Correcting curvature-density effects in the Hamilton-Jacobi skeleton

The Hainilton-Jacobi approach has proven to be a powerful and elegant method for extracting the skeleton of two-dimensional (2-D) shapes. The approach is based on the observation that the normalized flux associated with the inward evolution of the object boundary at nonskeletal points tends to zero as the size of the integration area tends to zero, while the flux is negative at the locations of skeletal points. Nonetheless, the error in calculating the flux on the image lattice is both limited by the pixel resolution and also proportional to the curvature of the boundary evolution front and, hence, unbounded near endpoints. This makes the exact location of endpoints difficult and renders the performance of the skeleton extraction algorithm dependent on a threshold parameter. This problem can be overcome by using interpolation techniques to calculate the flux with subpixel precision. However, here, we develop a method for 2-D skeleton extraction that circumvents the problem by eliminating the curvature contribution to the error. This is done by taking into account variations of density due to boundary curvature. This yields a skeletonization algorithm that gives both better localization and less susceptibility to boundary noise and parameter choice than the Hamilton-Jacobi method

数学的形態学手法による定量的ミクロ組織解析に関する研究

Tohoku University安斎浩一課

Defect and thickness inspection system for cast thin films using machine vision and full-field transmission densitometry

Quick mass production of homogeneous thin film material is required in paper, plastic, fabric, and thin film industries. Due to the high feed rates and small thicknesses, machine vision and other nondestructive evaluation techniques are used to ensure consistent, defect-free material by continuously assessing post-production quality. One of the fastest growing inspection areas is for 0.5-500 micrometer thick thin films, which are used for semiconductor wafers, amorphous photovoltaics, optical films, plastics, and organic and inorganic membranes. As a demonstration application, a prototype roll-feed imaging system has been designed to inspect high-temperature polymer electrolyte membrane (PEM), used for fuel cells, after being die cast onto a moving transparent substrate. The inspection system continuously detects thin film defects and classifies them with a neural network into categories of holes, bubbles, thinning, and gels, with a 1.2% false alarm rate, 7.1% escape rate, and classification accuracy of 96.1%. In slot die casting processes, defect types are indicative of a misbalance in the mass flow rate and web speed; so, based on the classified defects, the inspection system informs the operator of corrective adjustments to these manufacturing parameters. Thickness uniformity is also critical to membrane functionality, so a real-time, full-field transmission densitometer has been created to measure the bi-directional thickness profile of the semi-transparent PEM between 25-400 micrometers. The local thickness of the 75 mm x 100 mm imaged area is determined by converting the optical density of the sample to thickness with the Beer-Lambert law. The PEM extinction coefficient is determined to be 1.4 D/mm and the average thickness error is found to be 4.7%. Finally, the defect inspection and thickness profilometry systems are compiled into a specially-designed graphical user interface for intuitive real-time operation and visualization.M.S.Committee Chair: Tequila Harris; Committee Member: Levent Degertekin; Committee Member: Wayne Dale

A Geometric Approach for Deciphering Protein Structure from Cryo-EM Volumes

Electron Cryo-Microscopy or cryo-EM is an area that has received much attention in the recent past. Compared to the traditional methods of X-Ray Crystallography and NMR Spectroscopy, cryo-EM can be used to image much larger complexes, in many different conformations, and under a wide range of biochemical conditions. This is because it does not require the complex to be crystallisable. However, cryo-EM reconstructions are limited to intermediate resolutions, with the state-of-the-art being 3.6A, where secondary structure elements can be visually identified but not individual amino acid residues. This lack of atomic level resolution creates new computational challenges for protein structure identification. In this dissertation, we present a suite of geometric algorithms to address several aspects of protein modeling using cryo-EM density maps. Specifically, we develop novel methods to capture the shape of density volumes as geometric skeletons. We then use these skeletons to find secondary structure elements: SSEs) of a given protein, to identify the correspondence between these SSEs and those predicted from the primary sequence, and to register high-resolution protein structures onto the density volume. In addition, we designed and developed Gorgon, an interactive molecular modeling system, that integrates the above methods with other interactive routines to generate reliable and accurate protein backbone models

Efficiently Storing Well-Composed Polyhedral Complexes Computed Over 3D Binary Images

A 3D binary image I can be naturally represented by a combinatorial-algebraic structure called cubical complex and denoted by Q(I ), whose basic building blocks are vertices, edges, square faces and cubes. In Gonzalez-Diaz et al. (Discret Appl Math 183:59–77, 2015), we presented a method to “locally repair” Q(I ) to obtain a polyhedral complex P(I ) (whose basic building blocks are vertices, edges, specific polygons and polyhedra), homotopy equivalent to Q(I ), satisfying that its boundary surface is a 2D manifold. P(I ) is called a well-composed polyhedral complex over the picture I . Besides, we developed a new codification system for P(I ), encoding geometric information of the cells of P(I ) under the form of a 3D grayscale image, and the boundary face relations of the cells of P(I ) under the form of a set of structuring elements. In this paper, we build upon (Gonzalez-Diaz et al. 2015) and prove that, to retrieve topological and geometric information of P(I ), it is enough to store just one 3D point per polyhedron and hence neither grayscale image nor set of structuring elements are needed. From this “minimal” codification of P(I ), we finally present a method to compute the 2-cells in the boundary surface of P(I ).Ministerio de Economía y Competitividad MTM2015-67072-

Generating Second Order (Co)homological Information within AT-Model Context

In this paper we design a new family of relations between (co)homology classes, working with coefficients in a field and starting from an AT-model (Algebraic Topological Model) AT(C) of a finite cell complex C These relations are induced by elementary relations of type “to be in the (co)boundary of” between cells. This high-order connectivity information is embedded into a graph-based representation model, called Second Order AT-Region-Incidence Graph (or AT-RIG) of C. This graph, having as nodes the different homology classes of C, is in turn, computed from two generalized abstract cell complexes, called primal and dual AT-segmentations of C. The respective cells of these two complexes are connected regions (set of cells) of the original cell complex C, which are specified by the integral operator of AT(C). In this work in progress, we successfully use this model (a) in experiments for discriminating topologically different 3D digital objects, having the same Euler characteristic and (b) in designing a parallel algorithm for computing potentially significant (co)homological information of 3D digital objects.Ministerio de Economía y Competitividad MTM2016-81030-PMinisterio de Economía y Competitividad TEC2012-37868-C04-0