2020-06-23

Attending: Josh, Will, Frances, Mark, Chris, Simon, Petr, Melissa, Sebastien, Wilma,

David, Dominik, Jason, Jean-Marie, Andreas, Emil,

Start: 2:00 pm

1. Accepting minutes from last meeting

2. Project Status

(2-3 minutes each)

• IDR

  • Idr0071 needs more testing: Simon:

    • Imported to incorrect datasets due to

      https://github.com/ome/omero-blitz/issues/91

    • 32 images have excess metadata: Potential workaround

    • Duplicate Project/Dataset names causing issues

    • Plan to import then assess

    • Frances: plan was for prod84 (with idr0079, idr0077,

      idr0070)

    • Could release prod84 with those. Need to contact idr0071

      submitter

    • Simon - import during this week. Discuss options on Monday

• NGFF (Josh)

  • Notes from [yesterday's

    meeting</u>](https://docs.google.com/document/d/1kCTxl9LpuDjDoF4hXayahbAkR8aM2IfTbXunOCE-tJc/edit#).

    • Goal is to have masks in ome-zarr, i.e. bottom portion of:

    • 

    • Simon working on spec

    • Dundee team working on ‘bottom’ path above

    • GS working on ‘top’ path.

    • Omero-rois (python, OME team) used in IDR

    • Omero-roitool (Java, GS) uses existing Java libs

  • ITK

    inquiry about location of spec to add support

  • From napari zulip,

    https://github.com/tlambert03/napari-omero

    • Good to support masks

  • Discussion with Erich Bremer - Stony Brook.

    • Mostly were discussing the intersection of RDF with binary

      data

      • See [\[2005.06469\] Representing Whole Slide Cancer

        Image Features with Hilbert Curves</u>](https://arxiv.org/abs/2005.06469)

      • Spatially indexed representation of polygons to overlay

        on images

      • Done via a column store-like representation which could

        be used within Zarr.

      • … > Pathology … > … > DICOM …
    • But: Was unclear on tile server feature. Upcoming

      publication of one (IIF-compatible) which could be submitted back. Also has an CECOG-like HTTP implementation for Bio-Formats.

    • Also, successfully using

      native-image (from GraalVM) to compile Bio-Formats to native code.

      • Doesn’t support reflection - manual effort required
    • Awaiting publication etc.

• SA (learning/mail)

  • VMWare hypervisor and firmware updates

    • Rolling update of hypervisors, due to firmware updates will

      require VMs to be updated at our leisure (proposed timescale: over two week period following start of work by UoD IT)

    • Downtime needed. In touch with UoD IT.

  • Mail migration: Last week’s testing passed, list migration

    underway this week.

    • In retiring ome-nitpick in favor of omero-team, add Andreas,

      Emil, Wilma to latter? Maybe Kevin? Happy to go with what works for Glencoe. Current omero-team members are Chris, Melissa, Stick.

    • Chris: will discuss with GS team

• Glencoe (Chris):

  • Bioformat2raw work on Plates and Memoizer

  • n5/zarr usage in Java investigation

• Community

  • Workshop videos? July?

    • JM: video recording? Quality? zoom vs OBS etc?

    • Jason: needs discussion later

  • Community meetings? More frequent meetings suggested.

    • Get some more work done first

    • September

  • Collaboration proposals

1. AOB

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

• Office seating:

  • If desk is taped off, choose another

  • If you want to work in office, let Jason know.

1. Main Topic

(20-25 minutes plus 15 minutes questions max)