2019-11-26

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

Remote: Andreas, Wilma, J-m, Seb, Josh, David, Emil, Liza, Chris, Melissa

Start: 2:00 pm

1. Accepting minutes from last meeting

2. Project Status

(2-3 minutes each)

• IDR (Seb)

  • Data availability and archival updates.

    • Solution working for most use-cases, but could be improved

      in future

  • Prod72 updates

    • Last release for this year.

    • Currently loading, rendering, annotating.

    • 2 experiments to be completed this week for review when

      Frances back

• Python3: table for demo (see below)

  • Post-demo (training + idr)

    • Generally state of the software

  • Operating systems

    • Recommended platforms: Ubuntu 18.04, CentOS 7

    • Some work on Debian, Ubuntu 16.0.4 but not recommended

  • Next steps

    • Requirements page updated

    • Copy of documentation to be published

    • Using some pre-releases probably. If comfortable, getting

      omero-py 5.6.0 released next week

    • Chris: installation process? Pip vs bundle?

      • Web should be fully pip-installable, barring

        configuration variable

      • Server easier to download as a whole bundle at the

        moment

    • Question of dropping Python from the bundle

      • Main downside is which plugins would be picked up

        (lib/python vs pip installed component)

    • Tests only covering Python 3.6

      • Not possible to run them in Travis (other Python)

        primarily for memory reasons

• SA (learning/mail): N/A

• Glencoe (Chris)

  • Mrxs repo updates - more generic. Renamed

    bioformats2raw

    • Various WSI formats supported -> OME-TIFF

    • High-performance, multi-threaded, supports downsampling.

    • Can add more readers in future as needed

    • Preparing announcement - next week - 10 days

    • Could be used for pyramid generation in future - not tested

      yet

  • Requests for admin tool improvements for managing large number

    of users.

    • Lots of groups and users - many have left.

• Community

  • JRS: feedback from the road

    • Folders: defining the actual requirement. Some

      appreciation of what is currently available. Lots of note taking around mapr, etc.

      • JRS: Also just a matter of working with the metadata.

      • Will: requires reading the manual which probably isn’t

        the norm.

1. AOB

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

1. Main Topic - Python Demo

(20-25 minutes plus 15 minutes questions max)

• Josh: deployed with all plugins now ‘working’. Dev versions tagged.

• Petr:

• ‘Outreach’ DB on ome-training-4 (py3)

• Following typical workshop workflow - all seems to be working.

• Downloads (failed on last demo) working (original file, metadata,

  OME-TIFF, jpeg, png) for single/multiple images.

• Parade not working

• Figure working - saving, reload, export as PDF working.

  • But not if figure name contains unicode characters. (PR is open

    to fix this)

• Jason - demo of idr-experimental (py3):

• Thumbnails not loading on gallery front page.

• Mapr results page thumbs loading OK

• Filter results page thumbnails intermittant

• Iviewer working OK (playing projected movie).

• Mapr - Organism page - top level of tree not loading (too slow)?

• Idr0047 masks not loading in iviewer

• Deployment testing - Ubuntu 18 and CentOS 7 supported. Debian not

  tested yet.

• Omero-web will be purely pip installable

• OMERO.server zip currently includes the python libs (phase1). Phase

  2 will be pip install omero-py