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Gene expression detection and expression visualization in in-situ hybridized cross-sectional images of the mouse brain

Gene expression detection and expression visualization in in...

引用

Medical Imaging 2005 conference

作者： Pathak, S Lein, E Smith, S Haynor, DR Hawrylycz, M Allen Inst Brain Sci Seattle WA 98103 USA

ISBN: (纸本)0819457213

Understanding gene expression in the mouse brain should provide a better understanding of the underlying topology of the mammalian brain, thereby opening previously unexplored avenues in neuroscience and brain informatics. An important step in this direction is to develop robust algorithms to quantify gene expression in in-situ hybridization (ISH) data. ISH methodology involves the use of labeled nucleic acid probes that bind to specific mRNA transcripts in tissue sections. The bound probe is detected using colorimetric methods and the resulting stained tissue sections are imaged at high resolution. The goals of the present study are to first identify a staining method that produces maximum signal to noise ratio (SNR), and second to develop a method for gene expression detection for a wide range of ISH images spanning different intensity and expression patterns. A simple k-means based clustering method is used to separate foreground labeling from background and non-expressing tissues in a variety of images stained with different staining/ counter staining techniques. We found NBT/BCIP with no counterstain produces the best signal to background separation. The foreground cluster detected using the k-means algorithm was further modeled using a normal distribution. A novel one sided Mahalanobis distance based metric with majority partial ordered voting method was then developed to generate a fuzzy segmentation of the gene expression in each ISH image. This algorithm is fully automatic and facilitates high throughput analysis of large amount of image data. Using this methodology a cluster of 10 PCs was able to process approximately 10% of the mouse genome (17 TBytes of JPEG2000 lossless compressed images) over a period of 2 weeks. The results may be visualized at the Allen Institute for Brain Science web site ***.

关键词： gene expression detection statistical modeling expression visualization

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Multi-aspect data analysis in brain informatics

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1st International conference on Pattern Recognition and Machine Intelligence

作者： Zhong, N Maebashi Inst technol Int WIC Inst Maebashi Gumma 3710816 Japan Maebashi Inst technol Dept Informat Engn Maebashi Gumma 3710816 Japan

ISBN: (纸本)3540305068

In order to investigate human information processing mechanism systematically, various methods of brain data measurement and analysis are required. It has been observed that multiple brain data such as fMRI brain images and EEG brain waves extracted from human multiperception mechanism involved in a particular task are peculiar ones with respect to a specific state or the related part of a stimulus. Based on this point of view, we propose a way of peculiarity oriented mining for multi-aspect analysis in multiple human brain data, without using conventional image processing to fMRI brain images and frequency analysis to brain waves. The proposed approach provides a new way in Brain Informatics for automatic analysis and understanding of human brain data to replace human-expert centric visualization. We attempt to change the perspective of cognitive scientists from a single type of experimental data analysis towards a holistic view.

关键词： Neurology

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Flink: Semantic Web technology for the extraction and analysis of social networks

Flink: Semantic Web technology for the extraction and analys...

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Selected Papers from the International Semantic Web conference 2004 ISWC, 2004

作者： Mika, Peter De Boelelaan 1081 1081HV Amsterdam Netherlands

We present the Flink system for the extraction, aggregation and visualization of online social networks. Flink employs semantic technology for reasoning with personal information extracted from a number of electronic information sources including web pages, emails, publication archives and FOAF profiles. The acquired knowledge is used for the purposes of social network analysis and for generating a web-based presentation of the community. We demonstrate our novel method to social science based on electronic data using the example of the Semantic Web research community. © 2005 Elsevier B.V. All rights reserved.

关键词： Semantics

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An interoperable, agricultural information system based on satellite remote sensing data

An interoperable, agricultural information system based on s...

