Diamond-based models for scientific visualization

Hierarchical spatial decompositions are a basic modeling tool in a variety of application domains including scientific visualization, finite element analysis and shape modeling and analysis. A popular class of such approaches is based on the regular simplex bisection operator, which bisects simplices (e.g. line segments, triangles, tetrahedra) along the midpoint of a predetermined edge. Regular simplex bisection produces adaptive simplicial meshes of high geometric quality, while simplifying the extraction of crack-free, or conforming, approximations to the original dataset. Efficient multiresolution representations for such models have been achieved in 2D and 3D by clustering sets of simplices sharing the same bisection edge into structures called diamonds. In this thesis, we introduce several diamond-based approaches for scientific visualization. We first formalize the notion of diamonds in arbitrary dimensions in terms of two related simplicial decompositions of hypercubes. This enables us to enumerate the vertices, simplices, parents and children of a diamond. In particular, we identify the number of simplices involved in conforming updates to be factorial in the dimension and group these into a linear number of subclusters of simplices that are generated simultaneously. The latter form the basis for a compact pointerless representation for conforming meshes generated by regular simplex bisection and for efficiently navigating the topological connectivity of these meshes. Secondly, we introduce the supercube as a high-level primitive on such nested meshes based on the atomic units within the underlying triangulation grid. We propose the use of supercubes to associate information with coherent subsets of the full hierarchy and demonstrate the effectiveness of such a representation for modeling multiresolution terrain and volumetric datasets. Next, we introduce Isodiamond Hierarchies, a general framework for spatial access structures on a hierarchy of diamonds that exploits the implicit hierarchical and geometric relationships of the diamond model. We use an isodiamond hierarchy to encode irregular updates to a multiresolution isosurface or interval volume in terms of regular updates to diamonds. Finally, we consider nested hypercubic meshes, such as quadtrees, octrees and their higher dimensional analogues, through the lens of diamond hierarchies. This allows us to determine the relationships involved in generating balanced hypercubic meshes and to propose a compact pointerless representation of such meshes. We also provide a local diamond-based triangulation algorithm to generate high-quality conforming simplicial meshes

Exposure Render: An Interactive Photo-Realistic Volume Rendering Framework

The field of volume visualization has undergone rapid development during the past years, both due to advances in suitable computing hardware and due to the increasing availability of large volume datasets. Recent work has focused on increasing the visual realism in Direct Volume Rendering (DVR) by integrating a number of visually plausible but often effect-specific rendering techniques, for instance modeling of light occlusion and depth of field. Besides yielding more attractive renderings, especially the more realistic lighting has a positive effect on perceptual tasks. Although these new rendering techniques yield impressive results, they exhibit limitations in terms of their exibility and their performance. Monte Carlo ray tracing (MCRT), coupled with physically based light transport, is the de-facto standard for synthesizing highly realistic images in the graphics domain, although usually not from volumetric data. Due to the stochastic sampling of MCRT algorithms, numerous effects can be achieved in a relatively straight-forward fashion. For this reason, we have developed a practical framework that applies MCRT techniques also to direct volume rendering (DVR). With this work, we demonstrate that a host of realistic effects, including physically based lighting, can be simulated in a generic and flexible fashion, leading to interactive DVR with improved realism. In the hope that this improved approach to DVR will see more use in practice, we have made available our framework under a permissive open source license

Time-varying volume visualization

Volume rendering is a very active research field in Computer Graphics because of its wide range of applications in various sciences, from medicine to flow mechanics. In this report, we survey a state-of-the-art on time-varying volume rendering. We state several basic concepts and then we establish several criteria to classify the studied works: IVR versus DVR, 4D versus 3D+time, compression techniques, involved architectures, use of parallelism and image-space versus object-space coherence. We also address other related problems as transfer functions and 2D cross-sections computation of time-varying volume data. All the papers reviewed are classified into several tables based on the mentioned classification and, finally, several conclusions are presented.Preprin

