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Towards real-time visualization of detailed neural tissue models: View frustum culling for parallel rendering

Towards real-time visualization of detailed neural tissue mo...

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2nd ieee symposium on Biological Data visualization, BioVis 2012

作者： Hernando, Juan B. Schürmann, Felix Pastor, Luis CeSViMa Universidad Politécnica de Madrid Spain Blue Brain Project École Polytechnique Fédérale de Lausanne Switzerland GMRV Universidad Rey Juan Carlos Spain

ISBN: (纸本)9781467347303

Recent efforts to model neural tissue in great anatomical detail play an important role in the shift towards simulation-based brain research. visualization of those detailed models is an important part of the scientific workflow, allowing domain scientists to inspect and analyze the models as a virtual tissue. However, these visualizations pose several computational and interface challenges, from issues such as data size and geometrical and visual complexity. Manual or query driven selection of visual attributes such as color, transparency, transfer functions, visibility are important components for the usability of those visualizations, yet this requires the rendering to be as responsive as possible. Given the data complexity (several million triangles) - despite the power of current GPUs - parallel rendering is the only choice to visualize the full circuits at interactive levels. In particular, sort-first is an appropriate choice to deal with transparency, however it requires efficient view frustum culling. This paper presents two novel techniques for view frustum culling based on a bounding volume skeleton which is created from the geometrical skeleton of the neurons. These skeletons are combined with spatial partitions and some GPU processing to extract the portions of the neurons that need to be rendered while still facilitating interactive changes in the attributes. Experimental results show that the proposed method yields better results than classical approaches such as OBB-trees and looks promising for sort-first environments. © 2012 ieee.

关键词： visualization

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Epithelial cell reconstruction and visualization of the developing Drosophila wing imaginal disc

Epithelial cell reconstruction and visualization of the deve...

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2nd ieee symposium on Biological Data visualization, BioVis 2012

作者： Breen, David E. Widmann, Thomas Bai, Linge Jülicher, Frank Dahmann, Christian Drexel University Philadelphia PA United States Centro de Genómica e Investigación Oncológica Granada Spain Max Planck Institute for the Physics of Complex Systems Dresden Germany Dresden University of Technology Dresden Germany

ISBN: (纸本)9781467347303

Quantifying and visualizing the shape of developing biological tissues provide information about the morphogenetic processes in multicellular organisms. The size and shape of biological tissues depend on the number, size, shape, and arrangement of the constituting cells. To better understand the mechanisms that guide tissues into their final shape, it is important to investigate and measure the cellular arrangements within tissues. Here we present a set of techniques that produces detailed 3D models of the individual cells in an epithelial sheet. The inputs to the techniques are a volumetric model of an epithelium and a mesh model of the cell boundaries lying on its apical surface. The techniques include: definition of a Region of Interest (ROI), projection of the ROI vertices first to the basal surface then to the apical surface, projection of apical cell faces to the basal surface, creation of 3D epithelial cell models, and calculation and visualization of length and volume for each cell. In their first utilization we have applied these techniques to construct the individual epithelial cells of the wing imaginal disc of Drosophila melanogaster. To date, 3D epithelial cell models have been created, allowing for the calculation and visualization of cell parameters. The results show position-dependent patterns of cell shape in the wing imaginal disc. Our procedures should offer a general data processing pipeline for the construction of detailed 3D models of a wide variety of epithelial tissues. © 2012 ieee.

关键词： visualization

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Interactive transfer function design on large multiresolution volumes

Interactive transfer function design on large multiresolutio...

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ieee symposium on Large Data Analysis and visualization (LDAV)

作者： Steven Martin Han-Wei Shen Ohio State University USA

Interactive transfer function design techniques seek to leverage user knowledge to facilitate the discovery of data salience. In this process, interactive volume rendering is typically a necessity. Interactive volume rendering of large-scale data on workstations is often accomplished through the use of level of detail techniques, prioritizing information deemed to be salient over information deemed to be unimportant. If salience is not known a priori, and interactive transfer function design techniques that depend on volume rendering are to be applied to large-scale data using level of detail selection, then there is a cyclic dependency. Techniques must be applied that can support simultaneous development of salience both for the transfer function design technique and the level of detail selection technique. Building on recent work in LOD selection, we propose an interactive transfer function design technique that enables incremental salience discovery to support simultaneous construction of transfer functions and LOD selections on large-scale data.

关键词： Histograms Transfer functions Rendering (computer graphics) Data visualization Color Image color analysis graphics processing units

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Porosity maps - Interactive exploration and visual analysis of porosity in carbon fiber reinforced polymers

Porosity maps - Interactive exploration and visual analysis ...

