2021-07-13
Attending: Josh, Seb, Petr, Dom, Will, June, Khaled, Frances, Melissa, Jean-Marie, Wilma, Andreas, Muhanad, Chris, David
Start: 2:00 pm UK
Project Status
(2-3 minutes each)
- IDR
- prod99: 3 studies. Not ready yet. Planning for first week of August
- EMBL-EBI workshop this week. IDR workshop on Thursday. Two lectures (Jason, Frances), one practical (J-M, Petr, Frances)
- Tweets. Content to be recorded. Don’t know if it will be public
- resource migration (Seb): IDR resources to be migrated by end of September.
- Copy of IDR to be deployed by end of this week (or maybe month) and to be validated by IDR team.
- Releases can be migrated when ready
- NGFF
- v0.3 progress, PRs, etc. EMBL/MoBIE motivation
- Sample EMBL dataset available
- omero-cli-zarr PR - can be used for v0.3 data from IDR
- bf2raw not needed urgently
- BIDS for microscopy (cf. DICOM vs OME_NGFF?)
- Releases
- OMERO.insight 5.6.1 out - can connect to IDR
- omero-py 5.9.3 out - table race condition fix
- contributions from external need CLA to be signed
- easy to forget. Needs automation. e.g. github action
- Organisation-wide GHA would be handy
- preparing iviewer release ahead of next IDR prod
- Glencoe
- JPEG-LS compression now in DICOM spec. Testing compression in Python.
- Libs expect interleaved rgb. Requires re-slicing arrays. Issues with compression of 3D data (if z chunk size > 1)
- Codec will have associated caveats
- Tricky to configure compression params with JPEG2000 and JPEG-LS
- Upcoming DICOM work. Spec is complex
- Kevin - OMERO.tables read-only PR - next week
- Josh: see https://asv.readthedocs.io/en/stable/writing_benchmarks.html re: compression benchmarking
- Community
- Workshops: East-Bio 18th Nov 2021 (on-line) & TIM2022 - March, Germany
AOB
(5 min. max; tech. Discussion should be highlighted to relevant people and rescheduled)
Main Topic
(20-25 minutes plus 15 minutes questions max)
