2025-12-01 Technical Meeting

[sbliven]

The December technical meeting will be Monday, 1 December at 16:00 CET. Zoom link.

November minutes ◀️ ▶️ February minutes

[sbliven]

Updates since last month

• Schemas are now officially released as version 1.0.0! A formal release announcement will follow.
• @despadam has created a beautiful website for us at https://osc-em.github.io/. This nicely integrates the schema documentation. Please use the homepage when citing OSC-EM.
• Persistent URLs are available for all schemas and release artifacts through https://w3id.org/. See https://github.com/osc-em/oscem-schemas for details.
• Repositories have been renamed following the discussion at last month's meeting. Please update links and git repositories.
• Extractor and converter tools have been transferred to the osc-em organization, reflecting our commitment to sustaining and growing OSC-EM beyond any individual project or institute.

Agenda

1. Summary of renamed repositories
2. Review w3id PURLs
3. Discuss writing a paper
4. Review open PRs

[sbliven]

Release announcement draft

I would like to send a release announcement to some mailing lists. Here is the current text (slightly revised since today's meeting):

The Open Science Community for Electron Microscopy (OSC-EM) is excited to announce the stable release of the OSC-EM schema. The schemas aim to be an interoperable format for electron microscopy metadata, allowing key information to be preserved from acquisition through to publication. The format has been adopted by Swiss EM Facilities and INSTRUCT I2PC as the format for metadata exchange.

The release includes support for five experimental techniques:

1. general: General metadata schema. Used for materials science and general EM data.
2. spa: Single particle analysis, including processing steps
3. subtomo: Subtomogram averaging
4. cellular_tomo: Cellular tomography with a well-characterized sample
5. env_tomo: Environmental tomography on samples taken from the environment.

A number of tools are available to work with data in the OSC-EM format. Extractor programs are currently available to produce OSC-EM metadata from cryoEM (SerialEM, EPU, and TOMO5) datasets, material science (prz and emd files), and to convert to PDBx/mmCIF. Scipion has support for exporting SPA processing workflows in OSC-EM format. Finally, a web viewer can help visualize the data.

For more information, visit osc-em.github.io or email our list. We are actively looking for collaborators to add additional techniques, identify missing terms, or contribute to our monthly online meetings.

Spencer Bliven on behalf of the OSC-EM community

@lolasanchezzz @cossorzano Can you review and approve this, especially the INSTRUCT and Scipion portions?

Paper

We will start drafting a paper describing OSC-EM on google docs.

Possible journals:

• JSB
• Acta Xtal section D
• IUCR-J

I will send a link via email.

Next meeting

🎆 We will skip the January meeting, making our next appointment 2 February, 2026. 🎆