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PointCloudXplore 2: Visual exploration of 3D gene expression

PointCloudXplore 2: Visual exploration of 3D gene expression

引用

2nd Workshop of the DFG's International research Training group on visualization of Large and Unstructured Data Sets - Applications in Geospatial Planning, Modeling, and Engineering, VLUDS 2007

作者： Rübel, O. Weber, G.H. Huang, M.-Y. Bethel, E.W. Keränen, S.V.E. Fowlkes, C.C. Hendriks, C.L. Luengo DePace, Angela H. Simirenko, L. Eisen, M.B. Biggin, M.D. Hagen, H. Malik, J. Knowles, D.W. Hamann, B. International Research Training Group University of Kaiserslautern Germany Institute for Data Analysis and Visualization University of California Davis United States Computational Research Division Lawrence Berkeley National Laboratory Berkeley United States Genomics Division Lawrence Berkeley National Laboratory Berkeley United States Computer Science Department University of California Irvine United States Computer Science Division University of California Berkeley United States Lawrence Berkeley National Laboratory Life Sciences Division Berkeley United States Department of Molecular and Cellular Biology Center for Integrative Genomics University of California Berkeley United States

ISBN: (纸本)9783885794417

To better understand how developmental regulatory networks are defined in the genome sequence, the Berkeley Drosophila Transcription Network Project (BDNTP ) has developed a suite of methods to describe 3D gene expression data, i.e., the output of the network at cellular resolution for multiple time points. To allow researchers to explore these novel data sets we have developed PointCloudXplore (PCX). In PCX we have linked physical and information visualization views via the concept of brushing (cell selection). For each view dedicated operations for performing selection of cells are available. In PCX, all cell selections are stored in a central management system. Cells selected in one view can in this way be highlighted in any view allowing further cell subset properties to be determined. Complex cell queries can be defined by combining different cell selections using logical operations such as AND, OR, and NOT. Here we are going to provide an overview of PointCloudXplore 2 (PCX2), the latest publicly available version of PCX. PCX2 has shown to be an effective tool for visual exploration of 3D gene expression data. We discuss (i) all views available in PCX2, (ii) different strategies to perform cell selection, (iii) the basic architecture of PCX2., and (iv) illustrate the usefulness of PCX2 using selected examples.

关键词： visualization

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1 Course description

1 Course description

引用

ACM SIGGRAPH 2007 - International Conference on computer graphics and Interactive Techniques

作者： Kasik, Dave Gobbetti, Enrico Marton, Fabio Manocha, Dinesh Yoon, Sung-Eui Correa, Wagner Bruderlin, Beat Stephens, Abe Slusallek, Philipp Dietrich, Andreas Quilez, Iñigo Boeing Enterprise Visualization China Italy Department of Computer Science University of North Carolina Chapel Hill United States Lawrence Livermore National Laboratory United States Visualization Systems Group United States United States Department of Computer Science Technical University of Ilmenau Germany University of Utah's SCI Institute United States Department of Computer Graphics and Digital Media Saarland University Germany Computer Graphics Group Saarland University Germany

No abstract available

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Feature Emphasis and Contextual Cutaways for Multimodal Medical visualization

Feature Emphasis and Contextual Cutaways for Multimodal Medi...

引用

9th Joint Eurographics/IEEE VGTC Symposium on visualization, EuroVis 2007

作者： Burns, Michael Haidacher, Martin Wein, Wolfgang Viola, Ivan Gröller, M. Eduard Imaging and Visualization Department Siemens Corporate Research PrincetonNJ United States Computer Science Department Princeton University United States Institute of Computer Graphics and Algorithms Vienna University of Technology Austria Department of Informatics University of Bergen Norway

ISBN: (纸本)9783905673456

Dense clinical data like 3D Computed Tomography (CT) scans can be visualized together with real-time imaging for a number of medical intervention applications. However, it is difficult to provide a fused visualization that allows sufficient spatial perception of the anatomy of interest, as derived from the rich pre-operative scan, while not occluding the real-time image displayed embedded within the volume. We propose an importance-driven approach that presents the embedded data such that it is clearly visible along with its spatial relation to the surrounding volumetric material. To support this, we present and integrate novel techniques for importance specification, feature emphasis, and contextual cutaway generation. We show results in a clinical context where a pre-operative CT scan is visualized alongside a tracked ultrasound image, such that the important vasculature is depicted between the viewpoint and the ultrasound image, while a more opaque representation of the anatomy is exposed in the surrounding area. © The Eurographics Association 2007.

关键词： visualization

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Phantom based flow analysis by means of dynamic angiography, CFD and laser-doppler-velocimetry

Phantom based flow analysis by means of dynamic angiography,...

