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Image and Informatics Group, LBNL : Home

BioSig: An Imaging and Informatic System for Phenotypic Studies

IEEE Transaction on Systems, Man, Cybernetics, Oct. 2003..

    B. Parvin
    Q. Yang
    G. Fontenay
    M. H. Barcellos-Hoff

    ABSTRACT

    Organisms express their genomes in a cell-specific manner, resulting in a variety of cellular phenotypes or phenomes. Mapping cell phenomes under a variety of experimental conditions is necessary in order to understand the responses of organisms to stimuli. Representing such data requires an integrated view of experimental and informatic protocols. The proposed system, named BioSig, provides the foundation for cataloging cellular responses as a function of specific conditioning, treatment, staining, etc. for either fixed tissue or living cell studies. A data model has been developed to capture experimental variables and map them to image collections and their computed representation. This representation is hierarchical and spans across sample tissues, cells, and organelles, which are imaged with l ight microscopy. At each layer, content is represented with an attributed graph, which contains information about cellular morphology, protein localization, and cellular organization in tissue or cell culture. The web-based multilayer informatics architecture uses the data model to p rovide guided workflow access for content exploration.
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    Publication number: LBNL-51202