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A tree index to support clustering based exploratory data analysis

Communications in Computer and Information Science 2008年 13卷 1-15页

作者： Martin, Christian Nattkemper, Tim W. AG Applied Neuroinformatics Bielefeld University Germany

ISBN: (纸本)9783540705987

In microarray data analysis, visualizations based on agglomerative clustering results are widely applied to help biomedical researchers in generating a mental model of their data. In order to support a selection of the to-be-applied algorithm and parameterizations, we propose a novel cluster index, the tree index (TI), to evaluate hierarchical cluster results regarding their visual appearance and their accordance to available background information. Visually appealing cluster trees are characterized by splits that separate those homogeneous clusters from the rest of the data, which have low inner cluster variance and share a medical class label. To evaluate clustering trees regarding this property, the TI computes the likeliness of every single split in the cluster tree. computing TIs for different algorithms and parameterizations allows to identify the most appealing cluster tree among many possible tree visualizations obtained. Application is shown on simulated data as well as on two public available cancer data sets. © Springer-Verlag Berlin Heidelberg 2008.

关键词： visualization

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A virtual imaging system for colour research

A virtual imaging system for colour research

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2008 23rd International conference Image and Vision computing New Zealand, IVCNZ

作者： Chalmers, A.N. Wang, L. Ramos, M.V. Department of Electrical and Computer Engineering Manukau Institute of Technology Manukau 2241 New Zealand Institute for Biomedical Technologies Auckland University of Technology Auckland 1142 New Zealand

ISBN: (纸本)9781424425822

A visualization system has been constructed to provide an accurate representation of a group of surface colours under a range of different light sources. The impetus for this work has come from the burgeoning supply of new high-output LED (light-emitting diode) sources now entering the market. The system will be used to test the validity of the CIE (International Commission on Illumination) colour rendering index (CRI) for these and other sources. The system computes and displays each colour from a knowledge of the light-source spectrum and the spectral reflectance of each surface, and can simultaneously display the resultant colours from two different sources as well as computing the colour differences for the two sets of colours. Subjective tests are being undertaken to validate the computed results. © 2008 IEEE.

关键词： Color

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An Efficient Method for Sampling and computing Molecular Surface

An Efficient Method for Sampling and Computing Molecular Sur...

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International conference on biomedical Engineering and Informatics (BMEI)

作者： Junping Xiang Maolin Hu Key Laboratory of Intelligent Computing & Signal Processing Ministry of Education and School of Mathematics and Computational Science Anhui University China

An atom-centered protocol based method for surface sampling in grid space is proposed. Van der Waals, solvent-accessible and solvent-excluded surface can be generated in a unified framework. A spherical hash function is used to mark whether the points are inside a sphere, and the hash tables are used to record which spheres the surface points locate on. The proposed method can be modified to apply in the parallel computation directly, which is useful for molecular dynamics simulation, docking and surface comparison and so on. Our tests indicate that the proposed method is efficient and the generated surfaces are suitable for quantitative analysis and visualization.

关键词： Sampling methods Synthetic aperture sonar Solvents Atomic measurements Grid computing Probes biomedical computing Signal sampling Concurrent computing visualization

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MedVis: A Real-Time Immersive visualization Environment for the Exploration of Medical Volumetric Data

MedVis: A Real-Time Immersive Visualization Environment for ...

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International conference on biomedical visualization, MEDIVIS

作者： Rui Shen Pierre Boulanger Michelle Noga Department of Computing Science University of Alberta Edmonton AB Canada Department of Radiology & Diagnostic Imaging University of Alberta Edmonton AB Canada

ISBN: (纸本)9780769532844

This paper describes the Medical Visualizer, a real-time visualization system for analyzing medical volumetric data in various virtual environments, such as autostereoscopic displays, dual-projector screens and immersive environments such as the CAVE. Direct volume rendering is used for visualizing the details of medical volumetric data sets without intermediate geometric representations. By interactively manipulating the color and transparency functions through the friendly user interface, radiologists can either inspect the data set as a whole or focus on a specific region. In our system, 3D texture hardware is employed to accelerate the rendering process. The system is designed to be platform independent, as all virtual reality functions are separated from kernel functions. Due to its modular design, our system can be easily extended to other virtual environments, and new functions can be incorporated rapidly.

