The Open Microscopy Environment (OME) is an open-source software framework for addressing informatics challenges in biological imaging and analysis: proprietary file formats, lack of storage, and analysis facilities and standards for sharing image data and results. The Java-based OMERO client-server platform and its model-based architecture is applicable to a range of imaging domains, including light and electron microscopy, high-content screening, and recently into applications using non-image data from clinical and genomic studies.
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. The Open Microscopy Environment (OME) is an open-source software framework developed to address these challenges [1]. OME has three components—an open data model for biological imaging; standardised file formats (OME-TIFF) and software libraries for file conversion (Bio-Formats [2]); and a software platform for image data management and analysis (OMERO [3]). In this presentation, we discuss the design and use of OMERO.
The Java-based OMERO client-server platform [3] comprises an image metadata store, an image data repository, visualization and analysis by remote access, enabling sharing and publishing of image data. OMERO.grid [4] facilitates distributed computing including scripting facility for image processing. OMERO.grid manages processes across nodes, providing distributed background processing, log handling, and several other features, using ZeroC’s IceGrid framework [5]. Several third-party applications use the OMERO API (e.g. image-based searching, tracking and automatic image tagging; sophisticated image analysis modules [6]). OMERO’s model-based architecture has enabled its extension into a range of imaging domains, including light and electron microscopy, high-content screening, and recently into applications using non-image data from clinical and genomic studies [7].
Our next version, OMERO-5 improves support for large datasets, and reads images directly from their original file format, allowing access by third-party software.
OMERO and Bio-Formats run the JCB DataViewer [8] online scientific image publishing system and other institutional image data repositories [9], [10].
