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| tags: Tuesday | ||
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| # 2024-05-07 | ||
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| Attending: Will, Petr, JM, June, Khaled, Josh, Tom, David, Andreas, Kyle, Erin, Melissa, Chris, Chris M, David S, Seb, | ||
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| Start: 2:00 pm UK | ||
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| ## Accepting minutes from [last meeting](https://hackmd.io/team/ome?nav=overview) | ||
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| ## Project Status | ||
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| (2-3 minutes each) | ||
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| - IDR: | ||
| - JM: next release end of this week | ||
| - searchengine indexer took longer than expected, needs some investigation / validation | ||
| - ZarrReader PR review in progress | ||
| - JM: docs etc need to manage expectations | ||
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| - OMERO | ||
| - JM: started releasing various Java components, starting with BF 7.3.0 bump, then openmicroscopy etc. | ||
| - Modified devspace to test with Java 11, 17 & 21 in rotation. | ||
| - TODO: update docs with info on how to run OMERO on Java 17 etc, and move to dropping Java 8 | ||
| - New private devspace setup | ||
| - Andreas: tagging PRs for next omero-web release. Some still needing review. | ||
| - Will: OMERO.figure upgrade (vite) PR merged. Holding off release for now to catch any outstanding bugs (1 just fixed) | ||
| - iviewer: 2 PRs for IDR mostly ready to merge | ||
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| - Bio-Formats | ||
| - David: Flex PR investigation for IDR | ||
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| - NGFF | ||
| - RFC-1 (process) rebuttal underway | ||
| - some useful responses | ||
| - Transforms alt-proposal (https://forum.image.sc/t/ome-ngff-update-postponing-transforms-previously-v0-5/95617/2) | ||
| - Proposal to drop max 5D requirement. How much consensus in the community? Currently a blocker for some users. | ||
| - Metadata update. Proposal in prep for OME meeting | ||
| - Zarr update | ||
| - 2.18.0 forthcoming (https://github.com/zarr-developers/zarr-python/pull/1843). Last expected for 2.x.x. | ||
| - v3 still moving along | ||
| - kerchunk / chunk manifests (https://github.com/zarr-developers/zarr-specs/issues/287) | ||
| - variable chunk size (ZEP3). TBD: can this be combined with sharding? | ||
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| - GerBI (Tom) | ||
| - finished tests for KVP scripts update. Ready for review | ||
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| - Glencoe (Chris) | ||
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| - Community | ||
| - OME meeting: registrations picking up | ||
| - JM: post-meeting discussions on Java support? (2 from Glencoe will be coming) | ||
| - Tuesday meeting next tech discussion? Chris: maybe on omero-web, but nothing prepared | ||
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| ## AOB | ||
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| (5 min. max; tech. Discussion should be highlighted to relevant people and rescheduled) | ||
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| ## Main Topic | ||
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| (20-25 minutes plus 15 minutes questions max) |
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| tags: Tuesday | ||
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| # 2024-05-14 | ||
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| Attending: Will, Dom, David, Khaled, June, Frances, Andreas, Petr, Tom, Kyle, Melissa, Chris, Seb, David S, Erin, | ||
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| Start: 2:00 pm UK | ||
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| ## Accepting minutes from [last meeting](https://hackmd.io/team/ome?nav=overview) | ||
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| ## Project Status | ||
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| (2-3 minutes each) | ||
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| - IDR (Frances) | ||
| - prod121 release (Rocky 9) pending issues with DB performance during searchengine indexing - timeout errors etc. Also timeout with mapr queries in webclient. | ||
| - Khaled upgraded Postgres 13 -> 16 (including dump and restore the DB), seems to resolve issues. Improved indexing times, but some mapr queries still slow. | ||
| - After release, new idr-testing for NGFF upgrade test | ||
| - Chris: important to identify what the issue was for update of other OMERO servers on Rocky 9. | ||
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| - OMERO | ||
| - Andreas: preparing next omero-web release | ||
| - Seb: OMERO.server recent release 5.6.11, Insight 5.8.4, etc. | ||
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| - Bio-Formats | ||
| - ZarrReader PR review nearly done | ||
| - OME meeting prep in progress | ||
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| - NGFF | ||
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| - GerBI | ||
| - Tom: OME and ELMI meeting prep... | ||
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| - Glencoe | ||
| - Chris: tables work: exploring backends etc. | ||
| - poor interaction with webclient with large amounts of data | ||
| - Erin: will present some OMERO.tables workflows at OME meeting, omero2pandas, QuPath, NGFF label images etc. | ||
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| - Community (June) | ||
| - Google drive for [OME meeting registrants](https://docs.google.com/spreadsheets/d/1MDZcWCBNdc795vX7MoCh5Sehm99_Sg4m/edit#gid=762533928) | ||
| - Attendees have signed up for Posters, Lightning talks etc. | ||
| - Need a plan for signing-up workshop participants. Ask attendees when registration closes? | ||
