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tags: Tuesday | ||
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# 2024-03-12 | ||
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Attending: Will, Josh, JM, Dominik, June, Khaled, Tom, Melissa, Andreas, Seb, Jason, Petr, Muhanad, Kevin, David, Chris, Kyle, Erin, | ||
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Start: 2:00 pm UK | ||
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## Accepting minutes from [last meeting](https://hackmd.io/team/ome?nav=overview) | ||
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## Project Status | ||
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(2-3 minutes each) | ||
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- IDR (Seb): | ||
- Migration to rockyLinux 9. Going well. | ||
- Plan to announce to community once complete, announce docs etc. | ||
- One more non-NGFF release with Rocky 9 with idr0151. Then update to NGFF support. | ||
- Khaled has prepared ansible role for deploying microservices | ||
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- OMERO | ||
- [OMERO.web 5.25.0 release](https://github.com/ome/omero-web/pulls?q=is%3Apr+milestone%3A5.25.0) | ||
- Remove old Python 2 code, add Python 3.12 support | ||
- Fix activities API issue | ||
- Chris: form field PR? Andreas: yes, can include | ||
- JM: will switch merge-ci to rocky-9 Docker | ||
- JM: other python releases, e.g. dropbox etc to follow | ||
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- Bio-Formats | ||
- David: ZarrReader PR open - reading s3 directly. AWS SDK new dependency. | ||
- Also adds static method for loading plane without using memo file | ||
- Currently on merge-ci, not idr-testing yet | ||
- Will require regeneration of memo files | ||
- Jason: testing plan TBD? JM: will comment on PR | ||
- Chris: AWS SDK versions picking? We're using v1, same for n5 and scaleable minds. | ||
- v1 deprecated (EOL 2025) and v2 has new features. Different performance, thread pools | ||
- Java 21 changes: all working - plan to release in 7.3.0 in early April | ||
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- NGFF (Josh) | ||
- RFC Reviews starting (process) | ||
- e-mails sent to reviewers for RFC-1, positive responses so far. Deadline end of March | ||
- Melissa: process to volunteer reviewing? Josh to update RFC-1 | ||
- Event-based files (data) FLIM etc. | ||
- Josh: do we want to support this? | ||
- German working group maybe? | ||
- Zarr & ro-crate (data to metadata) | ||
- Both are directories with metadata (JSON). | ||
- Might open a ZEP with proposal | ||
- RDF (metadata) | ||
- [FDP](https://www.fairdatapoint.org/) with [DCAT](https://www.w3.org/TR/vocab-dcat-3/) at [SWAT](https://www.swat4ls.org/workshops/leiden2024/) | ||
- DICOM-RDF thread: DICOM community questions | ||
- JRS: https://bigpicture.eu/ and https://pypi.org/project/wsidicomizer/ | ||
- [Zeiss XSD](https://github.com/ZEISS/czicheck/blob/main/CZICheck/checkers/schema/ZEN/flatten/ImageMetadata.xsd) | ||
- Can we try to turn this into LinkML? Same as with our XSD? | ||
- [ARC](https://nfdi4plants.org/nfdi4plants.knowledgebase/docs/implementation/AnnotatedResearchContext.html) and a ["process" model](https://github.com/BioSchemas/specifications/pull/669) - Layer on top of ro-create for Experimental metadata. | ||
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- GerBI (Tom) | ||
- PR for PlateAcquisition display in webclient | ||
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- Glencoe (Chris) | ||
- webclient PR - fields maxlength (see above) | ||
- More updates to follow to avoid duplication etc. | ||
- webclient cleanup: webgateway-cache etc, handling "server busy" | ||
- Open-sourcing Zarr pixelbuffer - designed for private s3 access | ||
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- Community | ||
- Indonesia trip success: Workshop went well. Lots of demand but lack of resources. | ||
- https://gamapath.fkkmk.ugm.ac.id/ | ||
- Targeting OME Community Meeting May 29-31 | ||
- Finalising Room and registration details | ||
- Themes (or really current musings): | ||
- Petascale bioimage data resources (IDR, NL BioImaging, BioImage Archive, NFDI, FBI, SSBD) | ||
- NGFF Updates (Josh: --> "FAIR" would be an option but of course well-chewed) | ||
- Workflows and Analysis (Galaxy, etc.) - Björn Grüning? | ||
- Training with OMERO (UGM?) | ||
- Future of OMERO | ||
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## AOB | ||
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(5 min. max; tech. Discussion should be highlighted to relevant people and rescheduled) | ||
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## Main Topic | ||
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(20-25 minutes plus 15 minutes questions max) |