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14th Eurographics Conference on visualization 2012, EuroVis 2012

作者： Reh, A. Plank, B. Kastner, J. Gröller, E. Heinzl, C. University of Applied Sciences Upper Austria Campus Wels Austria Vienna University of Technology Institute of Computer Graphics and Algorithms Vienna Austria

In this work a novel method for the characterization of porosity in carbon fiber reinforced polymers (CFRP) is presented. A visualization pipeline for the interactive exploration and visual analysis of CFRP specimens is developed to enhance the evaluation workflow for non-destructive testing (NDT) practitioners based on specified tasks. Besides quantitative porosity determination and the calculation of local pore properties, i.e., volume, surface, dimensions and shape factors, we employ a drill-down approach to explore pores in a CFRP specimen. We introduce Porosity Maps (PM), to allow for a fast porosity evaluation of the specimen. Pores are filtered in two stages. First a region of interest is selected in the porosity maps. Second, pores are filtered with parallel coordinates according to their local properties. Furthermore a histogram-based best-viewpoint widget was implemented to visualize the quality of viewpoints on a sphere. The advantages of our approach are demonstrated using real world CFRP specimens. We are able to show that our visualization-driven approach leads to a better evaluation of CFRP components than existing reference methods. © 2012 The Author(s).

关键词： Porosity

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A flexible Java GPU-enhanced visualization framework and its applications

A flexible Java GPU-enhanced visualization framework and its...

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Annual ieee symposium on Computer-Based Medical Systems

作者： Ruida Cheng Justin Senseney Nishith Pandya Evan McCreedy Matthew J. McAuliffe Alexandra Bokinsky Imaging Sciences Laboratory Center for Information Technology National Institutes of Health DHHS USA Geometric Tools Inc. Chapel Hill NC USA

A flexible biomedical visualization framework implemented with Java, OpenGL, and OpenCL performs efficient volume rendering with large, multi-modal datasets. The framework takes advantage of the parallel processing power on modern graphics hardware with novel OpenCL and GLSL shading language implementations. The Java and GPU environment provide portable advanced biomedical image visualization applications. Several applications built on top of the GPU framework are also presented to show the extensibility of the application. These include multi-surface rendering, stereoscopic rendering, image fusion, and diffusion tensor visualization.

关键词： Rendering (computer graphics) graphics processing unit Surface treatment Image color analysis Java visualization Pipelines

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Automating transfer function design with valley cell-based clustering of 2D density plots

Automating transfer function design with valley cell-based c...

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14th Eurographics Conference on visualization 2012, EuroVis 2012

作者： Wang, Yunhai Zhang, Jian Lehmann, Dirk J. Theisel, Holger Chi, Xuebin Shenzhen Institutes of Advanced Technology Chinese Academy of Sciences China Computer Network Information Center Chinese Academy of Sciences China Department of Simulation and Graphics University of Magdeburg Germany

Two-dimensional transfer functions are an effective and well-accepted tool in volume classification. The design of them mostly depends on the user's experience and thus remains a challenge. Therefore, we present an approach in this paper to automate the transfer function design based on 2D density plots. By exploiting their smoothness, we adopted the Morse theory to automatically decompose the feature space into a set of valley cells. We design a simplification process based on cell separability to eliminate cells which are mainly caused by noise in the original volume data. Boundary persistence is first introduced to measure the separability between adjacent cells and to suitably merge them. Afterward, a reasonable classification result is achieved where each cell represents a potential feature in the volume data. This classification procedure is automatic and facilitates an arbitrary number and shape of features in the feature space. The opacity of each feature is determined by its persistence and size. To further incorporate the user's prior knowledge, a hierarchical feature representation is created by successive merging of the cells. With this representation, the user is allowed to merge or split features of interest and set opacity and color freely. Experiments on various volumetric data sets demonstrate the effectiveness and usefulness of our approach in transfer function generation. © 2012 The Author(s).

关键词： Cells

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Gaussian mixture model based volume visualization

Gaussian mixture model based volume visualization

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ieee symposium on Large Data Analysis and visualization (LDAV)

作者： Shusen Liu Joshua A. Levine Peer-Timo Bremer Valerio Pascucci

Representing uncertainty when creating visualizations is becoming more indispensable to understand and analyze scientific data. Uncertainty may come from different sources, such as, ensembles of experiments or unavoidable information loss when performing data reduction. One natural model to represent uncertainty is to assume that each position in space instead of a single value may take on a distribution of values. In this paper we present a new volume rendering method using per voxel Gaussian mixture models (GMMs) as the input data representation. GMMs are an elegant and compact way to drastically reduce the amount of data stored while still enabling realtime data access and rendering on the GPU. Our renderer offers efficient sampling of the data distribution, generating renderings of the data that flicker at each frame to indicate high variance. We can accumulate samples as well to generate still frames of the data, which preserve additional details in the data as compared to either traditional scalar indicators (such as a mean or a single nearest neighbor down sample) or to fitting the data with only a single Gaussian per voxel. We demonstrate the effectiveness of our method using ensembles of climate simulations and MRI scans as well as the down sampling of large scalar fields as examples.

