2022-05-31
Attending: Petr, Josh, Dom, Seb, Khaled, Frances, Jean-Marie, June, Andreas, Will, Davids Gault & Stirling, Jason, Kyle, Emil, Mina, Muhanad, Kevin
Start: 2:00 pm UK
Project Status
(2-3 minutes each)
- IDR
- Will: new search on IDR front page: https://github.com/IDR/idr-gallery/pull/8 (deployed on idr-testing)
- weblient search: https://github.com/ome/omero-web/pull/368
- https://github.com/ome/omero_search_engine_client/pull/18
- planning on exposing the search API and start consuming it internally as a first step
- current status (linked above) allows searching without knowing the key you’re looking for a priori
- feedback (& testing!) welcome
- also a version running on merge-ci which re-uses search_engine_client (since the lucene backend of IDR doesn’t work)
- good deal of pieces that need extracting / refactoring
- gone next 3 days but have temporarily made webclient search not depend on search_engine_client django app, just copied into the webclient PR for now
- tl;dr – start here –> https://idr-testing.openmicroscopy.org
- Bio-Formats
- 6.10.0 release out now - Slidebook7 reader. Tweets etc coming…
- Seb: follow with server release
- OMERO
- JM: Doc migrated to readthedocs. Work on redirecting docs.o.org to readthedocs as part of the next openmicroscopy release (floating point)
- Seb: floating point: testing looks good. Configuration - defaults not changed.
- Documentation to be updated
- JM: ZarrReader bumped. Further testing needed? Discuss at standup tomorrow
- work on metadata tables (MZ). Ramping up on testing, esp. sparse data in tables.
- NGFF
- Metadata work roadmap ok?
- retroactive for v0.2 - v0.4
- used by raw2ometiff and ZarrReader
- Will: tried to revive https://github.com/hms-dbmi/vizarr/pull/125
- FYI: https://idr.github.io/ome-ngff-samples/
- Use this template for other public samples
- FYI: https://ome.github.io/ome-ngff-validator/
- E.g. plate: https://ome.github.io/ome-ngff-validator/?source=https://uk1s3.embassy.ebi.ac.uk/idr/zarr/v0.1/plates/5966.zarr
- FYI: ZIC complete (barring JZarr)
- FYI: EOSS5 application going in Thursday
- S3 libraries (comments/thoughts welcome) - what repo where?
- Chris: fork s3 repo to ome?
- Chris: create a public HackMD to list repos/options
- Kevin: do we want to go with amazon s3 - performance?
- Josh: JZarr only supports s3. Other options NetCDF
- Glencoe
- 2nd phase of floating-point pyramids support…
- when / where to calculate min/max etc.
- Seb: roadmap? public docs?
- Chris: NGFF to store min/max? E.g. useful for a plate
- Seb: upgrade-check. Gives false positives/negatives (except for OMERO.server)
- Community
- FYI: ELMI next week (Jason, Josh, Petr) to Turku, Finland
- OME Meeting, Virtual, targetting early November.
- ideas? less focus on public data
AOB
(5 min. max; tech. Discussion should be highlighted to relevant people and rescheduled)
- OME Team on UoD RestDay/Jubilee Day Friday June 3
-
Main Topic
(20-25 minutes plus 15 minutes questions max)