引用

IEEE Symposium on Nuclear science (NSS/MIC)

作者： Torsten Bolke Santhosh Seshadhri Ozlem Gurvit Ragnar Bade Bernhard Preim Gabor Janiga Martin Skalej Steffen Serowy Georg Rose Healthcare Telematics & Medical Engineering Group Electrical Engineering Department Otto-von-Guericke University of Magdeburg Germany Laboratory of Fluid Dynamics and Technical Flows Process and Systems Engineering Department Otto-von-Guericke University of Magdeburg Germany Institute for Neuroradiology Medical Department Otto-von-Guericke University of Magdeburg Germany Visualization Research Group Computer Science Department Otto-von-Guericke University of Magdeburg Germany

In this paper we investigate the dynamics of contrast agent concentration as blood flow estimation method utilizing contributions from three different fields: morphologic and dynamic angiographic X-ray scans, computational fluid dynamics (CFD) simulations and Laser-Doppler-Velocimetry (LDV) measurements. Based on dynamic angiographic X-ray measurements we exploit dedicated CFD simulations, carried out specifically for each target object, for the adaptation of the plain video densitometric results. Finally, a comparison with LDV is presented.

关键词： Imaging phantoms Angiography Computational fluid dynamics Blood flow X-ray lasers Fluid dynamics Computational modeling Analytical models Fluid flow measurement Image analysis

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Adaptive demosaicking using multiple neural networks

Adaptive demosaicking using multiple neural networks

引用

2006 16th IEEE Signal Processing Society Workshop on Machine Learning for Signal Processing, MLSP 2006

作者： Yangjing, Long Yizhen, Huang Department of Mathematics Shanghai Jiaotong University 800 Dongchuan Road Minhang District Shanghai 200240 China Department of Computer Science and Engineering Shanghai Jiaotong University 800 Dongchuan Road Minhang District Shanghai 200240 China Digital Media and Data Reconstruction Lab. Shanghai Jiaotong University Graphics Team of the Wireless Platform Engineering Cellular and Handheld Group Intel Asia-Pacific Research and Development Ltd.

ISBN: (纸本)1424406560

Demosaicking is one of the important tasks in the image-processing pipeline in digital cameras using a single electronic sensor overlaid with a Color Filter Array. We quantitatively shows that, demosaicking algorithms perform better in low-gradient flat areas than in high-gradient steep areas. Based on this, an adaptive scheme is proposed that uses more complex neural networks to tackle steep areas in larger sizes of neighborhoods. And interpolation is edge-directed with different networks for different chosen directions. Thus networks are specialized in learning and depicting non-linear spatial inter-pixel correlations at respective gradients and directions. Its performance surpasses Go's neural-network method greatly. Compared with 2 recent state-of-the-art methods, our method provides an excellent trade-off between computational expense and PSNR, and well preserves image edge information. As an extension, we compare the performance of these algorithms with and without Lukac's postprocessing. © 2006 IEEE.

关键词： Adaptive systems

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Super-resolution using neural networks based on the optimal recovery theory

Super-resolution using neural networks based on the optimal ...

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2006 16th IEEE Signal Processing Society Workshop on Machine Learning for Signal Processing, MLSP 2006

作者： Huang, Yizhen Long, Yangjing Department of Computer Science and Engineering Shanghai Jiaotong University 800 Dongchuan Road Minhang District Shanghai 200240 China Department of Mathematics Shanghai Jiaotong University 800 Dongchuan Road Minhang District Shanghai 200240 China Graphics Team of the Wireless Platform Engineering Cellular and Handheld Group Intel Asia-Pacific Research and Development Ltd. Digital Media and Data Reconstruction Lab. Shanghai Jiaotong University

ISBN: (纸本)1424406560

An optimal recovery based neural-network Super Resolution algorithm is developed. The proposed method is computationally less expensive and outputs images with high subjective quality, compared with previous neural-network or optimal recovery algorithms. It is evaluated on classical SR test images with both generic and specialized training sets, and compared with other state-of-the-art methods. Results show that our algorithm is among the state-of-the-art, both in quality and efficiency. © 2006 IEEE.

关键词： Image quality

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A system for real-time watercolour rendering

A system for real-time watercolour rendering

引用

computer graphics International 2005, CGI 2005

作者： Burgess, Jeremy Wyvill, Geoff King, Scott A. Computer Graphics and Vision Research Group Department of Computer Science University of Otago New Zealand Computing and Mathematical Sciences Texas A and M-Corpus Christi United States

ISBN: (纸本)0780393309

We present a system for the real-time rendering of scenes to produce images like watercolour paintings. Our system uses a hybrid of object space rendering techniques and image plane post processing to attain extremely good results very quickly. We achieve this through graphics Processing Unit (GPU) programming, hardware accelerated shadow volumes, and the use of noise for various different tasks. We manage to circumvent problems found in both previous image space and object space methods by combining the two. © 2005 IEEE.

