2019-11-19

Dundee: Will, Petr, Dom, Simon, Mark,

Remote: Seb, Josh, Ola, Andreas, Jean-Marie, David, Melissa, Liza, Wilma, Chris

Start: 2:00 pm

1. Accepting minutes from last meeting

2. Project Status

(2-3 minutes each)

• IDR (Seb):

  • Aim to release everything that is publishable before end of

    year.

  • Various archiving needs/issues (including performance)

  • Few datasets in progress in the background by various team

    members

• Python3: tabling for #4

• SA (learning/mail): N/A

• Glencoe

  • Digital Pathology formats

    • Isyntax2raw

      (https://github.com/glencoesoftware/isyntax2raw) & mrxs2raw (https://github.com/glencoesoftware/mrxs2raw) conversion repos now public

    • Works with Philips data, available when registered on

      website

    • n5 is default format, zarr also possible

    • Secondary repository to turn back into OME-TIFF

      https://github.com/glencoesoftware/raw2ometiff incl. compressions choice

    • Upcoming improvements to the compression scheme + Dockerized

      pipeline for the conversion

    • Use TiffSaver instead of TiffWriter and optimised code paths

      for improved performance

    • Preparing a public statement on why we’re using

      transformation (which blog? Cross post?)

  • Long-running user-tokens for OMERO in new repo.

  • Bio-Formats updates - PRs open

• Community

  • Lots of love on image.sc

1. AOB

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

• …

• The python-uninterested can run away.

1. Main Topic: VAE Python 3 demo (J-m)

(20-25 minutes plus 15 minutes questions max)

• Demo…. (JM)

  • Python3 changes not published to docker hub yet. Demo local

    code.

  • Notebooks all running, but need manual testing - volunteers?

  • Remains to look at ITR. CellProfiler is currently disabled.

  • Seb: upgrade to VAE independent of the IDR? Yes.

• General discussion

  • Working on various plugins - most plugins green with

    omero-test-infra testing

    • Still working on omero-mapr.

  • Next focus on documentation

    • Need to decide on supported platforms and python versions

    • Yes