OpenEM shares its software, metadata standards, training materials and conference contributions openly.
Software & repositories
The SwissOpenEM GitHub organization hosts the OpenEM services and infrastructure. Metadata schemas, extractors and converters are maintained with the Open Standards Community for Electron Microscopy (OSC-EM).
OpenEM services & infrastructure
| Repository | Purpose |
|---|---|
| Ingestor | Facility service and application for ingesting EM datasets into SciCat. |
| openem-deployment | Docker Compose deployment of the OpenEM Ingestor stack. |
| Depositor | Transfer files and metadata from SciCat to the OneDep deposition system for EMDB and PDB. |
| ScopeMArchiver | Archival service for ETH Zurich ScopeM. |
| scicat-globus-proxy | Request Globus transfers using SciCat authentication tokens. |
| globus | Go library for Globus transfers. |
| keycloak-admin-helper-plugin | Keycloak administration helper plugin. |
| epu_dataset_merger | EPU dataset merging utility. |
OSC-EM metadata tools
| Repository | Purpose |
|---|---|
| oscem-schemas | Shared metadata schemas for electron microscopy. |
| oscem-extractor-life | Extract metadata from life science acquisitions, including SerialEM, EPU and Tomo5. |
| oscem-extractor-materials | Extract metadata from materials science EM data. |
| oscem-converter-extracted | Map extracted metadata to the OSC-EM format. |
| oscem-converter-mmcif | Convert OSC-EM metadata to mmCIF for OneDep deposition. |
Related code & project resources
- SciCat upstream: frontend, backend and SciCat CLI.
- Project websites: OpenEM and OSC-EM.
Platforms & open data
- PSI SciCat Data Catalog: archive, share and manage electron microscopy datasets.
- Published datasets: publicly released data in the PSI Data Catalog.
- Apoferritin example dataset: a public example of data shared through OpenEM.
- OpenEM on the ETH ORD Data Portal: project background and programme context.
Standards & collaborations
OpenEM is a founding member and a main schema contributor to OSC-EM. The OSC-EM schemas and metadata mappings support interoperability between instruments, processing tools and repositories. OpenEM also contributes to the CryoET Geometry standard.
Collaborations include INSTRUCT and EMDB within OSC-EM, PREMISE, FAIRmat and the EM Glossary, and the CryoET Standards Working Group. OpenEM works with EMDB on OneDep deposition and with EMPIAR on raw-image deposition. It also follows the ETH-ORD M2 Identity Management Guidelines and coordinates with ETH-ORD M2 API projects and the ETH Zurich FAIR Research Data Board.
Documentation & training materials
- OpenEM documentation: guides for users, facility operators and developers.
- SciCat documentation: background on the data catalogue used by OpenEM.
Presentations & posters
| Event | Date | Materials & information |
|---|---|---|
| CCPEM Spring Symposium 2023 | 24–26 April 2023 | Open EM Data in Switzerland |
| CCP-EM Pipeliner/Doppio Workshop | 17–18 January 2024, Oxford, UK | Invited participant; event information. |
| Agreeing community standards for cryoET data preservation and reuse: data structure, metadata, ontologies etc. | 17–19 April 2024, EMBL-EBI, Hinxton, UK | Invited participant. |
| Machine-actionable data interoperability for the chemical sciences (MADICES 2) | 22–25 April 2024, Berlin, Germany | Workshop materials · Scientific report |
| ETH Domain ORD Establish project presentations | 13 June 2024, online | The Open Data Network for Electron Microscopy (OpenEM): ETH-ORD Establish presentation 2024 · Report & recording |
| SciCatCon User Meeting | 2–4 July 2024 | OpenEM slides |
| New Opportunities for Better User Group Software (NOBUGS) | 23–27 September 2024 | OpenEM: Open research data infrastructure for electron microscopy in Switzerland |
| EnhanceR Symposium 2024 | 7 November 2024 | OpenEM: Open research data infrastructure for electron microscopy in Switzerland (EnhanceR 2024) |
| Advancing Open Research Data (ORD) Practices: collaboration and innovation in the ETH Domain | 12 June 2025 | OpenEM: FAIR data practices for electron microscopy |
| SciCatCon 2025 | 24–26 June 2025 | The Open Data Network for Electron Microscopy (OpenEM): SciCatCon 2025 |
| Scipion for Facilities Workshop 2025 | 30–31 October 2025 | Programme · FAIR data collection with the Open Science Community for Electron Microscopy (OSC-EM) metadata standard |
| ETH Domain Data Stewardship Community Event | 4 November 2025 | Event information · FAIR Standards for Electron Microscopy Data |
| SciCatCon 2026 | 29 June–3 July 2026 | Enabling interoperability between SciCat and open research data infrastructure |
| New Opportunities for Better User Group Software (NOBUGS) 2026 | 24 September 2026 | Open Research Data services with the PSI Data Catalog and SciCat |
Conferences & workshops
| Event | Date | Materials & information |
|---|---|---|
| OSC-EM Standards Workshop at PSI | 22–23 February 2024 | Programme · Report |
| OpenEM All-Hands Workshop, University of Bern | 13 February 2025 | Event information · 2025-02-13 OpenEM Workshop · Report & recording |
| OpenEM Workshop for PSI users | 8 April 2026 | OpenEM Workshop: Archiving Raw EM Data with the PSI Data Catalog |
| OpenEM User Workshop 2026, University of Bern | 7 September 2026 | Programme & event information |