About EMPIAR

EMPIAR, the Electron Microscopy Public Image Archive, is a public resource for raw electron microscopy images. Here, you can browse, upload and download the raw images used to build a 3D structure.

The purpose of EMPIAR is to provide easy access to state-of-the-art raw data to facilitate methods development and validation, which will lead to better 3D structures. It complements the Electron Microscopy Data Bank (EMDB), where 3D volumes are stored, and uses the fault-tolerant Aspera platform for data transfers. EMPIAR is based on input from the EM community, notably at two workshops organized 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)).

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.

EMPIAR DOI

Individual EMPIAR entries have a DOI assigned that links to the corresponding entry page. These DOIs have the following format:
https://dx.doi.org/10.6019/EMPIAR-#####, e.g., https://dx.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 (2016). https://dx.doi.org/10.1038/nmeth.3806. See also the EMBL-EBI press releases of 21 March 2016 here and here. 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

You can see more details on how EMPIAR data is being re-used by the community by the following link.

EMPIAR and the EMBL-EBI BioImage Archive

On 2 July 2019, EMBL-EBI announced the launch of its BioImage Archive (press release). EMPIAR is an active component of this new initiative which will enable it to grow into a sustainable 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), from which EMPIAR will benefit. EMPIAR is already getting too big to be supported by NFS file systems and will therefore be migrating to the object store over the next few months. As the changes only involve the back-end of EMPIAR, we anticipate that they will not affect deposition or retrieval of EMPIAR data. The web-based user interfaces for both deposition and retrieval of EMPIAR data will appear unchanged.
Last year, EMPIAR became an official EMBL-EBI resource, which, together with its becoming part of the BioImage Archive, will improve the support for and long-term sustainability of EMPIAR. This will help EMPIAR transition from a small pilot archive with a relatively narrow scope (raw 2D image data related to EMDB entries) at its launch in 2014 to a versatile, integrated and sustainable resource for EM-related bioimaging data.
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 the archiving of light-microscopy data and EM data will enable transparent deposition and retrieval 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 is funded by a project grant awarded to EMBL-EBI by MRC and BBSRC. It further benefits from funding from the Wellcome Trust and EMBL-EBI.