| - Petr: OME meeting [workshop planning](https://docs.google.com/spreadsheets/d/1a2FiKXByXfDYMJVPBhyGcXq-9s_PmV6qnlhOa9gz6X8/edit#gid=0) | ||
| - Petr: ELMI and Panama workshops upcoming | ||
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| ## AOB | ||
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| (5 min. max; tech. Discussion should be highlighted to relevant people and rescheduled) | ||
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| ## Main Topic | ||
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||
| (20-25 minutes plus 15 minutes questions max) |
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| @@ -0,0 +1,56 @@ | ||
| --- | ||
| tags: Tuesday | ||
| --- | ||
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| # 2024-05-21 | ||
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| Attending: Will, JM, Petr, Josh, Dom, Frances, Jason, June, Khaled, Seb, Muhanad, Andreas, Kyle, Melissa, David S, Erin, Chris, | ||
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| Start: 2:00 pm UK | ||
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| ## Accepting minutes from [last meeting](https://hackmd.io/team/ome?nav=overview) | ||
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| ## Project Status | ||
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| (2-3 minutes each) | ||
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| - IDR (Frances): | ||
| - Khaled tested CentOS 7 with Postgres 13 against Rocky9 with Postgres 16: indexing time similar. | ||
| - Decided not to investigate why we saw slower Postgres 13 on Rocky Linux. Maybe due to Rocky9 needing more resources than CentOS 7 (therefore slower on same hardware) | ||
| - New release: 13 new organisms | ||
| - test 122 ready to test NGFF update | ||
| - Jason: please tweet, linked-in etc about new release | ||
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| - OMERO (JM) | ||
| - omero 5.6.11, omero.insight 5.6.4 (support BF 7.3.0) | ||
| - omero web 5.26.0 - includes security fix | ||
| - omero.iviewer 0.14.0 | ||
| - Re: security release: when to port tests from security repos into mainline (so they are regularly run)? e.g. after 2 major versions? | ||
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| - Bio-Formats (Melissa) | ||
| - OME talk prep - run-through on Monday 2pm | ||
| - | ||
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| - NGFF/GerBI (Josh) | ||
| - RFC-1 author response is late | ||
| - Reached out to RFC-2 reviewers (zarr v3) | ||
| - Reached out to RFC-3 author (Juan) | ||
| - re: https://github.com/ome/ngff/pull/235 | ||
| - Mostly focused on next week. | ||
| - iRODS meeting. Might try to use iRODS for managing S3 buckets related to NGFF. | ||
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| - Glencoe | ||
| - Erin - OME meeting prep: slides etc - will share soon | ||
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| - Community | ||
| - Prep for meeting underway. Access, admin, catering... | ||
| - Updated [Meeting Agenda and Workshops](https://www.openmicroscopy.org/events/ome-community-meeting-2024/) | ||
| - | ||
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| ## AOB | ||
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| (5 min. max; tech. Discussion should be highlighted to relevant people and rescheduled) | ||
|
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| ## Main Topic | ||
|
|
||
| (20-25 minutes plus 15 minutes questions max) |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,52 @@ | ||
| --- | ||
| tags: Tuesday | ||
| --- | ||
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| # 2024-06-04 | ||
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| Attending: Will, JM, David, Khaled, Dom, Chris, Seb, Kyle, Erin, Melissa, Kevin, Maadhav | ||
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| Start: 2:00 pm UK | ||
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| ## Accepting minutes from [last meeting](https://hackmd.io/team/ome?nav=overview) | ||
|
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| ## Project Status | ||
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| (2-3 minutes each) | ||
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| - IDR | ||
| - Discussions ongoing on converting more data to OME-Zarr | ||
| - Will: testing on idr-testing. Memo file generation taking multiple attempts | ||
| - Waiting on OMEZarrReader release to deploy on idr-next - Final reviews on PR please. | ||
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| - OMERO | ||
| - Focus on updating remaining CentOS 6 machines | ||
| - work on cookiecutter-web app for OME | ||
| - OMERO.figure changelog for vite release awaiting review | ||
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| - Bio-Formats | ||
| - will return to focus on 8.0.0 milestone | ||
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| - NGFF | ||
| - Will: starting to look at Zarr V3 and usage in ome-zarr-py | ||
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| - GerBI | ||
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| - Glencoe | ||
| - Chris: OME meeting de-brief etc. | ||
| - Erin: scheduling discussion of OME-Zarr strategies in OMERO: OMEZarrReader vv pixel-buffer | ||
| - JM: away next week | ||
| - Erin: week of 17th? | ||
| - Seb: various issues open for next OMERO 5.7 release, including archive flag for omero.web | ||
| - Any other requests for changes, DB, deps etc? | ||
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| - Community | ||
| - Team at ELMI in Liverpool this week | ||
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| ## AOB | ||
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| (5 min. max; tech. Discussion should be highlighted to relevant people and rescheduled) | ||
|
|
||
| ## Main Topic | ||
|
|
||
| (20-25 minutes plus 15 minutes questions max) |