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.
-
Data from: Computational 3D histological phenotyping of whole zebrafish by X-ray histotomographyDryad Digital Repository, doi:10.5061/dryad.4nb12g2.
-
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).
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.
Metrics
-
- 11,925
- views
-
- 1,095
- downloads
-
- 81
- citations
Views, downloads and citations are aggregated across all versions of this paper published by eLife.
Download links
A two-part list of links to download the article, or parts of the article, in various formats.
Downloads (link to download the article as PDF)
Open citations (links to open the citations from this article in various online reference manager services)
Cite this article (links to download the citations from this article in formats compatible with various reference manager tools)
Computational 3D histological phenotyping of whole zebrafish by X-ray histotomography
eLife 8:e44898.
https://doi.org/10.7554/eLife.44898
Further reading
-
- 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.
-
- Developmental Biology
- Genetics and Genomics
The establishment and growth of the arterial endothelium requires the coordinated expression of numerous genes. However, regulation of this process is not yet fully understood. Here, we combined in silico analysis with transgenic mice and zebrafish models to characterize arterial-specific enhancers associated with eight key arterial identity genes (Acvrl1/Alk1, Cxcr4, Cxcl12, Efnb2, Gja4/Cx37, Gja5/Cx40, Nrp1 and Unc5b). Next, to elucidate the regulatory pathways upstream of arterial gene transcription, we investigated the transcription factors binding each arterial enhancer compared to a similar assessment of non-arterial endothelial enhancers. These results found that binding of SOXF and ETS factors was a common occurrence at both arterial and pan-endothelial enhancers, suggesting neither are sufficient to direct arterial specificity. Conversely, FOX motifs independent of ETS motifs were over-represented at arterial enhancers. Further, MEF2 and RBPJ binding was enriched but not ubiquitous at arterial enhancers, potentially linked to specific patterns of behaviour within the arterial endothelium. Lastly, there was no shared or arterial-specific signature for WNT-associated TCF/LEF, TGFβ/BMP-associated SMAD1/5 and SMAD2/3, shear stress-associated KLF4 or venous-enriched NR2F2. This cohort of well characterized and in vivo-verified enhancers can now provide a platform for future studies into the interaction of different transcriptional and signalling pathways with arterial gene expression.
