Differentiable Surface Triangulation

Triangle meshes remain the most popular data representation for surface geometry. This ubiquitous representation is essentially a hybrid one that decouples continuous vertex locations from the discrete topological triangulation. Unfortunately, the combinatorial nature of the triangulation prevents taking derivatives over the space of possible meshings of any given surface. As a result, to date, mesh processing and optimization techniques have been unable to truly take advantage of modular gradient descent components of modern optimization frameworks. In this work, we present a differentiable surface triangulation that enables optimization for any per-vertex or per-face differentiable objective function over the space of underlying surface triangulations. Our method builds on the result that any 2D triangulation can be achieved by a suitably perturbed weighted Delaunay triangulation. We translate this result into a computational algorithm by proposing a soft relaxation of the classical weighted Delaunay triangulation and optimizing over vertex weights and vertex locations. We extend the algorithm to 3D by decomposing shapes into developable sets and differentiably meshing each set with suitable boundary constraints. We demonstrate the efficacy of our method on various planar and surface meshes on a range of difficult-to-optimize objective functions. Our code can be found online: https://github.com/mrakotosaon/diff-surface-triangulation

3D mesh processing using GAMer 2 to enable reaction-diffusion simulations in realistic cellular geometries

Recent advances in electron microscopy have enabled the imaging of single cells in 3D at nanometer length scale resolutions. An uncharted frontier for in silico biology is the ability to simulate cellular processes using these observed geometries. Enabling such simulations requires watertight meshing of electron micrograph images into 3D volume meshes, which can then form the basis of computer simulations of such processes using numerical techniques such as the Finite Element Method. In this paper, we describe the use of our recently rewritten mesh processing software, GAMer 2, to bridge the gap between poorly conditioned meshes generated from segmented micrographs and boundary marked tetrahedral meshes which are compatible with simulation. We demonstrate the application of a workflow using GAMer 2 to a series of electron micrographs of neuronal dendrite morphology explored at three different length scales and show that the resulting meshes are suitable for finite element simulations. This work is an important step towards making physical simulations of biological processes in realistic geometries routine. Innovations in algorithms to reconstruct and simulate cellular length scale phenomena based on emerging structural data will enable realistic physical models and advance discovery at the interface of geometry and cellular processes. We posit that a new frontier at the intersection of computational technologies and single cell biology is now open.Comment: 39 pages, 14 figures. High resolution figures and supplemental movies available upon reques