minutes from August/Sept 2024

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diff --git a/2024/2024-08-06.md b/2024/2024-08-06.md
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+---
+title: '2024-08-06'
+tags: [Tuesday]
+
+---
+
+---
+tags: Tuesday
+---
+
+# 2024-08-06
+
+Attending: Will, Dom, Frances, Khaled, Chris, Jason, Kyle, Melissa, David, Andreas, Erin, Kevin, David S,
+
+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)
+    - ongoing work on ngff-challenge
+    - idr00157 plant study. v2 conversion needed first. Initial upload to s3 embassy bucket
+    - idr0090 already in v2. Dom testing conversion to v3
+    - idr0044 - sharding example
+    - Dom, using a [nextflow workflow](https://github.com/dominikl/nf_ngff_conv) on pilot-zarr3-dev. Was looking into [BatchConvert](https://github.com/Euro-BioImaging/BatchConvert) which is nextflow based as well, but in my option too complex for the task.
+    - Will: idr0044 images very big - can't load all at once
+    - idr0138 unlikely to be included in next release
+    - David looking at microservices. svs fix for idr0043. bioformats2raw dependency resolved. To be included in release next week
+
+- OMERO (Chris)
+    - omero-py PRs open for review
+    - server build including old jars due to ivy upgrade from 2.4 to 2.6. Seems to include some test dependencies https://forum.image.sc/t/critical-old-and-unsafe-log4j-jar-file-in-omero-5-6-12/100016/3
+        - plan to release 5.6.13 next week when JM/Seb back
+        - Not a security issue as jars aren't used
+
+- Bio-Formats (Melissa)
+    - 7.3.1 release notes updated
+    - Some PRs open
+
+- NGFF
+    - ngff challenge slides at https://drive.google.com/file/d/1rGh5zkA7jD42ehNTbJh4BXN1G8nRpOVB/view
+
+- GerBI
+
+- Glencoe
+    - few people off over next week(s)
+
+- Community (Jason)
+    - BINA Community Meeting OME meeting end of May at MBL
+    - OME Resources, e.g. who runs artifactory?
+        - Chris - hard decsions on what we can support
+
+## AOB
+
+(5 min. max; tech. Discussion should be highlighted to relevant people and rescheduled)
+
+## Main Topic
+
+(20-25 minutes plus 15 minutes questions max)
diff --git a/2024/2024-08-13.md b/2024/2024-08-13.md
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+---
+title: '2024-08-13'
+tags: [Tuesday]
+
+---
+
+---
+tags: Tuesday
+---
+
+# 2024-08-13
+
+Attending: Will, Andreas, Frances, Khaled, Kyle, Melissa, David, Muhanad, Seb, 
+
+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: software release (svs idr0043 fix and Microservices deployment).
+    - Deploy on idr-testing today and team testing tomorrow. If OK, then update production server directly.
+    - Will: ome2024-ngff-challenge. Testing conversions from zarr v2 -> v3, fixing issues at https://github.com/ome/ome2024-ngff-challenge/pull/23
+    - Added a couple of examples to README at https://github.com/ome/ome2024-ngff-challenge/pull/26
+    - Trying to convert idr0048 image (>100 GB) have failed (OOM) on pilot-zarr3-dev. Now manually writing chunks one at a time (see last commit above). Will take over 3 hours (still running).
+    - Goal is to convert idr0044 image (9TB). Not ready yet! Only 4TB free on pilot-zarr3-dev
+    - Not tested plate conversions yet (Dom looking at that).
+
+- OMERO:
+    - Seb: upcoming server release to address old log4j jar included in the build (unintented artifact of the build system). image.sc post describes how to remove extra jars. No security risk AFA we can tell.
+        - release on JM's return (end of this week or early next week at latest)
+        - Don't hold up IDR release. Can remove extra jars manually
+
+- Bio-Formats
+    - David: see IDR update above. Final checks this afternoon. Wider team testing tomorrow.
+    - External PR (imaris) from Bitplane. Needs feedback.
+
+- NGFF
+
+- GerBI
+
+- Glencoe
+
+- Community
+    - BINA OME meeting, May 2025.
+    - Grants submitted and positive feedback, witing on final confirms.
+    - Paper with UGM team to be submitted this week.
