From abf39e300aa7291b5b3ca8d0a588f39afdb6dd65 Mon Sep 17 00:00:00 2001 From: Jean-Marie Burel Date: Tue, 9 Jan 2024 15:44:26 +0000 Subject: [PATCH] add 2023-01-09 --- 2023/2023-01-09.md | 71 ++++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 71 insertions(+) create mode 100644 2023/2023-01-09.md diff --git a/2023/2023-01-09.md b/2023/2023-01-09.md new file mode 100644 index 0000000..024aa64 --- /dev/null +++ b/2023/2023-01-09.md @@ -0,0 +1,71 @@ +--- +tags: Tuesday +--- + +# 2023-01-09 + +Attending: J-M, Petr, Seb, Chris, Jason, Andreas, Kyle, Kevin, Melissa, David, Khaled, June, Tom, Erin, Dom + +Start: 2:00 pm UK + +## Accepting minutes from [last meeting](https://hackmd.io/team/ome?nav=overview) + +## 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](https://github.com/IDR/idr-metadata/issues/675#issuecomment-1878828866) so all NGFF data should now be valid. + - Will: I have [run check_pixels.py](https://github.com/IDR/idr-utils/pull/55#issuecomment-1879859634) 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](https://github.com/IDR/idr-metadata/issues/675#issuecomment-1881406444) 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](https://github.com/ome/bioformats/pull/3537). Will: converted one Plate but [has issues with Field count per Well](https://github.com/IDR/idr-metadata/issues/683#issuecomment-1882669352). 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](https://github.com/ome/ansible-role-postgresql-client/pull/13) + - rename repository or + - re-activate own GHA with workaround + + - Upgrading [omero-test-infra](https://github.com/ome/omero-test-infra/pull/66) 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 + - cf. ZarrReader timeline + +- 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. + - looking at options + +## AOB + +(5 min. max; tech. Discussion should be highlighted to relevant people and rescheduled) + +## Main Topic + +(20-25 minutes plus 15 minutes questions max)