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Advances in imaging methods such as electron microscopy, tomography and othermodalities are enabling high-resolution reconstructions of cellular andorganelle geometries. Such advances pave the way for using these geometries forbiophysical and mathematical modeling once these data can be represented as ageometric mesh, which, when carefully conditioned, enables the discretizationand solution of partial differential equations. In this study, we outline thesteps for a na\"ive user to approach GAMer 2, a mesh generation code written inC++ designed to convert structural datasets to realistic geometric meshes,while preserving the underlying shapes. We present two example cases, 1) meshgeneration at the subcellular scale as informed by electron tomography, and 2)meshing a protein with structure from x-ray crystallography. We furtherdemonstrate that the meshes generated by GAMer are suitable for use withnumerical methods. Together, this collection of libraries and tools simplifiesthe process of constructing realistic geometric meshes from structural biologydata.

An Open Source Mesh Generation Platform for Biophysical Modeling Using Realistic Cellular Geometries