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

(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
- 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 reads zeiss or scanr
- 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

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

(20-25 minutes plus 15 minutes questions max)