PT  - JOURNAL ARTICLE
AU  - Stephan Daetwyler
AU  - Ulrik Günther
AU  - Carl D. Modes
AU  - Kyle Harrington
AU  - Jan Huisken
TI  - Multi-sample SPIM image acquisition, processing and analysis of vascular growth in zebrafish
AID  - 10.1101/478149
DP  - 2018 Jan 01
TA  - bioRxiv
PG  - 478149
4099  - http://biorxiv.org/content/early/2018/11/24/478149.short
4100  - http://biorxiv.org/content/early/2018/11/24/478149.full
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.