I am pleased to inform you on the seminar by Prof. Jason Swedlow, hosted by Prof. Michael Sheetz “OME’s Bio-Formats, OMERO, & IDR: Open Tools for Accessing, Integrating, Mining and Publishing Image Data @ Scale” on 12th Mar (Monday) @2pm at T-Lab Level 5 Seminar Rooms.
OME’s Bio-Formats, OMERO, & IDR: Open Tools for Accessing, Integrating, Mining and Publishing Image Data @ Scale
by Jason R. Swedlow1 and the OME Consortium2
1Centre for Gene Regulation & Expression and Division of Computational Biology, University of Dundee, Dundee, Scotland, UK
2 https://www.openmicroscopy.org/teams/
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. OME releases specifications and software for managing image datasets and integrating them with other scientific data. OME’s Bio-Formats and OMERO are used in 1000’s of labs worldwide to enable discovery with imaging.
We have used Bio-Formats and OMERO to build solutions for sharing and publishing imaging data. The Image Data Resource (IDR; http://idr.openmicroscopy.org) includes image data linked to >40 independent studies from genetic, RNAi, chemical, localisation and geographic high content screens, super-resolution microscopy, and digital pathology. Datasets range from several GBs to tens of TBs. Wherever possible, we have integrated image data with all relevant experimental, imaging and analytic metadata. 89% of the phenotypes recorded by study authors are mapped to ontological annotations, primarily using the CMPO and EFO ontologies. With this metadata integration, we have run queries across studies to identify gene networks that link to cellular phenotypes. We are currently testing the hypotheses that result from these queries using human induced pluripotent stem cell-based models of proliferation and differentiation.
