Frequently asked questions

What are the file formats accepted?

The IDR uses the Bio-Formats library for reading imaging data. Bio-Formats supports over 150 proprietary and open file formats (see the full list). At a minimum, your data should be readable by an up-to-date version of Bio-Formats e.g. using the showinf utility or the Image/Fiji plugin.

What are the preferred formats for submission?

We strongly encourage imaging data deposition using open file formats such as OME-TIFF. Where possible the original raw data should be submitted, though you can also submit analyzed or processed data if you think it is more usable.

Is there a size limit for data deposition?

There is no size limit to the data that can be published in IDR. However for very large depositions (>10TB), please contact us as early as possible as special arrangements may be needed for data transfer.

Is it possible to restrict access to the data for some period? For example, is it possible for data to be embargoed until publication of the manuscript?

IDR holds and serves public data. IDR cannot take data that will remain private indefinitely, e.g. data that can only be shared with a specific set of collaborators. Please see info on OME’s OMERO if you require project-specific, controlled data access.
IDR can embargo data for a defined period of time, usually so that data publication is coordinated with the publication of the associated peer-reviewed paper. Contact the IDR team for more info.

Is it possible to schedule a release date?

Scheduling a release date is possible, but will often be provisional. However, advance notice is required as we will only schedule a release date once all data has been submitted, validated, and all our data integrity and consistency checks are satisfied. The amount of work and time this requires and our ability to honor an agreed publication date depends on the complexity of the datasets and, in many cases, how quickly authors respond to requests for clarifications, missing data etc. We’re happy to discuss all aspects of data submission at idr [at]

Is it possible to give access to embargoed data to authorized persons only?

At the moment we do not provide any private access to embargoed data.

Can my dataset be published under a non-commercial license?

IDR's mission is to make reference image datasets as widely available as possible. We believe the industrial research and commercial imaging communities are critical parts of the larger scientific enterprise. Indeed our funders put a high premium on engagement with these communities. IDR policy is to use CC0 or CC-BY licensing on its data exactly to promote the widest re-use and impact of the several million GBPs of public and charity investment that has supported and continues to support the IDR.

Why are some datasets published under more restrictive licenses?

There are some studies in IDR published under CC-BY-NC. These are largely datasets that IDR has re-published that used CC-BY-NC (or similar) in their original publication, specifically the JCB DataViewer, which ran from 2009 - 2016. However our policy is to use CC0 or CC-BY wherever possible.

How much does it cost to publish data in IDR?

Data deposition and publication is free-of-charge to the authors and is supported by grants from the BBSRC, Wellcome Trust and the European Commission.

Does the repository have a long-term data preservation plan?

IDR is currently funded by BBSRC and Wellcome as a collaboration between the OME Consortium and EMBL-EBI. It is a central component of EMBL-EBI’s open data mission in the domain of biological images (see and for more information).

Has the repository implemented a security policy regarding its information system?

The repository is hosted on EMBL-EBI infrastructure and as such a large portion of the security policy comes from EBI’s own policies. The IDR team has its own internal security policy which includes the protection of sensitive data such as embargoed submissions.

How does IDR handle private health identifiers (PHI) or personal identifying information (PII) that may be included in the data or metadata?

IDR publishes fully anonymized data. We require that the submitters transfer to us data fully de-identified from PHI and PII. This is definitely the submitters' responsibility, since only the submitter will have sufficient knowledge of the data type to fully guarantee de-identification.

When can I get an IDR accession number?

An IDR accession number can be provided when we receive all image data along with completed metadata templates.

When can I get a DOI?

A Data DOI will be minted following the public release of the data in IDR. A DOI cannot be provided before the data is publicly available in IDR.

How do I cite the IDR as a resource?

The IDR is described in the following publication: Williams E, Moore J, Li SW, Rustici G, Tarkowska A, Chessel A, Leo S, Antal B, Ferguson RK, Sarkans U, Brazma A, Salas REC, Swedlow JR. The Image Data Resource: A Bioimage Data Integration and Publication Platform. Nat Methods. 2017 Aug;14(8):775-781. doi: 10.1038/nmeth.4326. PMID: 28775673; PMCID: PMC5536224.

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