The Modified Direct Method: an Approach for Smoothing Planar and Surface Meshes

The Modified Direct Method (MDM) is an iterative mesh smoothing method for smoothing planar and surface meshes, which is developed from the non-iterative smoothing method originated by Balendran [1]. When smooth planar meshes, the performance of the MDM is effectively identical to that of Laplacian smoothing, for triangular and quadrilateral meshes; however, the MDM outperforms Laplacian smoothing for tri-quad meshes. When smooth surface meshes, for trian-gular, quadrilateral and quad-dominant mixed meshes, the mean quality(MQ) of all mesh elements always increases and the mean square error (MSE) decreases during smoothing; For tri-dominant mixed mesh, the quality of triangles always descends while that of quads ascends. Test examples show that the MDM is convergent for both planar and surface triangular, quadrilateral and tri-quad meshes.Comment: 18 page

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

Anisotropic Mesh Adaptation for Image Representation

Triangular meshes have gained much interest in image representation and have been widely used in image processing. This paper introduces a framework of anisotropic mesh adaptation (AMA) methods to image representation and proposes a GPRAMA method that is based on AMA and greedy-point removal (GPR) scheme. Different than many other methods that triangulate sample points to form the mesh, the AMA methods start directly with a triangular mesh and then adapt the mesh based on a user-defined metric tensor to represent the image. The AMA methods have clear mathematical framework and provides flexibility for both image representation and image reconstruction. A mesh patching technique is developed for the implementation of the GPRAMA method, which leads to an improved version of the popular GPRFS-ED method. The GPRAMA method can achieve better quality than the GPRFS-ED method but with lower computational cost.Comment: 25 pages, 15 figure