2018-08-14

Dundee (zoom): Will, Jean-Marie, Jason, Mark, June, Riad, Petr,

Remote: Sebastien, Melissa, Josh, Liza,

Start: 2:00 pm

1. Accepting minutes from last meeting

2. Project Status

(2-3 minutes each)

• Summer epics

  • Bio-Formats 5.9.1 - Seb

    • “Done”. Updates site updated etc

    • Potential regressions to go into 5.9.2

  • OME-TIFF pyramids - Seb

    • Secondary pyramids generated with various compression

      algorithms etc.

    • Next: heavy performance testing and validation and other

      pyramidal file formats

  • OMERO import / OMERO 5.4.8 - Riad

    • Server-side changes to change thumbnail loading

    • Slow progress

    • JM/Josh - decide on PR freeze / release next week when more

      people back

  • Training - J-m

    • Focusing on Basel prep - 2 x long days

    • On-going work website to add training section. See

      https://snoopycrimecop.github.io/www.openmicroscopy.org/training/

    • Figure 4.0.1 to go before with few bug fixes

    • Parade 0.2.0 (see report below) Discussed last week

    • Jason: Sydney training soon after Basel.

    • Starting to organise Japan trip too.

    • Cambridge in December?

    • JM: Neubias (Graeme Ball)

  • VAE 0.5.1 - J-m

    • release last week:

      itr

    • few todos post release

    • Convert release process from paper to Trello board

  • IDR 0.5.1 - Seb

    • Curator interview Friday

    • Expecting 2 datasets (new + update) in next release

    • Ongoing work on HPA first upload

      • Not in next release but aim to have it releasable ASAP

• Glencoe

  • Working on getting some Parade changes in as discussed with

    Jean-Marie and Will before I go on holiday next Monday; these will be useful for the upcoming series of demos

  • We’ll be working on a Material UI theme for React plugins that

    will adhere to the current OMERO.web look and feel

  • Couple image region microservice updates based on Ice

    asynchronous call handling; currently causes hangs on session `close()`, will report when we know more

  • Melissa has opened a PR outlining a change to trust Bio-Formats

    channel colour assignments more explicitly

  • Pyramid work is ongoing

  • Looking to try and open an omero-metadata PR based on Kevin’s

    work for discussion by the end of the week

    • Potential conflicts
  • Currently shipping 5.4.7 to customers

• Community

  • HCA:

    spacetx-fov-writer (on gitlab) - Josh

    • Docker image stored on gitlab registry (single command)

    • Uses bio-Formats-tools repository etc

    • ImageConverter needs refactoring to make it publicly

      available (currently using reflection)

    • 20-22nd call with Data-wranglers. Try to show them this.

1. AOB

• Invite Wei Ouyang, developed of ANNAPALM

  (paper, code) at Pasteur for Tuesday Presentation?

  • Useful segmentation tools for e.g. IDR.

  • JMB: 28 August?

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

1. Main Topic

(20-25 minutes plus 15 minutes questions max)