---
# System prepended metadata

title: '2024-03-12'
tags: [Tuesday]

---

---
tags: Tuesday
---

# 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

## Accepting minutes from [last meeting](https://hackmd.io/team/ome?nav=overview)

## 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](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

- 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](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.

- 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)
