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Evolutionary morphing

Evolutionary morphing

引用

VIS 05: IEEE visualization 2005, Proceedings

作者： Wiley, David F. Amenta, Nina Alcantara, Dan A. Ghosh, Deboshmita Kil, Yong J. Delson, Eric Harcourt-Smith, Will Rohlf, F. James John, Katherine St. Hamann, Bernd Institute for Data Analysis and Visualization Department of Computer Science University of California Davis American Museum of Natural History Lehman College City University of New York Department of Ecology and Evolution State University of New York Stony Brook

ISBN: (纸本)0780394623

We introduce a technique to visualize the gradual evolutionary change of the shapes of living things as a morph between known three-dimensional shapes. Given geometric computer models of anatomical shapes for some collection of specimens - here the skulls of the some of the extant members of a family of monkeys - an evolutionary tree for the group implies a hypothesis about the way in which the shape changed through time. We use a statistical model which expresses the value of some continuous variable at an internal point in the tree as a weighted average of the values at the leaves. The framework of geometric morphometrics can then be used to define a shape-space, based on the correspondences of landmark points on the surfaces, within which these weighted averages can be realized as actual surfaces. Our software provides tools for performing and visualizing such an analysis in three dimensions. Beginning with laser range scans of crania, we use our landmark editor to interactively place landmark points on the surface. We use these to compute a "tree-morph" that smoothly interpolates the shapes across the tree. Each intermediate shape in the morph is a linear combination of all of the input surfaces. We create a surface model for an intermediate shape by warping all the input meshes towards the correct shape and then blending them together. To do the blending, we compute a weighted average of their associated trivariate distance functions and then extract a surface from the resulting function. We implement this idea using the squared distance function, rather than the usual signed distance function, in a novel way.

关键词： Computer graphics

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HDF5-FastQuery: Accelerating complex queries on HDF datasets using fast bitmap indices

HDF5-FastQuery: Accelerating complex queries on HDF datasets...

引用

18th International Conference on Scientific and Statistical database Management, SSDBM 2006

作者： Gosink, Luke Shalf, John Stockinger, Kurt Wu, Kesheng Bethel, Wes Institute for Data Analysis and Visualization University of California at Davis One Shields Ave Davis CA 95616 United States Computational Research Division Lawrence Berkeley National Laboratory One Cyclotron Road Berkeley CA 94720 United States

ISBN: (纸本)0769525903

Large scale scientific data is often stored in scientific data formats such as FITS, netCDF and HDF. These storage formats are of particular interest to the scientific user community since they provide multi-dimensional storage and retrieval. However, one of the drawbacks of these storage formats is that they do not support semantic indexing which is important for interactive data analysis where scientists look for features of interests such as "Find all supernova explosions where energy > 105 and temperature > 106". In this paper we present a novel approach called HDF5-FastQuery to accelerate the data access of large HDF5 files by introducing multi-dimensional semantic indexing. Our implementation leverages an efficient indexing technology called bitmap indexing that has been widely used in the database community. Bitmap indices are especially well suited for interactive exploration of large-scale readonly data. Storing the bitmap indices into the HDF5 file has the following advantages: a) Significant performance speedup of accessing subsets of multi-dimensional data and b) portability of the indices across multiple computer platforms. We will present an API that simplifies the execution of queries on HDF5 files for general scientific applications and data analysis. The design is flexible enough to accommodate the use of arbitrary indexing technology for semantic range queries. We will also provide a detailed performance analysis of HDF5-FastQuery for both synthetic and scientific data. The results demonstrate that our proposed approach for multi-dimensional queries is up to a factor of 2 faster than HDF5. © 2006 IEEE.

关键词： Semantics

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visualization of scene structure uncertainty in multi-view reconstruction

Visualization of scene structure uncertainty in multi-view r...

引用

Applied Imagery Pattern Recognition Workshop (AIPR)

作者： Shawn Recker Mauricio Hess-Flores Mark A. Duchaineau Kenneth I. Joy Institute of Data Analysis and Visualization University of California Davis Davis CA USA Google Inc. USA

This paper presents an interactive visualization system, based upon previous work, that allows for the analysis of scene structure uncertainty and its sensitivity to parameters in different multi-view scene reconstruction stages. Given a set of input cameras and feature tracks, the volume rendering-based approach creates a scalar field from reprojection error measurements. The obtained statistical, visual, and isosurface information provides insight into the sensitivity of scene structure at the stages leading up to structure computation, such as frame decimation, feature tracking, and self-calibration. Furthermore, user interaction allows for such an analysis in ways that have traditionally been achieved mathematically, without any visual aid. Results are shown for different types of camera configurations for real and synthetic data as well as compared to prior work.

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Multimodal visualization of DTI and fMRI data using illustrative methods

Multimodal visualization of DTI and fMRI data using illustra...