关键词： Uncertainty Rendering (computer graphics) Data visualization Data models Computational modeling Transfer functions graphics processing units

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Combined surface and volumetric occlusion shading

Combined surface and volumetric occlusion shading

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Pacific (formerly Asia-Pacific APVIS) visualization symposium

作者： Mathias Schott Tobias Martin A.V. Pascal Grosset Carson Brownlee Thomas Höllt Benjamin P. Brown Sean T. Smith Charles D. Hansen University of Utah USA King Abdullah University for Science and Technology Saudi Arabia University of Wisconsin USA

In this paper, a method for interactive direct volume rendering is proposed that computes ambient occlusion effects for visualizations that combine both volumetric and geometric primitives, specifically tube shaped geometric objects representing streamlines, magnetic field lines or DTI fiber tracts. The proposed algorithm extends the recently proposed Directional Occlusion Shading model to allow the rendering of those geometric shapes in combination with a context providing 3D volume, considering mutual occlusion between structures represented by a volume or geometry.

关键词： Geometry Rendering (computer graphics) Educational institutions Diffusion tensor imaging Image color analysis Lighting Transfer functions

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FluoRender: An application of 2D image space methods for 3D and 4D confocal microscopy data visualization in neurobiology research

FluoRender: An application of 2D image space methods for 3D ...

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Pacific (formerly Asia-Pacific APVIS) visualization symposium

作者： Yong Wan Hideo Otsuna Chi-Bin Chien Charles Hansen SCI Institute and the School of Computing University of Utah USA Department of Neurobiology and Anatomy University of Utah USA

2D image space methods are processing methods applied after the volumetric data are projected and rendered into the 2D image space, such as 2D filtering, tone mapping and compositing. In the application domain of volume visualization, most 2D image space methods can be carried out more efficiently than their 3D counterparts. Most importantly, 2D image space methods can be used to enhance volume visualization quality when applied together with volume rendering methods. In this paper, we present and discuss the applications of a series of 2D image space methods as enhancements to confocal microscopy visualizations, including 2D tone mapping, 2D compositing, and 2D color mapping. These methods are easily integrated with our existing confocal visualization tool, FluoRender, and the outcome is a full-featured visualization system that meets neurobiologists' demands for qualitative analysis of confocal microscopy data.

关键词： Data visualization Rendering (computer graphics) Transfer functions Image color analysis Biology Three dimensional displays Brightness

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Interference microscopy volume illustration for biomedical data

Interference microscopy volume illustration for biomedical d...

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Pacific (formerly Asia-Pacific APVIS) visualization symposium

作者： Hanqi Guo Xiaoru Yuan Jie Liu Guihua Shan Xuebin Chi Fei Sun Center for Computational Science and Engineering Peking University China Peking University Beijing Beijing CN Key Laboratory of Machine Perception (Ministry of Education) and School of EECS Peking University China Content Technology NVidia Corporation USA Computer Network Information Center Chinese Academy of Sciences China Institute of Biophysics Chinese Academy of Sciences China

In this paper, we propose a novel volume illustration technique inspired by interference microscopy, which has been successfully used in biological, medical and material science over decades. Our approach simulates the optical phenomenon in interference microscopy that accounts light interference over transparent specimens, in order to generate contrast enhanced and illustrative volume visualization results. Specifically, we propose PCVR (Phase- Contrast volume Rendering) and DICVR (Differential Interference Contrast volume Rendering) corresponding to Phase-Contrast microscopy and Differential Interference Contrast (DIC) microscopy respectively. Without complex transfer function design, our proposed method can enhance the image contrast and structure details according to the subtle change of Optical Path Differences (OPD), and illustrate the thickness change and occluded structures with interferometry metaphors. In addition, we also develop a user interface to enable slicing specimen sections in volume data. Focus+ context lens are also included in the system for convenient data navigation and exploration. As the proposed methods are based upon widely applied microscopy techniques, they are intuitive for domain experts to explore and analyze the volume data with the proposed methods. The feedbacks from domain users suggest our proposed techniques are useful volume visualization approaches complimentary to the traditional ones.

关键词： Microscopy Interference Optical microscopy Rendering (computer graphics) Optical imaging Data visualization Optical refraction

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