+    - 
+
+## AOB
+
+(5 min. max; tech. Discussion should be highlighted to relevant people and rescheduled)
+
+## Main Topic
+
+(20-25 minutes plus 15 minutes questions max)
diff --git a/2024/2024-08-20.md b/2024/2024-08-20.md
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+---
+title: '2024-08-20'
+tags: [Tuesday]
+
+---
+
+---
+tags: Tuesday
+---
+
+# 2024-08-20
+
+Attending: Will, JM, Josh, Andreas, Tom, David G, Seb, Khaled, Erin, David S, 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
+    - Seb: software release last week: image-region microservice, ZarrReader bump etc.
+    - Will: https://github.com/IDR/deployment/issues/432 
+    - Will: idr0001 NGFF conversion. omero-cli-zarr export from prod121 server 
+
+- OMERO
+  - Adding release process instruction to https://github.com/ome/ome-contributing for the various components. Server done. Now for web etc.
+  - Something similar for IDR release will also be useful
+
+- Bio-Formats
+    - Reviewing release process docs
+    - Seb: working on docs for pre-compressed formats support. ndpi, DICOM, etc.
+
+- NGFF
+    - Josh reviewing and merging Will's recent PRs
+    - "Ready to run on TB of data?" - we'll see...
+    - TensorStore needs memory management tweaks
+    - Imaris - concerns of working with NGFF
+
+- GerBI (Tom)
+    - Restart friday omero-web meetings? JM: Yes.
+    - Tom: looking at in-place import. [Script to trigger import](https://github.com/German-BioImaging/omero_fileserver-import) from omero-web.
+    - FocalPlane talk coming up
+
+- Glencoe
+    - Spatial Biology meeting (also went last year) to talk about OMERO.tables
+    - meeting
+    - Seb: image-render update, fixing missing rdefs (e.g. after chown)
+    - Seb: Insight download Fileset [loses file structure](https://github.com/ome/omero-gateway-java/issues/89) 
+
+- 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)
diff --git a/2024/2024-08-27.md b/2024/2024-08-27.md
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+---
+title: '2024-08-27'
+tags: [Tuesday]
+
+---
+
+---
+tags: Tuesday
+---
+
+# 2024-08-27
+
+Attending: Will, JM, Jason, Dom, Tom, Seb, Andreas, David, Khaled, Kyle, Melissa, David S, Maadhav, 
+
+Start: 2:00 pm UK
+
+## Accepting minutes from [last meeting](https://hackmd.io/team/ome?nav=overview)
+
+## Project Status
+
+(2-3 minutes each)
+
+- IDR:
+   - 1.0.0 ngff-tools (challenge)
+     -  used to convert idr0090  
+     -  looking into converting into a nextflow workflow using Dom's repo as starting point https://github.com/dominikl/nf_ngff_conv 
+     - Seb: using idr-testing to test microservices deployment
+
+- OMERO
+    - Discussion how best to deal with change to internal _marshal_image() method.
+    - Tom: updating autotag
+    - Chris: best to revert archive changes, change API to use a map instead of a row
+        - maintain existing API but add more robust API
+        - Don't need to update other apps at this point
+        - Aim to release fix in next few days
+    - Java gateway PR (Seb) approved. Can now be consumed by Insight
+
+- Bio-Formats Melissa
+    - ome-common java component release tomorrow
+    - Seb & Melissa reviewing open PRs
+    - David - last week at OME. Thanks to all.
+        - drop-in session 11:00 - 1:00 on Zoom for any questions on formats
+        - Details for drop in session: https://docs.google.com/document/d/18WBjFslaOIqnEV9-eg2IXnwyOUuarfVPZvb6gurGzQo/edit
+    - JM: release processes (BF & OMERO) moved to contributing repo (public) and testing scenarios. Alongside contributing guidelines etc.
+
+- NGFF
+    - NGFF Hackathon-- https://forum.image.sc/t/ome-ngff-workflows-hackathon-2024-november-18th-22nd-in-zurich/100843
+
+- GerBI
+
+- Glencoe
+    - omero2pandas release, supports upload from csv. Announce once used/tested more etc.
+
+- Community
+    - Dundee outages
+    - Indonesia/Dundee Paper continues, under OME publications
+    - Wellcome, UKRI Funding
+    - BINA OME Meeting-- MBL, April 28-May 1, 2025
+    - Brno workshop in 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)
diff --git a/2024/2024-09-03.md b/2024/2024-09-03.md
@@ -0,0 +1,64 @@
+---
+title: '2024-09-03'
+tags: [Tuesday]
+
+---
+
+---
+tags: Tuesday
+---
+
+# 2024-09-03
+
+Attending: Will, Petr, Josh, JM, Khaled, Seb, Dom, Frances, Melissa, Chris, Kyle, 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):
+    - Testing of idr-testing microservices deployment. Mostly good with a couple of errors - Khaled looking into it...
