Educational Symposium

Jason Swedlow

OME’s Bio-Formats, OMERO, & IDR: Open Tools for Accessing, Integrating, Mining and Publishing Image Data @ Scale

Bio

Jason S Swedlow received a BA in Chemistry from Brandeis University (1982) and a P Ph.D. in Biophysics from UC San Francisco (1994). He joined the Wellcome Trust Biocentre at the University of Dundee, Scotland (1998) and is currently Professor of Quantitative Cell Biology in Dundee's School of Life Sciences. His research interests are the mechanisms and regulation of chromosome segregation during mitotic cell division, and the development of software for handling and sharing large scientific image datasets. Prof Swedlow is a co-founder of the Open Microscopy Environment (OME), an international consortium that develops and releases open source software for biological imaging. He also founded Glencoe Software, Inc., which commercializes and customizes OME technology for use in biopharma and data publishing, and BioImagingUK, a consortium of UK imaging scientists that define priorities for imaging in the life sciences. In 2011, Dr. Swedlow was named Social and Overall Innovator of the Year by the BBSRC. In 2012, Dr. Swedlow was named a Fellow of the Royal Society of Edinburgh.

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. 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 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; https://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. With this metadata integration, we have run queries across studies to identify gene networks that link to cellular phenotypes. We have also built cloud-based analysis tools portals to catalyse the re-use and re-analysis of published imaging data.  

To catalyse commercial access to OME's tools, we formed Glencoe Software in 2005 as a commercial arm of OME. Glencoe provides commercial licenses of OME software, along with guaranteed support and customisation. 

In our latest work, OME and Glencoe have collaborated to build Parade, a web-based data mining application that uses data analytics stored in OMERO to query, select and analyse large collection of images in drug discovery and digital pathology.