---
tags: Tuesday
---

# 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

## 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)