ZFIN ID: ZDB-PUB-190508-9
Computational 3D histological phenotyping of whole zebrafish by X-ray histotomography
Ding, Y., Vanselow, D.J., Yakovlev, M.A., Katz, S.R., Lin, A.Y., Clark, D.P., Vargas, P., Xin, X., Copper, J.E., Canfield, V.A., Ang, K.C., Wang, Y., Xiao, X., De Carlo, F., van Rossum, D.B., La Riviere, P., Cheng, K.
Date: 2019
Source: eLIFE   8: (Journal)
Registered Authors: Canfield, Victor, Cheng, Keith C.
Keywords: developmental biology, zebrafish
MeSH Terms:
  • Animals
  • Histological Techniques/methods*
  • Imaging, Three-Dimensional/methods*
  • X-Ray Microtomography/methods*
  • Zebrafish/anatomy & histology*
PubMed: 31063133 Full text @ Elife
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.