2024-04-30

Attending: Will, Dom, JM, Petr, Andreas, Frances, June, Josh, Kevin, Khaled, David, Erin, David S, Kyle, Melissa, Seb, Chris, Maadhav,

Start: 2:00 pm UK

Accepting minutes from last meeting

(2-3 minutes each) Brief report 15mins max for all.

IDR (Frances)
- prod121 release tomorrow idr0157 large plant study
- also includes rocky9 upgrades
- will deploy fresh idr-testing after release for final round of NGFF testing
OMERO
- Working on nightshade migration to Rocky 9
- Web PRs in progress, close to merging
Bio-Formats
- ZarrReader PR in review, then tag and release for IDR
- Flex PR (idr0001) assess scope of fix needed
NGFF
- https://forum.image.sc/t/ome-ngff-update-postponing-transforms-previously-v0-5/95617
- https://github.com/ome/ngff/pull/227
- Zarr v3 RFC PR to be merged and e-mail reviewers soon.
- FYI https://github.com/AllenNeuralDynamics/jomezarr
GerBI
- writing papers: promote data management and funding for it
Glencoe
- JSONp discussion, deprecation?
- Erin: recent meetings: ACR, BioIT, ABRF, https://aacrjournals.org/cancerres/article/84/6_Supplement/4933/736512
  - Upcoming Janelia blog on formats
Community
- June: meeting registrations picking up
- Monday: OME team (Dundee) day off

(5 min. max; tech. Discussion should be highlighted to relevant people and rescheduled)

Feedback on process welcome
Java programming language - LTS releases
Core OME repos in Java. Require Java 8+, Some Java 11
Users need JRE to run apps
Devs need JDK - OpenJDK released 2007 by Sun Microsystems
Now multiple JDK distributions
JDK builds only get support for 6 months
Other vendors ship their own OpenJKD releases with different EOL
- e.g. RedHat JDK 11 EOL Oct 2024
Bio-Formats 6.12.0 added support for Java 17
- recently added support for Java 21
OMERO server doesn’t yet support Java 17 - reflection issue
- Strongly encapsulated - can’t access protected/private Java API methods
- workaround: use –add-opens to JVM
- also need –add-exports to avoid IllegalAccessError
- This allows us to run OMERO.server on Java 17
- These options not supported for Java 8.
Next steps:
- review dependencies etc to remove need for reflection