Add notes 2024-10-15 -> 2024-11-12

2024/2024-10-15.md

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+---
+title: '2024-10-15'
+tags: [Tuesday]
+
+---
+
+---
+tags: Tuesday
+---
+
+# 2024-10-15
+
+Attending: Will, Dom, JM, Petr, Frances, David, Jason, Khaled, Maadhav, Melissa, Chris, Andres, Kyle, 
+
+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): antibody supplementary cleanup (idr0073 and idr0155), applied on idr-next. Should improve antibody search results. Also re-annotate "Antibody 1": ... etc on idr0158.
+    - Will: NGFF challenge samples viewer. https://deploy-preview-53--ngff-challenge.netlify.app/ ongoing. Feedback at https://docs.google.com/document/d/107XnRIcHhhJW2lUeFqJF3_mEiOMEMvLgzsIJL73YP9o/edit 
+    - Search meeting last Thursday. Migrate away from mapr. First steps: Will to add redirect from mapr pages to search engine results pages.
+    - GerBI data stewards: expecting to hear about doodle poll for first meeting
+
+- OMERO
+    - JM: migration of CentOS6 machine on hold till IT staff back next week.
+    - nightshade storage issue identified and fixed
+    - Storage performance issues - cause identified (high demands from other users of shared resources)
+    - Petr: crunching numbers for quotas. Growth numbers higher than predicted.
+
+- Bio-Formats
+    - Holding off on final PR merges till next week (Seb back)
+        - Jason: TBD timeline - chat after...
+
+- NGFF (see above)
+
+- GerBI
+
+- Glencoe
+    - Nothing to update
+
+- Community
+    - Petr: started working on Japan workshop - November.
+
+## AOB
+
+Jason: processing grants etc.
+(5 min. max; tech. Discussion should be highlighted to relevant people and rescheduled)
+
+## Main Topic
+
+(20-25 minutes plus 15 minutes questions max)

2024/2024-10-22.md

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+---
+title: '2024-10-22'
+tags: [Tuesday]
+
+---
+
+---
+tags: Tuesday
+---
+
+# 2024-10-22
+
+Attending: Will, Dom, Petr, Frances, JM, Seb, Chris, Khaled, Maadhav, Tom, Melissa, Kevin, Erin, David, Kyle, Jason,
+
+Start: 2:00 pm UK
+
+## Accepting minutes from [last meeting](https://hackmd.io/team/ome?nav=overview)
+
+## Project Status
+
+(2-3 minutes each)
+
+- IDR
+    - Antibody cleanup in idr-next.
+    - NGFF viewer (see below)
+    - Dom/Will: redirect from mapr to gallery search https://github.com/IDR/idr-gallery/pull/45 deployed on idr-testing
+
+
+- OMERO
+  - JM: First part of ome-web-prod migration complete. Any issues, let us know?
+  - Petr: QA in progress: DB dump (2hrs), switched DNS, now restoring DB, then spin up QA backup. Expect to be working again later today
+
+- Bio-Formats
+    - Melissa: plan 8.0.0 release on Thursday if infrastructure is ready. Make the call tomorrow
+
+- NGFF
+    - Will: Testing NGFF challenge viewer: https://will-moore.github.io/ome2024-ngff-challenge
+    - Plan to merge this later today if no blockers found (existing https://ome.github.io/ome2024-ngff-challenge/)
+    - Add feedback at bottom of https://docs.google.com/document/d/107XnRIcHhhJW2lUeFqJF3_mEiOMEMvLgzsIJL73YP9o/edit
+
+- GerBI
+    - Tom: workshop last week. Core facility and IT from various locations in Germany. Good discussion about planning OMERO deployment. Plan to repeat in a year or two. Ansible playbook used to install OMERO: https://github.com/I3D-bio/fit-for-omero_ansible-playbook . Slides on zenodo to come.
+
+- Glencoe
+    - Chris: Node cleanup on npsc
+    - Crick bioimage symposium planning - sponsoring and presenting https://www.crick.ac.uk/whats-on/crick-bioimage-analysis-symposium-2024 
+
+- Community 
+    - Jason: traveling Asia: Singapore, Yogyakarta Indonesia, Japan
+    - Frances: presenting to Malaysia potential collaborators next Wednesday
+
+## AOB
+
+(5 min. max; tech. Discussion should be highlighted to relevant people and rescheduled)
+
+## Main Topic
+
+(20-25 minutes plus 15 minutes questions max)

