Connecting and Expanding RIKEN's Systems Science of Biological Dynamics and OME's Image Data Resource Databases

Lead Research Organisation: University of Dundee



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Description The Swedlow group has led the OME Consrotium for many years and developed and released Bio-Formats and OMERO software platforms and the Image Data Resource (IDR;, the world's open, comprehensive public resource for reference imaging datasets in the life and biomedical sciences. The Onami Group (RIKEN, Japan) has developed the Systems Science of Biological Dynamics Database (SSBD;, public image data resource based on OME's OMERO and Bio-Formats software. The funding allowed the two groups to spend 10 days together, reviewing each other's progress and identifying avenues for future collaboration.
Exploitation Route Both IDR and SSBD are publishing imaging data on the scale fof 10s to 100s of TBytes, and these datasets can be re-used by others for benchmarks and re-analysis. The cited preprint reflects our views of requirements for public image data formats and resources. The preprint is now in press at Nature Methods.
Sectors Digital/Communication/Information Technologies (including Software),Pharmaceuticals and Medical Biotechnology

Description They have informed a discussion in Global BioImaging, leading to the preprint cited above.
First Year Of Impact 2020
Sector Digital/Communication/Information Technologies (including Software)
Impact Types Policy & public services

Title Image Data Repository (IDR) 
Description A collection of image data and metadata, including all experimental, acquisition, and analytic metadata. 
Type Of Material Database/Collection of data 
Year Produced 2015 
Provided To Others? Yes  
Impact The scripts used for importing datasets into the IDR form the basis of proposed standards for experimental and analytic metadata image-based phenotypic studies. A proposal to fund the full development of these standards has been submitted. 
Description IDR 
Organisation EMBL European Bioinformatics Institute (EMBL - EBI)
Country United Kingdom 
Sector Academic/University 
PI Contribution We have built the OMERO and Bio-Formats technology that forms the basis of the IDR.
Collaborator Contribution Alvis Brazma is a collaborator on our BBSRC IDR award (BB/M018423/1).
Impact The IDR is the major current output. Publications are now in prep.
Start Year 2015