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Workshops Bildverarbeitung fur die Medizin: Algorithmen - Systeme - Anwendungen, BVM 2009 - Workshop on Image Processing for Medicine: Algorithms - Systems - Applications, BVM 2009

作者： Born, Silvia Jainek, Werner Hlawitschka, Mario Scheuermann, Gerik Trantakis, Christos Meixensberger, Jürgen Bartz, Dirk ICCAS / VCM Universität Leipzig Germany Institute for Data Analysis and Visualization University of California Davis United States Institut für Informatik Universität Leipzig Germany Klinik für Neurochirurgie Universitätsklinikum Leipzig Germany

ISBN: (纸本)9783540938590

Designing multimodal visualizations combining anatomical and functional brain data is a demanding task. Jainek et al. [1] applied illustrative rendering techniques to obtain a high-quality representation of the location and characteristic of brain activation areas (derived from MRI and fMRI). Here, we present the integration of DTI data into this system. Reconstructed nerve fibers connecting functional areas with each other and lower brain areas are embedded into the complex rendering pipeline. Further, we enhanced perception of depth and shape by applying silhouettes and dithered halftoning.

关键词： data visualization

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Partitioning and mapping a fast level-set algorithm on the GPU

Partitioning and mapping a fast level-set algorithm on the G...

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IEEE International Workshop on Intelligent data Acquisition and Advanced Computing Systems: Technology and Applications

作者： Julián Lamas-Rodríguez Dora B. Heras Francisco Argüello Stefan Zachow Dagmar Kainmueller CITIUS University of Santiago de Compostela Spain Visualization and Data Analysis Zuse Institute Berlin (ZIB) Germany

Level-set methods are commonly used to segment regions of interest within images or volumes. These tasks usually involve a high number of operations. GPUs nowadays feature high computation and data throughput capabilities. In this work we present two GPU implementations of the level-set-based segmentation method called Fast Two Cycle. Our solutions partition the computational domain in tiles that can be processed in parallel. The original algorithm is adapted to the special features of the GPU, and performance is optimized by keeping a record of the tiles that require processing at any given time. We have tested our implementations with a set of 3D CT images of brain vessels and we show that we can obtain competitive results using commodity hardware.

关键词： Graphics processing units Tiles Instruction sets Kernel Image segmentation Proposals Three-dimensional displays

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Maximizing adaptivity in hierarchical topological models using cancellation trees

Maximizing adaptivity in hierarchical topological models usi...

引用

Workshop on Mathematical Foundations of Scientific visualization, Computer Graphics, and Massive data Exploration, 2004

作者： Bremer, Peer-Timo Pascucci, Valerio Hamann, Bernd Department of Computer Science University of Illinois Urbana-Champaign United States Center for Applied Scientific Computing Lawrence Livermore National Laboratory United States Institute for Data Analysis and Visualization Department of Computer Science University of California Davis United States

ISBN: (纸本)9783642543005

We present a highly adaptive hierarchical representation of the topology of functions defined over two-manifold domains. Guided by the theory of Morse–Smale complexes, we encode dependencies between cancellations of critical points using two independent structures: a traditional mesh hierarchy to store connectivity information and a new structure called cancellation trees to encode the configuration of critical points. Cancellation trees provide a powerful method to increase adaptivity while using a simple, easy-to-implement data structure. The resulting hierarchy is significantly more flexible than the one previously reported (IEEE Trans. Vis. Comput. Graph. 10(4):385–396, 2004). In particular, the resulting hierarchy is guaranteed to be of logarithmic height. © 2009 Springer-Verlag Berlin Heidelberg.

关键词： Trees (mathematics)

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A Maya use case: Adaptable scientific workflows with ADIOS for general relativistic astrophysics 13

A Maya use case: Adaptable scientific workflows with ADIOS f...

引用

Conference on Extreme Science and Engineering Discovery Environment, XSEDE 2013

作者： Slawinska, Magdalena Bode, Tanja Logan, Jeremy Clark, Michael Zou, Hongbo Kinsey, Matthew Wolf, Matthew Laguna, Pablo Klasky, Scott Georgia Institute of Technology College of Computing Atlanta GA United States Georgia Institute of Technology School of Physics Atlanta GA United States Remote Data Analysis and Visualization Center University of Tennessee Oak Ridge TN United States Oak Ridge National Laboratory Scientific Data Group Oak Ridge TN United States

ISBN: (纸本)9781450321709

There are many challenges in analyzing and visualizing data from current cutting-edge general relativistic astrophysics simulations. Many of the associated tasks are time-consuming with large performance degradation due to the magnitude and complexity of the data. The Adaptable I/O System (ADIOS) is a componentization of the I/O layer that has demonstrated remarkable I/O performance improvements on applications running on leadership class machines while also offering new in-memory "staging" operations for transforming data in-situ. We have been incorporating ADIOS staging technologies into our Maya numerical relativity code based on Cactus infrastructure and Carpet mesh refinement. Incorporating ADIOS into the Maya code is the first step toward enabling a more adaptable Maya workflow. We provide descriptions how we intend to leverage FlexPath (an ADIOS transport method) to provide a richer user experience in real-time visualization and interactive steering. © 2013 by the Association for Computing Machinery, Inc.

