The QBI Seminar Series is presenting Jason Swedlow, co-founder of the Open Microscopy Environment (OME), a community-led open source software project that develops specifications and tools for biological imaging. His lab focuses on studies of mitotic chromosome structure and dynamics and has published numerous leading papers in the field.

Seminar Focus:

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. OME is developed to address these challenges and 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.

Swedlow's lab has used Bio-Formats and OMERO to build solutions for sharing and publishing imaging data. The Image Data Resource (IDR) 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, they have integrated image data with all relevant experimental, imaging and analytic metadata. With this metadata integration, they have identified gene networks that link to cellular phenotypes. They have also built cloud-based analysis tool portals to catalyze the re-use and re-analysis of published imaging data. Through OME’s commercial arm, Glencoe Software, they have built 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.  

Dr. Swedlow will present his lab's latest work on linking genotypes and phenotypes in IDR, and their proposals for next generation data formats and public resources for imaging.   

Background:

Swedlow earned a BA in Chemistry from Brandeis University in 1982 and PhD in Biophysics from UCSF in 1994. After a postdoctoral fellowship with Dr T. J. Mitchison at UCSF and then Harvard Medical School, Dr Swedlow established his own laboratory in 1998 at the Wellcome Trust Biocentre, University of Dundee, as a Wellcome Trust Career Development Fellow. He was awarded a Wellcome Trust Senior Research Fellowship in 2002 and named Professor of Quantitative Cell Biology in 2007.

In 2005, he founded Glencoe Software, Inc., a commercial start-up that provides commercial licenses and customization for OME software. In 2011, Prof Swedlow and the OME Consortium were named BBSRC's Social Innovator of the Year and Overall Innovator of the Year. In 2012, he was named Fellow of the Royal Society of Edinburgh. Prof Swedlow has organized or directed several courses in quantitative microscopy at the Marine Biological Laboratory, Woods Hole, USA, Cold Spring Harbor Laboratory, USA and the National Centre for Biological Science, Bangalore. India.