Biomedical visual computing: case studies and challenges

pre-printAdvances in computational geometric modeling, imaging, and simulation let researchers build and test models of increasing complexity, generating unprecedented amounts of data. As recent research in biomedical applications illustrates, visualization will be critical in making this vast amount of data usable; it's also fundamental to understanding models of complex phenomena

Verifying volume rendering using discretization error analysis

pre-printWe propose an approach for verification of volume rendering correctness based on an analysis of the volume rendering integral, the basis of most DVR algorithms. With respect to the most common discretization of this continuous model (Riemann summation), we make assumptions about the impact of parameter changes on the rendered results and derive convergence curves describing the expected behavior. Specifically, we progressively refine the number of samples along the ray, the grid size, and the pixel size, and evaluate how the errors observed during refinement compare against the expected approximation errors. We derive the theoretical foundations of our verification approach, explain how to realize it in practice, and discuss its limitations. We also report the errors identified by our approach when applied to two publicly available volume rendering packages

A new isosurface extraction method on arbitrary grids

The development of interface-capturing methods (such as level-set, phase-field or volume of fluid (VOF) methods) for arbitrary 3D grids has further highlighted the need for more accurate and efficient interface reconstruction procedures. In this work, we propose a new method for the extraction of isosurfaces on arbitrary polyhedra that can be used with advantage for this purpose. The isosurface is extracted from volume fractions by a general polygon tracing procedure, which is valid for convex or non-convex geometries, even with non-planar faces. The proposed method, which can be considered as an extension of the marching cubes technique, produces consistent results even for ambiguous situations in polyhedra of arbitrary shape. To show the reproducibility of the results presented in this work, we provide the open source library isoap, which has been developed to implement the proposed method and includes test programs to demonstrate the successful extraction of isosurfaces on several grids with polyhedral cells of different types. We present results obtained not only for isosurface extraction from discrete volume fractions resulting from a volume of fluid method, but also from data sets obtained from implicit mathematical functions and signed distances to scanned surfaces. The improvement provided by the proposed method for the extraction of isosurfaces in arbitrary grids will also be very useful in other fields, such as CFD visualization or medical imaging.The authors gratefully acknowledge the support of the Spanish Ministerio de Ciencia, Innovación y Universidades - Agencia Estatal de Investigación and FEDER through projects DPI2017-87826-C2-1-P and DPI2017-87826-C2-2-P

Topology verification for isosurface extraction

Journal ArticleThe broad goals of verifiable visualization rely on correct algorithmic implementations. We extend a framework for verification of isosurfacing implementations to check topological properties. Specifically, we use stratified Morse theory and digital topology to design algorithms which verify topological invariants. Our extended framework reveals unexpected behavior and coding mistakes in popular publicly available isosurface codes

Doctor of Philosophy

dissertationIn this dissertation, we advance the theory and practice of verifying visualization algorithms. We present techniques to assess visualization correctness through testing of important mathematical properties. Where applicable, these techniques allow us to distinguish whether anomalies in visualization features can be attributed to the underlying physical process or to artifacts from the implementation under verification. Such scientific scrutiny is at the heart of verifiable visualization - subjecting visualization algorithms to the same verification process that is used in other components of the scientific pipeline. The contributions of this dissertation are manifold. We derive the mathematical framework for the expected behavior of several visualization algorithms, and compare them to experimentally observed results in the selected codes. In the Computational Science & Engineering community CS&E, this technique is know as the Method of Manufactured Solution (MMS). We apply MMS to the verification of geometrical and topological properties of isosurface extraction algorithms, and direct volume rendering. We derive the convergence of geometrical properties of isosurface extraction techniques, such as function value and normals. For the verification of topological properties, we use stratified Morse theory and digital topology to design algorithms that verify topological invariants. In the case of volume rendering algorithms, we provide the expected discretization errors for three different error sources. The results of applying the MMS is another important contribution of this dissertation. We report unexpected behavior for almost all implementations tested. In some cases, we were able to find and fix bugs that prevented the correctness of the visualization algorithm. In particular, we address an almost 2 0 -year-old bug with the core disambiguation procedure of Marching Cubes 33, one of the first algorithms intended to preserve the topology of the trilinear interpolant. Finally, an important by-product of this work is a range of responses practitioners can expect to encounter with the visualization technique under verification

Verifiable Visualization for Isosurface Extraction

Fig. 1. Through the verification methodology presented on this paper we were able to uncover a convergence problem within a publicly available marching-based isosurfacing code (top left) and fix it (top right). The problem causes the mesh normals to disagree with the known gradient field when refining the voxel size h (bottom row). The two graphs show the convergence of the normals before and after fixing the code. Abstract—Visual representations of isosurfaces are ubiquitous in the scientific and engineering literature. In this paper, we present techniques to assess the behavior of isosurface extraction codes. Where applicable, these techniques allow us to distinguish whether anomalies in isosurface features can be attributed to the underlying physical process or to artifacts from the extraction process. Such scientific scrutiny is at the heart of verifiable visualization – subjecting visualization algorithms to the same verification process that is used in other components of the scientific pipeline. More concretely, we derive formulas for the expected order of accuracy (or convergence rate) of several isosurface features, and compare them to experimentally observed results in the selected codes. This technique is practical: in two cases, it exposed actual problems in implementations. We provide the reader with the range of responses they can expect to encounter with isosurface techniques, both under “normal operating conditions ” and also under adverse conditions. Armed with this information – the results of the verification process – practitioners can judiciously select the isosurface extraction technique appropriate for their problem of interest, and have confidence in its behavior. Index Terms—Verification, V&V, Isosurface Extraction, Marching Cubes.