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;
http://openmicroscopy.org) 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 thousands 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;
https://idr.openmicroscopy.org) includes image data linked to >70 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. With this metadata integration, we have identified gene networks that link to cellular phenotypes. We have also built cloud-based analysis tool portals to catalyse the re-use and re-analysis of published imaging data. Through OME’s commercial arm, Glencoe Software, we have built PathViewer (
http://www.glencoesoftware.com/products/pathviewer/), a web-based WSI visualisation and annotation tool that is used in academic medical centres and 10 pharmaceutical companies and for digital pathology data sharing, atlases, analysis, and also for e-learning in medical education.
I’ll present our latest work on linking genotypes and phenotypes in IDR, and our proposals for next generation data formats and public resources for imaging.
