ZFIN ID: ZDB-PUB-190303-6
Multi-sample SPIM image acquisition, processing and analysis of vascular growth in zebrafish
Daetwyler, S., Günther, U., Modes, C.D., Harrington, K., Huisken, J.
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
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.