RT Journal Article
SR Electronic
T1 3D quantification of zebrafish cerebrovascular architecture by automated image analysis of light sheet fluorescence microscopy datasets
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 2020.08.06.239905
DO 10.1101/2020.08.06.239905
A1 E. C. Kugler
A1 J. Frost
A1 V. Silva
A1 K. Plant
A1 K. Chhabria
A1 T. J.A. Chico
A1 P. A. Armitage
YR 2020
UL http://biorxiv.org/content/early/2020/08/06/2020.08.06.239905.abstract
AB Zebrafish transgenic lines and light sheet fluorescence microscopy allow in-depth insights into vascular development in vivo and 3D. However, robust quantification of the zebrafish cerebral vasculature in 3D remains a challenge, and would be essential to describe the vascular architecture. Here, we report an image analysis pipeline that allows 3D quantification of the total or regional zebrafish brain vasculature. This is achieved by landmark- or object-based inter-sample registration and extraction of quantitative parameters including vascular volume, surface area, density, branching points, length, radius, and complexity. Application of our analysis pipeline to a range of sixteen genetic or pharmacological manipulations shows that our quantification approach is robust, allows extraction of biologically relevant information, and provides novel insights into vascular biology. To allow dissemination, the code for quantification, a graphical user interface, and workflow documentation are provided. Together, we present the first 3D quantification approach to assess the whole 3D cerebrovascular architecture in zebrafish.Competing Interest StatementThe authors have declared no competing interest.