2024-07-30
Attending: Petr, Josh, Dom, Frances, Andreas, Melissa, Jason, David Gault, Khaled, Kyle, Erin, Chris, Kevin
Start: 2:00 pm UK
Project Status
(2-3 minutes each)
- IDR (Frances)
- Identified 3 candidate studies for starting the challenge:
- idr0090: compound screen with 5 channels, already in Zarr v2. Looking at channel metadata
- idr0157: phenotypic plant, non-screen; not yet converted to Zarr v2. 14 organisms to explore.
- idr0044: McDole lightsheet data; partially converted to Zarr v2. Looking at chunking and sharding.
- Dom looking at this on a pilot
- Josh: pilot is slow. Dom to try a restart.
- OMERO (Andreas)
- OMERO.web release on Monday
- Tag pushed to Docker repo
- Announcement on website
- Bio-Formats
- David: following on from the OMERO release
- otherwise, back to PR review
- ZarrReader: integrating zarr-java beside jzarr for testing the API
- Chris: watch out with 7.3.1 due to the metadata changes
- behavior of Bio-Formats when things are missing is quite different
- good thing since things don’t blow up
- files that did fail, no longer do
- Josh: re-release as 7.4? something to think about.
- David: unclear on where
- Chris: specifically, all changes of
new Double(). new behavior
- but we don’t have broken stuff in the repo that should stay broken
- Melissa: will find another time to follow up on that
- NGFF (Josh)
- Challenge:
- ro-crate
- Few new PRs opened. Thoughts welcome.
- rust > ts
- various performance issues (memory & partial reads)
- script to generate?
- codecs (issues)
- “ergonomics” of the configuration (as well as the specification) leaves much to be desired
- Transforms
- https://github.com/InsightSoftwareConsortium/GetYourBrainTogether
- Hopefully PRs etc. filtering into the public soon.
- Glencoe (Chris)
- Various releases going in
- Community
- JRS: paper hopefully done soon
- Using OMERO for training / clinical residents (continuing education)
- e.g., archipelago makes it hard to travel
AOB
(5 min. max; tech. Discussion should be highlighted to relevant people and rescheduled)
Main Topic
(20-25 minutes plus 15 minutes questions max)
