2019-01-08

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

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

Start: 2:00 pm

1. Accepting minutes from last meeting

2. Project Status

(2-3 minutes each)

• Data-In

  • IDR prod62: Two

    new IDR datasets imported. Working on annotations.

    • Dom: images for 0047 and 0053 are imported.

    • Batch 3 of HPA going into idr-testing. Testing chown/chgrp

      workflow.

• Data-Out:

  • Build column on

    5.5.0

    • JM: Still working on OMERO build system, aiming for a

      working server by end of week

    • JM: Updating runtime dependencies in deployment related

      repos, but testing limited until Ice 3.7 works

    • Potential next steps: extract Insight and Ice slice files

  • VAE 0.5.3:

    • upgrading to latest jupyter/jupyterhub by end of January.

    • Upgrade of other dependencies

    • Notebook work (including testability, porting other

      notebooks into main repo)

    • JM: R and Orbit should work

  • Iviewer:

    • working on OpenLayers upgrade. Getting ready for more work

      on ROIs

    • JM: Plan to get rid of Closure compiler and improve ROI

      support

  • EASTBIO workshop on Friday 11/01

    • JM: Dundee workshop for students. Focus on Figure and Parade

• Glencoe

  • More microservice work, will be ported once open-source build

    work is complete

• Community

  • HCA/SpaceTx: working towards 0.1.0. Documentation and usability

    time. Upcoming face-to-face in Santa Cruz discussing imaging use cases and the internal imaging file format.

    • Josh: Working on docs prior to release. What are Bio-Formats

      Series? Meeting in Feb to discuss image management, maybe.

  • N5/Zarr emails and

    https://www.scipy2019.scipy.org/ (July 8-14)

    • Josh: Conference call next week to discuss N5/Zarr

      integration. SciPy proposed as a potential meeting location

  • UKLMF’19

    • File formats

    • IDR: facility provenance as annotation, quality control

    • Seb: as always people using lots of different file formats

      in different ways which may or may not work with OME. Reference libraries are critical. Several groups/companies working on standardising quality control, may need to be stored in OMERO

    • JM: Basel have a recent QC publication on a plugin
  • Jason: Several different IDR presentations with different

    emphases, would be worth going through them all

1. AOB

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

1. Main Topic: User Meeting, the Next Generation (Jason) - 14:23

Make choices for 2019 OME Meetings

1. The Same Old Thing

   1. It’s Great (focused target)

   2. It Costs Alot

      1. In £$

      2. In Time (especially June and non-Wilma)

   3. Alot of the same people (maybe good, maybe a problem)

   4. Value vs Cost?

2. Alternatives

   1. 2-3 User Training Sessions?

      1. Rooms at Dalhousie

      2. 8-12 people per session

   2. Deploying and Running OMERO for an Imaging Facility

   3. Application Integration

      1. The Dreaded Hackathon

   4. Engaging with Vendors

      1. OME-TIFF Usage and Integration
   5. “Satellite” meetings (cF. Basel), may attract people local to

      the meeting who can’t travel to Dundee

   6. All these could be in-person, webinar, interactive Zoom, etc.

   7. Periodically larger…?