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

Journal Article (Journal Article)

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.

Full Text

Duke Authors

Cited Authors

  • Ding, Y; Vanselow, DJ; Yakovlev, MA; Katz, SR; Lin, AY; Clark, DP; Vargas, P; Xin, X; Copper, JE; Canfield, VA; Ang, KC; Wang, Y; Xiao, X; De Carlo, F; van Rossum, DB; La Riviere, P; Cheng, KC

Published Date

  • May 7, 2019

Published In

Volume / Issue

  • 8 /

PubMed ID

  • 31063133

Pubmed Central ID

  • PMC6559789

Electronic International Standard Serial Number (EISSN)

  • 2050-084X

Digital Object Identifier (DOI)

  • 10.7554/eLife.44898


  • eng

Conference Location

  • England