BioImage Archive - a new hub for biological images

Credit: EMBL-EBI

BioImage Archive - a new hub for biological images

2 Jul 2019 - 14:52


  • High-resolution imaging technologies are essential for life scientists studying how life works at a molecular level
  • EMBL-EBI is setting up a central, open data resource for biological images, called BioImage Archive
  • Researchers will be able to freely store, share and access biological images in the new resource, which is set to accelerate scientific discoveries

July 2, Cambridge – EMBL’s European Bioinformatics Institute (EMBL-EBI) is expanding its remit to include bioimaging data. Through its new, dedicated resource for biological images, called the BioImage Archive, EMBL-EBI aims to make it easier for researchers around the world to store, share, access and analyse biological images. Easy access to bioimaging data could offer new insights into how life works at a molecular level and could advance knowledge in fields such as human health and disease, food security and biodiversity.

New opportunities and challenges

Developments in microscopy and imaging technologies, such as cryogenic electron microscopy, volume electron microscopy and super-resolution light microscopy, are allowing life-science researchers to observe biological structures and processes in completely new ways. These new data types present many exciting opportunities but also several challenges, including:

  • Sharing – access to and reuse of images is essential for biologists because it improves research quality and significantly speeds up scientific discovery
  • Diversity – imaging is not a single technology, but an umbrella term for many different methods, scales and resolutions
  • Analysis – any new type of data requires new analysis tools and methods that are easily accessible to the research community

EMBL-EBI has been collaborating with the wider bioimaging community to address some of these challenges. Pilot projects coordinated by EMBL-EBI, such as EMPIAR, and collaborations such as the Cell- and Tissue- Image Data Resource (IDR), have laid the groundwork for the creation of the BioImage Archive. The project has been made possible through capital support from a recent Strategic Priority Fund award from UK Research and Innovation.

“Imaging has huge potential for the life sciences, but only if the data can be shared and accessed easily by the global research community,” explains Ewan Birney, Director of EMBL-EBI. “The BioImage Archive acts as a broker or an intermediary, facilitating the sharing of bioimages and connecting with other resources that add value to these data.”

The next steps

In the initial phase, the BioImage Archive will make available images from EMBL-EBI’s EMPIAR and BioStudies resources, as well as IDR. In the future, other added-value resources will be connected to the BioImage Archive, enhancing the scientific value of the archived images through curation and the development of new analytical methods.

“EMBL-EBI’s expertise in data coordination and its links to the wider imaging community make it ideally-placed to coordinate and support the creation of a centralised data resource for imaging data,” says Melanie Welham, Executive Chair of BBSRC. “We are pleased to support this initiative and are looking forward to seeing it grow.”

The BioImage Archive is part of a wider EMBL drive to improve access to imaging technology and data. EMBL is in the process of building a new Imaging Centre in Heidelberg, Germany, which will enable researchers to access the latest microscopy technologies.

“Imaging is revolutionising the life sciences, facilitating new and exciting discoveries,” says Jan Ellenberg, Head of EMBL's Cell Biology and Biophysics Unit and Coordinator of Euro-BioImaging’s Preparatory Phases I and II. “Image data archiving and sharing is a high priority for EMBL and for the wider European scientific community, so we welcome the creation of EMBL-EBI’s BioImage Archive.”

EMBL is also a founding member of Euro-BioImaging ERIC – the European Research Infrastructure for Imaging Technologies in Biological and Biomedical Sciences. Euro-BioImaging provides access to its imaging Nodes across Europe, enabling researchers to access state-of-the art imaging technologies. It also provides the link to the imaging communities in Europe and beyond, which will use EMBL-EBI’s BioImage Archive to store and share their data. Euro-BioImaging ERIC is foreseen to be launched by its 14 member countries and EMBL in 2019.

Background information

One of the drivers for the BioImage Archive is a joint image data strategy concluded between Euro-BioImaging and ELIXIR. ELIXIR is a pan-European infrastructure for biological data, which includes EMBL-EBI as a leading Node.

