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visualization for validation and improvement of three-dimensional segmentation algorithms

Visualization for validation and improvement of three-dimens...

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7th Joint Eurographics - IEEE VGTC Symposium on visualization, VisSym 2005

作者： Weber, G.H. Luengo Hendriks, C.L. Keränen, S.V.E. Dillard, S.E. Ju, D.Y. Sudar, D. Hamann, B. Berkeley Drosophila Transcription Network Project Visualization and Computer Graphics Research Group Institute for Data Analysis and Visualization University of California Davis One Shields Avenue DavisCA95616 United States Genomics and Life Sciences Division Lawrence Berkeley National Laboratory One Cyclotron Road BerkeleyCA94720 United States

ISBN: (纸本)3905673193

The Berkeley Drosophila Transcription Network Project (BDTNP) is developing a suite of methods that will allow a quantitative description and analysis of three dimensional (3D) gene expression patterns in an animal with cellular resolution. An important component of this approach are algorithms that segment 3D images of an organism into individual nuclei and cells and measure relative levels of gene expression. As part of the BDTNP, we are developing tools for interactive visualization, control, and verification of these algorithms. Here we present a volume visualization prototype system that, combined with user interaction tools, supports validation and quantitative determination of the accuracy of nuclear segmentation. visualizations of nuclei are combined with information obtained from a nuclear segmentation mask, supporting the comparison of raw data and its segmentation. It is possible to select individual nuclei interactively in a volume rendered image and identify incorrectly segmented objects. Integration with segmentation algorithms, implemented in MATLAB, makes it possible to modify a segmentation based on visual examination and obtain additional information about incorrectly segmented objects. This work has already led to significant improvements in segmentation accuracy and opens the way to enhanced analysis of images of complex animal morphologies. © The Eurographics Association 2005.

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Volumetric data analysis using Morse-Smale complexes

Volumetric data analysis using Morse-Smale complexes

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International Conference on Shape Modeling and Applications

作者： V. Natarajan V. Pascucci Institute for Data Analysis and Visualization University of California슠Davis USA Lawrence Livemore National Laboratory Livermore CA USA

The 3D Morse-Smale complex is a fundamental topological construct that partitions the domain of a real-valued function into regions having uniform gradient flow behavior. In this paper, we consider the construction and selective presentation of cells of the Morse-Smale complex and their use in the analysis and visualization of scientific datasets. We take advantage of the fact that cells of different dimension often characterize different types of features present in the data. For example, critical points pinpoint changes in topology by showing where components of the level sets are created, destroyed or modified in genus. Edges of the Morse-Smale complex extract filament-like features that are not explicitly modeled in the original data. Interactive selection and rendering of portions of the Morse-Smale complex introduces fundamental data management challenges due to the unstructured nature of the complex even for structured inputs. We describe a data structure that stores the Morse-Smale complex and allows efficient selective traversal of regions of interest. Finally, we illustrate the practical use of this approach by applying it to cryo-electron microscopy data of protein molecules.

关键词： data analysis Shape Isosurfaces data visualization Topology data mining data structures Microscopy Clustering algorithms Partitioning algorithms

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End-to-end data reduction and hardware accelerated rendering techniques for visualizing time-varying non-uniform grid volume data 05

End-to-end data reduction and hardware accelerated rendering...

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International Workshop on Volume Graphics, VG

作者： H. Akiba Kwan-Liu Ma J. Clyne Institute for Data Analysis and Visualization University of California슠Davis USA Scientific Computing Devision National Center for Atmospheric Research CO USA

ISBN: (纸本)3905673266

We present a systematic approach for direct volume rendering terascale-sized data that are time-varying, and possibly non-uniformly sampled, using only a single commodity graphics PC. Our method employs a data reduction scheme that combines lossless, wavelet-based progressive data access with a user-directed, hardware-accelerated data packing technique. data packing is achieved by discarding data blocks with values outside the data interval of interest and encoding the remaining data in a structure that can be efficiently decoded in the GPU. The compressed data can be transferred between disk, main memory, and video memory more efficiently, leading to more effective data exploration in both spatial and temporal domains. Furthermore, our texture-map based volume rendering system is capable of correctly displaying data that are sampled on a stretched, Cartesian grid. To study the effectiveness of our technique we used data sets generated from a large solar convection simulation, computed on a non-uniform, 504/spl times/504/spl times/2048 grid.

