2018-01-16

Dundee: Helen, Kenny, Will, Mark, June, Dom, Petr, Simon, Roger, Riad, Emil, Balaji,

Remote: Seb, Jean-Marie, Josh, Wilma, David, Mark, Andreas, Chris, Melissa

Start: 2:00 pm

1. Accepting minutes from last meeting

2. Project Status

(2-3 minutes each)

• “Now”

  • Robot in devspace. Looking at improving speed and stabilizing

    tests

    • Looked at running them in parallel

      (pabot). New library (0.4)

    • Down to 4 failures on Firefox. Close to stability
  • Working on [Facility Manager

    workflow</u>](https://trello.com/c/GJiuntTK/92-workflow-vi-facility-managerlight-admin) for next training (end of January)

    • Preparing for Trends in Microscopy (March)
  • Figure release later this month. Working on final PRs and Help

    docs

    • Polygon support not in this release.

  • Kubernetes presentation. Simon, 6th Feb.

    • Assume knowledge of Docker & Docker-compose

    • Set aside time to consolidate Docker & other training

  • Chris: looking for potential dates for microservices training

• “Next”

  • ROI/HDF5 (PRs & Grants)

  • Update on 5.4.2 timeline

    • Targeting release for Tuesday

      • Docs

      • Code

      • (Apps?)

      • Etc.

      • Any final changes to get in?

      • Last PRs on Thursday

    • Public user testing

      • Enable public user temporarily on web-dev-merge

      • Need a way to test other server configs

  • Read-only work - to mainline OR IDR branch

    • Currently captured in

      https://trello.com/b/Z3y5ty8o/idr-050

  • Likely 5.4.3 (maybe 5.4.4) by Users’ meeting.

  • Roger - HDF data from ROIs in sample files.

    • Ready to try import these into OMERO

• Glencoe (Chris):

  • Changing process wrt Bio-Formats in particular

    • Will try to open all PRs initially against opensource

      Bio-Formats github

    • Adding some formats in the near future

    • Want to test against next major version etc.

  • Try same approach with OMERO too.

    • Features related to scripts and scripts UI

    • More new hires involved

    • Run scripts in parallel, show progress/feedback to user etc.

    • Use as much real test data as possible

  • Microservices- rendering regions. Improving scalability

• Community

  • IDR Next Release (Seb)

    • 0.4.5 planned for February - 2 new Datasets.

    • Create new production server and start import soon

    • Need to update/fix all notebooks

    • Mid-term future - moving to OMERO 5.4.x

    • Need to improve tracking of data submission requests.

    • Looking at redmine as an option to manage these

  • Meltdown/Spectre (Josh)

    • Send out response? Chris: no big gain in recycling existing

      security advisories.

    • Patching our systems is in progress (completion needs

      scheduling)

    • Restart devspace to update

1. AOB

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

• Breaking jobs & devspaces

  • Ci cleanup. Remove breaking jobs (been disabled for a while now)

  • Now: Define branches for large feature development and use

    devspace for testing

  • Mark: will anything test DB upgrade paths?

  • Seb: no - this will still need to be a manual setup

  • JM: ported Training testing to devspace - except Matlab

  • Simon: testing DB upgrade is similar to testing server config

    (above).

• Kenny: taking DB dumps etc from old nightshade2 and rsync to squig.

• June: Should be able to confirm user meeting dates next week

1. Main Topic

(20-25 minutes plus 15 minutes questions max)

• [Binary

  Vessels</u>](https://docs.google.com/presentation/d/11fThpeiVHPkp26XCTF4C9FxHFgtQMW31zB8dTAZNWto/edit) (Seb)

• Recent discussions on team priorities…

• 3 main areas of work: OMERO ecosystem, scaling IDR and Binary

  vessels

• Current state (of the art):

  • OME-TIFF - tiff files with ome.xml file for metadata etc

  • BigDataViewer (BDV) - HDF5 file with bdv.xml

• BDV is efficient for pixel storage, multi-dimensional etc

• But, BDV is not versioned, no upgrade path, limited metadata support

• Combine best features from OME-TIFF and BDV.

• Requirements:

  • Target Users’ meeting 2018

  • Supported components(core)

    • Containers: TIFF, H5, KLB

    • Codecs

  • Workflows

    • Reading BDV v1 filesets

    • Reading writing OME-BDV v2 filesets

    • Clients (ImageJ/BDV stack, OMERO?)

    • Implementation languages - Java, C++?

• Tech choices:

  • OME Data Model / spec

    • Add BDV xml elements

    • OME Pixels elements - deprecate vs upgrade

    • Subresolutions handling [design

      #74</u>](https://github.com/openmicroscopy/design/issues/74)

  • Container formats

  • Reader/writer API

    • Binary data access: plates -> blocks

    • OME-XML code generation (Metadatastore API)

    • Codecs: detection/extensibility

    • Thread-safety

  • Next steps

• What about Bio-Formats?

  • B-F 5.7.3

    • Included in OMERO 5.4.2

  • Moving towards B-F 5.8.0

    • New format readers (Glencoe software)

    • Community contributions

  • Beyond 5.8.0

    • Releases as needed

    • Open-source team - no planned work, maintenance/support

• Mark: What about ROI storage?

• Seb: masks stored as for images

  • But ROI storage is not a priority, given size of other tasks.