关键词： visualization

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Geometry-preserving topological landscapes

Geometry-preserving topological landscapes

引用

Workshop at SIGGRAPH Asia 2012, WASA 2012

作者： Beketayev, Kenes Weber, Gunther H. Morozov, Dmitriy Abzhanov, Aidos Hamann, Bernd Computational Research Division Lawrence Berkeley National Laboratory United States Institute for Data Analysis and Visualization Computer Science Department University of California Davis CA United States Computer Science Department Center for Energy Research Nazarbayev University Kazakhstan

ISBN: (纸本)9781450318358

We propose a novel technique for building geometry-preserving topological landscapes. Our technique creates a direct correlation between a scalar function and its topological landscape. This correlation is accomplished by introducing the notion of geometric proximity into the topological landscapes, reflecting the distance of topological features within the function domain. Furthermore, this technique enables direct comparative analysis between scalar functions, as long as they are defined on the same domain. We describe a construction technique that consists of three stages: contour tree computation, contour tree layout, and landscape construction. We provide a detailed description for the latter two steps. For the contour tree layout stage, we discuss dimension reduction and edge routing techniques that produce a drawing of the contour tree on the plane that preserves the geometric proximity. For the landscape construction stage, we develop a contour construction algorithm that takes the contour tree layout as an input, adds contours at heights that correspond to saddles of the contour tree, and produces a contour map. After an additional triangulation step, this construction method results in the landscape that has the same contour tree as the original function. © 2012 ACM.

关键词： Trees (mathematics)

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visualization of Biomolecular Structures: State of the Art 17

Visualization of Biomolecular Structures: State of the Art

引用

17th Eurographics Conference on visualization - State of the Art Reports, EuroVis-STAR 2015

作者： Kozlíková, B. Krone, M. Lindow, N. Falk, M. Baaden, M. Baum, D. Viola, I. Parulek, J. Hege, H.-C. Faculty of Informatics Masaryk University Czech Republic Visualization Research Center University of Stuttgart Germany Department of Visual Data Analysis Zuse Institute Berlin Germany Immersive Visualization Group Linköping University Sweden Laboratoire de Biochimie Théorique UPR 9080 CNRS France Department of Informatics University of Bergen Norway Institute of Computer Graphics and Algorithms Vienna University of Technology Austria

ISBN: (纸本)9783905674996

Structural properties of molecules are of primary concern in many fields. This report provides a comprehensive overview on techniques that have been developed in the fields of molecular graphics and visualization with a focus on applications in structural biology. The field heavily relies on computerized geometric and visual representations of three-dimensional, complex, large, and time-varying molecular structures. The report presents a taxonomy that demonstrates which areas of molecular visualization have already been extensively investigated and where the field is currently heading. It discusses visualizations for molecular structures, strategies for efficient display regarding image quality and frame rate, covers different aspects of level of detail, and reviews visualizations illustrating the dynamic aspects of molecular simulation data. The report concludes with an outlook on promising and important research topics to enable further success in advancing the knowledge about interaction of molecular structures. © The Eurographics Association 2015.

关键词： visualization

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Dynamic channels in biomolecular systems: Path analysis and visualization

Dynamic channels in biomolecular systems: Path analysis and ...

引用

IEEE Symposium on Biological data visualization (BioVis)

作者： Norbert Lindow Daniel Baum Ana-Nicoleta Bondar Hans-Christian Hege Department of Visualization and Data Analysis Zuse Institute Berlin Germany Department of Physiology and Biophysics University of California Irvine USA

analysis of protein dynamics suggests that internal cavities and channels can be rather dynamic structures. Here, we present a Voronoi-based algorithm to extract the geometry and the dynamics of cavities and channels from a molecular dynamics trajectory. The algorithm requires a pre-processing step in which the Voronoi diagram of the van der Waals spheres is used to calculate the cavity structure for each coordinate set of the trajectory. In the next step, we interactively compute dynamic channels by analyzing the time evolution of components of the cavity structure. Tracing of the cavity dynamics is supported by timeline visualization tools that allow the user to select specific components of the cavity structures for detailed exploration. All visualization methods are interactive and enable the user to animate the time-dependent molecular structure together with its cavity structure. To facilitate a comprehensive overview of the dynamics of a channel, we have also developed a visualization technique that renders a dynamic channel in a single image and color-codes time on its extension surface. We illustrate the usefullness of our tools by inspecting the structure and dynamics of internal cavities in the bacteriorhodopsin proton pump.

关键词： Cavity resonators Proteins Trajectory visualization Skin data visualization Retina

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