RT Journal Article
SR Electronic
T1 Multi-sample SPIM image acquisition, processing and analysis of vascular growth in zebrafish
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 478149
DO 10.1101/478149
A1 Stephan Daetwyler
A1 Ulrik Günther
A1 Carl D. Modes
A1 Kyle Harrington
A1 Jan Huisken
YR 2018
UL http://biorxiv.org/content/early/2018/11/24/478149.abstract
AB 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.Summary statement We present a dedicated multi-sample light sheet imaging, processing and analysis platform and demonstrate its value for studies of vascular growth in zebrafish.