Frequently asked questions

Frequently asked questions about the BioImage Archive.

About BioImage Archive

What is the BioImage Archive?

The BioImage Archive is a new public data resource at EMBL-EBI that archives and makes available biological image data, of all scales, from molecules to entire organisms.

A central archive promotes open data, provides reference data for the research community and allows for new scientific discoveries to be made with existing data across all imaging modalities and accelerates the development of new and improved image-analysis methods.

How do I access the BioImage Archive?

All publically available data in the BioImage Archive are accessible via https://www.ebi.ac.uk/biostudies/BioImages/studies. Data that are not yet public (e.g., with ‘hold until published’ status) can be accessed if you have the correct login credentials.

How do I stay in touch with developments?

You can subscribe to the mailing list.

Data submission

What data can and should be submitted to the BioImage Archive?

We welcome submissions of biological image data across all imaging modalities, from the molecular to the organism scale, which are associated with a publication, as well as large systematic reference image datasets (where reference data is defined as data that have value beyond a single experiment or project because they also can serve as a resource for the larger community). We also host submissions of annotations that label images (e.g. segmentation masks).

Please use our data deposition tools, or contact us to discuss establishing a data pipeline in the case of a large volume of multiple datasets, e.g. as generated by an ongoing project.

We are also developing a dedicated image-data-submission tool for the BioImage Archive with community-driven standards for both data and metadata.

Is there a cost to deposit data in the BioImage Archive?

No, both deposition of data to the Archive, and data access are free of charge.

What image formats does the BioImage Archive support?

The BioImage Archive accepts all image data formats, although formats that are understood by the Bio-Formats library, are preferable.

What is the best way to submit large volumes of information?

We recommend Aspera transfer for medium to large (10 GiB+) volumes of data.

How do I receive a BioImage Archive accession number?

Accession numbers are assigned during the submission process, and do not change upon dataset publication or revision.

How long on average does it take to receive an accession number?

Accession numbers are assigned after data are uploaded and the submission processed finalised. For small datasets, this can be a same day process, however for larger data volumes it will depend on transfer speeds (see above).

Do you assign Digital Object Identifiers (DOIs)?

Yes, DOIs are assigned automatically for new submissions. For old submissions, please email us to request a DOI.

Can I keep my dataset private (e.g. until publication)?

Yes. When you submit your data, you can choose a release date. Until that date, your data will not be publicly visible. However, you can choose to share your data with specific people (e.g. reviewers) using the share icon in the top right region of the page.

Can I add a publication to my dataset at a later point?

Yes. You can edit the publication field of your dataset’s metadata to add a publication, for example if your initial publication was a preprint.

How should I acknowledge my funder when submitting data?

Our submission template includes form elements in which you can acknowledge funding for your data. For Horizon Europe grants, please ensure to include the following information:

• Funding stream
• Project name
• Project acronym
• Grant PID

Citation and ORCIDs

How should I cite the BioImage Archive?

Citing BioImage Archive in general: please use the following publication:

• Hartley M, Kleywegt GJ, Patwardhan A, Sarkans U, Swedlow JR, Brazma A. The BioImage Archive – Building a Home for Life-Sciences Microscopy Data. J. Mol. Biol. 2022 June;434(11). doi:10.1016/j.jmb.2022.167505. PMID: 35189131.

Citing EMPIAR:

• Iudin A, Korir PK, Salavert-Torres J, Kleywegt GJ, Patwardhan A. EMPIAR: a public archive for raw electron microscopy image data. Nat Methods. 2016 May;13(5) 387-388. doi:10.1038/nmeth.3806. PMID: 27067018.

Citing BioStudies:

• Sarkans U, Gostev M, Athar A, Behrangi E, Melnichuk O, Ali A, Minguet J, Rada JC, Snow C, Tikhonov A, Brazma A, McEntyre J. The BioStudies database-one stop shop for all data supporting a life sciences study. Nucleic Acids Res. 2018 Jan;46(D1) D1266-D1270. doi:10.1093/nar/gkx965. PMID: 29069414; PMCID: PMC5753238.

Citing a particular dataset in the BioImage Archive:

• Please include your dataset accession number and the URL to BioImage Archive home page, e.g., “Image data are available in the BioImage Archive (https://www.ebi.ac.uk/bioimage-archive) under accession number S-BIAD-12345.”

How are ORCIDs used in the BioImage Archive?

Data depositors can include their ORCIDs in contact details; these will be searchable in the data access interface. If you are an author of a dataset, you can also claim it through the accession browsing interface.

Searching the Bioimage Archive

Can I search by publication/ accession/ study/ area of interest?

Yes, search by any metadata field is possible. Include multi-word phrases in double quotes; see more information on search capabilities.

How do I browse available datasets?

You can browse datasets here.

How do I link to a dataset?

Use https://www.ebi.ac.uk/biostudies/BioImages/studies/<accession_number> to link to a particular dataset in the BioImage Archive, e.g.

• https://www.ebi.ac.uk/biostudies/BioImages/studies/S-BIAD1.

How can I link to individual images?

Each image or file submitted to the BioImage Archive has an individual URI. The ~disnURIs keep to the following structure: https://www.ebi.ac.uk/biostudies/files/<accession-id>/<file-path> To learn the uri of a file in a submission, go to the webpage for that submission, then hover over the file or right click the file you want, and select “Copy Link Address”.

Downloading data

What is the easiest way to download large data volumes from the BioImage Archive?

For general help with downloading see downloading section of Biostudies help page or downloading data section on BioImage Archive help page. Aspera transfers are supported, and are particularly useful for large data volumes.

Under what license(s) is the BioImage Archive data available?

Some accessions have individual licenses - these are explicitly stated on the page for that accession. Where no license is stated, data are available under the EMBL-EBI Terms of Use which places no restrictions on use or redistribution.

What image data formats do you support for downloading?

The BioImage Archive does not currently provide format transformations, so users can download data in the same formats as used by data depositors.

How can the BioImage Archive support archiving of data that is in my community-specific value-added data resource?

In the future, capabilities will be available to connect other added-value resources that aim to enhance the scientific value of the archived images through curation, integrative analysis and the development of new analytical methods. Please write to [email protected] to discuss your ideas or subscribe to the mailing list.