Topological approaches for 3D object processing and applications

The great challenge in 3D object processing is to devise computationally efficient algorithms for recovering 3D models contaminated by noise and preserving their geometrical structure. The first problem addressed in this thesis is object denoising formulated in the discrete variational framework. We introduce a 3D mesh denoising method based on kernel density estimation. The proposed approach is able to reduce the over-smoothing effect and effectively remove undesirable noise while preserving prominent geometric features of a 3D mesh such as sharp features and fine details. The feasibility of the approach is demonstrated through extensive experiments. The rest of the thesis is devoted to a joint exploitation of geometry and topology of 3D objects for as parsimonious as possible representation of models and its subsequent application in object modeling, compression, and hashing problems. We introduce a 3D mesh compression technique using the centroidal mesh neighborhood information. The key idea is to apply eigen-decomposition to the mesh umbrella matrix, and then discard the smallest eigenvalues/eigenvectors in order to reduce the dimensionality of the new spectral basis so that most of the energy is concentrated in the low frequency coefficients. We also present a hashing technique for 3D models using spectral graph theory and entropic spanning trees by partitioning a 3D triangle mesh into an ensemble of submeshes, and then applying eigen-decomposition to the Laplace-Beltrami matrix of each sub-mesh, followed by computing the hash value of each sub-mesh. Moreover, we introduce several statistical distributions to analyze the topological properties of 3D objects. These probabilistic distributions provide useful information about the way 3D mesh models are connected. Illustrating experiments with synthetic and real data are provided to demonstrate the feasibility and the much improved performance of the proposed approaches in 3D object compression, hashing, and modeling

A Bayesian Approach to Manifold Topology Reconstruction

In this paper, we investigate the problem of statistical reconstruction of piecewise linear manifold topology. Given a noisy, probably undersampled point cloud from a one- or two-manifold, the algorithm reconstructs an approximated most likely mesh in a Bayesian sense from which the sample might have been taken. We incorporate statistical priors on the object geometry to improve the reconstruction quality if additional knowledge about the class of original shapes is available. The priors can be formulated analytically or learned from example geometry with known manifold tessellation. The statistical objective function is approximated by a linear programming / integer programming problem, for which a globally optimal solution is found. We apply the algorithm to a set of 2D and 3D reconstruction examples, demon-strating that a statistics-based manifold reconstruction is feasible, and still yields plausible results in situations where sampling conditions are violated

Visualization, Exploration and Data Analysis of Complex Astrophysical Data

In this paper we show how advanced visualization tools can help the researcher in investigating and extracting information from data. The focus is on VisIVO, a novel open source graphics application, which blends high performance multidimensional visualization techniques and up-to-date technologies to cooperate with other applications and to access remote, distributed data archives. VisIVO supports the standards defined by the International Virtual Observatory Alliance in order to make it interoperable with VO data repositories. The paper describes the basic technical details and features of the software and it dedicates a large section to show how VisIVO can be used in several scientific cases.Comment: 32 pages, 15 figures, accepted by PAS

3D time series analysis of cell shape using Laplacian approaches

Background: Fundamental cellular processes such as cell movement, division or food uptake critically depend on cells being able to change shape. Fast acquisition of three-dimensional image time series has now become possible, but we lack efficient tools for analysing shape deformations in order to understand the real three-dimensional nature of shape changes. Results: We present a framework for 3D+time cell shape analysis. The main contribution is three-fold: First, we develop a fast, automatic random walker method for cell segmentation. Second, a novel topology fixing method is proposed to fix segmented binary volumes without spherical topology. Third, we show that algorithms used for each individual step of the analysis pipeline (cell segmentation, topology fixing, spherical parameterization, and shape representation) are closely related to the Laplacian operator. The framework is applied to the shape analysis of neutrophil cells. Conclusions: The method we propose for cell segmentation is faster than the traditional random walker method or the level set method, and performs better on 3D time-series of neutrophil cells, which are comparatively noisy as stacks have to be acquired fast enough to account for cell motion. Our method for topology fixing outperforms the tools provided by SPHARM-MAT and SPHARM-PDM in terms of their successful fixing rates. The different tasks in the presented pipeline for 3D+time shape analysis of cells can be solved using Laplacian approaches, opening the possibility of eventually combining individual steps in order to speed up computations