2023-08-22
Attending: Will, Josh, JM, Dom, Frances, Khaled, Jason, Melissa, Andreas, Kevin, Kyle, Emil, Maadhav
Start: 2:00 pm UK
Project Status
(2-3 minutes each)
- IDR (Frances):
- 2 new studies 139, 149 released last week
- working towards software upgrade for NGFF
- Conversions nearly done
- Some historical fixes needed: idr0004 and idr0010
- Will: backlog on the BIA side. mostly incomplete studies (only 2-3 studies complete)
- https://uk1s3.embassy.ebi.ac.uk/bia-integrator-data/pages/test_zarr_pipeline.html
- OMERO
- omero-insight 5.8.2 release last week - bump Bio-Formats
- ongoing work on certificates (GS - Seb)
- doc upgrade and full stack upgrade
- CENTOS7 connection issues (e.g. from Ubuntu 22.04) doesn’t need full stack upgrade - server side only
- TLS update - need server and client updates
- Bio-Formats (Melissa)
- NGFF
- Java fun: bftools and update sites (Josh)
- Workshop prep - OME-Zarr support not easy in standalone Bio-Formats.
- Also https://forum.image.sc/t/getting-started-with-ome-zarr-in-java/85333/3 blosc, QPath etc.
- Documentation could be improved
- blosc not available on maven, needs env variable
- Needs to be usable by regular users, not just devs
- Josh: created tickets
- Do we ship s3 support? (currently stripped out)
- old libs and didn’t work with OMERO
- Seb: auth etc on s3 is hard - restrict scope
- Will: tables spec - any updates?
- Warwick:
- Rajpoot lab repo: https://github.com/TissueImageAnalytics
- API for H&E models, including HoverNet segmentation: https://github.com/TissueImageAnalytics/tiatoolbox
- WSI file converter, including support for writing OME-Zarr and DICOM WSI, allegedly 10-100x faster than bioformats2raw: https://github.com/John-P/wsic
- GerBI
- RDM4mic https://gerbi-gmb.de/activities/rdm4mic/ starting again
- NFDI - EOSC discussions
- Glencoe
- Kevin: will start to look at Shape stats…
- Community
AOB
(5 min. max; tech. Discussion should be highlighted to relevant people and rescheduled)
Main Topic
(20-25 minutes plus 15 minutes questions max)