Funding information

The IDR project was funded by the BBSRC (BB/M018423/1, BB/R015384/1), the Wellcome Trust (212962/Z/18/Z) and Horizon 2020 Framework Programme of the European Union under grant agreements No. 688945 (Euro-BioImaging Prep Phase II) and No. 653493 (Global BioImaging). Updates to OMERO and Bio-Formats used in IDR were supported by the Wellcome Trust (095931/Z/11/Z) and Horizon 2020 Framework Programme of the European Union under grant agreement No. 634107 (MULTIMOT).

European Bioinformatics Institute (EMBL-EBI)

The European Bioinformatics Institute (EMBL-EBI) is a global leader in the storage, analysis and dissemination of large biological datasets. We help scientists realise the potential of ‘big data’ by enhancing their ability to exploit complex information to make discoveries that benefit humankind.

We are at the forefront of computational biology research, with work spanning sequence analysis methods, multi-dimensional statistical analysis and data-driven biological discovery, from plant biology to mammalian development and disease.

We are part of EMBL and are located on the Wellcome Genome Campus, near Cambridge, UK, one of the world’s largest concentrations of scientific and technical expertise in genomics.

European Molecular Biology Laboratory (EMBL)

EMBL is Europe’s leading laboratory for the life sciences. We are an intergovernmental organisation, established in 1974 and are supported by over 20 member states.

EMBL performs fundamental research in molecular biology, studying the story of life. We offer services to the scientific community, train the next generation of scientists, and strive to integrate the life sciences across Europe.

We are international, innovative, and interdisciplinary. We are more than 1700 people, from over 80 countries, operating across six sites in Barcelona (Spain), Grenoble (France), Hamburg (Germany), Heidelberg (Germany), Hinxton (UK), and Rome (Italy). Our scientists work in independent groups and conduct research and offer services in all areas of molecular biology.

Our research drives the development of new technology and methods in the life sciences. We work to transfer this knowledge for the benefit of society.

UK Research and Innovation

UK Research and Innovation is a new body which works in partnership with universities, research organisations, businesses, charities, and government to create the best possible environment for research and innovation to flourish. We aim to maximise the contribution of each of our component parts, working individually and collectively. We work with our many partners to benefit everyone through knowledge, talent and ideas.

Operating across the whole of the UK with a combined budget of more than £7 billion, UK Research and Innovation brings together the Arts and Humanities Research Council; Biotechnology and Biological Sciences Research Council; Engineering and Physical Sciences Research Council; Economic and Social Research Council; Innovate UK; Medical Research Council; Natural Environment Research Council; Research England; and Science and Technology Facilities Council.


Euro-BioImaging is a fully distributed research infrastructure that offers open access to imaging technologies, training and data services in biological and biomedical imaging. Euro-BioImaging consists of imaging facilities, called Nodes, located across Europe that have opened their doors to all life science researchers.

In 2018, Euro-BioImaging achieved “landmark” status on the ESFRI (European Strategy Forum on Research Infrastructures) Roadmap and, as such, is recognised as “a European Hub of scientific excellence, generating new ideas and pushing the boundaries of science and technology.” All scientists, regardless of their affiliation, area of expertise or field of activity can benefit from these pan-European open access services. Visit the interim web access portalfor more information.


ELIXIR unites Europe’s leading life science organisations in managing and safeguarding the increasing volume of data being generated in publicly funded research. It coordinates, integrates and sustains bioinformatics resources across its member states and enables users in academia and industry to access vital data, tools, standards, compute, and training services for their research.

Image Data Resource (IDR)

The Image Data Resource (IDR) is a public repository of image datasets from published scientific studies, where the community can submit, search and access high-quality bio-image data. Currently, the IDR hosts cell imaging data in the Cell-IDR and tissue imaging data in the Tissue-IDR.


EMPIAR, the Electron Microscopy Public Image Archive, is an EMBL-EBI public resource for raw electron microscopy images.


EMBL-EBI’s BioStudies database holds descriptions of biological studies, links to data from these studies in other databases at EMBL-EBI or outside, as well as data that do not fit in the structured archives at EMBL-EBI.

Contact the news team

Vicky Hatch | Communications Officer

Oana Stroe | Senior Communications Officer

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