About EMPIAR

EMPIAR (https://empiar.org/ or https://www.ebi.ac.uk/empiar), the Electron Microscopy Public Image Archive, is a public resource for raw images underpinning 3D cryo-EM maps and tomograms (themselves archived in EMDB). EMPIAR also accommodates 3D datasets obtained with volume EM techniques and soft and hard X-ray tomography. All data archived in EMPIAR can be re-used freely without any conditions or restrictions ("CC0" license model). Detailed information about EMPIAR policies and procedures is available.
The purpose of EMPIAR is to provide easy access to state-of-the-art data to facilitate methods development, validation and re-use, e.g., for Machine Learning applications. EMPIAR data is also used for training and teaching purposes and as part of community challenges.
EMPIAR owes much to input from the EM community, notably at two workshops organised by EMBL-EBI and the Open Microscopy Environment (OME) - "Data Management Challenges in Three-dimensional EM" (Patwardhan et al., Nat. Struct. Mol. Biol. 19, 1203-1207 (2012)) and "A 3D Cellular Context for the Macromolecular World" (Patwardhan et al., Nat. Struct. Mol. Biol. 21, 841-845 (2014)). We are developing a timeline with highlights of EMPIAR's history.
An overview of the status of and plans for EMPIAR as of August 2021 is available in this 20 minute recorded presentation.

EMPIAR accession codes

Accession codes for EMPIAR entries have the format: EMPIAR-#####, e.g., EMPIAR-10009. Please use the accession code in this format when citing EMPIAR entries. Your support in maintaining consistency will greatly aid discoverability of entries on the web and in full-text articles.
After the public release, your deposition will be issued a DOI that can be cited too, see the section below for details.
You can also claim EMPIAR entries to your ORCID record. Please see more information here.

EMPIAR DOI

Individual EMPIAR entries have a DOI (Digital Object Identifier) assigned that links to the corresponding entry page. These DOIs have the following format:
10.6019/EMPIAR-10016, where EMPIAR-10016 is the entry accession code. This points to https://doi.org/10.6019/EMPIAR-10016.

Citing EMPIAR

Please cite the following publication in your papers and on websites: A. Iudin, P.K. Korir, J. Salavert-Torres, G.J. Kleywegt & A. Patwardhan. "EMPIAR: A public archive for raw electron microscopy image data." Nature Methods 13, 387-388 (2016). https://dx.doi.org/10.1038/nmeth.3806. To cite individual entries, please quote the EMPIAR accession code (see above; in addition, you can also use the DOI to provide a direct link to the entry) and cite the original publication.

EMPIAR data re-use case study

Examples of how EMPIAR data is being re-used by the community are described here.

EMPIAR and the EMBL-EBI BioImage Archive

On 2 July 2019, EMBL-EBI announced the launch of its BioImage Archive (press release). EMPIAR is a major component of this initiative which enables it to grow into a sustainable multi-petabyte-scale resource over the next few years.
Using funding from the UK Research and Innovation Strategic Priorities Fund, EMBL-EBI is building IT infrastructure to support the BioImage Archive, including a scalable storage architecture (object store), which EMPIAR already uses.
As the BioImage Archive is being built up over the next few years, EMPIAR users and depositors will experience additional benefits. For instance, integration of light-microscopy data and electron and X-ray microscopy data will enable transparent deposition, retrieval and visualisation of data for correlative imaging modalities such as CLEM and CLXM. It will also enable linking and integration of diverse bioimaging datasets from a variety of modalities and on a range of length scales.

More information

EMPIAR in the news

Funding

The work on EMPIAR was funded from 2014 to 2021 by two project grants awarded to EMBL-EBI by MRC and BBSRC. Since 2021, it benefits from funding from the Wellcome Trust. The EMBL-EBI IT infrastructure supporting EMPIAR is funded by the UK Research and Innovation Strategic Priorities Fund. Additional funding for EMPIAR has been provided since its inception by EMBL-EBI with support from the EMBL Member States.
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