diff --git a/2024/2024-05-07.md b/2024/2024-05-07.md new file mode 100644 index 0000000..de2aaed --- /dev/null +++ b/2024/2024-05-07.md @@ -0,0 +1,65 @@ +--- +tags: Tuesday +--- + +# 2024-05-07 + +Attending: Will, Petr, JM, June, Khaled, Josh, Tom, David, Andreas, Kyle, Erin, Melissa, Chris, Chris M, David S, 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: + - 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 + +- 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 + +- Bio-Formats + - David: Flex PR investigation for IDR + +- 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? + + +- GerBI (Tom) + - finished tests for KVP scripts update. Ready for review + +- Glencoe (Chris) + + +- 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 + +## 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/2024/2024-05-14.md b/2024/2024-05-14.md new file mode 100644 index 0000000..6d9b8c8 --- /dev/null +++ b/2024/2024-05-14.md @@ -0,0 +1,54 @@ +--- +tags: Tuesday +--- + +# 2024-05-14 + +Attending: Will, Dom, David, Khaled, June, Frances, Andreas, Petr, Tom, Kyle, Melissa, Chris, Seb, David S, 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 (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. + +- OMERO + - Andreas: preparing next omero-web release + - Seb: OMERO.server recent release 5.6.11, Insight 5.8.4, etc. + +- Bio-Formats + - ZarrReader PR review nearly done + - OME meeting prep in progress + +- NGFF + +- GerBI + - Tom: OME and ELMI meeting prep... + +- 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. + +- 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 + +## 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/2024/2024-05-21.md b/2024/2024-05-21.md new file mode 100644 index 0000000..29d8dfe --- /dev/null +++ b/2024/2024-05-21.md @@ -0,0 +1,56 @@ +--- +tags: Tuesday +--- + +# 2024-05-21 + +Attending: Will, JM, Petr, Josh, Dom, Frances, Jason, June, Khaled, Seb, Muhanad, Andreas, Kyle, Melissa, David S, 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): + - 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 + +- 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? + +- Bio-Formats (Melissa) + - OME talk prep - run-through on Monday 2pm + - + +- 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. + +- Glencoe + - Erin - OME meeting prep: slides etc - will share soon + +- Community + - Prep for meeting underway. Access, admin, catering... + - Updated [Meeting Agenda and Workshops](https://www.openmicroscopy.org/events/ome-community-meeting-2024/) + - + +## 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/2024/2024-06-04.md b/2024/2024-06-04.md new file mode 100644 index 0000000..ffcd71a --- /dev/null +++ b/2024/2024-06-04.md @@ -0,0 +1,52 @@ +--- +tags: Tuesday +--- + +# 2024-06-04 + +Attending: Will, JM, David, Khaled, Dom, Chris, Seb, Kyle, Erin, Melissa, Kevin, 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 + - 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. + +- OMERO + - Focus on updating remaining CentOS 6 machines + - work on cookiecutter-web app for OME + - OMERO.figure changelog for vite release awaiting review + +- Bio-Formats + - will return to focus on 8.0.0 milestone + +- NGFF + - Will: starting to look at Zarr V3 and usage in ome-zarr-py + +- GerBI + +- 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? + +- Community + - Team at ELMI in Liverpool 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)