CRIMSON: An open-source software framework for cardiovascular integrated modelling and simulation

Christopher J. Arthurs; Rostislav Khlebnikov; Alex Melville; Marija Marčan; Alberto Gomez; Desmond Dillon-Murphy; Federica Cuomo; Miguel Silva Vieira; Jonas Schollenberger; Sabrina R. Lynch; Christopher Tossas-Betancourt; Kritika Iyer; Sara Hopper; Elizabeth Livingston; Pouya Youssefi; Alia Noorani; Sabrina Ben Ahmed; Foeke J.H. Nauta; Theodorus M.J. van Bakel; Yunus Ahmed; Petrus A.J. van Bakel; Jonathan Mynard; Paolo Di Achille; Hamid Gharahi; Kevin D. Lau; Vasilina Filonova; Miquel Aguirre; Nitesh Nama; Nan Xiao; Seungik Baek; Krishna Garikipati; Onkar Sahni; David Nordsletten; C. Alberto Figueroa

doi:10.1371/journal.pcbi.1008881

CRIMSON: An open-source software framework for cardiovascular integrated modelling and simulation

Christopher J. Arthurs^*, Rostislav Khlebnikov, Alex Melville, Marija Marčan, Alberto Gomez, Desmond Dillon-Murphy, Federica Cuomo, Miguel Silva Vieira, Jonas Schollenberger, Sabrina R. Lynch, Christopher Tossas-Betancourt, Kritika Iyer, Sara Hopper, Elizabeth Livingston, Pouya Youssefi, Alia Noorani, Sabrina Ben Ahmed, Foeke J.H. Nauta, Theodorus M.J. van Bakel, Yunus AhmedPetrus A.J. van Bakel, Jonathan Mynard, Paolo Di Achille, Hamid Gharahi, Kevin D. Lau, Vasilina Filonova, Miquel Aguirre, Nitesh Nama, Nan Xiao, Seungik Baek, Krishna Garikipati, Onkar Sahni, David Nordsletten, C. Alberto Figueroa

^*Corresponding author for this work

Research output: Contribution to journal › Article › peer-review

34 Citations (Scopus)

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 preoperative surgical planning to medical device design optimization.

Original language	English
Article number	e1008881
Journal	PLoS Computational Biology
Volume	17
Issue number	5
DOIs	https://doi.org/10.1371/journal.pcbi.1008881
Publication status	Published - May 2021

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Arthurs, C. J., Khlebnikov, R., Melville, A., Marčan, M., Gomez, A., Dillon-Murphy, D., Cuomo, F., Vieira, M. S., Schollenberger, J., Lynch, S. R., Tossas-Betancourt, C., Iyer, K., Hopper, S., Livingston, E., Youssefi, P., Noorani, A., Ahmed, S. B., Nauta, F. J. H., van Bakel, T. M. J., ... Alberto Figueroa, C. (2021). CRIMSON: An open-source software framework for cardiovascular integrated modelling and simulation. PLoS Computational Biology, 17(5), [e1008881]. https://doi.org/10.1371/journal.pcbi.1008881

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title = "CRIMSON: An open-source software framework for cardiovascular integrated modelling and simulation",

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 preoperative surgical planning to medical device design optimization.",

author = "Arthurs, {Christopher J.} and Rostislav Khlebnikov and Alex Melville and Marija Mar{\v c}an and Alberto Gomez and Desmond Dillon-Murphy and Federica Cuomo and Vieira, {Miguel Silva} and Jonas Schollenberger and Lynch, {Sabrina R.} and Christopher Tossas-Betancourt and Kritika Iyer and Sara Hopper and Elizabeth Livingston and Pouya Youssefi and Alia Noorani and Ahmed, {Sabrina Ben} and Nauta, {Foeke J.H.} and {van Bakel}, {Theodorus M.J.} and Yunus Ahmed and {van Bakel}, {Petrus A.J.} and Jonathan Mynard and {Di Achille}, Paolo and Hamid Gharahi and Lau, {Kevin D.} and Vasilina Filonova and Miquel Aguirre and Nitesh Nama and Nan Xiao and Seungik Baek and Krishna Garikipati and Onkar Sahni and David Nordsletten and {Alberto Figueroa}, C.",

note = "Publisher Copyright: Copyright: {\textcopyright} 2021 Arthurs et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Copyright: Copyright 2021 Elsevier B.V., All rights reserved.",

year = "2021",

month = may,

doi = "10.1371/journal.pcbi.1008881",

language = "English",

volume = "17",

journal = "PLoS Computational Biology",

issn = "1553-734X",

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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, Ahmed, SB, Nauta, FJH, van Bakel, TMJ, Ahmed, Y, van Bakel, PAJ, Mynard, J, Di Achille, P, Gharahi, H, Lau, KD, Filonova, V, Aguirre, M, Nama, N, Xiao, N, Baek, S, Garikipati, K, Sahni, O, Nordsletten, D & Alberto Figueroa, C 2021, 'CRIMSON: An open-source software framework for cardiovascular integrated modelling and simulation', PLoS Computational Biology, vol. 17, no. 5, e1008881. https://doi.org/10.1371/journal.pcbi.1008881

TY - JOUR

T1 - CRIMSON

T2 - An open-source software framework for cardiovascular integrated modelling and simulation

AU - Arthurs, Christopher J.

AU - Khlebnikov, Rostislav

AU - Melville, Alex

AU - Marčan, Marija

AU - Gomez, Alberto

AU - Dillon-Murphy, Desmond

AU - Cuomo, Federica

AU - Vieira, Miguel Silva

AU - Schollenberger, Jonas

AU - Lynch, Sabrina R.

AU - Tossas-Betancourt, Christopher

AU - Iyer, Kritika

AU - Hopper, Sara

AU - Livingston, Elizabeth

AU - Youssefi, Pouya

AU - Noorani, Alia

AU - Ahmed, Sabrina Ben

AU - Nauta, Foeke J.H.

AU - van Bakel, Theodorus M.J.

AU - Ahmed, Yunus

AU - van Bakel, Petrus A.J.

AU - Mynard, Jonathan

AU - Di Achille, Paolo

AU - Gharahi, Hamid

AU - Lau, Kevin D.

AU - Filonova, Vasilina

AU - Aguirre, Miquel

AU - Nama, Nitesh

AU - Xiao, Nan

AU - Baek, Seungik

AU - Garikipati, Krishna

AU - Sahni, Onkar

AU - Nordsletten, David

AU - Alberto Figueroa, C.

N1 - Publisher Copyright: Copyright: © 2021 Arthurs et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Copyright: Copyright 2021 Elsevier B.V., All rights reserved.

PY - 2021/5

Y1 - 2021/5

N2 - 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 preoperative surgical planning to medical device design optimization.

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 preoperative surgical planning to medical device design optimization.

UR - http://www.scopus.com/inward/record.url?scp=85106060879&partnerID=8YFLogxK

U2 - 10.1371/journal.pcbi.1008881

DO - 10.1371/journal.pcbi.1008881

M3 - Article

C2 - 33970900

AN - SCOPUS:85106060879

SN - 1553-734X

VL - 17

JO - PLoS Computational Biology

JF - PLoS Computational Biology

IS - 5

M1 - e1008881

ER -

CRIMSON: An open-source software framework for cardiovascular integrated modelling and simulation

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