Attending: Will, Dom, David, Frances, Chris, Seb, Melissa, June, Khaled, Kevin, Kyle, Wilma, Josh, J-m, Erin, Gina, Petr
Start: 2:00 pm UK
(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-py release last week
- wait for next release of BioFormats before updating in OMERO (J-M explained process to Petr)
- release planned for week after next 6.11.0 (instead of patch release as previously planned)
- 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
- 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
(5 min. max; tech. Discussion should be highlighted to relevant people and wrescheduled)
(20-25 minutes plus 15 minutes questions max)