2019-08-20

Dundee: Will, Dominik, Petr, June, Jason, Mark, Riad, JM,

Remote: Frances, Josh, Seb, Andreas, Melissa

Start: 2:00 pm

1. Accepting minutes from last meeting

2. Project Status

(2-3 minutes each)

• Data-In (Ingest)

  • IDR (Prod70) in good shape

    • Software upgraded and Bio-Formats cache files regenerated

    • New OMERO 5.5 functionalities available e.g. websockets

      • J-M: important concept in-place for next-gen VAE

        proposal (mybinder)

      • Dominik has PR for Java Gateway using websockets
    • Restarted thumbnail generation of idr0022 big screen,

      finalizing annotations.

    • Scheduled release for early/mid-September

  • IDR metadata: authorship discussion

    • Standardizing author formatting using MEDLINE/Pubmed style

    • Next: modelling of study vs publication authorship - e.g. 1

      Study -> 2 Publications

    • Jason: Use Pubmed-central or Europe PMC style formatting?

      • Seb: All studies are on Pubmed, but not for PMC or

        Europe PMC

• Data-Out (UI/Search)

  • Prepared for iviewer release - movie, changelog etc - release

    tomorrow

  • Docs - Training guides. Use separate repo for each guide. E.g.

    cellprofiller, fiji etc

    • Use readthedocs for easy deployment

    • Each repo is a submodule - separate repos allow different

      configs for myBinder

    • Combined into a single omero-guide repo / front page, index

      etc.

    • Josh: Usage statistics?

      • JM: No, not out of the box

      • Jason: is important for the project. Use e.g. google

        analytics (don’t write our own)

• Python3 (Josh)

  • omero-web still stuck on various manage.py-style errors

    • Need help with hard-coded assumptions, structuring, internal

      import statements etc

  • omero-py testing strategy fairly sound

  • Decoupling of OmeroPy - all PRs excluded.

    • Jobs to merge decoupled repos and run tests

  • PR to remove from openmicroscopy on its way

  • JM: submodules? Scripts?

    • PRs won’t get merged till jobs updated

• SA (learning/mail)

  • Seb: starting to archive old services. E.g Trac -> readonly.

    Need to decide what we want to keep. E.g. many versions of trac pages?

  • Can turn-off and enable read-only in short term if needed.

  • Melissa: Old trac tickets are useful (don’t need to be public)

• Glencoe

  • Glencoe-con etc.

• Community

  • EMBL (CBA/ilastik) & File Formats (Josh)

    • Nice use-cases

    • Last time: pattern files (“star5”)

    • This time: spatial context - Affine transform etc.

      • Stitching and overlaying

      • Example of Affine transform for whole image

        • Tricky to handle transform for each tile. Apply in

          what order etc?

    • Ended up coming back to BDV and a practical use case

    • Use case Images -> Add metadata -> to IDR

      • Help to have Illastik attach metadata - no manual steps
    • Tischi’s “triple” plugin: intensity + segmentation + table

      (cf. Parade)

      • Click on ROI - show in table and vice versa

      • Can we try to get and IDR dataset into a BDV file

    • BDVWriter with extended API

      • E.g. reading & writing tables

    • Create BDV with OME-XML

    • Segment image and write back to BDV

    • Fiji/BF to open - ask which series/segmentations to open

    • Josh: do we write any Fiji/IJ code outside of BF?

  • Petr: visiting INDEPTH / Lisbon. Zoom link is a MUST (2/Sep)

    • 4-6/Sep link will be re-used or needs to be re-issued.

    • Purchasing another month of webinar zoom

1. AOB

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

1. Main Topic

(20-25 minutes plus 15 minutes questions max)