University of Dundee

The Open Microscopy Environment: Share and share alike

Led in Dundee by Prof. Jason Swedlow FRSE, the Open Microscopy Environment is an international consortium has revolutionised the ability of researchers and industrial partners to handle, analyse, share and interpret vast amounts of image data.

Share and share alike is the core philosophy of the Open Microscopy Environment (OME) that is delivering software solutions for life sciences research. From identifying biological structures in cells to examining animal behaviour, high-resolution imaging has become a critical technology across all of Biomedical and Life Sciences. The amount of imaging data generated in research labs in academia, pharma and biotech has reached gargantuan proportions. The explosion in the quantity and quality of data is further complicated by variation in file formats and size.

Founded by Professor Jason Swedlow at the University of Dundee in 2000, the Open Microscopy Environment is an open source, community-led consortium that is now a leading provider of software solutions for biological image management. When Professor Swedlow initiated this project he had two ambitious aims “First-- whatever technology we developed would be open source, allowing us to share applications, tools, and know-how to the largest possible number of users, developers and scientists, all around the world. The second-- we should build the most powerful and innovative software we could and ensure that it worked and could be used for as many different problems as possible.”

The OME Consortium developed a software tool called Bio-Formats that can be used for converting images and metadata from different platforms to a standardised open format. Bio-Formats is currently the most comprehensive scientific image file format translator available and is used in >60,000 sites worldwide.

OME also developed OMERO, a data management system that enables access, sharing, analysis and publication of complex multi-dimensional image data. Scientists in >3,000 sites worldwide use OMERO to securely access their data from anywhere and apply whatever methods they need to analyse their image data.

A major impact is the uptake of OME image software and management tools by multinational companies, which is provided to them through the Glencoe Software spin-out, founded in late 2005 by Prof Swedlow. Examples of companies currently distributing software platforms developed by OME and provided by Glencoe Software include Applied Precision Inc, PerkinElmer and Rockefeller University Press. The latter incorporated a customised version of OMERO in the world’s first web-based publication system for original multi-dimensional image data.

The impact of Prof. Swedlow’s work and the OME team was recognised in 2011 when he was named BBSRC “Innovator of the Year” for its economic and social impacts.