---
# System prepended metadata

title: '2023-10-24'
tags: [Tuesday]

---

---
tags: Tuesday
---

# 2023-10-24

Attending: Will, JM, Dom, Petr, Frances, Tom, Chris, Khaled, Seb, Melissa, David, Kyle, Maadhav, Andreas, David S, Muhanad,

Start: 2:00 pm UK

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

## Project Status

(2-3 minutes each)

- IDR:
    - ZarrReader. In order for a memo file to be generated from mkngff data (no OriginalFiles for zarr chunks are created in the mkngff Filesets) we need getUsedFiles() to return a list that doesn't include chunks (otherwise server throws SecurityViolation). However, regular import of NGFF data fails with this option. What options exist?
    - Testing [spreadsheet]( https://docs.google.com/spreadsheets/d/1KhIars5aqRu4Pos8uNfZgEO6akoNj8JBTQ62j9po2T4/edit#gid=0)
    - Chris: use env variables to interact with ZarrReader
        - default is to include chunks (matches existing API)
    - Seb: `*.bfoptions` file in the data, understood by ZarrReader, e.g. [FormatReader](https://github.com/ome/bioformats/blob/e484e1faefd6c7590fa5dbb56e56f3cc360d9139/components/formats-api/src/loci/formats/FormatReader.java#L252-L258) reads [zeiss](/uod/idr/repos/curated/zeiss-czi/options/) or [scanr](/uod/idr/repos/curated/scanr/options/)
    - These options shouldn't require a separate IDR-specific fork

- OMERO
  - OMERO server/web deployed on RHEL 9 using ansible
  - migration process tested
  - To discuss with IT GPFS upgrade
  - Andreas: OMERO.web PRs getting merged for upcoming release

- Bio-Formats
    - patch release last week
    - next week review PRs for next minor release

- NGFF

- GerBI - Tom
    - OMERO.figure workshop at I2K - 1 hour with training server
    - Working on OMERO.scripts - Key-Value pairs to csv etc.
    - JM: looking to deprecate Make-Movie script menencoder not supported on RHEL etc.

- Glencoe
    - Glencoe con next week.
    - SBI2 next week.
    - Writing up Ice/Python work
    - Python 3.11 has been out for a year - still don't support it. pytables etc dropping python 3.8 support.

- Community
    

## AOB

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

## Main Topic

(20-25 minutes plus 15 minutes questions max)
