Subject-specific, multiscale simulation of electrophysiology: a software pipeline for image-based models and application examples.
Many simulation studies in biomedicine are based on a similar sequence of processing steps, starting from images and running through geometric model generation, assignment of tissue properties, numerical simulation and visualization of the results--a process known as image-based geometric modelling and simulation. We present an overview of software systems for implementing such a sequence both within highly integrated problem-solving environments and in the form of loosely integrated pipelines. Loose integration in this case indicates that individual programs function largely independently but communicate through files of a common format and support simple scripting, so as to automate multiple executions wherever possible. We then describe three specific applications of such pipelines to translational biomedical research in electrophysiology.
MacLeod
R S
RS
Nora Eccles Harrison Cardiovascular Research and Training Institute (CVRTI), University of Utah, Salt Lake City, UT 84112, USA. macleod@cvrti.utah.edu
Stinstra
J G
JG
Lew
S
S
Whitaker
R T
RT
Swenson
D J
DJ
Cole
M J
MJ
Krüger
J
J
Brooks
D H
DH
Johnson
C R
CR
D003198:Computer Simulation; D003952:Diagnostic Imaging; D004594:Electrophysiology; D012984:Software