2024/2024-10-29.md

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+---
+title: '2024-10-29'
+tags: [Tuesday]
+
+---
+
+---
+tags: Tuesday
+---
+
+# 2024-10-29
+
+Attending: Will, JM, Dom, Petr, Josh, Frances, Khaled, Kevin, Jason, Andreas, Kyle, Seb, Erin, Chris, 
+
+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: idr0161 testing for next release next month
+    - Will: NGFF samples viewer
+    - Will: replacing mapr with searchengine - testing deployment on idr-testing
+
+- OMERO
+  - Migration of ome-web-prod (QA and downloads, docs etc( done, ironing out a few issues due to port not opened from merge-ci
+      - old machine CentOS6 to be shut down at end of Nov
+  - Follow-up from B-F release last week: fixed conda repos to release BF related libraries
+  - Prep for workshops in Kobe next week on-going
+  - Andreas: 4 PRs ready to go for upcoming release. Group-User menu update is outstanding. Will: commented on PR.
+
+- Bio-Formats
+    - Seb: release went well. 1 hour or less.
+    - Ironed out post-release steps. Fiji
+    - Next: Bump BF in omero.server. Also include new LUTs in next server release?
+
+- NGFF
+    - Will: just started making [notes on RFC-5](https://docs.google.com/document/d/12twRs-ooWBthDHlVagpi8d5gYDKF5mDHAjwlOAj2zxA/edit).
+    - Josh: Good general reception of challenge *et al.* 
+    - RFC-3 demo (jupyter notebook) Juan. Lots of other notes to be written up.
+    - Zarrcade - similar idea https://github.com/JaneliaSciComp/zarrcade 
+    - Jason: good response to OME's work
+
+- GerBI
+    - Data stewards meeting with IDR scheduled 13th November
+    - NFDI asked to consult on law on metadata standards
+
+- Glencoe
+    - Pixelbuffer for Zarr - work to support downsampling pyramids in Z.
+
+- Community
+    - Czech republic workshop prep.
+    - Looking at using Tom's playbooks in Kobe workshop
+
+## AOB
+
+(5 min. max; tech. Discussion should be highlighted to relevant people and rescheduled)
+
+## Main Topic
+
+(20-25 minutes plus 15 minutes questions max)

2024/2024-11-05.md

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+---
+title: '2024-11-05'
+tags: [Tuesday]
+
+---
+
+---
+tags: Tuesday
+---
+
+# 2024-11-05
+
+Attending: Will, Dom, Frances, Khaled, Andreas, Kevin, Kyle, Seb, Chris, David S, Jason, 
+
+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: idr0161 multiplex study for next release (week or 2). Imported on idr-next today. Checks and rendering..
+    - mapr redirects to searchengine - tested on idr-testing last week. Needs update to current database. Seb spinning up new deployment from scratch
+
+- OMERO: Andreas: working on omero-web release. Plan for next week to coincide with other releases.
+
+- Bio-Formats: Melissa: discussed 8.0.1 patch release with Seb. Week of 18th. To be discussed with formats team when available.
+
+- NGFF
+    - Jason: NGFF challenge next steps TBD
+    - Will: looking at ome-zarr-py update to work with Zarr v3 
+
+- GerBI
+
+- Glencoe
+
+- Community
+    - Jason: GBI meeting last week; imaging facilities from around the world. Theme: Image Data. Most talks mentioned OME/OMERO/NGFF.
+        - Josh presented OME-Zarr. Federated image repo - positive reception. Discussions on what's next...
+    - Retweets or whatever: https://x.com/openmicroscopy/status/1853634849078460860
+    - Update from GBI Meeting
+
+## AOB
+
+(5 min. max; tech. Discussion should be highlighted to relevant people and rescheduled)
+
+## Main Topic
+
+(20-25 minutes plus 15 minutes questions max)

2024/2024-11-12.md

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+---
+title: '2024-11-12'
+tags: [Tuesday]
+
+---
+
+---
+tags: Tuesday
+---
+
+# 2024-11-12
+
+Attending: Will, Dom, JM, Maadhav, Khaled, Josh, Melissa, Kyle, Frances, Andreas, Chris, Seb, Petr, Kevin, David, Erin, Muhanad
+
+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:
+    - Preparing for NFDI data stewards meeting tomorrow morning 8am
+    - idr-testing is back up with latests DB. Testing search with updated Antibody KVPs.
+
+- OMERO
+    - Java Oracle email UoD: implication on software stack. Please check and remove.
+    - See also https://github.com/ome/omero-artifact-plugin/pull/25. Already jumped from Java 8 to Java 11. More will need a gradle upgrade.
+    - omero-web 5.28.0 release ready to go when suitable. JM: let's aim for early next week (Tues) - also release openmicroscopy following BF release this week (see below)
+
+- Bio-Formats
+    - Melissa: 8.0.1 - all PRs in Milestone have been merged. Ready to pick a date. Could be Thursday this week.
+        - JM: yes, Thursday
+    - Reviewing items for 8.1.0, including 1 external contribution
+
+- NGFF
+  - I2K/GBI/FoundingGIDE: challenge well received. Lots of enthusiasm. Number of groups want to get involved.
+    - Offers of new data
+    - Keeping data around
+  - In need of a **roadmap** (perhaps as an RFC), e.g.,
+    - 0.5: Zarr v3
+    - 0.6: transforms
+    - 0.7: RO-Crate?
+    - ... 1.0/2.0/LTS/etc.
+    - Vendors interested in support etc.
+  - [Hackathon](https://biovisioncenter.notion.site/OME-NGFF-Workflows-Hackathon-2024-dde32a032adf49b4a53b4b014586b678) next week. Focus on Java, Python, and Workflows though multimodality perhaps as a unifying topic.
+  - Seb: community call before end of year? Josh: yes, we have offers to run calls 
+  - J-M: useful to have the challenge data in March
+  - Will: looking to update ome-zarr-py. found one issue in zarr-python. https://github.com/zarr-developers/zarr-python/pull/2480
+
+- GerBI
+  - Josh: NFDI4BIOIMAGE project to compare and document repository submissions. E.g. Zenodo AND BIA etc.
+
+- Glencoe
+    - Erin: heading to CBIAS (Crick) last week of November
+
+- Community
+    - OMERO workshop in Japan went fine, see https://x.com/openmicroscopy/status/1853634849078460860
+    - OMERO workshop in Brno in preparation. 1-day workshop on 6th December
+
+## AOB
+
+(5 min. max; tech. Discussion should be highlighted to relevant people and rescheduled)
+
+## Main Topic
+
+(20-25 minutes plus 15 minutes questions max)