BioMesh3D: A Meshing Pipeline for Biomedical Computing

Biomedical computing applications often follow a computational pipeline: experimental data or image acquisition, mathematical modeling, geometric modeling (segmentation, mesh generation), material modeling, numerical approximation (finite element analysis, linear solvers, nonlinear optimization), visualization (of the geometric model, material model, and solutions), and validation. An important requirement of the numerical approximation and visualization methods is the need to create a discrete decomposition of the model geometry into a mesh. The meshes produced are used as input for computational simulation, as well as, the geometric basis for which many of the visualization results are displayed. Historically, the generation of these meshes has been a critical bottleneck in efforts to efficiently generate biomedical simulations which can be utilized in understanding, planning, and diagnosing biomedical conditions. In this paper, we will outline a pipeline for more efficiently generating meshes suitable for biomedical simulations. Because of the wide array of geometries and phenomena encountered in biomedical computing, this pipeline will incorporate a flexible suite of tools that will offer some generality to mesh generation of biomedical models. We will discuss several tools that have been successfully used in past problems and how these tools have been incorporated into the suite of other tools. We will demonstrate mesh generation for a couple of example problems along with methods for verifying the quality of the meshes generated. Finally, we will discuss on-going and future efforts to bring all of these tools into a common environment to dramatically reduce the difficulty of mesh generation for biomedical simulations. BioMesh3D: A Meshing Pipeline for Biomedical Computing Michael Callahan, Martin J. Cole, Jason F. Shepherd, Jeroen G. Stinstra, and Chris R. Johnson 1 Scientific Computing and Imaging Institute, Salt Lake City, UT [email protected] 2 Scientific Computing and Imaging Institute, Salt Lake City, UT [email protected] 3 Scientific Computing and Imaging Institute, Salt Lake City, UT [email protected] 4 Scientific Computing and Imaging Institute, Salt Lake City, UT [email protected] 5 Scientific Computing and Imaging Institute, Salt Lake City, UT