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Depositing data in EMPIAR

You can deposit your data in EMPIAR using the EMPIAR deposition system. This tool can be accessed from the EMPIAR homepage (Figure 2). Alternatively, you can use empiar-depositor script (can be installed with “pip install empiar-depositor”) to make an automatic deposition. This will require a specially prepared JSON file that describes the metadata. This JSON file can be filled in manually according to the JSON schema or generated with Scipion – an image processing framework for obtaining 3D models of macromolecular complexes using Electron Microscopy (3DEM).

Your data remains private until you tell us to release it.
Figure 2 Accessing the EMPIAR deposition system.

It is possible to register an EMPIAR account or sign in with your ORCiD, Google or Facebook accounts.

When you deposit your data in EMPIAR you will need to fill in a form to capture metadata about the image/dataset. An example submission form is shown below. EMPIAR entries have one of the following types: 

  • EMDB – raw image data relating to structures deposited to the Electron Microscopy Data Bank,
  • INSILICO  – simulated data, for instance, created using InSilicoTEM (note: we only accept simulated data in special circumstances such as test/training sets for validation challenges: you are required to ask for and be granted permission before depositing),
  • SBF-SEM – image data collected using serial block-face scanning electron microscopy (like the Gatan 3View system),
  • SXT – image data collected using soft x-ray tomography,
  • FIB SEM – image data collected using focused ion beam scanning electron microscopy,
  • IHM – integrative hybrid modelling data,
  • CLEM – correlative light-electron microscopy – please deposit the relevant data to BioStudies first and then provide us with a cross-reference,
  • CLXM – correlative light X-ray microscopy and
  • MicroED – microcrystal electron diffraction

The options for releasing entry to the public are:

1) REL – directly after the submission has been processed,

2) EMDBPUB – after the related EMDB entry has been released,

3) HPUB – after the related primary citation has been published and

4) HOLD – delay release of entry by one year from the date of deposition. Once the year elapses the entry will automatically be published with notice.

Uploading data and capturing metadata with the EMPIAR deposition tool

The image data is uploaded using Globus. This is a simple and secure way of making electron microscopy data and the associated metadata publicly available.

Help Other options for uploading your data include the Aspera command line and Aspera web interface. If neither of these are suitable for you, please contact us and we can discuss the best way to submit your data to EMPIAR.