2019-04-30

Dundee: Petr, June, Riad, Seb, Mark, Will, Simon, Dom

Remote: Jean-Marie, Frances, Josh, Will, Chris, Andreas, David, Melissa

Start: 2:00 pm

1. Accepting minutes from last meeting

2. Project Status

(2-3 minutes each)

• Data-In

  • Bio-Formats 6.1 (Seb)

    • Near drawing a line on contents of 6.1

    • BDVReader is 95% done

    • Most of the Java dependencies are done. NetCDF being tested,

      but looks positive

    • Legacy OmeroPyramid format issue has been reproduced without

      OMERO

    • Couple of unknowns. RC within next week?

      • JMB: pyramid fix in B-F or OMERO? David: likely fix in

        B-F but reader in OMERO.

  • IDR 0.6.7 (Seb)

    • HPA run plus likely one more screen. (No complete

      data+metadata)

    • Work on UI will be ongoing concurrently.

  • IDR 0.7.0 - new UI (Will)

    • See [extensive

      notes</u>](https://docs.google.com/document/d/1HHQbMKT3N5yGAOfKHjEuGJX19nBW_ldOXmKPN3q14FU/edit#) or screenshots on design issue

    • Will: multiple rounds iterating over different ideas

      covering front page for IDR allowing to explore the IDR.

    • Currently based on omero-gallery. Might fully supersede the

      old gallery (primarily used as an example previously)

    • next step: deployment of new UI so that team can test it

• Data-Out

  • Tags omero-* repo late friday after build/dependencies issues,

    m3 of omero-java-gateway is the last addition. Java clients (Insight and matlab immediately) use it.

  • Working on docs and ironing bits. Moving towards release in

    coming weeks. Timeline to set in stones, we need BF 6.1 with omero pyramid fix so it can be included

    • Expecting openmicroscopy milestone to be tagged tomorrow

  • Insight:

    • Package importer: might need to decide on the usage by

      consumers. Chris: not heavily used by a few customers still rely on it.

    • Readme
  • Josh: python 3 initial work. Easy to get started but eventually

    hit Python gateway.

    • Started breaking it gateway into files

    • Will need no other PRs touching that piece of code

    • Will: probably limited amount of changes to the gateway.

    • JM: OMERO 5.5 will probably be short-lived. More work into

      the pipeline (Python 3)

  • OMERO.downloader release coming this week to fix export bug

    before coming training workshops.

    • Current release version has bug in TIFF export. Testing

      ongoing and targetted for the upcoming training.

    • Also includes download of map annotations.

• Glencoe (Chris)

  • Bio-Formats, Micro-services, upgrading

  • New webinar coming up in a few weeks

  • Josh: progress with migrating on top of backbone ms

    • Pixelbuffer and image-region use backbone on master branch

    • Remaining one to upgrade to backbone it thumbnail

• Community

  • Seattle report (Josh)

    • Future of OMERO discussions

      • E.g. Conversation with Allen Institute for Cell Science

      • Created their own stack based on SpringBoot

      • Also have data in several location

      • Interest in keeping the discussions e.g. can parts of

        the stack be re-used without needing everything (micro-services)

    • Flexible model (EBI & Allen)

      • Discussions around RDF.

      • EBI primarily using JSON-schema, discussed the support

        problem

      • CZI converting everything to OME-TIFF. Unclear whether

        they have all the metadata of the PFF.

    • Zarr & N-DIM stitching (SpaceTx, Allen, etc) cF. BigStitcher

      • Problem of the metadata connecting the blobs together

      • BigStitcher uses GUI based approach to make inferences

    • Registration & coordinate frameworks (SpaceTx, Sanger, etc.)

      E.g.:

      • https://github.com/spacetx/starfish/issues/1286 -

        coords in CSV

      • https://github.com/spacetx/starfish/issues/1121 -

        sparse dimensions

      • Registration between two coordinate systems e.g. 2

        separate acquisitions with shifted coordinate systems

    • Significant amount of spatial transcriptomics. Not yet

      public data

  • Workshops (June)

    • Petr/Dom going to Oxford next week

    • Deadline for next Dundee workshop is May 10th

  • GPFS upgrade

    • Still finishing central clusters upgrade. Cannot perform

      nightshade upgrade

    • West-ci is down. Cannot be rebooted. Ticket open with LSC.

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)