Bootstrap Based Surface Reconstruction

Surface reconstruction is one of the main research areas in computer graphics. The goal is to find the best surface representation of the boundary of a real object. The typical input of a surface reconstruction algorithm is a point cloud, possibly obtained by a laser 3D scanner. The raw data from the scanner is usually noisy and contains outliers. Apart from creating models of high visual quality, assuring that a model is as faithful as possible to the original object is also one of the main aims of surface reconstruction. Most surface reconstruction algorithms proposed in the literature assess the reconstructed models either by visual inspection or, in cases where subjective manual input is not possible, by measuring the training error of the model. However, the training error underestimates systematically the test error and encourages overfitting. In this thesis, we provide a method for quantitative assessment in surface reconstruction. We integrate a model averaging method from statistics called bootstrap and define it into our context. Bootstrapping is a resampling procedure that provides statistical parameter. In surface fitting, we obtained error estimate which detect error caused by noise or bad fitting. We also define bootstrap method in context of normal estimation. We obtain variance and error estimates which we use as a quality measure of normal estimates. As application, we provide smoothing algorithm for point clouds and normal smoothing that can handle feature area. We also developed feature detection algorithm

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