+    - Will be released with software upgrades from David, along with idr0138. Imported on idr-next with annotations. Looking at rendering settings now.
+    - ngff-challenge conversions. Deadline of 20th September for idr0090, idr0044, idr0157
+
+- OMERO
+    - omero.web released last week with 'archived' fix
+    - omero.figure released with various external contributions and max-projection limits.
+    - Java gateway released yesterday. Insight release in prep, expected by end of week.
+
+- Bio-Formats (Melissa)
+    - Extended formats meeting yesterday. Cleaning up open PRs.
+    - Planning 8.0.0 release timeline. Likely weeks rather than months.
+    - External contributions:
+    - Josh: Readers & Tools
+        - Some parts of the code are not maintained now. Extract into separate repo? Get other maintainers involved?
+        - External readers in separate jars. How to handle this list? e.g. environment variables
+
+- NGFF (Josh)
+  - Challenge: meetings tomorrow. Some conversion activity from contributors
+  - RFCs: RFC-1 response to reviewers. Please endorse! https://github.com/ome/ngff/pull/258
+  - RFC-2: waiting on final reviewer comments
+  - RFC-3: few edits coming
+  - RFC-4 & 5 final edits then to be created
+
+- GerBI (Josh)
+    - TIM meeting prep (March 2025). Building on OMERO deployment on Hive from last year. Lots of ideas on how to add to this! LDAP, registration, NGFF, IRODs etc.
+
+- Glencoe (Chris)
+    - see webclient API fix above. Ideas for refactoring & improving API
+
+- Community
+    - Global bioimaging Japan. 27th Oct. Josh going. Registration open.
+    - Followed by founding GIDE. Interest in OMERO 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)
diff --git a/2024/2024-09-10.md b/2024/2024-09-10.md
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+---
+title: '2024-09-10'
+tags: [Tuesday]
+
+---
+
+---
+tags: Tuesday
+---
+
+# 2024-09-10
+
+Attending: Will, Petr, JM, Frances, Andreas, Seb, Tom, Khaled, Melissa, Kyle, Jason, Josh, Chris, Maadhav
+
+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)
+  - Prod123 released this morning.  Includes new study (idr0138), software upgrades and microservices.
+  - NGFF Challenge: all plates in idr0090 converted as well as idr0044. Moving on to all existing OME-Zarr data.
+    - JRS: where do we do announcements? Twitter, LinkedIn?
+    - FW: idr0138 already announced on Twitter this morning.
+
+- OMERO
+  - Andreas: several things tagged. Few outstanding PRs. Will get those released when there's a green light
+  - Petr (UoD IT): migrating aged GPFS to ESS. Testing performance, etc.
+    - Melissa: https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-test-repo/182/ as a valid build?
+  - J-M: insight build is red which blocked release. Pushing as soon as Dom is back.
+
+- Bio-Formats
+  - Melissa: looking into policies for community response, etc.
+    - JRS: working on additional public response (comments welcome when able)
+  - OME-TIFF writing performance as a next topic
+
+- NGFF
+  - RFCs
+  - Meshes, etc.
+  - Jülich
+
+- GerBI
+  - [ontop](https://github.com/andrawaag/omero-ontop-mappings/blob/main/idr_r2rml.ttl) & uniprot (Josh)
+    - Needs
+      - extending that configuration
+      - figure out security (or public data only)
+      - having a mechanism for discovering endpoints
+    - JRS: links to IDR is interesting.
+      - linking to random OMERO's is ... in a different category
+      - perhaps for LLMs?
+  - Tom: helping people with data at HHU
+
+- Glencoe
+    - Gaining experience with large OMERO.tables using the latest improvements and endpoints introduced in OMERO.py and OMERO.web
+
+- Community 
+    - Wellcome Funding
+      - few positions funded and a few elsewhere
+      - was a Foundation / Scale-up model.
+      - currently rebudgeting
+      - focus on NGFF
+    - Few other grants pending
+      - structure consistent with bridging the OME org to include others who have resources committed
+    - BINA org of OME2025 Community Meeting 
+      - MBL, April 28 - May 1 (or so)
+      - 
+
+## AOB
+
+(5 min. max; tech. Discussion should be highlighted to relevant people and rescheduled)
+
+## Main Topic
+
+(20-25 minutes plus 15 minutes questions max)