Project developments

BioImaging project scope

EMBL has been supported via the UK Research and Innovation (UKRI) Strategic Project Fund to develop the internal infrastructure and image resources hosted at EMBL’s European Bioinformatics Institute (EMBL-EBI). The project will reach out to community experts to develop sustainable technologies to support image submission, retrieval and efficient image storage, across the biological imaging community.

Objectives

• Promote open imaging data and reproducibility of analyses. This allows authors to provide a complete record of their original data and analysis methods, and enables other interested scientists to explore alternative analyses of the same raw data.
• Provide reference data for the research community. These data, along with rules of community use and analysis methods, avoid the redundant production of replica datasets and can be the basis for added-value resources (e.g., atlases). They will provide a large efficiency gain for routine experiments and, over time, build a comprehensive scientific reference image resource for cells, tissues, organs, and organisms.
• Allow new scientific discoveries to be made using existing data, via novel or integrated analysis of datasets that were originally generated for a different purpose.
• Accelerate the development of image analysis methods against a broad range of benchmark datasets, thus encouraging validation and robustness of the computational methods and enabling well-structured image analysis challenges.

Development milestones

BioImage Archive Development Principles

• The BioImage Archive should store and make available imaging datasets from molecular to organism scale, excluding medical imaging in its initial development
• Image datasets submitted should be directly related to results included in a publication or have clear value beyond a single experiment or project with high re-use value to the research community (‘reference datasets’).
• Access for community data resources should be provided.
• A scalable storage solution will be adopted for the archive with a direct web interface for data retrieval.
• Image submission formats will be as inclusive as feasible with the ability to retrieve data exactly as submitted. The image formats delivered and hosted will remain as flexible as feasible until community cohesion is found.
• The archive will enable cloud-based analyses.

BioImaging Project Governance

The BioImaging Project is one project supporting the wider Data Infrastructure Programme. It will follow the below governance model with UKRI-BBSRC assuming the external Senior Responsible owner role for the capital investment and EMBL-EBI taking on Internal Sponsorship to provide the operational investment required to successfully deliver the project.

Community input will be gathered via an Imaging Ecosystem Working Group, which will provide an assurance role.

Community engagement

Working with community experts throughout the development process is paramount to ensure that the BioImage Archive serves the needs of life-science researchers, data scientists, software engineers, funders and the wider public.

Developing the technical and biological metadata required for successful image-data submission, as well as the best methods to store, link and serve image data to enable wider image re-use, is one of the first, essential steps in making the BioImage Archive a reality. For this purpose, specialists from EMBL-EBI and colleagues over 30 other institutions have compiled a series of metadata guidelines called Recommended Metadata for Biological Images (REMBI). These were published in a comment in Nature Methods on 21st May 2021. The standard will be adopted by the BioImage Archive.

The guidelines are a result of a series of meetings with representatives from the different bioimaging communities, including light, electron and X-ray microscopy communities. The aim of the proposed guidelines is to provide a framework for discussing imaging data sharing. The hope is to reach community-wide consensus on the level of detail that is optimal.

The current version of REMBI is available online

Imaging Ecosystem Working Group

Funders

Ongoing development is enabled by capital investment from the UKRI Strategic Priorities Fund and operational costs supported by EMBL member state funding.

The BioImage Archive builds on a history of funding from BBSRC, Wellcome Trust, MRC, Global BioImaging, Euro-BioImaging, Horizon 2020, and previous UK Government technical infrastructure investment.