Computational 3D histological phenotyping of whole zebrafish by X-ray histotomography

Author:

Ding Yifu123ORCID,Vanselow Daniel J12ORCID,Yakovlev Maksim A12ORCID,Katz Spencer R123ORCID,Lin Alex Y12ORCID,Clark Darin P4,Vargas Phillip5,Xin Xuying12,Copper Jean E12,Canfield Victor A12ORCID,Ang Khai C12ORCID,Wang Yuxin6,Xiao Xianghui7,De Carlo Francesco8,van Rossum Damian B12,La Riviere Patrick5ORCID,Cheng Keith C12ORCID

Affiliation:

1. The Jake Gittlen Laboratories for Cancer Research, Penn State College of Medicine, Hershey, United States

2. Division of Experimental Pathology, Department of Pathology, Penn State College of Medicine, Hershey, United States

3. Medical Scientist Training Program, Penn State College of Medicine, Hershey, United States

4. Center for In Vivo Microscopy, Duke University, Durham, United States

5. Department of Radiology, The University of Chicago, Chicago, United States

6. Imaging Group, Omnivision Technologies, Inc., Santa Clara, United States

7. National Synchrotron Light Source II, Brookhaven National Laboratory, Upton, United States

8. Advanced Photon Source, Argonne National Laboratory, Lemont, United States

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.

Funder

NIH Office of the Director

National Institutes of Health

Huck Institutes of the Life Sciences

Institute for Cyber Science, PSU

Jake Gittlen Memorial Golf Tournament

Pennsylvania Tobacco Fund

Publisher

eLife Sciences Publications, Ltd

Subject

General Immunology and Microbiology,General Biochemistry, Genetics and Molecular Biology,General Medicine,General Neuroscience

Reference64 articles.

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