tags: Tuesday
—
2025-04-15
Attending: Will, Josh, Frances, Melissa, Petr, Dom, Andreas, Kyle, Khaled, David, Erin, Jason, Kevin
Start: 2:00 pm UK
Project Status
(2-3 minutes each)
- IDR (Frances):
- next release 3 new studies and fixes to broken images. Big release, expected end of the month
- idr0164 fourth study from HDBR
- idr0160 single big plate
- idr0156 embryonic stem cells etc.
- Next IDR meeting Wednesday 23rd 10am
-
OMERO
- Bio-Formats
- builds status: waiting on quote for hardware for Glencoe.
- Data sync ongoing. 5 or 6 days to go. Weekly restart of Dundee servers keeps interrupting transfer.
- Petr: this can be configured with sudo; it’s a cron job
- NGFF
- Working on an abstract for CoRDI: https://www.nfdi.de/cordi-2025/call/ (deadline: Thursday)
- ngff-zarr now supports sharding: https://forum.image.sc/t/ngff-weekly-dev-update-thread/110810/11
- More updates welcome, e.g. Zarr-pixel-buffer?
- Hugging Face and storage: https://huggingface.co/docs/hub/en/storage-limits e.g. 100 TB datasets (smaller datasets are free)
- We could possibly direct users to store OME-Zarrs there?
- Also https://github.com/mlcommons/croissant/pull/848 etc. Markup language for deep learning.
- GerBI
- Lots of focus on CoRDI
- Also looking at various new use cases (cellpainting, light sheet)
- Whole-mouse cleared imaging datasets - interesting challenge for conversion/storage in OME-Zarr
-
Glencoe
- Community
AOB
- Dundee systems
- Passwords (Josh)
- did not receive prompt to change
- Melissa and Jason: also did not receive prompt
- open tickets? Unclear.
- Petr: was prompted by eduroam to change password. Then updated to use new password for MS outlook and elsewhere
Main Topic
(20-25 minutes plus 15 minutes questions max)
