Electron Microscopy Public Image Archive
Electron Microscopy Public Image Archive
The final 3D reconstruction from a single-particle, electron tomography or electron diffraction experiment can be deposited to EMDB. Image data related to EMDB entries, e.g., micrographs, particle-stacks and tilt-series can be deposited to EMPIAR. EMPIAR also supports the following experimental methods (taking image data and final reconstructions where available):
For these experimental methods we require that the data set is directly related to a publication or is a part of a community initiative, e.g. as benchmarking data.
ORCID iDs are shown on entry pages for every author that has provided us with such during the deposition process. This allows a quick and easy way to access the list of the author's publications from Europe PMC search or directly from the author's ORCID profile page.
EMPIAR has now integrated ORCID into the deposition system. The user can sign in into the system using their ORCID account. This would automatically populate user profile fields like ORCID iD, first and last names and email.
All data in EMPIAR is freely and publicly available to the global community under the CC0 license (https://creativecommons.org/share-your-work/public-domain/cc0/).
We accept data from a range of imaging modalities in EMPIAR, including cryo-EM, cryo-ET, and various volume EM, X-ray microscopy and correlative imaging studies. In the case of cryo-EM/ET, the recommendation is to deposit the “rawest” form of your data to EMPIAR (e.g., for single-particle studies, unaligned multi-frame micrographs). This enables wide data re-use and re-processing, e.g., for validation, methods development, teaching, and community challenges. Providing additional downstream intermediate files (e.g., motion-corrected micrographs, particle coordinates, particle stacks, particle Star files with assigned Euler angles and alignments) is also encouraged as these will aid users interested in specific steps of the EM workflow.
Ideally, as much as possible should be provided. For example:In terms of metadata, EMPIAR’s deposition forms already collect information on numbers of images, frames per image, image format, dimensions, pixel spacing and type. Further information, for example, on parameters essential for reprocessing such as Cs, electron dose per frame and gain-reference orientation (for any deposited gain-reference images) can be provided in the “Details” fields. Additionally, workflows from Scipion (and in the future hopefully from other packages as well) can be uploaded as part of your submissions.
The full list of EMPIAR requirements is available online, including data and file types, formats, and extensions. For information on EMPIAR’s policies and processing procedures, please see {{emdb_global.ebi_ebi_empiaries. For guidance on EMPIAR’s deposition process, please refer to our deposition manual.
Note: for non-cryo data, there are different requirements and recommendations.
Pressing the "Submit" button sends the deposition for review by the EMPIAR annotation team. They will communicate with the depositor regarding any issues and may choose to unlock the deposition if complementary details or data are required. Once this is complete, the depositor will be sent a request to approve the curation by the EMPIAR annotation team. Upon receiving the depositor's approval the entry will enter the release phase following the instructions provided by the depositor. The time it takes to get the entry released depends on the size of the entry, the number of files, the current load on EMBL-EBI resources and the availability of the annotation staff. The depositor will be notified by email once the entry is publicly available.
Please cite the original publication and cite the EMPIAR entry using the guidelines provided here
Yes, EMPIAR entry pages offer three options - Aspera, download of a tarball via http, and download of individual files via ftp. The file browsers on the EMPIAR entry pages allow you to select files and sub-directories to be downloaded via Aspera or http. Aspera is the recommended option and can be used for any size of download. Please note that the download will be an as-is structure of the selected files and directories and not an archive (tar-ball)! The http download option will create a tarball that can be downloaded. This option only works for tarballs < 1.5GB. You can also download individual files (but not sub-directories) using Ftp (select "Browse Ftp").
Yes! To download data use endpoint:
EMPIAR schema is described here. It consists of the main empiar.xsd XML schema file and additional requirements in empiar.sch in Schematron format.
Make sure that your Firewall does not block your transfer.
For Globus ensure that hx-gridftp-*.ebi.ac.uk addresses are whitelisted.
For Aspera you might need to modify the rules to accommodate the following:
permit TCP outbound to 193.62.197.71 on port 33001
permit UDP outbound to 193.62.197.71 on port 33001
permit UDP inbound from 193.62.197.71 on port 33001
Our web transfer interface has the target rate set to 200 000 Kbps and the policy to adaptive. Similarly, the command line displayed above. In case you are having issues with transferring data, it might help to reduce the target rate.
To do so, please use the command line transfer and change the value of '-l' parameter. For example: ascp -QT -l 10M -P33001 -i ~/.aspera/connect/etc/asperaweb_id_dsa.openssh emp_ext3@fasp.ebi.ac.uk:/test testset
Please get in touch if the issue persists. If possible, provide us Aspera logs.
