view while still maintaining a high image resolution by using a high magnification over numerical aperture ratio ODT set-up. With the inclusion of phase shifting we demonstrate that 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 8•10-5. In this way, high RI sensitivity can be achieved that is necessary for phase tomography of optically cleared tissue structures, which we can identify for features with RI down to 6•10-4. Third, we optimize the optical clearing procedure to prevent scattering and refraction to deteriorate our large scale images. We demonstrate our technique by imaging a 3 day old zebrafish and an adult cryoinjured zebrafish heart in a large 5.5 x 5.5 x 4.1 mm3 volume with 4 micrometer resolution. Various tissue structures can be clearly identified. The volume of the cryoinjured heart is segmented and quantified based on the refractive index distribution.",
author = "{van Rooij}, Jos and Jeroen Kalkman",
year = "2019",
doi = "10.1117/12.2526612",
language = "English",
volume = "11076",
editor = "Emmanuel Beaurepaire and Pavone, {Francesco Saverio}",
booktitle = "Proceedings of SPIE",
publisher = "SPIE",
address = "United States",

}

RIS

TY - GEN

T1 - Large scale high sensitivity optical diffraction tomography of zebrafish

AU - van Rooij, Jos

AU - Kalkman, Jeroen

PY - 2019

Y1 - 2019

N2 - In this work we demonstrate large scale high sensitivity optical diffraction tomography (ODT) of zebrafish. Compared to previous work the scale and sensitivity are enhanced by the following steps. First, we obtain a large field of view while still maintaining a high image resolution by using a high magnification over numerical aperture ratio ODT set-up. With the inclusion of phase shifting we demonstrate that 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 8•10-5. In this way, high RI sensitivity can be achieved that is necessary for phase tomography of optically cleared tissue structures, which we can identify for features with RI down to 6•10-4. Third, we optimize the optical clearing procedure to prevent scattering and refraction to deteriorate our large scale images. We demonstrate our technique by imaging a 3 day old zebrafish and an adult cryoinjured zebrafish heart in a large 5.5 x 5.5 x 4.1 mm3 volume with 4 micrometer resolution. Various tissue structures can be clearly identified. The volume of the cryoinjured heart is segmented and quantified based on the refractive index distribution.

AB - In this work we demonstrate large scale high sensitivity optical diffraction tomography (ODT) of zebrafish. Compared to previous work the scale and sensitivity are enhanced by the following steps. First, we obtain a large field of view while still maintaining a high image resolution by using a high magnification over numerical aperture ratio ODT set-up. With the inclusion of phase shifting we demonstrate that 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 8•10-5. In this way, high RI sensitivity can be achieved that is necessary for phase tomography of optically cleared tissue structures, which we can identify for features with RI down to 6•10-4. Third, we optimize the optical clearing procedure to prevent scattering and refraction to deteriorate our large scale images. We demonstrate our technique by imaging a 3 day old zebrafish and an adult cryoinjured zebrafish heart in a large 5.5 x 5.5 x 4.1 mm3 volume with 4 micrometer resolution. Various tissue structures can be clearly identified. The volume of the cryoinjured heart is segmented and quantified based on the refractive index distribution.

UR - http://www.scopus.com/inward/record.url?scp=85074257784&partnerID=8YFLogxK

U2 - 10.1117/12.2526612

DO - 10.1117/12.2526612

M3 - Conference contribution

VL - 11076

BT - Proceedings of SPIE

A2 - Beaurepaire, Emmanuel

A2 - Pavone, Francesco Saverio

PB - SPIE

ER -

ID: 66540430