Notes 30th Jan, and 6th Feb

2024/2024-01-30.md

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+---
+tags: Tuesday
+---
+
+# 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
+
+## Accepting minutes from [last meeting](https://hackmd.io/team/ome?nav=overview)
+
+## Project Status
+
+(2-3 minutes each)
+
+- IDR
+    - Will: adapting [check_pixels.py](https://github.com/IDR/idr-utils/pull/55#issuecomment-1915051356) 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
+    - todo: web and web apps 
+  - 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
+    - Petr: OMERO.figure workshop Karolinska, 14th February (remote)
+    - Indonesia trip planning
+    - [Wellcome BioImaging Technology Development Awards](https://wellcome.org/grant-funding/schemes/bioimaging-technology-development-awards)
+
+## 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?
+

2024/2024-02-06.md

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+---
+tags: Tuesday
+---
+
+# 2024-02-06
+
+Attending: Will, Dom, Petr, Frances, Muhanad, Andreas, JM, June, David, Josh, Khaled, Seb, Kyle, Kevin, Jason, Melissa, Chris, David S, Maadhaav
+
+Start: 2:00 pm UK
+
+## Accepting minutes from [last meeting](https://hackmd.io/team/ome?nav=overview)
+
+## Project Status
+
+(2-3 minutes each)
+
+- IDR (Frances):
+    - Looking at 2 fixes for NGFF perf
+        - configuration changes:
+        - large memory usage when loading NGFF data
+        - e.g. 20 Threads of 1GB memory each
+        - Ice threads and DB connections. e.g:
+        - config set -- omero.db.poolsize 40
+        - config set -- Ice.ThreadPool.Server.SizeMax 25
+        - config set -- Ice.ThreadPool.Client.SizeMax 25
+        - When Django gives up (timeout) server doesn't give up, then Django tries again!
+    - Also looking at microservices deployment
+    - BioFormats - David looking at sizes of memo files but minimal space for improvements. E.g. some memos 100MB. 95% of what's stored is ome.xml
+    - Jason: target publication dates? Frances: some pressing dates coming up. Feb release would be nice.
+    - Won't add any more studies to the 2 new ones in this release.
+
+- OMERO:
+    - waiting on omero-web python 3.12 changes before full testing with omero-py
+    - RHEL9 - preparing switch of ci infrastructure
+
+- Bio-Formats (David):
+    - 7.2.0 release should go ahead this week on Thursday
+
+- NGFF (Josh):
+  - Zarr v3 status: zarr-python v3 branch is active. Major review coming up. Any users should have a look. Try to get blog post on changes for users.
+  - Movement on other ZEPs. Zep4 on conventions.
+  - Unidata update (netCDF etc) devs left.
+  - Will: started looking at v0.5 support for ome-ngff-validator...
+
+- GerBI
+  - Conferences, etc.
+
+- Glencoe (Chris):
+  - python 3.12 (see above)
+  - Erin presenting tables etc at SLAS in Boston. Will add poster to website
+
+- Community (Petr):
+    - Karolinska workshop 14th Feb
+    - Wellcome BioImaging 
+
+## AOB
+
+(5 min. max; tech. Discussion should be highlighted to relevant people and rescheduled)
+
+## Main Topic
+
+(20-25 minutes plus 15 minutes questions max)