Completed Cells, Biochemistry & Physiology Computing & AI

A2O - Transforming EMPIAR into an Essential Resource for EM Data Spanning Scales from Atoms to Organisms

Funder Wellcome Charity-funded
Recipient organisation European Molecular Biology Laboratory
Funding £1.5M
Period Oct 2020 — Sept 2025

In plain English

AI plain-English summary

EMPIAR, a public archive for electron microscopy images, now holds 284 terabytes of data across 286 entries, and this project will overhaul how scientists deposit and reuse those massive datasets. The problem is straightforward: as electron microscopy expands from imaging single proteins to whole tissues and organisms, the data files have become enormous—some spanning entire animal brains at nanoscale resolution. Researchers currently struggle to upload these volumes, and others struggle to download and view them efficiently. Without better infrastructure, valuable data sits unused or is never shared at all. If this succeeds, EMPIAR will handle tissue- and organism-level 3D volumes, support interactive viewing of multiscale images, and simplify the deposition workflow to encourage mandatory data sharing. The project will also test compression methods to prepare for future growth. For most people, this work will remain invisible—it improves the pipes, not the product. But for structural biologists, neuroscientists, and drug developers, faster access to high-quality electron microscopy data could accelerate discoveries in everything from viral mechanisms to neural connectivity. The archive already has over 180 citations; this upgrade ensures it can keep pace with the field.

View original technical description
The Electron Microscopy Public Image Archive (EMPIAR) was developed following consultations with the cryo-EM community highlighting the pressing need for public dissemination of image data underpinning cryo-EM structures. Since 2014, EMPIAR has quickly grown in volume (286 entries; 284 terabytes as of 01/04/2020) and established its role and value for the community (>180 EMPIAR citations). Its remit now includes micro-crystal electron diffraction (microED), soft-X-ray tomography (SXT), and volume-EM (including Focused Ion Beam and Serial Block-Face SEM) data. The main goals of this grant are to streamline and facilitate the deposition process (encouraging deposition and improving quality and quantity of deposited information) and to enhance and facilitate data reuse. All hardware and IT infrastructure will be provided by EMBL-EBI. Specific aims: - Fully support deposition of volume-EM data; - Support handling large (tissue- and organism-level) 3D-volumes by pump-priming EMPIAR with flagship connectomics and non-connectomics datasets; - Enable efficient and interactive reuse of large 3D-volumes by supporting multiscale imaging formats; - Facilitate potential mandatory deposition by simplifying the deposition workflow and enhancing data reuse; - Improve support for correlative imaging data, working with stakeholder communities and the EMBL-EBI BioImage Archive; - Prepare for rapid growth of data volumes by evaluating and implementing data-compression methods.

View the original record at the funder ↗

Researchers

Ardan Patwardhan (EPMC Awardee)Gerard Kleywegt (EPMC Awardee)

Related Research

Grants with similar aims, by meaning.

EMDB: dealing with the cryo-EM data deluge
Public archiving and data integration in the era of multi-modal imaging
The Electron Microscopy Data Bank
Integrating 3D biological data on scales from molecules to cells
Collaborative Computational Project for cryo electron microscopy (CCP-EM): expanding the reach of cryoEM

Original classification

Biomedical Resources Grant

Plain English summaries and category classifications on this site are generated by AI and may not perfectly reflect the original research.