2024-01-30
Attending: Will, David, JM, Dom, Josh, Chris, Frances, Khaled, Kevin, Muhanad, Melissa, Jason, June, Petr, Tom, Maadhav, Seb, David S, Kyle, Erin,
Start: 2:00 pm UK
Project Status
(2-3 minutes each)
- IDR
- Will: adapting check_pixels.py script, running in parallel to try and reproduce issues we’ve seen from web. getPlane() doesn’t cause issues but renderImage() does. Need to look into stack traces.
- Also been looking at using vizarr to view NGFF data from s3 directly.
- Chris: options for goofys, caching etc? Seb: not looked at it much.
- Josh: jstack doesn’t show long-running threads. Other threads deadlocked at login.
- OMERO
- Petr: repeating the error Re: Rendering on OMERO https://github.com/ome/omero-server/issues/174 causing errors with OMERO.figure and
sleepOpenBytes
- JM: all used ansible roles now upgraded (RHEL 9) and released
- figure release last week
- Python 2/3 cleanup (thanks Glencoe) first step towards Python 3.12
- test-infra adjustments
- working on CI migration to rhel 9
- recent Jenkins secvuln doesn’t affect us
- Bio-Formats
- Melissa: reviewing 7.2.0 release…
- NGFF
- Josh: SpatialData grant report. Table spec divergence.
- GeoZarr: multiscale ZEP forthcoming
- GerBI
- Tom: Ongoing: annotation scripts documentation
- ELMI: plan workshop on REMBI and OMERO
- Glencoe
- Jenkins upgrades
- Python cleanup (see above)
- Society for Lab Automation systems meeting - present OMERO.tables work
- 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)
- Erin: Tissue clearing workshop last week - 100 attendees.
- Presented our Webknosses work
- Users typically use desktop apps - remote Desktop etc
- Advantages of web browser access
- Most viewers aren’t 3D
- Users are familiar with Webknosses
- Webknosses: orthogonal views and volume view
- OMERO.script tells Webknosses where the s3 NGFF data is and gets a URL to open Webknosses.
- Webknosses server provides auth etc to access s3 but web viewer does consume zarr data.
- 3D chunk data 32 x 32 x 32 doesn’t open in PathViewer
- OMERO.script is very fast & light - could be done with Open-with plugin instead of a script?
