2019-07-09

Dundee: Petr, Dom, Ilaria, June, Riad,

Remote: Jason, Frances, Seb, Will, Andreas, David, Chris, Melissa

Start: 2:00 pm

1. Accepting minutes from last meeting

2. Project Status

(2-3 minutes each)

• Data-In (Ingest)

  • IDR 0.6.8 downtime before end of business today - 1 day

    hopefully

    • Needs checking that we are back to normal tomorrow

  • Bio-Formats 6.2.0

    • Testing and integrating. New readers.

    • New release next week.

  • IDR upgrade to OMERO 5.5/BF 6

    • Next couple of weeks

• Data-Out (UI/Search)

  • OMERO 5.5.1 release

    • Mid-way through the release currently

    • Public downloads etc. Final Insight testing now

    • Should be ready tomorrow for public announcement

• SA (learning/mail)

  • Learning

    • Petr: meeting with Paul Pfelts on Thursday

    • Will: investigating slowness of systems with many users. Try

      to reduce unnecessary loading.

      • Problem of loading all group/experiments details loaded

        when using -1 as group context

      • Probably best fixed server-side

    • Seb: blocker for learning?

      • Will: easiest fix is to remove any users that haven’t

        logged in.

      • Ultimate decision about usability on Thursday with Paul
    • Will: impact of the change will impact every single query.

      Only looked at a few ones so far.

    • Possibly move inactive users to a different group

      • Petr: not obvious how to make the query

      • Jason: Just move All users (except Paul) to another

        group?

• Glencoe

  • Chris: working through micro-services tracking deadlocks.

    Traceing tech to help.

• Community

  • Jason: more workshop opportunities

  • Discussion about loss on notifications on expired Lifesci

    accounts

  • Jason in London then EBI - discuss EuroBioImaging

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)

• Ilaria’s presentation: OMERO steps in the field of Environmental

  Science

  • Images to be documented, analysed, shared, published

  • Actions:

    • Use demo account to try OMERO functionalities

    • Install OMERO

    • Install Orbit and Fiji for image analysis

    • Test Orbit (with help from Manuel Stritt)

  • Orbit worked well for identifying e.g. penguins, albatrosses

    etc.

    • ROIs saved back to OMERO

  • Get feedback from data users and image collectors

    • Demonstration of OMERO with request for comments

    • Create wish-list - mostly automation of key-value pairs and

      tagging

  • Joined the OME team office

    • Developed custom scripts for Tag & Map Annotation management

    • Better understanding of groups, permissions etc.

  • Github repo of scripts

  • Github fork of domik’s omero-R for analysing shapes

  • To come:

    • Deploy OMERO in real environment using docker. Pilot

      projects to test

    • Assess OMERO performance and what works and what doesn’t.

      Worth proceeding?

    • If OMERO is good solution for Environmental Science: invest

      more time…

  • Considerations:

    • OMERO.py not easy to learn - learning python and OMERO at

      same time

    • Users will need training - will want more automation (means

      learning python)

  • Will: suggest to write some instructions about scripts. Easy to

    forget expectations