关键词： Color image processing

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Illustrative visualization

Illustrative visualization

引用

VIS 05: IEEE visualization 2005, Proceedings

作者： Viola, Ivan Gröller, Meister E. Hadwiger, Markus Bühler, Katja Preim, Bernhard Sousa, Mario Costa Ebert, David S. Stredney, Don Kanitsar, Armin Bruckner, Stefan Grimm, Sören Svakhine, Nikolai A. Jang, Yun Gaithert, Kelly Tietjen, Christian Krüger, Arno Peitgen, Heinz-Otto Isenberg, Tobias Hintze, Jana Hertel, Ilka Strauß, Gero Institute of Computer Graphics and Algorithms Vienna University of Technology Austria VRVis Research Center Vienna Austria Department of Simulation and Graphics University of Magdeburg Germany Department of Computer Science University of Calgary Canada School of Electrical and Computer Engineering Purdue University United States Ohio Supercomputer Center United States Institute of Computer Graphics and Algorithms Vienna University of Technology Austria VRVis Research Center Vienna Austria Electrical and Computer Engineering Purdue University United States IEEE Austria Department of Computer Science University of Calgary Canada Department of Computer Science Computer Graphics Research Lab. University of Calgary Canada Purdue University United States Ohio Supercomputer Center United States University of Texas Austin United States Interface Laboratory United States Biomedical Applications United States Department of Simulation and Graphics Otto-von-Guericke-University of Magdeburg Germany Otto-von-Guericke-University of Magdeburg FIN/ISG Germany Institute for Simulation and Graphics Department for Computer Science Otto-von-Guericke-University of Magdeburg Universitaetsplatz 2 39106 Magdeburg Germany Center for Medical Diagnosic Systems and Visualization Universitaetsallee 29 28359 Bremen Germany Department of Simulation and Graphics Otto-von-Guericke University of Magdeburg Germany ENT Department University Hospital of Leipzig Germany

ISBN: (纸本)0780394623

The tutorial presents state-of-the-art visualization techniques inspired by traditional technical and medical illustrations. Such techniques exploit the perception of the human visual system and provide effective visual abstractions to make the visualization clearly understandable. Visual emphasis and abstraction has been used for expressive presentation from prehistoric paintings to nowadays scientific and medical illustrations. Many of the expressive techniques used in art are adopted in computer graphics, and are denoted as illustrative or non-photorealistic rendering. Different stroke techniques, or brush properties express a particular level of abstraction. Feature emphasis or feature suppression is achieved by combining different abstraction levels in illustrative rendering. Challenges in visualization research are very large data visualization as well as multi-dimensional data visualization. To effectively convey the most important visual information there is a significant need for visual abstraction. For less relevant information the dedicated image space is reduced to enhance more prominent features. The discussed techniques in the context of scientific visualization are based on iso-surfaces and volume rendering. Apart from visual abstraction, i.e., illustrative representation, the visibility of prominent features can be achieved by illustrative visualization techniques such as cut-away views or ghosted views. The structures that occlude the most prominent information are suppressed in order to clearly see more interesting parts. A different smart way to provide information on the data is using exploded views or other types of deformation. Furthermore intuitive feature classification via 3D painting and manipulation with the classified data including label placement is presented. Discussed non-photorealistic and illustrative techniques from visualization and graphics are shown from the perspective as tools for illustrators from medicine, botany, archeology

关键词： visualization

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A system for real-time watercolour rendering

A system for real-time watercolour rendering

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computer graphics International

作者： J. Burgess G. Wyvill S.A. King Computer Graphics and Vision Research Group Department of Computer Science University of Otago New Zealand Computing & Mathematical Sciences Texas A and M Corpus Christi USA

We present a system for the real-time rendering of scenes to produce images like watercolour paintings. Our system uses a hybrid of object space rendering techniques and image plane post processing to attain extremely good results very quickly. We achieve this through graphics processing unit (GPU) programming, hardware accelerated shadow volumes, and the use of noise for various different tasks. We manage to circumvent problems found in both previous image space and object space methods by combining the two.

关键词： Real time systems Rendering (computer graphics) Painting Layout Paints computer graphics computer science Pigmentation computer vision Acceleration

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A new fractal-based approach for 3D visualization of mountains in VRML standard

A new fractal-based approach for 3D visualization of mountai...

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Proceedings GRAPHITE 2004 - 2nd International Conference on computer graphics and Interactive Techniques in Australasia and South East Asia

作者： Sharifi, Mohsen Golpaygani, Fatemeh Hashemi Esmaeli, Mehdi Visualization Research Group Computer Engineering Department Iran Univ. of Science and Technology Iran

ISBN: (纸本)1581138849

Several factors currently limit the size of Virtual Reality Modeling Language (VRML) models that can be effectively visualized over the Web. Main factors include network bandwidth limitations and inefficient encoding schemes for geometry and its associated properties. The delays caused by these factors reduce the attractiveness of VRML usage for a large range of virtual reality models, CAD data, and scientific visualizations. To solve this problem, we have tried to decrease the size of data by deploying fractal geometry in VRML standard. A novel approach is proposed for generating a "fractal mountain" using a random Midpoint-Displacement method in VRML standard. Our VRML 2.0 implementation, which is based on two newly defined nodes, TriangleGrid and FractMountain, and uses PROTO mechanism and Java in the Script nodes for the logic, is presented too. It is shown that our approach is more flexible and memory efficient than other approaches for computing mountain structures. Besides, mountains visualized by this approach look much more natural than those generated by other approaches.

关键词： Virtual reality

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