RT Journal Article
SR Electronic
T1 CRIMSON: An Open-Source Software Framework for Cardiovascular Integrated Modelling and Simulation
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 2020.10.14.339960
DO 10.1101/2020.10.14.339960
A1 C.J. Arthurs
A1 R. Khlebnikov
A1 A. Melville
A1 M. Marčan
A1 A. Gomez
A1 D. Dillon-Murphy
A1 F. Cuomo
A1 M.S. Vieira
A1 J. Schollenberger
A1 S.R. Lynch
A1 C. Tossas-Betancourt
A1 K. Iyer
A1 S. Hopper
A1 E. Livingston
A1 P. Youssefi
A1 A. Noorani
A1 S. Ben Ahmed
A1 F.J.H. Nauta
A1 T.M.J. van Bakel
A1 Y. Ahmed
A1 P.A.J. van Bakel
A1 J. Mynard
A1 P. Di Achille
A1 H. Gharahi
A1 K. D. Lau
A1 V. Filonova
A1 M. Aguirre
A1 N. Nama
A1 N. Xiao
A1 S. Baek
A1 K. Garikipati
A1 O. Sahni
A1 D. Nordsletten
A1 C.A. Figueroa
YR 2020
UL http://biorxiv.org/content/early/2020/10/15/2020.10.14.339960.abstract
AB In this work, we describe the CRIMSON (CardiovasculaR Integrated Modelling and SimulatiON) software environment. CRIMSON provides a powerful, customizable and user-friendly system for performing three-dimensional and reduced-order computational haemodynamics studies via a pipeline which involves: 1) segmenting vascular structures from medical images; 2) constructing analytic arterial and venous geometric models; 3) performing finite element mesh generation; 4) designing, and 5) applying boundary conditions; 6) running incompressible Navier-Stokes simulations of blood flow with fluid-structure interaction capabilities; and 7) post-processing and visualizing the results, including velocity, pressure and wall shear stress fields. A key aim of CRIMSON is to create a software environment that makes powerful computational haemodynamics tools accessible to a wide audience, including clinicians and students, both within our research laboratories and throughout the community. The overall philosophy is to leverage best-in-class open source standards for medical image processing, parallel flow computation, geometric solid modelling, data assimilation, and mesh generation. It is actively used by researchers in Europe, North and South America, Asia, and Australia. It has been applied to numerous clinical problems; we illustrate applications of CRIMSON to real-world problems using examples ranging from pre-operative surgical planning to medical device design optimization. CRIMSON binaries for Microsoft Windows 10, documentation and example input files are freely available for download from www.crimson.software, and the source code with compilation instructions is available on GitHub https://github.com/carthurs/CRIMSONFlowsolver (CRIMSON Flowsolver) under the GPL v3.0 license, and https://github.com/carthurs/CRIMSONGUI (CRIMSON GUI), under the AGPL v3.0 license. Support is available on the CRIMSON Google Groups forum, located at https://groups.google.com/forum/#!forum/crimson-users.Competing Interest StatementCJA and CAF have a joint interest in CRIMSON Technologies LLC, a supporting company for CRIMSON, providing software and services to researchers. This is in addition to the open-source version of CRIMSON which is freely available.