关键词： Hardware Acceleration data visualization Rendering (computer graphics) Time varying systems Graphics Encoding Decoding Video compression Mesh generation

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Maximizing adaptivity in hierarchical topological models

Maximizing adaptivity in hierarchical topological models

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International Conference on Shape Modeling and Applications

作者： P.-T. Bremer V. Pascucci B. Hamann Department of Computer Science University of Illinois Urbana-Champaign USA Lawrence Livermore National Laboratory Center for Applied Scientific Computing USA Institute for Data Analysis and Visualization Department of Computer Science University of California Davis USA

We present an approach to hierarchically encode the topology of functions over triangulated surfaces. Its Morse-Smale complex, a well known structure in computational topology, describes the topology of a function. Following concepts of Morse theory, a Morse-Smale complex (and therefore a function's topology) can be simplified by successively canceling pairs of critical points. We demonstrate how cancellations can be effectively encoded to produce a highly adaptive topology-based multi-resolution representation of a given function. Contrary to the approach, we avoid encoding the complete complex in a traditional mesh hierarchy. Instead, the information is split into a new structure we call a cancellation forest and a traditional dependency graph. The combination of this new structure with a traditional mesh hierarchy proofs to be significantly more flexible than the one previously reported. In particular, we can create hierarchies that are guaranteed to be of logarithmic height.

关键词： Topology data visualization data analysis Computer science Encoding Level set Shape Scientific computing Laboratories Transfer functions

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Evolutionary morphing

Evolutionary morphing

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IEEE Conference on visualization

作者： D.F. Wiley N. Amenta D.A. Alcantara D. Ghosh Y.J. Kil E. Delson W. Harcourt-Smith F.J. Rohlf K. St John B. Hamann Institute for Data Analysis and Visualization and Department of Computer Science University of California Davis USA American Museum of Natural University of New York UK Department of Ecology and Evolution State University of New York Stony Brook USA

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： Shape Surface morphology Evolution (biology) Statistical analysis data visualization Genomics Bioinformatics Skull Humans data analysis

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An improved N-bit to N-bit reversible Haar-like transform

An improved N-bit to N-bit reversible Haar-like transform

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Pacific Conference on Computer Graphics and Applications

作者： J.G. Senecal P. Lindstrom M.A. Duchaineau K.I. Joy Inst. for Sci. Comput. Res. Lawrence Livermore Nat. Lab. CA USA Center for Applied Scientific Computing Lawrence Livemore National Laboratory USA Institute for Data Analysis and Visualization Computer Science Department University of California Davis USA

We introduce the piecewise-linear Haar (PLHaar) transform, a reversible n-bit to n-bit transform that is based on the Haar wavelet transform. PLHaar is continuous, while all current n-bit to n-bit methods are not, and is therefore uniquely usable with both lossy and lossless methods (e.g. image compression). PLHaar has both integer and continuous (i.e. non-discrete) forms. By keeping the coefficients to n bits PLHaar is particularly suited for use in hardware environments where channel width is limited, such as digital video channels and graphics hardware.

关键词： Wavelet transforms Continuous wavelet transforms Hardware Dynamic range Image coding Scientific computing Image reconstruction Laboratories data analysis data visualization

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visualization in Medicine and Life Sciences II 1

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丛书名： Mathematics and visualization

1000年

作者： Lars Linsen Hans Hagen Bernd Hamann Hans-Christian Hege

ISBN: (数字)9783642216084

ISBN: (纸本)9783642216077;9783662519691

For some time, medicine has been an important driver for the development of data processing and visualization techniques. Improved technology offers the capacity to generate larger and more complex data sets related to imaging and simulation. This, in turn, creates the need for more effective visualization tools for medical practitioners to interpret and utilize data in meaningful ways. The first edition of visualization in Medicine and Life Sciences (VMLS) emerged from a workshop convened to explore the significant data visualization challenges created by emerging technologies in the life sciences. The workshop and the book addressed questions of whether medical data visualization approaches can be devised or improved to meet these challenges, with the promise of ultimately being adopted by medical experts. visualization in Medicine and Life Sciences II follows the second international VMLS workshop, held in Bremerhaven, Germany, in July 2009. Internationally renowned experts from the visualization and driving application areas came together for this second workshop. The book presents peer-reviewed research and survey papers which document and discuss the progress made, explore new approaches to data visualization, and assess new challenges and research directions.

关键词： visualization Computer Graphics Computer Appl. in Life Sciences Mathematical Modeling and Industrial Mathematics Image Processing and Computer Vision Computational Science and Engineering

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visualization in Medicine and Life Sciences III 1

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丛书名： Mathematics and visualization

1000年

作者： Lars Linsen Bernd Hamann Hans-Christian Hege

ISBN: (数字)9783319245232

ISBN: (纸本)9783319245218;9783319796406

The book discusses novel visualization techniques driven by the needs in medicine and life sciences as well as new application areas and challenges for visualization within these fields. It presents ideas and concepts for visual analysis of data from scientific studies of living organs or to the delivery of healthcare. Target scientific domains include the entire field of biology at all scales - from genes and proteins to organs and populations - as well as interdisciplinary research based on technological advances such as bioinformatics, biomedicine, biochemistry, or biophysics. Moreover, they comprise the field of medicine and the application of science and technology to healthcare problems. This book does not only present basic research pushing the state of the art in the field of visualization, but it also documents the impact in the fields of medicine and life sciences.

关键词： visualization User Interfaces and Human Computer Interaction Computer Graphics Image Processing and Computer Vision

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