2024-01-09
Attending: J-M, Petr, Seb, Chris, Jason, Andreas, Kyle, Kevin, Melissa, David, Khaled, June, Tom, Erin, Dom
Start: 2:00 pm UK
Project Status
(2-3 minutes each)
- IDR
- NGFF upgrade:
- Will: pending re-processing of a handful of NGFF Plates by BioStudies, I have hosted these on our own uk1s3 buckets and used these from idr-next so all NGFF data should now be valid.
- Will: I have run check_pixels.py on 1 image per Plate or 2 images per Dataset across ALL data on idr-next. I see various Exceptions with
getPlane() but the only mismatching pixels detected were from idr0009. Seb: “The problem is that this data was originally loaded with a version of the ScanR reader that represents missing wells as black images while the default behavior in Bio-Formats is to represent these as sparse plates. When this was backported to OME Bio-Formats, an option was introduced to support both behaviors - see https://bio-formats.readthedocs.io/en/latest/formats/options.html
I think the action is to update all plates in this study to set scanr.skip_missing_wells to false , delete & regenerate the memo files and retest”. Will: tried this but no joy.
- Also Petr found that idr0001 images fail (except for the first Acquisition of each Plate), so we either need to convert to NGFF or reopen Flex: merge IDR changes. Will: converted one Plate but has issues with Field count per Well. Needs more testing etc. Conversion of 192 Plates might take 6 days with bioformats2raw (don’t know with omero-cli-zarr) and total 9TB. We probably don’t want to block release for this (TBD)?
- J-M: to be discussed tomorrow after standup and make decisions.
- Seb: storage in good place. Working on upgrading IDR to Rocky Linux 9. Plan for Q1
- Jason: Systems came back after power outage ahead of time. TOO: J-M add links to mirror in our doc for future reference.
- OMERO
- Issue with publication of ansible workflow to ansible galaxy: see discussion
- rename repository or
- re-activate own GHA with workaround
- Upgrading omero-test-infra so we can release applications like omero-figure
- Upgrade page for migrating systems
- OMERO.web looking at open PRs and cleaning up backlog.
- Bio-Formats
- Melissa: PRs review next week for release timeline. Backlog is “acceptable” state.
- David: Reviewing state to plan release timeline for ZarrReader to include 0.5 spec
- NGFF
- GerBI
- Tom: Working KVP scripts. Presentation next week of the current status. No progress on Web
- Glencoe
- Work on OMERO.tables
- Documentation
- API changes: dependencies issues using OMERO.py (client vs server ones).
- Review requirements in OMERO.web. Better minimum for dependencies
- Seb: CentOS 7/RHEL 7 upgrade
- Seb: Python 3.12 support coming, Python 3.8 EOL in 9 months
- Erin: Upcoming Harvard tissue workshop end of January: OME.zarr (public data) with Webnossos+OMERO plus.
- presentation after workshop
- Community
- Continuing efforts with UGM team
- no issue reported so far with the migration
- More tests to be done by Dewa.
- Grants submitted for working with HCS data (Wellcome), IDR at PSC (NIH), in progress for IDR maintenance (NIH).
- Contact from Erick Ratamero and Ken Ho– alternative hosts for OME meeting.
AOB
(5 min. max; tech. Discussion should be highlighted to relevant people and rescheduled)
Main Topic
(20-25 minutes plus 15 minutes questions max)
