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. Using micro-CT optimized for cellular characterization (histotomography), brain nuclei were computationally segmented and assigned to brain regions. Shape and volume were computed for populations of nuclei such as those of motor neurons and red blood cells. Striking individual phenotypic variation was apparent from color maps of computed cell density. Unlike histology, histotomography allows the detection of phenotypes that require millimeter scale context in multiple planes. We expect the computational and visual insights into 3D tissue architecture provided by histotomography to be useful for reference atlases, hypothesis generation, comprehensive organismal screens, and diagnostics.

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Work Title Computational 3D Histological Phenotyping of Whole Zebrafish by X-ray Histotomography
Access
Open Access
Creators
  1. Xuying Xin
  2. Keith C Cheng
Keyword
  1. Volumetric histology, micro-CT, 3D imaging, phenotypic variation, whole-organism phenomics, zebrafish
License Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)
Work Type Article
Publisher
  1. eLife
Publication Date May 7, 2019
Subject
  1. Biomedical research
Language
  1. English
Publisher Identifier (DOI)
  1. https://doi.org/10.7554/eLife.44898
Geographic Area
  1. US
Related URLs
Deposited May 24, 2019

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Version 1
published

  • Created
  • Added elife-44898-v2.pdf
  • Added Creator Xuying Xin
  • Added Creator Keith C Cheng
  • Published
  • Updated Subject, Language, Publisher, and 4 more Show Changes
    Subject
    • Biomedical research
    Language
    • English
    Publisher
    • eLife
    Geographic Area
    • US
    Publisher Identifier (DOI)
    • https://doi.org/10.7554/eLife.44898
    Related URLs
    • file:///Users/xzx1/Documents/CHV-markdown/XuyingDocs/Zebrafish_histotomography_eLife.pdf
    Publication Date
    • 2019-05-07
  • Deleted elife-44898-v2.pdf
  • Added Zebrafish_histotomography_eLife.pdf