Multi-sample SPIM image acquisition, processing and analysis of vascular growth in zebrafish.

First Authors Stephan Daetwyler
Authors Stephan Daetwyler, Ulrik G√ľnther, Carl D. Modes, Kyle Harrington, Jan Huisken
Corresponding Authors
Last Authors Jan Huisken
Journal Name Development (Cambridge, England) (Development)
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Article Number doi: 10.1242/dev.173757
PubMed ID 30824551
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Print Publication Date 2019-03-01
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Abstract To quantitatively understand biological processes that occur over many hours or days, it is desirable to image multiple samples simultaneously and automatically process and analyze the resulting datasets. Here, we present a complete multi-sample preparation, imaging, processing, and analysis workflow to determine the development of the vascular volume in zebrafish. Up to five live embryos were mounted and imaged simultaneously over several days using selective plane illumination microscopy (SPIM). The resulting large imagery dataset of several terabytes was processed in an automated manner on a high-performance computer cluster and segmented with a novel segmentation approach that uses images of red blood cells as training data. This analysis yielded a precise quantification of growth characteristics of the whole vascular network, head vasculature, and tail vasculature over development. Our multi-sample platform demonstrates effective upgrades to conventional single-sample imaging platforms and paves the way for diverse quantitative long-term imaging studies.
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Affiliated With Huisken, Modes, Postdoc first author, Postdocs
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Acknowledged Services Computer Department, Fish Facility
Publication Status Published
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DOI 10.1242/dev.173757
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Created By thuem
Added Date 2019-03-08
Last Edited By thuem
Last Edited Date 2019-03-08 14:51:05.999
Library ID 7354
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