We aim to publish reference image datasets, which have value beyond simply supporting an original publication according to the Euro-BioImaging - Elixir Image Data Strategy. This includes:
To make IDR datasets as widely re-usable as possible, we strongly recommend that submitters make their datasets available under a CC0 or CC-BY license. The licensing information should be included as part of the metadata .
Dataset size is typically not an issue, but for sizes significantly larger than 1000 GB special planning may be needed.
Metadata describing an imaging study is submitted using template files. These are available for download from https://github.com/IDR/idr0000-lastname-example/archive/master.zip.
There are template files for two different use cases:
For both types of study three files should be submitted:
Example files for HCS studies can be found here:
Example files for non-screen studies can be found here:
Each study is slightly different and advice on how to fill in the template can be given. Questions should be sent to email@example.com.
Imaging datasets can be remarkably complex. To the extent that it's well-structured and reusable by the community, we are interested in enriching your online dataset with your additional metadata, e.g.:
There are several options for having your image data transferred to the IDR:
A submission is considered complete only after your uploaded metadata and image data have been validated. Validation may itself take significant time depending on, e.g., the size of the dataset, the file formats used and the consistency in naming between files. During validation, frequent consultation with the author and/or data producer may be necessary.
Once your data is validated and ready for import, you will be notified that the publication pipeline can begin.
Your dataset in IDR will be given an accession number (e.g. “idr1234”) which you can use for informally referring to your entry. For more formal uses such as citing the imaging dataset in your publication, we suggest using a DOI:
Image files are available in the Image Data Resource (Williams et al 2017) under DOI https://doi.org/10.17867/10000105 .
DOIs can be made available upon request but require an additional depositor agreement and license form on top of your completed submission.
If you want to include a citation to the IDR in a paper or other publication, please use:
Williams et al (2017) Image Data Resource: a bioimage data integration and publication platform, https://doi.org/10.1038/nmeth.4326.
© 2016-2018 University of Dundee & Open Microscopy Environment. Creative Commons Attribution 4.0 International License.
OMERO is distributed under the terms of the GNU GPL. For more information, visit openmicroscopy.org