---
tags: Tuesday
---

# 2023-03-07

Attending: Will, Dom, JM, Petr, Josh, Frances, Tom B, David, Khaled, Melissa, Seb, Richard, Kevin, Kyle, David Stirling, Muhanad

Start: 2:00 pm UK

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

## Project Status

(2-3 minutes each)

- IDR (Frances):
- SSBD visit last week.
- lots of discussion comparing SSBD and IDR, potential bridges, common terms etc.
- IDR search for use in SSBD etc.
- Conversion of datasets to NGFF ongoing (for server upgrade)

- OMERO (JM)
- releasing omero-* Java components. Adjustments made to the release process.
- starting with omero-model
- omero-server discussion wrt [indexing PR](https://github.com/ome/omero-server/pull/156)
- Kevin: please comment on rendering PR if any more TODOs
- Josh: https://github.com/Qureator/omero-acquisition-transfer
- need to make this extensible/reusable
- Keep an eye out for other community forks
- https://github.com/ome/omero-cli-transfer/pull/43 (accident)

- Bio-Formats (David)
- focus back on ZarrReader, dealing with issues from conversions above
- chunk API for openbytes - PR open against Bio-Formats
- https://github.com/ome/bioformats/pull/3794

- NGFF
- 0.4/Paper
- not heard from submission - waiting on reviewer:
- Add authors: RIKEN (data), DKFZ/Helmholtz (tools), SciLifeLab (generation)
- scilifelab generating NGFF data from microscope (https://github.com/kasasxav/ImSwitch)
- 0.5/Tables:
- BDZ - tracking data in AnnData tables, view in napari Validator, etc
- Tables PR - discussion upcoming to check on progress
- 0.6+/Metadata: Chat next Wed. Requirements, etc.
- other binary files?

- GerBI
- Tom: TIM meeting in 2 weeks
- OMERO install on Hive looking good, with in-place import, 5TB of space, users created for all participants.
- Any config improvements for performance etc?
- Zarr in-place import not worked, but not needed for workshop
- Most users expected to use Insight
- I3D: first meeting
- ongoing training material creation. How to collaborate?
- cf. RDMKit and progress for submission
- discuss after TiM?
- Josh: NFDI launch. NGFF position.
- started. hiring people. Ad for position around ngff to go out later this month. Easier if based in Germany but not a must
- First meeting April

- Glencoe
- Erin: Chris at [meeting](https://www.eventbrite.co.uk/e/data-to-early-diagnosis-precision-medicine-centres-of-excellence-showcase-tickets-418790562847)
- Running OMERO.plus release. Lot of testing. including Bio-Formats and OMERO updates.
- Compatibility testing with plugins and OMERO.web 5.18 went well. Happy to share notes.
- New version of bioformats2raw and raw2ometiff (~2 weeks ago)
- https://github.com/glencoesoftware/bioformats2raw/releases/tag/v0.6.1
- https://github.com/glencoesoftware/raw2ometiff/releases/tag/v0.4.1
- Attending ABRF in Boston (Erin and Stick) and JupyterCon in Paris (Emil and David)
- OMERO search indexing needs a resolution. https://github.com/ome/omero-server/pull/156

- Community
- Training at TiM
- Talks from J-m
- EuBI workshop at the end of the month
- Richard: to be approaching regarding OMERO/IDR training (in-person slightly preferable to remote) later in the year. Petr: first come first serve :smile:

## AOB

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

## Main Topic

(20-25 minutes plus 15 minutes questions max)