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.
Ding, Yifu, et al. "Computational 3D histological phenotyping of whole zebrafish by X-ray histotomography." eLife, vol. 8, May. 2019. 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, & Cheng, Keith C. (2019). Computational 3D histological phenotyping of whole zebrafish by X-ray histotomography. eLife, 8. https://doi.org/10.7554/eLife.44898
Ding, Yifu, Vanselow, Daniel J., Yakovlev, Maksim A., et al., "Computational 3D histological phenotyping of whole zebrafish by X-ray histotomography," eLife 8 (2019), https://doi.org/10.7554/eLife.44898
@article{osti_1558992,
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 others},
title = {Computational 3D histological phenotyping of whole zebrafish by X-ray histotomography},
annote = {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},
url = {https://www.osti.gov/biblio/1558992},
journal = {eLife},
issn = {ISSN 2050-084X},
volume = {8},
place = {United States},
publisher = {eLife Sciences Publications, Ltd.},
year = {2019},
month = {05}}
2011 8th IEEE International Symposium on Biomedical Imaging (ISBI 2011), 2011 IEEE International Symposium on Biomedical Imaging: From Nano to Macrohttps://doi.org/10.1109/isbi.2011.5872394