26 July 2016 The Open Microscopy Environment: open image informatics for the biological sciences
Author Affiliations +
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).
© (2016) COPYRIGHT Society of Photo-Optical Instrumentation Engineers (SPIE). Downloading of the abstract is permitted for personal use only.
Colin Blackburn, Colin Blackburn, Chris Allan, Chris Allan, Sébastien Besson, Sébastien Besson, Jean-Marie Burel, Jean-Marie Burel, Mark Carroll, Mark Carroll, Richard K. Ferguson, Richard K. Ferguson, Helen Flynn, Helen Flynn, David Gault, David Gault, Kenneth Gillen, Kenneth Gillen, Roger Leigh, Roger Leigh, Simone Leo, Simone Leo, Simon Li, Simon Li, Dominik Lindner, Dominik Lindner, Melissa Linkert, Melissa Linkert, Josh Moore, Josh Moore, William J. Moore, William J. Moore, Balaji Ramalingam, Balaji Ramalingam, Emil Rozbicki, Emil Rozbicki, Gabriella Rustici, Gabriella Rustici, Aleksandra Tarkowska, Aleksandra Tarkowska, Petr Walczysko, Petr Walczysko, Eleanor Williams, Eleanor Williams, Jason R. Swedlow, 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); doi: 10.1117/12.2232291; https://doi.org/10.1117/12.2232291
PROCEEDINGS
8 PAGES


SHARE
RELATED CONTENT


Back to Top