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 will promote open data, provide reference data for the research community and allow for new scientific discoveries to be made with existing data across all imaging modalities and accelerate the development of new and improved image-analysis methods.

Currently, data from two resources are available: EMPIAR, the Electron Microscopy Public Image Archive, and image datasets in the BioStudies database.

How do I access the BioImage Archive?

All publically available data in the BioImage Archive data is available via www.ebi.ac.uk/bioimage-archive/browse. Data that is 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 image 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).

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. In the future, the first point of entry for all data depositions will be this new BioImage Archive data-submission tool, which will then dispatch submissions of different imaging modalities or biological context to the appropriate connected value-added databases.

What minimum metadata do I need to submit data?

For EMPIAR, the deposition tool will ask for all the necessary metadata, e.g., dataset title, authors, EMDB accession code if applicable, etc.

For a light microscopy data submission to BioStudies, please see two metadata templates available; we are working to enable template-driven image dataset submissions through the BioStudies submission tool.

What image formats does the BioImage Archive support?

The BioImage Archive accepts all image data formats. For EMPIAR submissions, the common formats in the field, such as MRC, MRCS, TIFF, DM4, IMAGIC, SPIDER, MRC FEI, and RAW FEI, are recommended. For light microscopy, formats that are understood by the Bio-Formats library, are preferable.

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

Aspera transfers are supported by both EMPIAR and BioStudies deposition tool; EMPIAR supports also Globus. We recommend these transfer methods over FTP also for smaller data volumes (in the GB range).

How do I receive a BioImage Archive accession number?

BioImage Archive does not currently assign accession numbers other than those assigned by the participating resources, EMPIAR and BioStudies.

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

For EMPIAR, the depositor receives an accession number as soon as the entry is submitted. The time it takes to do that depends mostly on the upload time (so on the dataset size). Filling in of the forms usually takes considerably less time, and it can also be sped up if the user has other EMPIAR / EMDB depositions or papers from which the metadata can be automatically imported.

The process currently takes around one week for BioStudies submissions; we are working towards a more automated submission process that will cut this time down to hours.

Citation and ORCIDs

How should I cite the BioImage Archive?

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

  • Ellenberg J, Swedlow JR, Barlow M, Cook CE, Sarkans U, Patwardhan A, Brazma A, Birney E. A call for public archives for biological image data. Nat Methods. 2018 Nov;15(11) 849-854. doi:10.1038/s41592-018-0195-8. PMID: 30377375.

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 (http://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. EMPIAR has integrated ORCIDs into the deposition system. The user can sign in into the system using their ORCID account. This would automatically populate user profile fields like ORCID iD, first and last names and email. If they prefer not to associate their ORCID profile with the EMPIAR account, they can still use ORCID to automatically fill in relevant forms in EMPIAR.

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. If you are interested only in electron microscopy (EM) and X-ray microscopy datasets, go to EMPIAR. All light microscopy datasets are available at BioStudies.

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/EMPIAR-10207
  • https://www.ebi.ac.uk/biostudies/BioImages/studies/S-BIAD1.

There are direct links to EMPIAR data available, e.g., empiar.org/10207.

Downloading data

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

See instructions on downloading EM and X-ray microscopy datasets in EMPIAR and instructions on downloading light microscopy datasets. Aspera transfers are supported by both EMPIAR and BioStudies deposition tool; EMPIAR supports also Globus. We recommend these transfer methods over FTP also for smaller data volumes (in the GB range).

What image data formats do you support for downloading?

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

How do I download a suitable image data set for method validation or testing purposes?

Subsets of larger datasets in EMPIAR can be downloaded in a number of ways:

  • The most visual one is the directory browser on EMPIAR entry pages. The page already has the data split into subsets as specified by the depositor. You can select the whole dataset, a subset or a part of it and press download button. This provides a choice of Aspera (good for all data sizes) or streamed HTTPS download (good only for smaller sizes).
  • If you know the directories/file names of the image set you are interested in, you can:
    • download the data using Aspera command line interface
    • browse the entry contents with Globus and select the directories/files
    • browse the entry on public FTP - this is not ideal since data loss is possible during such transfer.

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 bioimage-archive@ebi.ac.uk to discuss your ideas or subscribe to the mailing list.