Kavli Research & Enterprise Discussions (K.R.E.D)

Kavli Research & Enterprise Discussions (K.R.E.D)

Our Kavli Research and Enterprise Discussion (K.R.E.D.) will be presented by Professor Jason R. Swedlow, University of Dundee.

Date: 05 June 2025

Time: 14:00

Venue: Dorothy Crowfoot Hodgkin Building - Seminar Room 1 (20-026)

This is an event for University staff only.

Professor Jason R. Swedlow's Talk is entitled “Making BioImage Data FAIR on a Global Scale: OME’s Bio-Formats, OME-TIFF, OMERO, & IDR”

His abstract and biography are below.

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 which aims 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. OME-TIFF is an open, metadata-rich, multi-dimensional, multi-resolution data format for modern bioimaging that has been widely adopted across the bioimaging community. OME-Zarr is a new data format that enables new ways of storing and sharing data, and is especially optimised for cloud-based data resources. 

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 >420 TBytes of image data linked to >120 independent studies from genetic, RNAi, chemical, localisation and geographic high content screens, super-resolution microscopy, single cell profiling, light sheet microscopy of developing organisms and tissues, 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. These annotations make it possible to re-use IDR data, and to connect independent imaging datasets by molecular perturbations and phenotypes. IDR is part of a global effort to build public bioimage data resources and linked to EMBL-EBI’s BioImage Archive and RIKEN’s Systems Science of Biological Dynamics database. IDR, BIA and SSBD are adopting OME-Zarr, and in 2024, these, along with several global resources have used this new format to build the world’s first federated bioimage data resource.

Biography:  

Jason Swedlow is Professor of Quantitative Cell Biology in the School of Life Sciences, University of Dundee. He earned a BA in Chemistry from Brandeis (1982) and PhD in Biophysics from UCSF (1994). After postdocs at UCSF and Harvard, he established his laboratory at Dundee, focussed on mitotic chromosome dynamics and cell and tissue imaging informatics (1998). He founded the Open Microscopy Environment (OME) and Glencoe Software, Inc. He was previously the Program Director of Delta Tissue, the Wellcome LEAP program