Fast and Exact Fiber Surfaces for Tetrahedral Meshes

Isosurfaces are fundamental geometrical objects for the analysis and visualization of volumetric scalar fields. Recent work has generalized them to bivariate volumetric fields with fiber surfaces, the pre-image of polygons in range space. However, the existing algorithm for their computation is approximate, and is limited to closed polygons. Moreover, its runtime performance does not allow instantaneous updates of the fiber surfaces upon user edits of the polygons. Overall, these limitations prevent a reliable and interactive exploration of the space of fiber surfaces. This paper introduces the first algorithm for the exact computation of fiber surfaces in tetrahedral meshes. It assumes no restriction on the topology of the input polygon, handles degenerate cases and better captures sharp features induced by polygon bends. The algorithm also allows visualization of individual fibers on the output surface, better illustrating their relationship with data features in range space. To enable truly interactive exploration sessions, we further improve the runtime performance of this algorithm. In particular, we show that it is trivially parallelizable and that it scales nearly linearly with the number of cores. Further, we study acceleration data-structures both in geometrical domain and range space and we show how to generalize interval trees used in isosurface extraction to fiber surface extraction. Experiments demonstrate the superiority of our algorithm over previous work, both in terms of accuracy and running time, with up to two orders of magnitude speedups. This improvement enables interactive edits of range polygons with instantaneous updates of the fiber surface for exploration purpose. A VTK-based reference implementation is provided as additional material to reproduce our results

Live cell division dynamics monitoring in 3D large spheroid tumor models using light sheet microscopy

<p>Abstract</p> <p>Background</p> <p>Multicellular tumor spheroids are models of increasing interest for cancer and cell biology studies. They allow considering cellular interactions in exploring cell cycle and cell division mechanisms. However, 3D imaging of cell division in living spheroids is technically challenging and has never been reported.</p> <p>Results</p> <p>Here, we report a major breakthrough based on the engineering of multicellular tumor spheroids expressing an histone H2B fluorescent nuclear reporter protein, and specifically designed sample holders to monitor live cell division dynamics in 3D large spheroids using an home-made selective-plane illumination microscope.</p> <p>Conclusions</p> <p>As illustrated using the antimitotic drug, paclitaxel, this technological advance paves the way for studies of the dynamics of cell divion processes in 3D and more generally for the investigation of tumor cell population biology in integrated system as the spheroid model.</p

The analysis and application of dynamic MRI contrasts to grape berry biology

Magnetic resonance imaging (MRI) is a powerful, non-invasive imaging tool. When MRI is employed in the study biological systems, the acquired images reflect different aspects of system morphology and/or physiology. This thesis explores the application of relaxation and diffusion MRI to the study of different biological aspects of the fruit of the common grape vine, Vitis vinifera L., a highly valued botanical species. The results of this investigation have put forth a number of contributions to this area of research. The studies within this thesis began with a necessary validation for the application of diffusion MRI techniques to the grape berry using simulated cellular geometries to determine how broad plant cells could potentially influence the accurate reconstruction of the grape berry morphology. The result of this validation will also prove useful for other wide geometry applications wider than 10 μm. Relaxation and diffusion MRI was also used to study changes to berry morphology resulting from berry development and ripening. This study provided a novel perspective on grape berry development and demonstrated that diffusion anisotropy patterns correlated with the microstructure of the major pericarp tissues of grape berries, including the exocarp, outer and inner mesocarp, seed interior, as well as microstructural variations across grape berry development. This study also provided further evidence that the inner mesocarp striation patterns observed in the spin-spin relaxation weighted images of previous studies arise due to variations in cell width across the striation bands. Diffusion MRI was employed to investigate the morphological and physiological changes to occur within grape berries during fruit split, a costly source of fruit loss in vineyards. This study revealed water uptake through splits in the berry epidermis will result in the loss of parenchyma cell vitality about these wounds. The amount of water left standing on the surface of split grape berries may hence be an important determinant of the cellular response of the fruit to this trauma, and the subsequent establishment of adventitious fruit pathogens. Additionally, paramagnetically enhanced spin-lattice relaxation MRI was used to undertake a novel examination of the diffusive transport of manganese across the berry pericarp. The results of this study shows that the transport of manganese is within the berry xylem influences manganese exiting of ‘downstream’ of the pedicel, and that cellular membranes affect the spatial distribution of manganese across the berry pericarp. Manganese proved to be an excellent tracer for these experiments, and future investigations making use of paramagnetically enhanced relaxation MRI, perhaps employing other paramagnetic materials such as iron or copper, could prove to be valuable in determining how botanical species transport and store these materials within sink organs