2018-08-07

Dundee: Kenny, JM, Petr, Simon, Dom, June, Riad

Remote: Josh, David, Melissa, Jason, Chris, Wilma, Will, Seb, Liza

Start: 2:00 pm

1. Accepting minutes from last meeting

2. Project Status

(2-3 minutes each)

• Summer epics

  • Import / Thumbnail loading (Riad)

    • if the import requires, check import has completed before

      attempting to load thumbnail (possibly using “jobs”)

    • Add more server/client messages to provide information to

      users on progress of import

    • Add extra UI to display any errors when a user selects an

      image that’s failed to load, possibly new section to right panel or a dialog,

    • Trial changes on insight and see what functionality we can

      add to blitz for similar use in web & CLI

    • Milestone: 5.4.8 (end of the month)

    • Suzanne’s (external contributor) importer work needs to be

      reviewed for generality, to be discussed later

      • Attaching complex metadata at import time (IDR use

        cases?)

    • There’s some other import document with more

      information/ideas

      • Some ideas for speed ups but not straightforward, more

        discussions required

      • Start scoping and estimating time requirements

  • OME-TIFF pyramids (Seb)

    • Aim: Use BF converter tools to convert all pyramidal file

      formats in our possession into OME-TIFF pyramids, then compare imports of original and OME pyramids

    • Will likely affect CI servers

  • ITR (Simon)

    • Will be deployed this week

    • Notebooks and docker image updated

    • Preliminary test framework for notebooks

  • Training

    • Preparing for Basel

  • App releases

    • Figure: Bug in open PR, may affect release date

    • Parade

• Glencoe (Chris)

  • OMERO PRs open, including fix for file handle leakage, and

    improved documentation

  • More microservice work, including integrating Prometheus metrics

• Community

  • [Mike

    Wicks</u>](https://www.ed.ac.uk/pathology/people/staff-students/mike-wicks) visiting/presenting on August 21 to discuss Comparative Pathology Workbench (CPW)

    • Part of HCA/CZI project, building digital pathology

      prototype app on top of OMERO, aim is to provide a web UI for pathologists to browse and select data

    • May benefit from reusing Figure work

  • HCA: submission definition (Josh)

    • Forget everything about writing a SpaceTX reader

    • Instead use BFconvert to generate companion file and tiff

      stack, which in conjunction with their JSON metadata (which will have to be stored somewhere) equals SpaceTX

    • Therefore every HCA image with be an OME file, though on S3

      object store which will affect how OMERO reads the images

  • Japan/Riken: SSDB channel available along with Google Drive

    folders. Potential federation proposal

  • More training sessions ….

1. AOB

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

• ImageJ and CellProfiler are moving their forums to Discourse.

  Probably not suitable for OME at the moment.

1. Main Topic

(20-25 minutes plus 15 minutes questions max)