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FAQ

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] openmicroscopy.org.

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.

Do authors retain the rights to their data?

The authors of an IDR study retain copyright. IDR receives a license to publish the data on behalf of the authors. Every study in IDR is published using a permissive public license allowing to share and re-use the data, usually CC0 or CC BY 4.0.

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 https://www.nature.com/articles/s41592-018-0195-8 and https://www.ebi.ac.uk/bioimage-archive/our-roadmap/ 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.

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OMERO is distributed under the terms of the GNU GPL. For more information, visit openmicroscopy.org


IDR logo version: devel. Last updated: 2020-06-30.