2018-02-20

Dundee: Will, Kenny, Petr, Dominik, Mark, June, Helen, Balaji, Jean-Marie, Riad,

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

Start: 2:00 pm

1. Accepting minutes from last meeting

2. Project Status

(2-3 minutes each)

• West (Workflows)

  • Upcoming 5.4.4 release

    • rc thursday [testing

      sheet</u>](https://docs.google.com/spreadsheets/d/1lI4jVmocE-DuQhxS_EMqjcI2UeNrAoIq1TgM5HlIPnY/edit#gid=1254367109)

    • Last 2 PRs to go in

    • Main workflow PR against develop needs to be green.

    • Need fix to pyramid invalidation PR

    • History PR open tomorrow

  • Iviewer:

    • Good progress aiming for 1.0 after 5.4.4

    • Improvements in shape deletion, css tweaks etc.

    • Multi-viewer workflow - double-click to open new windows

    • Some merge conflicts to resolve

  • Next: prep for Trends in Microscopy

    • 12th-14th March - 2 hour workshop.

    • Jason: show iviewer!

    • Using outreach server - connection OK etc.

• East (infra/IDR 0.5.0)

  • Recursive builds (oh my)

    • Roger’s work on coupling & building multiple PRs.

    • Try this with submodules & a ‘super/meta repository’

  • IDR:

    • read-only work continuing on 5.4 session manager

    • mini-idr 2.0 - Scripts to import plate from each study

    • The dreaded Hibernate 5+ (Riad)

      • May support ‘old’ server and Hibernate 5 server together

  • Systems

    • Kubernetes:

      https://github.com/openmicroscopy/kubernetes-apps

      • Up and running

      • Redmine too

      • Naming discussion

      • Each user to create submodule on repo above

      • Coming: devspace k8s app

    • GPFS: migration

      • Fix downloads and docs timeouts -> migrate to our own

        GPFS

      • Move more resources - squig etc.

      • Want to get naming correct - hard to change once in

        place

      • Might get confusing, but we’ll mount everything under

        /ome on various boxes

      • Not sure if we’ll take the time to get Samba running

      • Jason: Use UoD IT resources where appropriate

• Glencoe

  • Training microservices on Thursday.

  • Prepping OMERO 5.4 updates for customers

  • Cross-group support for rendering plugin

  • Handling large number of channels, especially wrt ROIs

  • Exploring new tech e.g. communication between server components

    etc.

• Community

  • JRS: Scientific Data announcing IDR as a recommend (image) data

    repository

  • JRS: Increasing submissions so good to formalize tracking

    (redmine)

  • Elmi: workshops 2 slots of 1h June

  • Users meeting: Jason thinking about speakers…? Suggestions?

    • Aim for shorter talks, more community focus.

    • IDR update, community update, what else?

    • What examples do we know of users doing cool stuff? 10-15

      mins talks.

    • JM: publishing workflows, interactive figures etc?

    • Open registration to externals by end of week.

    • Liza is working on banner for website.

    • Registration fee - flat rate £115.

1. AOB

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

• Any update on when User meeting registration will be open to

  externals?

  • Covered above - end of the week likely

1. Webclient custom filtering plugin demo by Will

(20-25 minutes plus 15 minutes questions max)

• JRS: works on dataset? Yes

• PW: heatmap in grid? Could do. Single value

• PW: fantastic, exactly what’s wanted in recent feedback

  • Except they want for all data

  • E.g. search result data

  • WM: yes, center panel should be enabled for search results

  • JMB: even cross-plate or cross-project results.

  • WM: UI like in insight

  • WM: but center panel currently expects the tree to be there

  • WM: … search panel also has a mixture of stuff that’s not

    expected by the center panel

  • WM: … paging works differently

• PW: how will plugin work with paginated dataset?

  • WM: haven’t tried yet.

  • WM: assume previously we had pagination so that thumbnails can’t

    be loaded. Hope to adjust the page size.

  • JAM: cF. “human cells” on IDR (2.4M)

  • CA: Emil’s been looking at something similar in d3. As soon as

    you get beyond a trivial number of images (few hundred) [it] falls apart. Even for querying across a screen, will need to eventually filter server-side.

  • JAM: imagine we want both strategies. If you have the data

    and it’s small enough, then filter (render, etc.) locally. Otherwise, server-side.

  • JRS: bifurcation in usage patterns. Imagine many people would

    want it immediately for more reasonably sized datasets. Useful query would be across the screen, that’s the important experimental concept.

  • WM: worth trying to find the limits? JRS/CA/…: yes.

  • JMB: are the thumbnails even useful? CA: already had some

    feedback that below a certain size it’s not useful.

  • CA: try cellprofiler for real metrics? 30-40 columns.

  • CA: just letting someone write a query? WM: cF. Lucene but you

    wouldn’t want to type in map k/v CA: perhaps have a limited vocabulary, e.g `roi_count > 50`

• JMB: comments on central panel issue?

  https://github.com/openmicroscopy/design/issues/82

• CA: funded for very large use case. Would be nice to work on a

  single implementation.

• WM: do we keep adding to the current filtering functionality

  (rating, name), i.e. are we replacing the current center panel or maintaining both? JMB: similar to iviewer migration…

  • CA: already much better

  • WM: don’t currently support the multiple well at the bottom

  • JRS: evaluating replacing current with this next-generation

  • BR: “just a plugin” (with limitations) may make it manageable.

    Already get quite a lot.

  • JMB: buy us time.

• JMB: exporting the current view (PDF, JPEG) is good.

  • Export to figure? WM: Balaji’s been playing with a library for

    that.

  • PW: cF. buried Excel export (recently asked for)

  • KG: exporting the search results (search query itself)

  • CA: “subsets” (for easy Dataset creation). Saving views :+1:

• CA: need the repository to be migrated

  • MC: on gitlab?

  • JMB: also need pip installation

  • CA: interested before end of March

• JRS: actions

  • Find the limit

  • Show heat-maps as default (no thumbnails)

  • Cross-container ability

  • New name? (Several votes for “parade”)

    • PW: as a plugin, then discoverability is paramount. “I don’t

      have figure tab” Users may not be able to connect the dots to “parade” WM: googlable name is perhaps enough. PW: how to know what to google. CA: don’t know the name buys you much. PW: “filter(ing)” CA: but it’s searching

  • Trajectory of development

    • Repo actions

    • First releases for one set of use cases (smallish, local, …)

    • Scaling-up / server-side

    • Exporting

    • Persisting views