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Annual conference 2005 - Geospatial Goes Global: From Your Neighborhood to the Whole Planet

作者： Teng, William Chiu, Long Doraiswamy, Paul Kempler, Steven Liu, Zhong Pham, Long Rui, Hualan NASA Goddard Earth Sciences Data/Information Services Center Distributed Active Archive Center Code 902.2 Greenbelt MD 20771 United States Science Systems and Applications Inc. United States George Mason University United States Beltsville MD 20705 United States

ISBN: (纸本)1570830762

Monitoring global agricultural crop conditions during the growing season and estimating potential seasonal production are critically important for market development of U.S. agricultural products and for global food security. The Goddard Space Flight Center Earth Sciences data and Information Services Center Distributed Active Archive Center (GES DISC DAAC) is developing an Agricultural Information System (AIS), evolved from an existing TRMM Online visualization and analysis System (TOVAS), which will operationally provide satellite remote sensing data products (e.g., rainfall) and services. The data products will include crop condition and yield prediction maps, generated from a crop growth model with satellite data inputs, in collaboration with the USDA Agricultural Research Service. The AIS will enable the remote, interoperable access to distributed data, by using the GrADS-DODS Server (GDS) and by being compliant with Open GIS Consortium standards. Users will be able to download individual files, perform interactive online analysis, as well as receive operational data flows. AIS outputs will be integrated into existing operational decision support systems for global crop monitoring, such as those of the USDA Foreign Agricultural Service and the U.N. World Food Program.

关键词： Decision support systems

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Actor-oriented design of scientific workflows

引用

24th International conference on Conceptual Modeling

作者： Bowers, S Ludäscher, B Univ Calif Davis Genome Ctr Davis CA 95616 USA Univ Calif Davis Dept Comp Sci Davis CA 95616 USA

ISBN: (纸本)3540293892

Scientific workflows are becoming increasingly important as a unifying mechanism for interlinking scientific data management, analysis, simulation, and visualization tasks. Scientific workflow systems are problem-solving environments, supporting scientists in the creation and execution of scientific workflows. While current systems permit the creation of executable workflows, conceptual modeling and design of scientific workflows has largely been neglected. Unlike business workflows, scientific workflows are typically highly data-centric naturally leading to dataflow-oriented modeling approaches. We first develop a formal model for scientific workflows based on an actor-oriented modeling and design approach, originally developed for studying models of complex concurrent systems. Actor-oriented modeling separates two modeling concerns: component communication (dataflow) and overall workflow coordination (orchestration). We then extend our framework by introducing a novel hybrid type system, separating further the concerns of conventional data modeling (structural data type) and conceptual modeling (semantic type). In our approach, semantic and structural mismatches can be handled independently or simultaneously, and via different types of adapters, giving rise to new methods of scientific workflow design.

关键词： data flow analysis

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Metabolic visualization and intelligent shape analysis of the hippocampus

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International conference on Computational Intelligence and Security, CIS 2005

作者： Choi, Yoo-Joo Kim, Jeong-Sik Kim, Min-Jeong Choi, Soo-Mi Kim, Myoung-Hee Institute for Graphic Interfaces Ewha-SK Telecom Building 11-1 Daehyun-Dong Seodaemun-Ku Seoul Korea Republic of Department of Computer Science and Engineering Ewha Womans University Daehyun-Dong Seodaemun-Ku Seoul Korea Republic of Center for Computer Graphics and Virtual Reality Ewha Womans University Daehyun-Dong Seodaemun-Ku Seoul Korea Republic of School of Computer Engineering Sejong University Seoul Korea Republic of Department of Computer Application Technology Seoul University of Venture and Information Seoul Korea Republic of

ISBN: (纸本)3540308199

This paper suggests a prototype system for visualization and analysis of anatomic shape and functional features of the hippocampus. Based on the result of MR-SPECT multi-modality image registration, anatomical and functional features of hippocampus are extracted from MR and registered SPECT images, respectively. The hippocampus is visualized in 3D by applying volume rendering to hippocampus volume data extracted from the MR image with color coded by registered SPECT image. In order to offer the objective and quantitative data concerning to the anatomic shape and functional features of the hippocampus, the geometric volume and the SPECT intensity histogram of hippocampus regions are automatically measured based on the MR and the registered SPECT image, respectively. We also propose a new method for the analysis of hippocampal shape using an integrated Octree-based representation, consisting of meshes, voxels, and skeletons. © Springer-Verlag Berlin Heidelberg 2005.

关键词： Image analysis

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The deliver and visualization of geospatial information in mobile GIS

The deliver and visualization of geospatial information in m...

