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, 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.


Introduction to GIBBON:

The computational biomechanics toolbox for MATLAB, GIBBON ( 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)