关键词： Image generation Data visualization biomedical imaging Transfer functions Medical diagnostic imaging Three dimensional displays Image color analysis

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3D Multiscale Visualisation for Medical Datasets

3D Multiscale Visualisation for Medical Datasets

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International conference on biomedical visualization, MEDIVIS

作者： N. J. B. McFarlane G. J. Clapworthy A. Agrawal M. Viceconti F. Taddei E. Schileo F. Baruffaldi Department of Computing & Information Systems University of Bedfordshire Luton UK Laboratorio di Tecnologia Medica Istituti Ortopedici Rizzoli Bologna Italy

ISBN: (纸本)9780769532844

A 3D multiscale view has been developed for medical datasets that are composed of multiple images of very different spatial sizes. The example data consisted of 3 volume images of bone: a 400 mm femur; a 20 mm micro-CT image of trabeculae; and a 0.5 mm nano-CT image of a single trabecula. The images were nested, the nano-CT being inside the micro-CT, which was within the head of the femur. The images were visualised using a volume slice view. The dataset was multiscale in that each image could not be usefully resolved at the scale of the next larger image. The multiscale interaction within the system is based on the replacement of sub-scale images by small click-and-zoom tokens. Issues relating to interaction with the tokens are discussed and early outcomes from this form representation are described.

关键词： Cameras visualization Data visualization Three dimensional displays biomedical imaging Bones Image resolution

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Using Web Services for Distributed Medical Visualisation

Using Web Services for Distributed Medical Visualisation

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International conference on biomedical visualization, MEDIVIS

作者： Xia Zhao Enjie Liu Gordon Clapworthy Paolo Quadrani Debora Testi Marco Viceconti Department of Computing and Information Systems University of Bedfordshire Luton UK CINECA Supercomputing Centre Bologna Italy BioComputing Competence Centre SCS s.r.l. Bologna Italy Laboratorio di Tecnologia Medica Istituti Ortopedici Rizzoli Bologna Italy

ISBN: (纸本)9780769532844

Collaboration on the storage, processing and visualisation of medical data via the Internet is a considerable challenge and one that is growing in importance due to the escalating interest in the Virtual Physiological Human. Investigations into possible approaches for distributed, realtime visualisation are important in this context. This paper presents a Web Services approach to distributed visualisation that has been developed within the LHDL project. The processing and visualisation Web Services that have been created are based on existing MAF applications; this has formed a useful testbed for transforming legacy software into Web Services. On the client side, a Rich Internet Application concept was adopted, while a web-based, user friendly Flex client has been implemented.

关键词： Web services Data visualization Libraries Image generation Servers Service oriented architecture Software

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3D Lumbar visualization Based on VTK with Fusing Sagital Slices and Aixal Slices

3D Lumbar Visualization Based on VTK with Fusing Sagital Sli...

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International conference on Bioinformatics and biomedical Engineering (ICBBE)

作者： Shu Zhan Shijie Hao Jian-Guo Jiang Hong Li Hefei University of Technology Hefei Anhui China Anhui Medical University Hefei Anhui China

Based on the anatomical consistency in two series MRI images of a patient in different postures, an algorithm computing a spatially intersectant line of two images from each series is proposed. Furthermore, the anatomical corresponding section of 3D datasets formed by these series can be located. Finally, the datasets are 3D visualized with VTK (visualization ToolKits). This would be of great help to physicians when they give diagnoses. Also, the algorithm has its application in image registration, image segmentation and 3D visualization.

关键词： Magnetic resonance imaging Musculoskeletal system Data visualization biomedical imaging Medical diagnostic imaging Image registration Spine Image segmentation Focusing Rendering (computer graphics)

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CSV: Visualizing and mining cohesive subgraphs

CSV: Visualizing and mining cohesive subgraphs

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2008 ACM SIGMOD International conference on Management of Data 2008, SIGMOD'08

作者： Wangt, Nan Parthasarathy, Srinivasan Tan, Kian-Lee Tung, Anthony K. H. School of Computing National University of Singapore Singapore Dept. of Computer Science and Engineering and Department of Biomedical Informatics Ohio State University ColumbusOH United States

