PUBLICATION
Multi-sample SPIM image acquisition, processing and analysis of vascular growth in zebrafish
- Authors
- Daetwyler, S., Günther, U., Modes, C.D., Harrington, K., Huisken, J.
- ID
- ZDB-PUB-190303-6
- Date
- 2019
- Source
- Development (Cambridge, England) 146(6): (Journal)
- Registered Authors
- Huisken, Jan
- Keywords
- Growth models, Light sheet microscopy, Multi-sample imaging, SPIM, Segmentation, Vasculature, Zebrafish
- MeSH Terms
-
- Animals
- Biological Phenomena
- Cardiovascular System/embryology*
- Cluster Analysis
- Embryo, Nonmammalian
- Green Fluorescent Proteins/metabolism
- Image Processing, Computer-Assisted/methods*
- Microscopy, Fluorescence/methods*
- Software
- Zebrafish
- PubMed
- 30824551 Full text @ Development
Citation
Daetwyler, S., Günther, U., Modes, C.D., Harrington, K., Huisken, J. (2019) Multi-sample SPIM image acquisition, processing and analysis of vascular growth in zebrafish. Development (Cambridge, England). 146(6):.
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.
Genes / Markers
Expression
Phenotype
Mutations / Transgenics
Human Disease / Model
Sequence Targeting Reagents
Fish
Orthology
Engineered Foreign Genes
Mapping