The Open Microscopy Environment: Open image informatics for the biological sciences

Colin Blackburn, Chris Allan, Sébastien Besson, Jean Marie Burel, Mark Carroll, Richard K. Ferguson, Helen Flynn, David Gault, Kenneth Gillen, Roger Leigh, Simone Leo, Simon Li, Dominik Lindner, Melissa Linkert, Josh Moore, William J. Moore, Balaji Ramalingam, Emil Rozbicki, Gabriella Rustici, Aleksandra TarkowskaPetr Walczysko, Eleanor Williams, Jason R. Swedlow

    Research output: Chapter in Book/Report/Conference proceedingConference contribution

    1 Citation (Scopus)


    Despite significant advances in biological imaging and analysis, major informatics challenges remain unsolved: file formats are proprietary, storage and analysis facilities are lacking, as are standards for sharing image data and results. While the open FITS file format is ubiquitous in astronomy, astronomical imaging shares many challenges with biological imaging, including the need to share large image sets using secure, cross-platform APIs, and the need for scalable applications for processing and visualization. The Open Microscopy Environment (OME) is an open-source software framework developed to address these challenges. OME tools include: an open data model for multidimensional imaging (OME Data Model); an open file format (OME-TIFF) and library (Bio-Formats) enabling free access to images (5D+) written in more than 145 formats from many imaging domains, including FITS; and a data management server (OMERO). The Java-based OMERO client-server platform comprises an image metadata store, an image repository, visualization and analysis by remote access, allowing sharing and publishing of image data. OMERO provides a means to manage the data through a multi-platform API. OMERO's model-based architecture has enabled its extension into a range of imaging domains, including light and electron microscopy, high content screening, digital pathology and recently into applications using non-image data from clinical and genomic studies. This is made possible using the Bio-Formats library. The current release includes a single mechanism for accessing image data of all types, regardless of original file format, via Java, C/C++ and Python and a variety of applications and environments (e.g. ImageJ, Matlab and R).

    Original languageEnglish
    Title of host publicationSoftware and Cyberinfrastructure for Astronomy IV
    PublisherSPIE-International Society for Optical Engineering
    ISBN (Electronic)9781510602052
    Publication statusPublished - 26 Jul 2016
    EventSPIE Astronomical Telescopes + Instrumentation: Software and Cyberinfrastructure for Astronomy IV - Edinburgh International Conference Centre, Edinburgh, United Kingdom
    Duration: 26 Jun 201630 Jun 2016 (Link to Conference details)


    ConferenceSPIE Astronomical Telescopes + Instrumentation
    Country/TerritoryUnited Kingdom
    Internet address


    • Data management
    • File formats
    • Image analysis
    • Image management
    • Image repositories
    • Multi-dimensional data
    • Open-source software

    ASJC Scopus subject areas

    • Electronic, Optical and Magnetic Materials
    • Condensed Matter Physics
    • Computer Science Applications
    • Applied Mathematics
    • Electrical and Electronic Engineering


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