2018-09-25

Dundee: Petr, Mark, Simon, Dom, June, JM, Will, Riad,

Remote: Wilma, Josh, Seb, Frances, David, Andreas, Jason, Emil, Melissa, Chris, Liza

Start: 2:00 pm

1. Accepting minutes from last meeting

2. Project Status

(2-3 minutes each)

• (Summer?) Epics

  • OMERO 5.4.8: whew

    • Done!

    • OME production servers still need to be upgraded

  • No decision yet on 5.4.9

• Data In (Seb)

  • Bio-Formats 6.0.0 roadmap

    • M1: lots of non API breaking changes, KLB reader (required

      for an IDR submission)

    • M2: OME-TIFF pyramid reading/writing (feedback by tomorrow

      morning)

    • No more 5.9 releases planned, 5.10 will be released only if

      high demand

  • IDR 0.5.2

    • Working on batch of 1000 antibodies from HPA (500K 3Kx3K

      images)

      • Annotations and rendering settings in progress
    • New submission with image and ROI data including work on

      relaxed companion OME-TIFF

  • HCA (Josh)

    • s3-reader prototype

      • Aiming for a prototype repo to allow us to read a format

        such as OME-TIFF over S3

      • Main area of investigation will be latency of requests

• Data Out (Mark)

  • Collecting some initial thoughts in

    gdoc, certainly glad of suggestions, comments, redirection, etc. before turning those notes into a Trello board.

  • Turning omero-downloader into something that can be released to

    users

    • Current effort is to try to remove use of deprecated

      OmeroReader from omero-downloader; initial results seem promising. There are other small technical fixes to be made to the proof-of-concept downloader code before improving how it writes the structured data to make it a production tool but perhaps we want to go in a wholly different direction.

  • More input on requirements welcome

  • Petr: user in Australia has their own download script that

    should be public somewhere, along with several annotation scripts that might be interesting

  • Josh: another use case would be slurping from IDR as g. did.

  • Simon: potentially a demo? Sure, or some brief summary (docs?)

• Training (JM):

  • Upcoming Neubias meeting Edinburgh

  • Potential workshop in Finland in November

  • Heidelberg workshop in December

  • Cambridge training in December

  • Singapore workshop next year

• Web apps:

  • Will: preparing a handover of projects

  • JM: Preparing minor release of OMERO.figure

  • JM: Testing FPBioimage improvements

• Glencoe (Chris)

  • 5.4.8 testing, found some thumbnail bugs, probably related to

    read-only server, aiming to write integration tests

    • JM: may be related to known bugs

    • Riad: working on some open-source thumbnail integration

      tests too

  • Bug found with administrator sessions in OMERO.web

  • Doing some computer vision work with whole slide images,

    including new/updated file formats. Some work will be backported.

  • HMS teaching servers: 3-4 groups of 20 simultaneous users

  • Webinar next Tuesday

• Community (Josh)

  • RDF Love 💙💚❤️

  • People interested in JSON-LD, OME-OWL

  • Need to standardise OME terminology (OWL, JSON, API, etc)

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)