2024-01-16
Attending: Josh, Will, Dom, David Gault, Chris, Frances, Andreas, Khaled, David Stirling, June, Melissa, Jena Wendt (Münster), Tom, Seb, Kyle, Kevin, Maadhav, Petr, Jean-Marie, Jason
Start: 2:00 pm UK
Project Status
(2-3 minutes each)
- IDR:
- Next release: idr0138 (NGFF) and idr0154
- idr0138 imported over holidays, ROIs now created - rendering settings needed
- idr0154 import will be quick
- NGFF release: “stress testing” this morning. Some images felt like they are loading a bit slower than on IDR, but difficult to quantify. Performance seemed to improve with more browsing (caching??).
- idr0011 Plate failing, due to renaming/moving on BIA s3.
- Various other plates resubmitted to BIA are now available (we have hosted these on our custom s3 buckets in the meantime for idr-next). Now looking at updating these to use BIA data…
- Running mkngff again to update NGFF Fileset will add
_mkngff to templatePrefix, e.g. demo_2/2016-07/28/21-44-02.006_mkngff_mkngff.
- Some images didn’t load, but appeared OK when re-loaded.
- OMERO
- upcoming release omero-py: 3.8 Python is the minimum version.
- Fixes test-infra (Pillow version issue)
- Bio-Formats (David)
- PR reviews -
- Aim for 1st week of Feb for next 7.2.0 release (or 2 weeks later if date is missed)
- Nico Quick czi reader progressing
- ZarrReader moving towards NGFF v0.5 spec support
- will keep changes up to date with spec changes
- NGFF
- No word on transforms. Time limit/cutoff?
- implementations progressing, python, JavaScript, etc
- We should look at ome-ngff-validator (schemas now available)
- RFC proposal opened. Next step: identifer reviewers.
- Additionally ZEP0 is also undergoing review. Hopefully get this signed off by spring.
- Starting Office hours to restart the website meetings
- Will: currently open issues? Josh: ping me URLs or we can meet at a different time?
- Upcoming questions around implementations (e.g., ilastik)
- Glencoe Chris
- Django 5.0 released. More async features, some things deprecated. Requires python 3.10.
- omero-web cleanup needed, old apis, interactions etc.
- Seb: python 2 compatibility code cleanup, ‘future’ etc.
- character encoding in NGFF, reserved chars, unicode etc. How to handle during conversion?
- Community
- Josh: “OME data compatibility”, next Wednesday (the 24th), 10AM EST/3PM UK/4PM EU
- Ping Josh if you need invite/more info?
- GerBI (Tom)
- Key-Value pair scripts… See https://github.com/German-BioImaging/omero-scripts/tree/xtnd_support_kvpairs
- Editing exisitng KV scripts
- Users start KV workflow in webclient, but doesn’t work for SPW Wells.
- Single script to handle CSV -> P/D/I S/P/A/W and vice-versa (export KVP to csv)
- Also need Delete KVP script
- Namespace update “editable” vv protected from client editing
- Also option to add Tags instead of KVP
- Jens: Q: using Tags - should we try to use existing Tags? - input option for users to choose
AOB
(5 min. max; tech. Discussion should be highlighted to relevant people and rescheduled)
Main Topic
(20-25 minutes plus 15 minutes questions max)
