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Image data submission policy

  1. EMPIAR accepts raw images underpinning 3D cryo-EM maps and tomograms, 3D images obtained with volume EM techniques, and soft and hard X-ray tomography imaging. Image data in these categories should be deposited into EMPIAR.
  2. All other imaging data associated with a publication should be deposited in the BioImage Archive, using the BioStudies/BioImage Archive shared submission system with an imaging-specific metadata template.
  3. For studies that generate both data suitable for EMPIAR and other image data (for example correlative X-ray/light microscopy), datasets should be deposited separately into EMPIAR and the BioImage Archive. Linking information, such as registrations or transformations into common coordinate space, should be deposited in the BioImage Archive.
  4. Image data may be moved between the EBI image data resources, according to operational need. Accession identifiers will remain valid.

For queries, please get in touch at image-presubmission@ebi.ac.uk.

Examples

The table below is intended to provide reference examples showing how different data types are deposited to each archive (Table 2).

Data typeBioImage ArchiveEMPIARExamplesNotes
Light microscopy✅❌S-BIAD287, S-BIAD332Including many super-resolution techniques
2D Electron microscopy✅❌S-BIAD217, S-BIAD15Note that 3D (volume) EM data should be deposited to EMPIAR
High content screening images✅❌S-BIAD29, S-BIAD235See 1. below.
Other imaging, e.g. AFM, ultrasound✅❌S-BIAD189, S-BIAD194Includes all biological imaging methods not explicitly listed elsewhere
cryo-EM❌✅EMPIAR-10002, EMPIAR-10061
cryo-ET❌(✅)EMPIAR-10164 , EMPIAR-10164See 2. below.
Volume EM/XM❌✅EMPIAR-10462 (SBF-SEM), EMPIAR-10310 (FIB-SEM), EMPIAR-10087 (SXT)
Correlative microscopy where one component is 3D EM/XM✅(Light Microscopy data and correlation info)✅(EM/XM data)S-BIAD17 AND EMPIAR-10412, S-BSST729 AND EMPIAR-10847See 3. below
Patient identifiable imaging data❌❌❌
Table 2 Reference examples showing how different data types are deposited to appropriate data archive.

1. For high content screening studies, specific metadata templates are available for different screen types, e.g. compound screens, genetic knockout screens. Please contact us at bioimage-archive@ebi.ac.uk for more information.

2. For Cryo-ET, 3D tomograms: if there are only a small number, they should all be deposited to EMDB. If there are many, then one or a few representative tomograms should be deposited to EMDB; the rest can be deposited to EMPIAR. Raw data (tilt series): should only be deposited to EMPIAR.

3. For correlative studies:

  • 3D EM or X-ray images should be deposited into EMPIAR.
  • Other modalities (e.g. Light Microscopy) should be deposited into the BioImage Archive.
  • Information that describes the correlation between the images from modalities, e.g. transformations into a shared physical coordinate space, registrations etc. should be deposited into the BioImage Archive.

For more information, see Iudin et al 2021, though note that where the protocol references deposition to BioStudies, the “BioImaging” template should be used during deposition.