@article{67d894e653104daa9e60bb631249fe8a,
title = "PolNet: a tool to quantify network-level cell polarity and blood flow in vascular remodeling",
abstract = "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 endothelial 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 analysis 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.",
author = "Bernabeu, \{Miguel O.\} and Jones, \{Martin L.\} and Nash, \{Rupert W.\} and Anna Pezzarossa and Coveney, \{Peter V.\} and Holger Gerhardt and Franco, \{Claudio A.\}",
note = "Funding Information: M.L.J.{\textquoteright}s work was supported by the Francis Crick Institute, which receives its core funding from Cancer Research UK ( FC001999 ), the UK Medical Research Council ( FC001999 ), and the Wellcome Trust ( FC001999 ). H.G. was supported by a European Research Council consolidator grant called Reshape ( 311719 ) and by the British Council{\textquoteright}s Britain-Israel Research and Academic Exchange initiative . C.A.F. was supported by a European Research Council starting grant ( 679368 ), the H2020-Twinning grant ( 692322 ), the Funda{\c c}{\~a}o para a Ci{\^e}ncia e a Tecnologia funding grants ( IF/00412/2012 , EXPL-BEX-BCM-2258-2013 , PRECISE-LISBOA-01-0145-FEDER-016394 , and LISBOA-01-0145-FEDER-007391 ), and a project cofunded by FEDER through Programa Operacional Regional de Lisboa 2020 , PORTUGAL 2020 , and Funda{\c c}{\~a}o para a Ci{\^e}ncia e a Tecnologia . M.O.B. and P.V.C. acknowledge support from the UK Engineering and Physical Sciences Research Council under the project “UK Consortium on Mesoscale Engineering Sciences” (grant number EP/L00030X/1 ). M.O.B., H.G., and C.A.F. acknowledge support by a grant from the Fondation Leducq ( 17 CVD 03 ). R.W.N. was funded under the embedded CSE programme of the ARCHER UK National Supercomputing Service ( http://www.archer.ac.uk ). P.V.C. acknowledges support from the UK Medical Research Council (MR/L016311/1), the UCL Provost, and from European Research Council grants ComPat (671564) and CompBioMed (675451). Publisher Copyright: {\textcopyright} 2018 Biophysical Society",
year = "2018",
month = may,
day = "8",
doi = "10.1016/j.bpj.2018.03.032",
language = "English",
volume = "114",
pages = "2052--2058",
journal = "Biophysical Journal",
issn = "0006-3495",
publisher = "Elsevier Inc.",
number = "9",
}