2018-05-01

Dundee: Kenny, Simon, Will, Mark, Riad, Dom, Petr, Jason, June,

Remote: Chris, Josh, Seb, J-m, Melissa, Liza, Wilma, Andreas, David

Start: 2:00 pm

1. Accepting minutes from last meeting

2. Project Status

(2-3 minutes each)

• Community

  • *Moved to the top to free up those primarily interested in

    \#ome2018*

  • Users’ Meeting

    • 45 external registrants so far

    • Discussion of workshops (below)

    • Speakers’ schedule (Day 1)

      • Short talks: 10+5 to start

      • Lightning for 1.5 hours

      • Long talks: 20m talk + 10m questions

      • 1m poster talks

    • Kenny: Code of conduct? Yes. Card please.

  • Spam fun

    • Some fix made (.org, .org.uk whitelisted)

• West (Workflows)

  • OMERO 5.4.6: last call for PRs

    • Known read-only issues will be documented but won’t be fixed

      for 5.4.6

  • Figure:

    • Big image PR integrated. For full review see [testing

      sheet</u>](https://docs.google.com/spreadsheets/d/1qdOAv0wUgAVHEtlVroOwkeNUoNwst-APSPFJk6-3Sz8/edit#gid=0)

    • To be released before users’ meeting

  • IViewer:

    • No time for 1.0.0, will have intermediate release before

      users’ meeting

  • VAE:

    • Second round of notebooks testing on-going. Looking good.

    • One remaining Issue with

      (current idr-py). Not related to VAE.

    • Next: test with prod50

  • Working on workshop. [OME2018 Day 2

    workshops</u>](https://docs.google.com/document/d/1qXFzeIlijNUDxjRSAIEYZmmeiS4OCREyP_xq7BXOMBs/edit#) (Trello board)

    • Need to figure out room capacity if we run a single track

      workshop (“Metadata track”)

    • Some workshops will benefit from space to use laptops

    • Producing an “Import” handout for participants

    • Testing analysis workshop

• East (infra/IDR 0.5.0)

  • Prod50: last minute changes, re-caching, & publication, ETA next

    week

  • Beyond:

    • HPA (26,000 imports, antibody labelled TMAs, complex

      metadata)

    • mapr performance status (“endpoints”)

      • Postgres: Materialised views (Mark) to optimise queries

        with Vertex webmicroservice (Riad) in front

      • Tradeoff between PG changes vs Elasticsearch

        • Elasticsearch would allow indexing external

          ontologies

      • Naming….

      • New style of server (without Ice)

      • JRS: blog on improvement in metadata queries

      • cF. HPA antibody tagging as a use case

  • TIFF-Pyramids: Reading & Writing status as well as upcoming demo

    • Should be able to use BFConvert to generate pyramids for any

      OME-TIFF

• Glencoe

  • Promoting mapr and parade (upcoming release) to users with large

    datasets

  • Working with large per-objects tables (millions of rows)

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)

Report on the CZI meeting, Computational Tools for the HCA.

Discuss of slides that were presented. See Slides 37 & 38

• General description

  • Human Cell Atlas goals

  • CZI Computational Tools RFA

  • Dearth of imagers & imaging

• Datasets

  • Rohban (cellpainting): cf idr0033

  • *FISH (smFISH, etc)

  • Sanger (MERFISH, spatial transcriptomics)

  • JRS: “profile tissue in some state”

• Technical Parts

  • Purple: ingestion & validation

  • Blue: S3, Elasticsearch

  • Orange: file browser; handoffs

  • Green: still a bit unclear

  • Red: Portals

  • Misc services

• Concrete next steps

  • File formats: YAFF as well as S3/BDV

  • Image metadata json schema

  • An OMERO instance

    • QuPath?

  • Lots more talking