CRIMSON: An Open-Source Software Framework for Cardiovascular Integrated Modelling and Simulation

• Published in: bioRxiv
• Main Authors: Arthurs, Cj, Khlebnikov, R, Melville, A, Marčan, M, Gomez, A, Dillon-Murphy, D, Cuomo, F, Vieira, Ms, Schollenberger, J, Lynch, Sr, Tossas-Betancourt, C, Iyer, K, Hopper, S, Livingston, E, Youssefi, P, Noorani, A, S Ben Ahmed, Nauta, Fjh, Tmj Van Bakel, Ahmed, Y, Paj Van Bakel, Mynard, J, P Di Achille, Gharahi, H, Lau, K D, Filonova, V, Aguirre, M, Nama, N, Xiao, N, Baek, S, Garikipati, K, Sahni, O, Nordsletten, D, Figueroa, Ca
• Format: Paper
• Language: English
• Published: Cold Spring Harbor Cold Spring Harbor Laboratory Press 15.10.2020
• Subjects: Blood flow; Boundary conditions; Computer applications; Computer programs; Design optimization; Fluid flow; Fluid-structure interaction; Hemodynamics; Image processing; Mathematical models; Medical equipment; Open source software; Software
• DOI: 10.1101/2020.10.14.339960

Abstract 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 Statement CJA 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. Footnotes * https://drive.google.com/file/d/1kl0PHcwRClzUuyLOPzxRNqE_h8_TpeFQ/view?usp=sharing