BioImage Archive

Overview of the data flows in the BioImage Archive.

The BioImage Archive (BIA) is a research data repository hosting publicly accessible bioimaging datasets. It is hosted by the European Bioinformatics Institute, in the United Kingdom. It was first announced on 2 July 2019.

Its creation was proposed in 2018 to cater for the lack of a central public repository for microscopy images in the biosciences. In 2019, it was created based on the BioStudies database and extended the EMBL-EBI resources for imaging, which at the time included only EMPIAR (the Electron Microscopy Public Image Archive). BIA was also meant as a bridge between EMPIAR and the Image Data Resource, a public bioimaging database maintained by the Open Microscopy Environment consortium. In 2026, BioImage Archive entered the list of ELIXIR Core Data Resources.

The growth in data archived by BIA and EMPIAR.

As of 2026, BIA holds over 2,500 datasets and one petabytes of data. Datasets cover a wide range of subjects and are identified by alphanumeric identifiers of the format "S-BIAD0000". For example, a study about development of the Japanese eel is deposited under the identifier S-BIAD3325. Deposition on BioImage Archive is considered as a good practice for FAIR data in bioimaging.

BioImage Archive provides application program interfaces usable by the general public and other open-source software utilities.

The archive receives data submissions in a variety of file formats, including proprietary standards. As part of its FAIR data practices, BIA has a pipeline to normalize data and metadata, making use of the OME-Zarr data format and the RO-Crate metadata standard.

