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
Citation
Kugler, E., Plant, K., Chico, T., Armitage, P. (2019) Enhancement and Segmentation Workflow for the Developing Zebrafish Vasculature. Journal of imaging. 5(1):.
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.
Genes / Markers
Expression
Phenotype
Mutations / Transgenics
Human Disease / Model
Sequence Targeting Reagents
Fish
Orthology
Engineered Foreign Genes
Mapping