Open EM Data Network

Open EM Data Network

IMG_1967

Category

Establish

Institutions

ETH Zurich

Data type

Electron micrographs, tomograms, tilt series, diffraction images, spectrograms, electron density maps, atomic models, and processing workflows.

Field

Electron Microscopy

Researchers

Alexandra Radenovic, Andrzej J. Rzepiela, Bilal Qureshi, Christophe Copéret, Christophe Briand, Daniel Böhringer, Elisabeth Müller, Gebhard Schertler, Gregor Cicchetti, Henning Stahlberg, Marco Cantoni, Miroslav Peterek, Nicolas Blanc, Rolf Erni, Spencer Bliven, Stephan Egli, and Volodymyr Korkhov

Description

OpenEM is a national initiative designed to make electron microscopy (EM) data from Swiss research institutions openly available, well organized, and easy to reuse. Modern electron microscopes produce extremely large and valuable image datasets that are essential for research in areas such as structural and cell biology, materials science, and nanotechnology. Until now, these data were often stored locally, described inconsistently, and difficult to share or reuse beyond their original purpose. The OpenEM project addresses this challenge by establishing common standards, tools, and infrastructure for managing EM data according to the FAIR principles: data should be findable, accessible, interoperable, and reusable. By standardizing how metadata are collected and how datasets are published, OpenEM simplifies workflows for researchers, improves data quality, and supports reproducibility and long-term preservation. Importantly, open and well-described datasets can be reused in ways not originally anticipated, for example to train new AI-based analysis methods, reprocess data with improved algorithms, or combine results across multiple studies. At the core of OpenEM is the SciCat Data Catalog operated by the Paul Scherrer Institute (PSI). SciCat is already used for data from large-scale facilities such as synchrotrons and neutron sources and has now been extended to serve as a central repository for Swiss EM data. Facilities across the ETH domain and SwissUniversities contribute datasets using the Open Science Community for Electron Microscopy (OSC-EM) metadata standard developed within the project. This enables consistent data ingestion, discovery, and sharing across institutions. In addition, life science datasets can be deposited seamlessly into international repositories such as the Electron Microscopy Database (EMDB), the Electron Microscopy Public Image Archive (EMPIAR), and the Protein Data Bank (PDB), further increasing their visibility and impact. Through OpenEM, an estimated 6.4 petabytes of EM data generated annually in Switzerland can be systematically catalogued and, where appropriate, made openly available. By lowering barriers to data sharing and reuse, the project helps maximize the scientific value of costly EM infrastructure and supports new discoveries across disciplines, both within Switzerland and internationally
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