See also

References

  1. ↑ Zulueta-Coarasa, Teresa; Yoldas, Aybuke; Anita, Liviu; Babalola, Kolawole; Bircan, Karatug; Cattavitello, Cesare; Clementel, Damiano; Ma, Miao; Mandloi, Tushar; Marks, Daniel; Rookyard, Christopher; Sherwood, Francois; Somasundharam, Sriram; Velasquez, Melina; Weyand, Simone (2026-11-05). "BioImage Archive: bringing bioimaging data together". Nucleic Acids Research: gkag1108. doi:10.1093/nar/gkag1108. ISSN 1362-4962.{{cite journal}}: CS1 maint: article number as page number (link)
  2. 1 2 3 Hartley, Matthew; Kleywegt, Gerard J.; Patwardhan, Ardan; Sarkans, Ugis; Swedlow, Jason R.; Brazma, Alvis (2022). "The BioImage Archive – Building a Home for Life-Sciences Microscopy Data". Journal of Molecular Biology. 434 (11) 167505. bioRxiv 10.1101/2021.12.17.473169. doi:10.1016/j.jmb.2022.167505. PMID 35189131.
  3. ↑ Reither, Sabine (2019-07-02). "The Bioimage Archive has been announced today by EMBL-EBI". German BioImaging. Retrieved 2026-08-25.
  4. ↑ Ellenberg, Jan; Swedlow, Jason R.; Barlow, Mary; Cook, Charles E.; Sarkans, Ugis; Patwardhan, Ardan; Brazma, Alvis; Birney, Ewan (November 2018). "A call for public archives for biological image data". Nature Methods. 15 (11): 849–854. doi:10.1038/s41592-018-0195-8. ISSN 1548-7105. PMC 6884425. PMID 30377375.
  5. ↑ Iudin, Andrii; Korir, Paul K; Somasundharam, Sriram; Weyand, Simone; Cattavitello, Cesare; Fonseca, Neli; Salih, Osman; Kleywegt, Gerard J; Patwardhan, Ardan (2023-01-06). "EMPIAR: the Electron Microscopy Public Image Archive". Nucleic Acids Research. 51 (D1): D1503–D1511. doi:10.1093/nar/gkac1062. ISSN 0305-1048. PMC 9825465. PMID 36440762.
  6. ↑ Williams, Eleanor; Moore, Josh; Li, Simon W.; Rustici, Gabriella; Tarkowska, Aleksandra; Chessel, Anatole; Leo, Simone; Antal, Bálint; Ferguson, Richard K.; Sarkans, Ugis; Brazma, Alvis; Carazo Salas, Rafael E.; Swedlow, Jason R. (August 2017). "Image Data Resource: a bioimage data integration and publication platform". Nature Methods. 14 (8): 775–781. doi:10.1038/nmeth.4326. ISSN 1548-7105. PMC 5536224. PMID 28775673.
  7. ↑ "ELIXIR Core Data Resources | ELIXIR". elixir-europe.org. Retrieved 2026-08-25.
  8. ↑ "BioImage Archive receives new Core Data Resource and Deposition Database status by ELIXIR". Euro-BioImaging. 2026-01-13. Retrieved 2026-08-25.
  9. 1 2 Zulueta-Coarasa, Teresa; Yoldas, Aybuke; Anita, Liviu; Babalola, Kolawole; Bircan, Karatug; Cattavitello, Cesare; Clementel, Damiano; Ma, Miao; Mandloi, Tushar; Marks, Daniel; Rookyard, Christopher; Sherwood, Francois; Somasundharam, Sriram; Velasquez, Melina; Weyand, Simone (2026-11-05). "BioImage Archive: bringing bioimaging data together". Nucleic Acids Research: gkag1108. doi:10.1093/nar/gkag1108. ISSN 1362-4962.{{cite journal}}: CS1 maint: article number as page number (link)
  10. ↑ "BioImage Archive | re3data.org". www.re3data.org. Retrieved 2026-08-25.
  11. ↑ Zulueta-Coarasa, Teresa; Yoldas, Aybuke; Anita, Liviu; Babalola, Kolawole; Bircan, Karatug; Cattavitello, Cesare; Clementel, Damiano; Ma, Miao; Mandloi, Tushar; Marks, Daniel; Rookyard, Christopher; Sherwood, Francois; Somasundharam, Sriram; Velasquez, Melina; Weyand, Simone (2026-11-05). "BioImage Archive: bringing bioimaging data together". Nucleic Acids Research: gkag1108. doi:10.1093/nar/gkag1108. ISSN 1362-4962.{{cite journal}}: CS1 maint: article number as page number (link)
  12. ↑ "S-BIAD3325: Heterochrony of axis segmentation underlies extreme morphogenesis in the Japanese eel". beta.bioimagearchive.org. Retrieved 2026-08-25.
  13. ↑ FAIRsharing Team; Sarkans, Ugis; Hartley, Matthew (2018). "BioImage Archive | FAIRsharing". fairsharing.org. doi:10.25504/FAIRsharing.x38D2k. Retrieved 2026-08-25.
  14. ↑ Galinova, Vera; Seifi, Mehdi; Serrano Solano, Beatriz; Lidayová, Kristína; Dalle Nogare, Damian; Corbat, Agustín Andrés; Talks, Joshua; Giacomello, Edoardo; Gómez-de-Mariscal, Estibaliz (2026-07-22). "AI4Life Open Calls and Public Challenges: why, how, and what we have learned". bioRxiv 10.64898/2026.07.21.739486.
  15. ↑ Ambroset, Mélodie; Valades-Cruz, Cesar Augusto; Tonfack, Libert Brice; D'Antuono, Rocco; Fuster-Barceló, Caterina (2026). "Assessing the reproducibility of a bioimage analysis workflow characterising tissue flow in Drosophila". Journal of Microscopy. n/a (n/a) jmi.70125. doi:10.1111/jmi.70125. ISSN 1365-2818. PMID 42312811.
  16. ↑ Russell, Craig T; Burel, Jean-Marie; Athar, Awais; Li, Simon; Sarkans, Ugis; Swedlow, Jason; Brazma, Alvis; Hartley, Matthew; Uhlmann, Virginie (2025-08-01). "bia-binder: a web-native cloud compute service for the bioimage analysis community". Bioinformatics. 41 (8) btaf412. doi:10.1093/bioinformatics/btaf412. ISSN 1367-4811. PMC 12342736. PMID 40692175.