---
# System prepended metadata

title: '2022-09-13'
tags: [Tuesday]

---

---
tags: Tuesday
---

# 2022-09-13

Attending: Will, Dom, David, Frances, Chris, Seb, Melissa, June, Khaled, Kevin, Kyle, Wilma, Josh, J-m, Erin, Gina, Petr

Start: 2:00 pm UK

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

## Project Status

(2-3 minutes each)

- IDR (Frances):
    - Datasets still testing
    - Search UI phase 1 mostly there - testing ongoing
    - Release aiming for end of September (dataset and search)
    - Storage: FIRE testing with HPA data ongoing

- OMERO:
    - omero-py release last week
    - wait for next release of BioFormats before updating in OMERO (J-M explained process to Petr)

- Bio-Formats:
    - release planned for week after next 6.11.0 (instead of patch release as previously planned)

- NGFF
  - Chunks in OMERO:
    - Bug: https://github.com/ome/ZarrReader/issues/40 from idr-0125
    - Possible fix: https://github.com/ome/ZarrReader/pull/41 - ignore chunks at import time
    - Workaround: manually "in-place" chunks after import?
  - Fiji/N5 hackathon in Praque
    - See https://imagesc.zulipchat.com/#narrow/stream/329366-.5B2022-09.5D-Fiji.2BNGFF-Prague-hackathon
    - Teams interested in a low-level Java jar from github.com/ome which provides generated model classes
  - :warning: bioformats2raw.layout work is currently blocked bioformats2raw 0.5.0
    - Gathering & reviewing all PRs this week. Feedback & help welcome.
  - Will: acquisitions handling https://github.com/ome/ome-zarr-py/issues/225
    - How do users want to see acquisitions? slider? stacked as multiple channels? (cf. CyCIF)
    - Chris: depends on the use case. e.g. PerkinElmer for multiple day spaces between acquisitions
    - Will: then almost like an extra dimension
    - Chris: don't currently allow declaring how you want them displayed. for the moment, make a choice when *writing* the data
    - Seb: from issue, no problem from spec & impl. layer. but more how do you consume them? napari issue? (all clients)
      - are they asking for more metadata about display? (part of the rendering work?)
    - Josh: do we encourage them to write their own plugin?
    - Chris: try to extend the plugin so someone *could* extend

- GerBI

- Glencoe (Chris):
  - BioFormats and bioformats2raw updates in progress (PRs open) to be in 0.5.0.
  - OMERO plus releases
  - bioformats2raw metadata: rendering settings etc.

- Community (Petr):
  - TIM 2023 discussion: they will set up an OMERO server (Tom B)
  - EastBio masterclass in November (week)
  - JM to London on Friday for BioImaging UK Meeting

## AOB

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

## Main Topic

(20-25 minutes plus 15 minutes questions max)
