2023-07-04
Attending: Josh (notes), Frances, June, Jason, Chris, Andreas, Sébastien, Tom, David Stirling, Muhanad
Start: 2:00 pm UK
Project Status
(2-3 minutes each)
- IDR (Frances)
- idr0119 is still importing (big screen). Should finish tomorrow for annotations. ETA: 17th of July
- NGFF work is ongoing. current timeline is to have all datasets by September and upgrade by October
- new submission is also asking for conversion to OME-Zarr
- IDR invited for full application to Global Biocore Data Resource
- JRS: consortium of funders that are trying to understand resources
- previously reviewed for them
- short application submitted
- reviews picked up on needing more
- most relevant: “why are you not a deposition resource? why are you an added value resource?”
- will need usage stats, etc.
- likely we take for granted what people know (e.g. SAB on the website)
- OMERO (Andreas)
- couple of PRs re: Django 4.2 approved
- Seb doing more testing
- release slotted for when everyone returns from vacation
- Seb: questions for Will etc. on return - how much of app compatibility do we want to roll together (figure, etc)
- Bio-Formats (David)
- 6.14 release likely to go out tomorrow
- Few more deprecation warnings added
- One DICOM PR has been omitted. Slotted for 7.0.0
- JRS: will look at the notes later today
- NGFF (Josh)
- ZarrReader news
- Adding to Bio-Formats (DEV) update site (link
- CA: dependencies between update sites?
- JAM: no, can’t auto-activate
- Seb: additionally order matters (like readers.txt)
- Learning symlinks, etc. for IDR+NGFF
- Tables & transforms: upcoming community meetings
- “OMEZarr” object: EMBL HD and others
- GerBI (Tom)
- progressing on OMERO webtagging repositories
- split into two parts.
- next step: link pypi repositories for the next (automatic) release
- Josh created https://pypi.org/user/gerbot/
- Seb: re: transferring of repos, ETA for (mock) release so we can test?
- working on in-place imports at HHU
- see image.sc thread re: splitting with raw2ometiff
- specifically geared towards image analysis needs
- Glencoe (Chris)
- cleaning things up during the summer gap
- for when people are back, do we bump to Django 4.2 as a req (i.e. when do we drop 3.2?)
- infrastructure questions:
- gunicorn has been dropped for about 3 years
- new CGI protocol. need to see how it behaves with ICE
- NGFF-Converter (David)
- coming out with support for latest bioformats2raw
- working on 2.0 to expand usage and the new API tools
- no clear ETA (~few months)
- 1.1.5 will hopefully be the last in that series
- Community
- Ongoing workshop in Japan
- JRS: community discussions
- everything online, no objections to date
- still interest in a meeting in Dundee
AOB
(5 min. max; tech. Discussion should be highlighted to relevant people and rescheduled)
Main Topic
(20-25 minutes plus 15 minutes questions max)
