Computational 3D histological phenotyping of whole zebrafish by X-ray histotomography
- Penn State College of Medicine, United States
- Duke University, United States
- The University of Chicago, United States
- Motorola Mobility, United States
- Argonne National Laboratory, 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. 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.
Data availability
ViewTool is publically available (http://3D.fish). Digital histology is publicly available from our Zebrafish Lifespan Atlas (http://bio-atlas.psu.edu) (Cheng, 2004). Registered and unregistered 8-bit reconstructions of the heads of five zebrafish larvae involved in analysis are available on Dryad (https://datadryad.org/) along with scripts written for cell nuclei detection, analysis, and sample registration. Full resolution scans, including raw projection data, are available from researchers upon request as a download or by transfer to physical media.
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Data from: Computational 3D histological phenotyping of whole zebrafish by X-ray histotomographyDryad Digital Repository, doi:10.5061/dryad.4nb12g2.
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ViBE-Z: A Framework for 3D Virtual Colocalization Analysis in Zebrafish Larval Brainshttp://vibez.informatik.uni-freiburg.de.
Article and author information
Author details
Patrick La Riviere
Funding
NIH Office of the Director (R24-OD018559)
- Patrick La Riviere
- Keith Cheng
National Institutes of Health (R24-RR017441)
- Patrick La Riviere
- Keith Cheng
The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.
Ethics
Animal experimentation: All procedures on live animals were approved by the Institutional Animal Care and Use Committee (IACUC) at the Pennsylvania State University, ID: PRAMS201445659, Groundwork for a Synchrotron MicroCT Imaging Resource for Biology (SMIRB).
Reviewing Editor
- Richard M White, Memorial Sloan Kettering Cancer Center, United States
Publication history
- Received: January 5, 2019
- Accepted: May 4, 2019
- Accepted Manuscript published: May 7, 2019 (version 1)
- Version of Record published: June 11, 2019 (version 2)
Copyright
© 2019, Ding et al.
This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.
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Computational 3D histological phenotyping of whole zebrafish by X-ray histotomography
eLife 8:e44898.
https://doi.org/10.7554/eLife.44898
Further reading
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- Developmental Biology
By enabling researchers to image whole zebrafish with cellular resolution, X-ray histotomography will improve our understanding of the biological differences between individuals of the same species.
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- Developmental Biology
Coordination of cell proliferation and migration is fundamental for life, and its dysregulation has catastrophic consequences, such as cancer. How cell cycle progression affects migration, and vice versa, remains largely unknown. We address these questions by combining in silico modelling and in vivo experimentation in the zebrafish trunk neural crest (TNC). TNC migrate collectively, forming chains with a leader cell directing the movement of trailing followers. We show that the acquisition of migratory identity is autonomously controlled by Notch signalling in TNC. High Notch activity defines leaders, while low Notch determines followers. Moreover, cell cycle progression is required for TNC migration and is regulated by Notch. Cells with low Notch activity stay longer in G1 and become followers, while leaders with high Notch activity quickly undergo G1/S transition and remain in S-phase longer. In conclusion, TNC migratory identities are defined through the interaction of Notch signalling and cell cycle progression.
