---
tags: Tuesday
---

# 2023-11-14

Attending: Will, Dom, Petr, Josh, JM, David, Frances, Muhanad, Melissa, Seb, Khaled, Kyle, Andreas, June, David S, Chris, Erin,

Start: 2:00 pm UK

## Accepting minutes from [last meeting](https://hackmd.io/team/ome?nav=overview)

## Project Status

(2-3 minutes each)

- IDR
- Frances: public EBI folder now unblocked. Transfer in progress
- Will: Seb ran memo file generation on idr-testing last week. Found a bunch of failures, mostly due to a missed sql statements (now fixed) but also 8 NGFF plates that are missing files on EBI s3. Re-running the conversion for these now... Also memo file generation is re-running due to memo cache not working on readonly-X proxy servers.
- Decided to push NGFF release to early next year

- OMERO
- issue with omero-py building on Windows see [std: binary function](https://learn.microsoft.com/en-us/answers/questions/1348183/std-binary-function-is-missing-in-msvc-14-37-32822) - don't block release, create an issue to keep track
- ansible roles: a handful to be released.
- OMERO.web UI customization support: https://github.com/ome/omero-web/issues/510 feedback welcome!

- Bio-Formats
- ZarrReader - last few fixes
- Bio-Formats PR reviews, aim for 7.1.0 release mid December

- NGFF
- Hackathon ([stream](https://imagesc.zulipchat.com/#narrow/stream/408045-.5B2023-11.5D-Hackathon.3A-Next-gen-image-analysis-workflows) / [website](https://www.biovisioncenter.uzh.ch/en/events/hackathon_23.html))
- Summary forthcoming (image.sc) but tl;dr
- Presentations: nextflow, galaxy, spark, slurm, fractal, cellprofiler, as well as pydantic and spatialdata
- Breakout groups:
- Converters (mcd, MD Image Xpress, Cellvoyager, etc.) --> GitHub topics
- all in python.
- First nextflow workflows with OME-Zarr
- OME-Zarrs in PyTorch
- validators and hierarchical modelling (pydantic/linkml)
- Features ("NGFFF")
- OME-Zarrs in Galaxy
- NGFF reader/writer review
- Common place to work: https://github.com/bioimagetools
- review of various tools/python libs -gdoc
- NGFF spec discussions
- Proposed RFC like process. General agreement. Next steps.
- Extensions: Let us put other stuff into OME-Zarr
- Transforms: F-Order (computer vis libs) vv C-order (numpy)
- e.g. n5, itk and Matlab? are F-Order

- GerBI
- Training docs & a few repos (Tom?)
- Zenodo https://zenodo.org/records/8323588 and YouTube links
- Working on https://github.com/German-BioImaging/omero-scripts/tree/xtnd_support_kvpairs
- Hackathons (Josh)
- Cologne November and Bielefeld December
- Discussing importing & exporting from & to OMERO
- ARC, BIDS, RDF.
- Interest in more advanced annotation namespace usages

- Glencoe

- Community
- Good Feedback and engagement from Barcelona workshop https://docs.google.com/document/d/1j5YcLq86lEYHit-kC6jbC67A60kF-SwDVm8dVTR0L0Q/edit . Colour-blind support

## AOB

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

## Main Topic

(20-25 minutes plus 15 minutes questions max)