EMPIAR: the Electron Microscopy Public Image Archive.

Public archiving in structural biology is well established with the Protein Data Bank (PDB; wwPDB.org) catering for atomic models and the Electron Microscopy Data Bank (EMDB; emdb-empiar.org) for 3D reconstructions from cryo-EM experiments. Even before the recent rapid growth in cryo-EM, there was an expressed community need for a public archive of image data from cryo-EM experiments for validation, software development, testing and training. Concomitantly, the proliferation of 3D imaging techniques for cells, tissues and organisms using volume EM (vEM) and X-ray tomography (XT) led to calls from these communities to publicly archive such data as well. EMPIAR (empiar.org) was developed as a public archive for raw cryo-EM image data and for 3D reconstructions from vEM and XT experiments and now comprises over a thousand entries totalling over 2 petabytes of data. EMPIAR resources include a deposition system, entry pages, facilities to search, visualize and download datasets, and a REST API for programmatic access to entry metadata. The success of EMPIAR also poses significant challenges for the future in dealing with the very fast growth in the volume of data and in enhancing its reusability.

Ten recommendations for organising bioimaging data for archival.

Organised data is easy to use but the rapid developments in the field of bioimaging, with improvements in instrumentation, detectors, software and experimental techniques, have resulted in an explosion of the volumes of data being generated, making well-organised data an elusive goal. This guide offers a handful of recommendations for bioimage depositors, analysts and microscope and software developers, whose implementation would contribute towards better organised data in preparation for archival. Based on our experience archiving large image datasets in EMPIAR, the BioImage Archive and BioStudies, we propose a number of strategies that we believe would improve the usability (clarity, orderliness, learnability, navigability, self-documentation, coherence and consistency of identifiers, accessibility, succinctness) of future data depositions more useful to the bioimaging community (data authors and analysts, researchers, clinicians, funders, collaborators, industry partners, hardware/software producers, journals, archive developers as well as interested but non-specialist users of bioimaging data). The recommendations that may also find use in other data-intensive disciplines. To facilitate the process of analysing data organisation, we present bandbox, a Python package that provides users with an assessment of their data by flagging potential issues, such as redundant directories or invalid characters in file or folder names, that should be addressed before archival. We offer these recommendations as a starting point and hope to engender more substantial conversations across and between the various data-rich communities.

EMDB Web Resources.

The Electron Microscopy Data Bank (EMDB; http://emdb-empiar.org) is a global openly-accessible archive of biomolecular and cellular 3D reconstructions derived from electron microscopy (EM) data. EMBL-EBI develops web-based resources to facilitate the reuse of EMDB data. Here we provide protocols for how these resources can be used for searching EMDB, visualising EMDB structures, statistically analysing EMDB content and checking the validity of EMDB structures. Protocols for searching include quick link categories from the main page, links to latest entries released during the weekly cycle, filtered browsing of the entire archive and a form-based search. For visualisation, the 'Volume Slicer' enables slices of EMDB entries to be visualised interactively and in three orthogonal directions. The EMstats web service (https://emdb-empiar.org/emstats) provides up-to-date interactive statistical charts analysing EMDB. All EMDB entries have 'visual analysis' pages that provide basic validation information for the entry.