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a platform for platform for bioimage analysis



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BIOINFORMATICS ORIGINAL PAPER Vol 26 no 4 2010 pages 544 552 doi 10 1093 bioinformatics btp699 Databases and ontologies Bisque a platform for bioimage analysis and management Kristian Kvilekval1 Dmitry Fedorov1 Boguslaw Obara1 2 Ambuj Singh1 3 and B S Manjunath1 for Bio Image Informatics Electrical and Computer Engineering Department University of California Santa Barbara CA USA 2 Oxford e Research Centre and Oxford Centre for Integrative Systems Biology University of Oxford Oxford UK and 3 Department of Computer Science University of California Santa Barbara CA USA Received on May 28 2009 revised on December 11 2009 accepted on December 17 2009 Advance Access publication December 22 2009 Associate Editor John Quackenbush ABSTRACT Motivation Advances in the eld of microscopy have brought about the need for better image management and analysis solutions Novel imaging techniques have created vast stores of images and metadata that are dif cult to organize search process and analyze These tasks are further complicated by con icting and proprietary image and metadata formats that impede analyzing and sharing of images and any associated data These obstacles have resulted in research resources being locked away in digital media and le cabinets Current image management systems do not address the pressing needs of researchers who must quantify image data on a regular basis Results We present Bisque a web based platform speci cally designed to provide researchers with organizational and quantitative analysis tools for 5D image data Users can extend Bisque with both data model and analysis extensions in order to adapt the system to local needs Bisque s extensibility stems from two core concepts exible metadata facility and an open web based architecture Together these empower researchers to create develop and share novel bioimage analyses Several case studies using Bisque with speci c applications are presented as an indication of how users can expect to extend Bisque for



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