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Quantitative image analysis and the Open Microscopy Environment

Part 3. Proteomics

3.4. Functional Proteomics

Basic Techniques and Approaches

  1. Jason R. Swedlow,
  2. Chris Allan,
  3. Andrea Falconi,
  4. Jean-Marie Burel

Published Online: 15 APR 2005

DOI: 10.1002/047001153X.g304413

Encyclopedia of Genetics, Genomics, Proteomics and Bioinformatics

Encyclopedia of Genetics, Genomics, Proteomics and Bioinformatics

How to Cite

Swedlow, J. R., Allan, C., Falconi, A. and Burel, J.-M. 2005. Quantitative image analysis and the Open Microscopy Environment. Encyclopedia of Genetics, Genomics, Proteomics and Bioinformatics. 3:3.4:59.

Author Information

  1. University of Dundee, Dundee, UK

Publication History

  1. Published Online: 15 APR 2005


Many advances have been made in instrumentation and image analysis algorithms for light microscope, yet computational cell biology remains out of reach for many investigators. The use of proprietary file formats by commercial software complicates the storage, analysis, and querying of image data. Integration of new algorithms into proprietary packages is difficult at best, and there are inadequate standards for sharing image data and results with colleagues. We have developed an open-source software framework to address these limitations called the Open Microscopy Environment ( The foundation of our system is a data model that is specifically designed for five-dimensional microscope images (X, Y, Z, wavelengths, and time). This model is instantiated as an XML file that serves as a convenient data migration format for biological imaging. In addition, the OME Data Model is used to build an OME database and associated interfaces that serve as an integrated data storage, management, and analysis tool. The database stores all information regarding acquisition and all subsequent results from processing, analysis, and measurement. Using standard software interfaces, this design removes barriers of communication between different proprietary software packages. The Data Model, and by extension, the OME XML File and the OME database can be adapted to the requirements of local facilities. Finally, the system provides Web-based and stand-alone clients applications for visualizing image data and analytic results. OME is an open-source software project, and OME code is licensed under the Less GNU General Public License. The latest documentation for OME and software releases are at


  • imaging;
  • bioinformatics;
  • microscopy;
  • computational biology;
  • systems biology