---
tags: Tuesday
---

# 2023-01-31

Attending: Frances, Will, Petr, Muhanad, JM, David, Chris, Josh, Tom, Khaled, Jason, Andreas, Kyle, Kevin, Melissa, Erin, Seb, Wilma, David Stirling

Start: 2:00 pm UK

## Accepting minutes from [last meeting](https://github.com/ome/meeting-minutes)

## Project Status

(2-3 minutes each)

- IDR
- preparing next release:
- idr0146
- HPA - last few antibodies from previous release
- Search updates: backend and UI changes
- Bug fix and testing ongoing
- Plan to release on Thursday if all well, otherwise next week
- New search video
- SSBD visit prep
- New notebook, to harvest genes and use gene profiler to give enriched GO terms
- Jason: GO term enrichment analysis: standard approach. E.g. https://www.nature.com/articles/s41598-018-28948-z

- OMERO
- OMERO.insight release last week with new gateway release
- weekly OMERO.web meetings: Fridays 1:00 - 1:30 UK
- Andreas to handle next release
- may wait for Kevins channel rendering bugfix

- Bio-Formats (David)
- 6.12.0 release upcoming, end of next week
- Release process changing - may do a milestone release ahead of 6.12.0 to test.

- NGFF (Josh)
- Calls with NASA (POWER earth data on energy use, ZarrCon, ...)
- moving to use more Open Source
- Logos from Zarr users to add to zarr site
- Z3: use double underscores for escaping...
- NGFF v0.5 - will re-focus soon
- [SpatialData](https://spatialdata.scverse.org/)
- Catalogs of existing NGFF data.
- idr samples page re-use: needs refactor to not be IDR-specific
- NGFF Paper: Jason: OK to edit doc? Yes
- omero-cli-zarr: Big Images support [PR #134](https://github.com/ome/omero-cli-zarr/pull/134) (Will)
- still falling over (chunks all in one directory)
- caching helps.
- Chris/Seb: good to fix the underlying BDV reader issue https://github.com/glencoesoftware/bioformats2raw/issues/187
- JM: discuss zarr resources at Fridays: 1:30

- GerBI
- Tom: Not currently working on Hive install (server in use till next week)
- Josh: 22nd - 24th Feb: I3D meeting. Roadmap, requirements from OME team?

- Glencoe (Chris)
- See omero.web above
- OMERO.server threading issues: PR open, doc updates
- Background threads review & document
- Data compression with bioformats2raw: initial issues due to TIFF compression limitations. New features available since initial support
- JM: doc changes can be released anytime
- Docs generated from Blitz configs
- Kevin: javadocs are extensive, but not config properties

- Community
- UK Data Research Infrastructure
- SSBD Visit Feb 27 - Mar 3
- Josh: arriving on 28th

## AOB

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

## Main Topic

(20-25 minutes plus 15 minutes questions max)
- OMERO.figure & NGFF (Will) [slides](https://docs.google.com/presentation/d/1AAf3M5QcbjkZsp1QZZW3oW7EtSbwJGQ7ZxtnArnhSO0/edit#slide=id.p)
- JRS: 1. Let's consider decisions on updates not on number of changes of code but longer term maintenance. Effectively maintaining our own custom viewer in .figure seems not a great long-term plan.
- 2. Would the use of coordinateTransforms cause conflicts, e.g. with CLEM data? Maybe a naïve question.
- 3. The full detach from OMERO server maybe worth considering, but would a user ever want to use OMERO as the metadata source for a .figure workflow? I think we discussed this in the context of direct support for NGFF data in .figure. This is different than discussed-- is OK, just clarifying and trying to decide what we want to do first.
- 4. Scale bars.... are really important for a figure.