tags: Tuesday
—
2026-09-08
Attending: Will, Petr, Dom, Khaled, Andreas, Melissa, Damien, Seb, Frances, Joel, Chris, Kyle, Tiago, Kevin,
Start: 2:00 pm UK
Project Status
(2-3 minutes each)
- IDR (Frances)
- Zarr conversion of IDR data to v0.5 OME-Zarr and validating with https://chanzuckerberg.github.io/dynamic-cell-atlas-specs/v0.2/validator.html
- Working on new submission workflows: import from s3
- OMERO
- OMERO.web security release tomorrow (Andreas)
- https://forum.image.sc/t/action-required-reminder-security-release-of-omero-web-coming-this-wednesday-september-9th/122412
- OME-Zarr support (Seb)
- fixes against omero-zarr-pixel-buffer to restore backwards compatibility issues
- expecting omero-zarr-pixel-buffer 0.7.1 release later this week
- omero-label: open source library/CLI plugin for managing OME-Zarr labels
- Will be useful for https://github.com/ome/omero-iviewer/pull/532
- OMERO.figure 8.0.1 released. Last release before we split the “figure” app into a separate repo. See https://github.com/ome/omero-figure/pull/706
- No breaking changes for omero-figure users
- Joel: OME.zarr figure app could be good subject for open bio-imaging talks
- Petr: merge-ci has moved to a new VM-Ware.
- Trigger time has been set to 1pm (was previously 1am)
- Gives more time between Trigger and 9:30am standup.
- Melissa: not running Bio-Formats merge jobs at Dundee now, so no requirements on timing.
- Petr: we could go for e.g. 11pm.
- Currently about 6 hours total time. 3.5 hours for OMERO-test-integration. Mostly timing is OK, but occasional slower on “rainy days”
- Seb: do we need to migrate to more stable hardware anytime soon?
- Petr: reasonably confident in short/medium term. Only 4 cores but seems to be running fine just now.
- Bio-Formats (Melissa)
- 9.0.0rc1 will be tagged tomorrow
- NGFF
- OME-Zarr Hackathon in Dresden this week (Johannes attending, https://plan.events.mpg.de/event/775/)
- RFC-7 Channel Metadata scoping going on (https://github.com/ome/ngff/issues/580)
- Johannes: planning to get v0.6 release tagged soon (this week)
-
GerBI (Damien)
- New member of RSE (Bharti Arora) starting on Oct 1
- Damien: ongoing work on scoping of RFC-7
- Damien: Working on Quarep model into LinkML
- Glencoe (Chris)
- Infrastructure management, maintenance & migration ongoing
- TBD: proxy of maven central a good idea?
- Similar issues as the ones faced by SciJava Maven repository - https://forum.image.sc/t/maven-scijava-org-unavailable/120874
- BioVisionCenter
- November OME-Zarr hackathon: https://biovisioncenter.notion.site/2026-ome-zarr-hackathon
- Application window closing September 15th
- Working to expand size from 50 to 60 participants given large demand
- Provisionally upcoming Open Bioimaging Practices meetings for fall 2026:
- Late September: OME-Zarr Viewers, part 2
- Late October: Multiplexed image analysis in OME-Zarr
- Late November: Spatial OMICs & OME-Zarr
-
Community
- OMERO Latam Help desk last friday with little attendance; Petr gave helpful advice. Next ones, Tiago to attend solely and provide the initial support. Google Calendar Event
- October outreach Prague
- Petr & Tom to Panama: Both to give talk & workshop
- Brno outreach in December
AOB
(5 min. max; tech. Discussion should be highlighted to relevant people and rescheduled)
Main Topic
(20-25 minutes plus 15 minutes questions max)
