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The Open Microscopy Environment (OME) Data Model and XML file: open tools for informatics and quantitative analysis in biological imaging

Ilya G Goldberg1, Chris Allan2, Jean-Marie Burel2, Doug Creager3, Andrea Falconi2, Harry Hochheiser1, Josiah Johnston1, Jeff Mellen3, Peter K Sorger3 and Jason R Swedlow2*

Author Affiliations

1 Image Informatics and Computational Biology Unit, Laboratory of Genetics National Institute on Aging, National Institutes of Health, 333 Cassell Drive, Baltimore, MD 21224, USA

2 Division of Gene Regulation and Expression, University of Dundee, Dow Street, Dundee DD1 5EH, Scotland, UK

3 Department of Biology, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA

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Genome Biology 2005, 6:R47  doi:10.1186/gb-2005-6-5-r47

Published: 3 May 2005

Abstract

The Open Microscopy Environment (OME) defines a data model and a software implementation to serve as an informatics framework for imaging in biological microscopy experiments, including representation of acquisition parameters, annotations and image analysis results. OME is designed to support high-content cell-based screening as well as traditional image analysis applications. The OME Data Model, expressed in Extensible Markup Language (XML) and realized in a traditional database, is both extensible and self-describing, allowing it to meet emerging imaging and analysis needs.