PUBLICATION

Enhancement and Segmentation Workflow for the Developing Zebrafish Vasculature

Authors
Kugler, E., Plant, K., Chico, T., Armitage, P.
ID
ZDB-PUB-210902-2
Date
2019
Source
Journal of imaging   5(1): (Journal)
Registered Authors
Chico, Tim J.
Keywords
3D, analysis, development, in vivo, light sheet fluorescence microscopy (LSFM), segmentation, vasculature, zebrafish
MeSH Terms
none
PubMed
34465714 Full text @ J Imaging
Abstract
Zebrafish have become an established in vivo vertebrate model to study cardiovascular development and disease. However, most published studies of the zebrafish vascular architecture rely on subjective visual assessment, rather than objective quantification. In this paper, we used state-of-the-art light sheet fluorescence microscopy to visualize the vasculature in transgenic fluorescent reporter zebrafish. Analysis of image quality, vascular enhancement methods, and segmentation approaches were performed in the framework of the open-source software Fiji to allow dissemination and reproducibility. Here, we build on a previously developed image processing pipeline; evaluate its applicability to a wider range of data; apply and evaluate an alternative vascular enhancement method; and, finally, suggest a work-flow for successful segmentation of the embryonic zebrafish vasculature.
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