PolNet: A Tool to Quantify Network-Level Cell Polarity and Blood Flow in Vascular Remodeling

Miguel O. Bernabeu, Martin L. Jones, Rupert W. Nash, Anna Pezzarossa, Peter V. Coveney, Holger Gerhardt, and Claudio A. Franco

In this article, we present PolNet, an open-source software tool for the study of blood flow and cell-level biological activity during vessel morphogenesis. We provide an image acquisition, segmentation, and analysis protocol to quantify endo- thelial cell polarity in entire in vivo vascular networks. In combination, we use computational fluid dynamics to characterize the hemodynamics of the vascular networks under study. The tool enables, to our knowledge for the first time, a network-level anal- ysis of polarity and flow for individual endothelial cells. To date, PolNet has proven invaluable for the study of endothelial cell polarization and migration during vascular patterning, as demonstrated by two recent publications. Additionally, the tool can be easily extended to correlate blood flow with other experimental observations at the cellular/molecular level. We release the source code of our tool under the Lesser General Public License.