2023-01-31

Attending: Frances, Will, Petr, Muhanad, JM, David, Chris, Josh, Tom, Khaled, Jason, Andreas, Kyle, Kevin, Melissa, Erin, Seb, Wilma, David Stirling

Start: 2:00 pm UK

Accepting minutes from last meeting

Project Status

(2-3 minutes each)

• IDR
  • preparing next release:
    • idr0146
    • HPA - last few antibodies from previous release
    • Search updates: backend and UI changes
    • Bug fix and testing ongoing
    • Plan to release on Thursday if all well, otherwise next week
    • New search video
  • SSBD visit prep
    • New notebook, to harvest genes and use gene profiler to give enriched GO terms
    • Jason: GO term enrichment analysis: standard approach. E.g. https://www.nature.com/articles/s41598-018-28948-z
• OMERO
  • OMERO.insight release last week with new gateway release
  • weekly OMERO.web meetings: Fridays 1:00 - 1:30 UK
  • Andreas to handle next release
    • may wait for Kevins channel rendering bugfix
• Bio-Formats (David)
  • 6.12.0 release upcoming, end of next week
  • Release process changing - may do a milestone release ahead of 6.12.0 to test.
• NGFF (Josh)
  • Calls with NASA (POWER earth data on energy use, ZarrCon, …)
    • moving to use more Open Source
  • Logos from Zarr users to add to zarr site
  • Z3: use double underscores for escaping…
  • NGFF v0.5 - will re-focus soon
  • SpatialData
  • Catalogs of existing NGFF data.
    • idr samples page re-use: needs refactor to not be IDR-specific
  • NGFF Paper: Jason: OK to edit doc? Yes
  • omero-cli-zarr: Big Images support PR #134 (Will)
    • still falling over (chunks all in one directory)
    • caching helps.
    • Chris/Seb: good to fix the underlying BDV reader issue https://github.com/glencoesoftware/bioformats2raw/issues/187
  • JM: discuss zarr resources at Fridays: 1:30
• GerBI
  • Tom: Not currently working on Hive install (server in use till next week)
  • Josh: 22nd - 24th Feb: I3D meeting. Roadmap, requirements from OME team?
• Glencoe (Chris)
  • See omero.web above
  • OMERO.server threading issues: PR open, doc updates
    • Background threads review & document
  • Data compression with bioformats2raw: initial issues due to TIFF compression limitations. New features available since initial support
  • JM: doc changes can be released anytime
  • Docs generated from Blitz configs
  • Kevin: javadocs are extensive, but not config properties
• Community
  • UK Data Research Infrastructure
  • SSBD Visit Feb 27 - Mar 3
    • Josh: arriving on 28th

AOB

(5 min. max; tech. Discussion should be highlighted to relevant people and rescheduled)

Main Topic

(20-25 minutes plus 15 minutes questions max)

• OMERO.figure & NGFF (Will) slides
• JRS: 1. Let’s consider decisions on updates not on number of changes of code but longer term maintenance. Effectively maintaining our own custom viewer in .figure seems not a great long-term plan.
• 1. Would the use of coordinateTransforms cause conflicts, e.g. with CLEM data? Maybe a naïve question.
• 1. The full detach from OMERO server maybe worth considering, but would a user ever want to use OMERO as the metadata source for a .figure workflow? I think we discussed this in the context of direct support for NGFF data in .figure. This is different than discussed– is OK, just clarifying and trying to decide what we want to do first.
• 1. Scale bars…. are really important for a figure.