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 Tarkowska; Petr Walczysko; Eleanor Williams; Jason R. Swedlow

doi:10.1117/12.2232291

26 July 2016 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 Tarkowska, Petr Walczysko, Eleanor Williams, Jason R. Swedlow

Author Affiliations +

Proceedings Volume 9913, Software and Cyberinfrastructure for Astronomy IV; 991324 (2016) https://doi.org/10.1117/12.2232291
Event: SPIE Astronomical Telescopes + Instrumentation, 2016, Edinburgh, United Kingdom

Abstract

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).

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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 Tarkowska, Petr Walczysko, Eleanor Williams, and Jason R. Swedlow "The Open Microscopy Environment: open image informatics for the biological sciences", Proc. SPIE 9913, Software and Cyberinfrastructure for Astronomy IV, 991324 (26 July 2016); https://doi.org/10.1117/12.2232291

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