2024-03-12
Attending: Will, Josh, JM, Dominik, June, Khaled, Tom, Melissa, Andreas, Seb, Jason, Petr, Muhanad, Kevin, David, Chris, Kyle, Erin,
Start: 2:00 pm UK
Project Status
(2-3 minutes each)
- 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
- OMERO
- OMERO.web 5.25.0 release
- 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
- 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
- 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 with DCAT at SWAT
- DICOM-RDF thread: DICOM community questions
- JRS: https://bigpicture.eu/ and https://pypi.org/project/wsidicomizer/
- Zeiss XSD
- Can we try to turn this into LinkML? Same as with our XSD?
- ARC and a “process” model - Layer on top of ro-create for Experimental metadata.
- GerBI (Tom)
- PR for PlateAcquisition display in webclient
- 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
- 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
AOB
(5 min. max; tech. Discussion should be highlighted to relevant people and rescheduled)
Main Topic
(20-25 minutes plus 15 minutes questions max)
