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

Autor: Miguel Silva Vieira, Alberto Gomez, Rostislav Khlebnikov, Alex Melville, Christopher Tossas-Betancourt, Christopher J. Arthurs, Sara E Hopper, Pouya Youssefi, Seungik Baek, C. Alberto Figueroa, Marija Marčan, Jonathan Mynard, Vasilina Filonova, Paolo Di Achille, Jonas Schollenberger, Onkar Sahni, David Nordsletten, Miquel Aguirre, Elizabeth Renee Livingston, Sabrina Ben Ahmed, Alia Noorani, Federica Cuomo, Sabrina R. Lynch, Yunus Ahmed, Nitesh Nama, Krishna Garikipati, KD Lau, Theodorus M. J. van Bakel, Hamid Gharahi, Desmond Dillon-Murphy, Kritika Iyer, Petrus A. J. van Bakel, Foeke J. H. Nauta, Nan Xiao
Rok vydání: 2020
Předmět:
Man-Computer Interface
Models
Anatomic
Patient-Specific Modeling
Source code
Physiology
Computer science
Blood Pressure
02 engineering and technology
030204 cardiovascular system & hematology
Vascular Medicine
Computer Applications
Computer Architecture
User-Computer Interface
Electronics Engineering
Open Science
Postoperative Complications
0302 clinical medicine
Documentation
Software
Blood Flow
Medicine and Health Sciences
Computer Engineering
Graphical User Interfaces
Biology (General)
Graphical user interface
media_common
Ecology
Simulation and Modeling
Applied Mathematics
Models
Cardiovascular
Software Engineering
Hematology
Magnetic Resonance Imaging
Finite element method
Body Fluids
Alagille Syndrome
Blood
Computational Theory and Mathematics
Mesh generation
Modeling and Simulation
Physical Sciences
Engineering and Technology
Anatomy
Open Source Software
Research Article
Computer and Information Sciences
QH301-705.5
Science Policy
Computation
media_common.quotation_subject
Finite Element Analysis
0206 medical engineering
Image processing
Research and Analysis Methods
Computer Software
Cellular and Molecular Neuroscience
03 medical and health sciences
Imaging
Three-Dimensional
Genetics
Humans
Leverage (statistics)
Computer Simulation
Molecular Biology
Computerized Simulations
Ecology
Evolution
Behavior and Systematics
business.industry
Hemodynamics
Biology and Life Sciences
Computational Biology
Pipeline (software)
020601 biomedical engineering
Liver Transplantation
Heart Disease Risk Factors
Microsoft Windows
Blood Vessels
Software engineering
business
Mathematics
User Interfaces
Zdroj: PLoS Computational Biology
PLoS Computational Biology, Vol 17, Iss 5, p e1008881 (2021)
DOI: 10.1101/2020.10.14.339960
Popis: 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.
Author summary We provide the first full presentation in the literature of CRIMSON, the Cardiovascular Integrated Modelling and Simulation Package. CRIMSON consists of a graphical user interface desktop computer program for creating geometric models of blood vessels from medical imaging scans, specifying parameters such as the stiffness of the artery walls, the resistance of connected vessels which are not visible on the scans, and determining the appropriate parameters for all aspects of the model. CRIMSON additionally consists of the Flowsolver, a high-performance computing package which simulates the flow of blood through the models created in the graphical user interface. Whilst several packages which can simulate blood flow exist, most target general fluid simulations, and this lack of specialisation means that blood flow simulation is harder to perform, and can require ad hoc (and potentially scientifically-limiting) workflow decisions. CRIMSON’s specialisation deals with these problems, as well as presenting a number of unique features which are unavailable elsewhere.
Databáze: OpenAIRE
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