PT  - JOURNAL ARTICLE
AU  - C.J. Arthurs
AU  - R. Khlebnikov
AU  - A. Melville
AU  - M. Marčan
AU  - A. Gomez
AU  - D. Dillon-Murphy
AU  - F. Cuomo
AU  - M.S. Vieira
AU  - J. Schollenberger
AU  - S.R. Lynch
AU  - C. Tossas-Betancourt
AU  - K. Iyer
AU  - S. Hopper
AU  - E. Livingston
AU  - P. Youssefi
AU  - A. Noorani
AU  - S. Ben Ahmed
AU  - F.J.H. Nauta
AU  - T.M.J. van Bakel
AU  - Y. Ahmed
AU  - P.A.J. van Bakel
AU  - J. Mynard
AU  - P. Di Achille
AU  - H. Gharahi
AU  - K. D. Lau
AU  - V. Filonova
AU  - M. Aguirre
AU  - N. Nama
AU  - N. Xiao
AU  - S. Baek
AU  - K. Garikipati
AU  - O. Sahni
AU  - D. Nordsletten
AU  - C.A. Figueroa
TI  - CRIMSON: An Open-Source Software Framework for Cardiovascular Integrated Modelling and Simulation
AID  - 10.1101/2020.10.14.339960
DP  - 2020 Jan 01
TA  - bioRxiv
PG  - 2020.10.14.339960
4099  - http://biorxiv.org/content/early/2020/10/15/2020.10.14.339960.short
4100  - http://biorxiv.org/content/early/2020/10/15/2020.10.14.339960.full
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.