tags: Tuesday —

2025-06-24

Attending: Will, Jean-Marie, Andreas, Frances, Khaled, Seb, Kyle, Kevin, Chris,

Conflicts: Josh

Start: 2:00 pm UK

Accepting minutes from last meeting

Project Status

(2-3 minutes each)

• IDR (Frances)
  • prod128 with zarr-pixel-buffer. Landing pages looking good for next release.
  • Waiting for submitters to fix a couple of broken images (incorrect images with missing Channels in one study. Other has one broken OME-Zarr - thumbnail wasn’t created). Will delay release a bit. Annotations are OK.
• OMERO (Seb)
  • Proposed release notes for OMERO.server 5.6.16 - https://github.com/ome/openmicroscopy/pull/6434. Includes Bio-Formats 8.2.0, OMERO.py 5.21.0 and OMERO.web 5.29.1
• Bio-Formats (Seb)
  • Maven Central Portal migration
    • https://central.sonatype.org/news/20250326_ossrh_sunset/
    • EOL of OSSRH service used for publishing low-level OME Java libaries under the org.openmicroscopy namespace
    • Migrating to the Central Portal. Successfully tested on ome-common 6.0.26
    • Propagating changes to other components and updating the contributing pages
    • JM: will need update of build process & docs publishing for OMERO components
  • New internal #formats Slack channel created yesterday
    • Allows discussion between Glencoe and OME teams
• NGFF
  • Will: about to release omero-cli-zarr 0.6.0. Supports latest version on numpy.
  • JM/Will: register.py script for “import” of OME-Zarr images / plates
    • Needs discussion on s3 authentication for omero-zarr-pixel-buffer. How to store this info in OMERO?
  • OME-NGFF community call this morning (and repeated at 4pm today)
    • Tong Li presented High throughput workflows - mostly using OME-TIFF: users & IT find it easier to work with small numbers of files. Also users can e.g. drag and drop onto Fiji.

• GerBI

• Glencoe
  • Glencoe team meeting in person July 7-9. Will miss Tuesday meeting
• Community
  • Petr and Jean-Marie at GBI course in Pune, India last week:
    • Successful course: Lots of interest from countries where resources are limited - following Indonesia usage.
    • OMERO installation workshop: some users have very limited IT experience.
    • OMERO.server installed at Pune.
  • OME community meeting on OME website. Promoting/showcasing OME usage by members of the community

AOB

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

Main Topic

(20-25 minutes plus 15 minutes questions max)