ISBN: (纸本)9781605581026

Extracting dense sub-components from graphs efficiently is an important objective in a wide range of application domains ranging from social network analysis to biological network analysis, from the World Wide Web to stock market analysis. Motivated by this need recently we have seen several new algorithms to tackle this problem based on the (frequent) pattern mining paradigm. A limitation of most of these methods is that they are highly sensitive to parameter settings, rely on exhaustive enumeration with exponential time complexity, and often fail to help the users understand the underlying distribution of components embedded within the host graph. In this article we propose an approximate algorithm, to mine and visualize cohesive subgraphs (dense sub components) within a large graph. The approach, refereed to as Cohesive Subgraph visualization (CSV) relies on a novel mapping strategy that maps edges and nodes to a multi-dimensional space wherein dense areas in the mapped space correspond to cohesive subgraphs. The algorithm then walks through the dense regions in the mapped space to output a visual plot that effectively captures the overall dense sub-component distribution of the graph. Unlike extant algorithms with exponential complexity, CSV has a complexity of O(V 2logV) when fixing the parameter mapping dimension, where V corresponds to the number of vertices in the graph, although for many real datasets the performance is typically sub-quadratic. We demonstrate the utility of CSV as a stand-alone tool for visual graph exploration and as a pre-filtering step to significantly scale up exact subgraph mining algorithms such as CLAN [33]. Copyright 2008 ACM.

关键词： visualization

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A concept-driven automatic ontology generation approach for conceptualization of document corpora

A concept-driven automatic ontology generation approach for ...

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2008 IEEE/WIC/ACM International conference on Web Intelligence, WI 2008

作者： Zheng, Hai-Tao Borchert, Charles Kim, Hong-Gee Biomedical Knowledge Engineering Laboratory Seoul National University 28 Yeongeon-dong Jongro-gu Seoul Korea Republic of

ISBN: (纸本)9780769534961

In the age of increasing information availability, many techniques, such as document clustering and information visualization, have been developed to ease understanding of information for users. However, most of these methods do not help users directly understand key concepts and their semantic relationships in document corpora, which are critical for capturing their conceptual structures. Therefore, we propose a novel approach called 'Clonto' to identify the key concepts and automatically generate ontologies based on these concepts for conceptualization of document corpora. Clonto applies latent semantic analysis to identify key concepts, allocates documents based on these concepts, and utilizes WordNet to automatically generate a corpus-related ontology. The documents are linked to the ontology through the key concepts. The experimental results show that Clonto can identify key concepts with a high precision and the clustering results of Clonto outperform the STC (Suffix Tree Clustering) algorithm, the Lingo clustering algorithm, the Fuzzy Ants clustering algorithm, and clustering based on TRS (Tolerance Rough Set). Moreover, based on the same document corpus, the ontology generated by Clonto shows a significant informative conceptual structure. © 2008 IEEE.

关键词： Ontology

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Octree Based Representation and Volume Rendering of Three-Dimensional Medical Data Sets

Octree Based Representation and Volume Rendering of Three-Di...

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International conference on biomedical Engineering and Informatics (BMEI)

作者： Weiwei Song Shungang Hua Zongying Ou Hu An Kaifeng Song School of Mechanical Engineering University of Ji''nan Jinan China Key Laboratory of Precision & Non-traditional Machining of Ministry of Education Dalian University of Technology Dalian China

In many clinical applications, interactive exploration of three dimension medical data sets is required, but the huge amount of computational time and storage space needed for rendering do not allow the visualization of large medical data sets by now. In this paper we present a new algorithm for rendering large medical data sets on standard PC. The key technique is a new representation method of large medical dataset based on an efficient octree data structure. First, the input data is converted into a compressed hierarchical octree representation. Then, a template-based raycasting scheme using shear-warp factorization for expediting parallel viewing of volume datasets is employed. The algorithm exploits the uniform shape, orientation and size of the "nonempty" octree blocks by building templates for ray/block intersections in the case of raycasting. Experiment results display that high quality human body interior images of a large dataset can be generated by the proposed approach on a standard PC platform fast.

关键词： Data visualization biomedical imaging Mechanical engineering Encoding Space technology Image coding Power engineering computing biomedical engineering biomedical informatics Laboratories

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