CRIMSON

CRIMSON, the CardiovasculaR Modelling and SimulatiON Environment, is a complete software pipeline for segmenting blood vessels from medical imaging data, generating meshes, designing and specifying boundary conditions and material properties, and performing finite element simulation of blood flow on thousands of CPU cores, using the SUPG-stabilised incompressible Navier-Stokes equations. The software is used by researchers around the globe, and is freely available for users to download from our website, www.crimson.software. We believe that the calibre and interests of researchers in attendance at CMBBE 2019 make this conference an ideal place for a CRIMSON workshop.


In this workshop we will introduce the newest version of the FEBio software. FEBio is a finite element solver that was designed specifically for solving problems in computational biomechanics, bioengineering, and biophysics. It accomplishes this goal by providing constitutive models, loading conditions, and modeling scenarios that are relevant for these fields. The latest version of FEBio (version 3.0) has full multiphysics capabilities that allow users to model large deformation nonlinear analysis, multiphasic domains, fluid problems, chemical reactions, fluid-solid interactions, and more. 


SlicerSALT for Biomedical and Biomechanical Research

Quantitative morphologic assessment of individual anatomical structures in Medical Imaging is often based on volumetric measurements.Volume changes are intuitive features as they might explain atrophy or dilation due to illness. On the other hand, structural changes at specific locations are not sufficiently reflected in volume measurements. Shape analysis has thus become of increasing interest to the Medical Imaging community due to its potential to precisely locate morphological changes between healthy and pathological structures.

Slicer Shape AnaLysis Toolbox (SlicerSALT) is an open-source, free comprehensive software that allows biomedical scientists to precisely locate shape changes in their imaging studies. SlicerSALT enhances the intuitiveness and ease of use for such studies, as well as allow researchers to find shape changes with higher statistical power. Altogether this constitutes a crucial resource for the imaging field that will enable many and important new findings in biomedical imaging studies.


GIBBON

Introduction to GIBBON:

The computational biomechanics toolbox for MATLAB, GIBBON (https://www.gibboncode.org) is a free and open-source MATLAB toolbox for image-segmentation, advanced meshing, and finite element analysis (based on FEBio or ABAQUS).

Speaker:  Kevin M. Moerman Ph.D. M.Sc. B.Eng. (NUI Galway)


SimVascular

SimVascular is the only fully open source software package providing a complete pipeline from medical image data to cardiovascular blood flow simulation results and analysis (www.simvascular.org).  It offers capabilities for image segmentation, unstructured adaptive meshing, physiologic boundary conditions, and two Navier-Stokes finite element solvers with fluid structure interaction capabilities, including large deformation motion with an Arbitrary Lagrangian Eulerian (ALE) formulation.  An accompanying vascular model repository provides over 100 clinical data sets with simulation results from different parts of the vasculature to enable research.  Extensive online documentation and tutorials with clinical examples are provided online. In this workshop, we will interactively take new users through a step-by-step tutorial, covering basic steps of model construction, meshing, flow simulations, and best practices for high quality results. We will also introduce several new features of SimVascular, including a module for image segmentation with machine learning, a python scripting interface, and a pipeline for reduced-order modeling with a 1D solver.  Following a series of interactive demonstrations, we will moderate a question and answer session for current and potential users.