2018-06-26

Dundee: Will, Petr, Kenny, Simon, Mark, Dominik, Jean-Marie, Riad, Jason,

Remote: Josh, Sebastien, Melissa, David, Andreas, Chris, Wilma, Liza

Start: 2:00 pm

1. Accepting minutes from last meeting

2. Project Status

(2-3 minutes each)

• Summer epics

  • Import (Mark)

    • Mark: queried omero-team about import performance issues and

      provided simple utility wholly client-side to report duration metrics except for pyramids

      • Next step is likely performance testing on idr2-slot3

        (“north”)

    • Seb: suggested range of image data for testing different

      aspects of import

    • Insight:

      • Riad: Added options in UI to match “skip” options of

        import CLI

      • Dom: PR for importing large number of files (not 100%

        finished yet): \#5783

    • JM: need to contact Susanne Kunis about her work on Insight

      import UI to avoid conflicts. Dom to do this.

  • Formats

    • Bio-Formats 5.9.0 -

      https://github.com/openmicroscopy/bioformats/milestone/63

    • Status of the release tomorrow at the Formats meeting. Stick

      to date or push by a day or two?

    • High levels of community requests. Forums, QAs etc.

      • Need to reduce support burden

    • IDR HPA dataset to start importing

      • Jason: size of images?

      • Dom: 2-3k

  • Monitoring

    • → Main topic demo

      • https://trello.com/c/Zs77bh3X/49-omero-server-profiling-scripts

  • Analysis/Outreach (J-m)

    • TOPIM:

      • Use Petr’s laptop in case we cannot use outreach (no

        reply to our email about network)

      • Finalising notebooks and scripts - aim to tag this week

        and deploy.

      • [Print out for

        workshop</u>](https://docs.google.com/document/d/1XWRy7CzJ93Up-s0NVjckfAukH9ZRdgA7RXHsNojWUoI/edit#) (in-progress)

        • Including Orbit and CellProfiler.

    • ITR

      • Add link to materials (e.g. PDF, notebooks) to

        https://idr.openmicroscopy.org/about/itr.html. Work in progress: https://github.com/jburel/idr.openmicroscopy.org/tree/itr-material

      • Add R to idr-notebooks working of a [topic

        branch:itr</u>](https://github.com/IDR/idr-notebooks/tree/itr)

      • Looking at adding Orbit to the list

      • Jason: ITR (image tool resource) public list of tools

        • Want to link to working demo using IDR data.

        • Good showcase for OME, especially outreach work.

        • Notebooks to go in idr-notebooks repo

        • ITR also contains tools that are not linked to our

          work

      • Josh: OMERO federation: linking external data

  • OMERO 5.4.7 (Josh)

    • Several critical items on the board

    • Aim for August release - need to pick a date

• Glencoe

  • microservice testing & caching

  • Concurrency issues with high request counts

  • Melissa to work on OME-TIFF pyramid read/write in C++ & Java

  • Emil & JM looking at CellProfiler. Versions etc.

    • Jason: need URLs to illustrate the issues we’re having

  • Andreas. Exporting pathviewer views

    • Figure PRs coming soon.

• Community

  • EBI Imaging (HCA/BIA)

    • Upcoming meeting (Jason)

      • Scope of meeting being discussed and solidified.

      • Just Josh & Jason to attend

      • Series of short presentations. IDR, IDR - HCA, object

        stores, biostudies

      • Biostudies - IDR data linking solidified

      • Josh: try to limit number of points of interaction

    • Python/C++ efforts (Josh)

      • OME Files py Docker builds

      • [Starfish

        (python)</u>](https://github.com/spacetx/starfish)

      • See [ome-files build

        repo</u>](https://github.com/ome/ome-files-build)

    • Archiving images (paper)

      • See biorxiv and/or google drive

    • IDR (paper) - still not open

    • Long-term goals request. ETA for outline tomorrow(ish)

      • Everyone’s feedback before holidays
  • Riken (incl.

    BioHackathon) (Josh)

    • #OME-SSBD slack channel

    • Others discussing metadata issues via community

    • Bio-hackathons in Japan and Paris (see link above)

      • Instrument metadata in RDF

      • 12th July

  • FYI: Discussion with Marcus Fantham

    • New version of FPBioimage available

    • OMERO.fpbioimage to link to repo to load on-the-fly

    • Require some adjustment to our web plugin. Probably a summer

      job

  • Basel: workshop - Sept 3-4 proposed date

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)

• Simon: https://monitoring.openmicroscopy.org/<XXX>/

  Prometheus/Grafana demo

• Multiple Prometheus servers monitoring EBI resources and nightshade,

  demo etc in Dundee

• All send summary of data to prometheus-global in Dundee. Stores

  data.

• Grafana UI displays data from prometheus-global. Doesn’t store data.