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International conference on Wireless Communications, Networking and Mobile Computing

作者： Zuo, XQ Li, QQ Kunming Univ Sci & Technol Fac Land Resource Engn Kunming 650093 Peoples R China

ISBN: (纸本)078039335X

With the development of mobile communications and wireless Internet technology, the mobile computing environment makes it possible to get any information from Internet at anytime and anywhere. However, client of mobile GIS has the diversity including cellular telephones, PDAs and vehicle terminals, etc. Therefore, mobile GIS must take this diversity into consideration and offer the service of spatial information running in various terminals. A standard open descriptive format of spatial information data is very important. Scalable Vector Graphics (SVG), an effective approach in the era of mobile internet, can get all sorts of bountiful graph information at anytime and anywhere. In mobile GIS system, SVG is also a valid method of representation spatial information. Mapping relation between spatial information and SVG marker was firstly studied in the paper. Secondly, method on generation of spatial information expressed by SVG was researched. Thirdly, the paper proposed SVG analysis and rendering approach combined pull mode with DOM View for Render (DVR). Complex feature, such as water system of embedded island, was rendered by means of strategy of layer controlling. The experimental result shows that it is feasible to adopt SVG describing or representing spatial information. And SVG can solve the problem on the diversity of client during the mobile service of spatial information, which will promote to popularize the service of spatial information.

关键词： mobile GIS SVG visualization

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A novel application of data modeling for extracting mathematical ontologies and relationship matrix features from text documents

A novel application of data modeling for extracting mathemat...

引用

conference on Enabling Technologies for Simulation Science IX

作者： Jaenisch, HM Handley, JW Faucheux, JP Lamkin, K dtech Syst Inc Huntsville AL 35804 USA

ISBN: (纸本)0819457906

This paper presents a novel algorithm for extracting Who, Where, When, What, How, and Why information directly from text documents without the use of dictionaries. Our process converts text into mathematical representation and uses purely equation and functional based relationships to make all classification decisions. Applications include requirements matching, hypothesis generation, data mining, document summarization, and document understanding.

关键词： data modeling databases Associative arrays Computer programming Mathematical modeling visualization Fractal analysis data mining Genetic algorithms Internet

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Human-Computer Interaction - INTERACT 2005 - IFIP TC13 International conference, Proceedings

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1st International conference on Advanced data Mining and Applications, ADMA 2005

ISBN: (纸本)3540289437

The proceedings contain 56 papers. The topics discussed include: the future of Web interfaces;haptizing wind on a weather map with reactive force and vibration;responsive interaction based on sketch in concept styling;effects of display configurations on document triage;analysing user confusion in context aware mobile applications;mobile photo browsing with pipelines and spatial cues;analysis of user behavior on high-resolution tiled displays;using real-life troubleshooting interactions to inform self-assistance design;assessing interaction styles in web user interfaces;exposing middle school girls to programming via creative tools;and static visualization of temporal eye-tracking data.

关键词： Human computer interaction

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Robust visualization of the dental occlusion by a double scan procedure

Robust visualization of the dental occlusion by a double sca...

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8th International conference on Medical Image Computing and Computer-Assisted Intervention

作者： Schutyser, F Swennen, G Suetens, P Katholieke Univ Leuven Univ Hosp Gasthuisberg Dept Med Image Comp ESATPSIFac Med Louvain Belgium Katholieke Univ Leuven Univ Hosp Gasthuisberg Dept Med Image Comp ESATPSIFac Engn Louvain Belgium Univ Libre Bruxelles Univ Hosp Brugmann Dept Plast Surg Brussels Belgium

ISBN: (纸本)3540293272

A detailed visualization of the dental occlusion in 3D image-based planning environments for oral and maxillofacial planning is important. With CT imaging however, this occlusion is often deteriorated by streak artifacts caused by amalgam fillings. Moreover, more detailed surface information at the level of the dental cuspids is often desired. In this paper, a double scan technique is introduced to image the dental occlusion by means of a newly designed 3D splint. The patient wears this splint between the upper and lower teeth during CT-scan. In a second step, the splint is positioned between the plaster casts of the upper and lower jaw, and this setup is scanned. Based on markers in the 3D splint, both data sets are fused and a combined visualization is possible, The accuracy, robustness and applicability in clinical routine is shown. This technology enables meticulous 3D cephalometric analysis, detailed maxillofacial planning and opens possibilities towards intraoperative support.

关键词： Dentistry

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