Computational 3D histological phenotyping of whole zebrafish by X-ray histotomography
Abstract
Organismal phenotypes frequently involve multiple organ systems. Histology is a powerful way to detect cellular and tissue phenotypes, but is largely descriptive and subjective. To determine how synchrotron-based X-ray micro-tomography (micro-CT) can yield 3-dimensional whole-organism images suitable for quantitative histological phenotyping, we scanned whole zebrafish, a small vertebrate model with diverse tissues, at ~1 micron voxel resolutions. Micro-CT optimized for cellular characterization (histotomography) allows brain nuclei to be computationally segmented and assigned to brain regions, and cell shapes and volumes to be computed for motor neurons and red blood cells. Striking individual phenotypic variation was apparent from color maps of computed densities of brain nuclei. Unlike histology, the histotomography also allows the study of 3-dimensional structures of millimeter scale that cross multiple tissue planes. We expect the computational and visual insights into 3D cell and tissue architecture provided by histotomography to be useful for reference atlases, hypothesis generation, comprehensive organismal screens, and diagnostics.
- Authors:
-
[1];
[1];
[1];
[1];
[1];
[1];
[1];
[3];
[1]
- Penn State College of Medicine, Hershey, PA (United States)
- Duke Univ., Durham, NC (United States)
- The Univ. of Chicago, Chicago, IL (United States)
- Omnivision Technologies, Inc., Santa Clara, CA (United States)
- Brookhaven National Lab. (BNL), Upton, NY (United States)
- Argonne National Lab. (ANL), Lemont, IL (United States)
- Publication Date:
- Research Org.:
- Argonne National Laboratory (ANL), Argonne, IL (United States)
- Sponsoring Org.:
- National Institutes of Health (NIH); USDOE Office of Science (SC), Basic Energy Sciences (BES)
- OSTI Identifier:
- 1558992
- Grant/Contract Number:
- AC02-06CH11357
- Resource Type:
- Accepted Manuscript
- Journal Name:
- eLife
- Additional Journal Information:
- Journal Volume: 8; Journal ID: ISSN 2050-084X
- Publisher:
- eLife Sciences Publications, Ltd.
- Country of Publication:
- United States
- Language:
- English
- Subject:
- 59 BASIC BIOLOGICAL SCIENCES
Citation Formats
Ding, Yifu, Vanselow, Daniel J., Yakovlev, Maksim A., Katz, Spencer R., Lin, Alex Y., Clark, Darin P., Vargas, Phillip, Xin, Xuying, Copper, Jean E., Canfield, Victor A., Ang, Khai C., Wang, Yuxin, Xiao, Xianghui, De Carlo, Francesco, van Rossum, Damian B., La Riviere, Patrick, and Cheng, Keith C. Computational 3D histological phenotyping of whole zebrafish by X-ray histotomography. United States: N. p., 2019.
Web. doi:10.7554/eLife.44898.
Ding, Yifu, Vanselow, Daniel J., Yakovlev, Maksim A., Katz, Spencer R., Lin, Alex Y., Clark, Darin P., Vargas, Phillip, Xin, Xuying, Copper, Jean E., Canfield, Victor A., Ang, Khai C., Wang, Yuxin, Xiao, Xianghui, De Carlo, Francesco, van Rossum, Damian B., La Riviere, Patrick, & Cheng, Keith C. Computational 3D histological phenotyping of whole zebrafish by X-ray histotomography. United States. https://doi.org/10.7554/eLife.44898
Ding, Yifu, Vanselow, Daniel J., Yakovlev, Maksim A., Katz, Spencer R., Lin, Alex Y., Clark, Darin P., Vargas, Phillip, Xin, Xuying, Copper, Jean E., Canfield, Victor A., Ang, Khai C., Wang, Yuxin, Xiao, Xianghui, De Carlo, Francesco, van Rossum, Damian B., La Riviere, Patrick, and Cheng, Keith C. Tue .
"Computational 3D histological phenotyping of whole zebrafish by X-ray histotomography". United States. https://doi.org/10.7554/eLife.44898. https://www.osti.gov/servlets/purl/1558992.
@article{osti_1558992,
title = {Computational 3D histological phenotyping of whole zebrafish by X-ray histotomography},
author = {Ding, Yifu and Vanselow, Daniel J. and Yakovlev, Maksim A. and Katz, Spencer R. and Lin, Alex Y. and Clark, Darin P. and Vargas, Phillip and Xin, Xuying and Copper, Jean E. and Canfield, Victor A. and Ang, Khai C. and Wang, Yuxin and Xiao, Xianghui and De Carlo, Francesco and van Rossum, Damian B. and La Riviere, Patrick and Cheng, Keith C.},
abstractNote = {Organismal phenotypes frequently involve multiple organ systems. Histology is a powerful way to detect cellular and tissue phenotypes, but is largely descriptive and subjective. To determine how synchrotron-based X-ray micro-tomography (micro-CT) can yield 3-dimensional whole-organism images suitable for quantitative histological phenotyping, we scanned whole zebrafish, a small vertebrate model with diverse tissues, at ~1 micron voxel resolutions. Micro-CT optimized for cellular characterization (histotomography) allows brain nuclei to be computationally segmented and assigned to brain regions, and cell shapes and volumes to be computed for motor neurons and red blood cells. Striking individual phenotypic variation was apparent from color maps of computed densities of brain nuclei. Unlike histology, the histotomography also allows the study of 3-dimensional structures of millimeter scale that cross multiple tissue planes. We expect the computational and visual insights into 3D cell and tissue architecture provided by histotomography to be useful for reference atlases, hypothesis generation, comprehensive organismal screens, and diagnostics.},
doi = {10.7554/eLife.44898},
journal = {eLife},
number = ,
volume = 8,
place = {United States},
year = {Tue May 07 00:00:00 EDT 2019},
month = {Tue May 07 00:00:00 EDT 2019}
}
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