The Open Microscopy Environment (2024)

Dundee: Will, Petr, Roger, Dominik, Simon, Helen, Balaji, Mark, Riad,Jason, Andrea,

Remote: Sebastien, Jean-Marie, Josh, Wilma, Melissa, David, Liza,Eleanor, Emil

Start: 2:00 pm

1. Accepting minutes from last meeting

2. Project Timelines

(2-3 minutes each)

A. Spaces

• Files/Formats

  • Unidata server changes - breaks build. First round of fixes

    worked. More rounds of fixes needed. Only affects thosebuilding with ant (not maven)

  • Model documentation CI adjustments - Update to latest version of

    Sphinx

  • Upcoming Dresden meeting - December. Java community IJ, Knime

    etc. BDV format discussion.

  • PR review/cleanup across format repositories

• Metadata

  • Upcoming training (IDR training at EBI 23rd Nov). See #training

  • Licensing updates. Authors of IDR data. Most cc by. See

    idr-submissions list.

  • One dataset ready IDR-38 (Light-sheet); few getting close. See

    idr-project board.

• OMERO 5.4.1

  • Board needs to be cleaned up. Try to keep “essential” card

    • Release date will need to be discussed

    • 5.4.1 probably after Cambridge training.

  • Will: thumbnail caching may be a major (pre-training) blocker:

    https://trello.com/c/2fQFE3Lb/99-bug-thumbnail-caching

  • Simon: try to avoid a pre-holidays release

  • Josh: might consider a milestone release if needed

• Outreach

  • Will:

    SMGnext week

  • Balaji: Cambridge 33 registered for 1st day. 21 for day 2.

  • 20 registered for Eleanor’s Jupyter notebook IDR training

  • Misc training discussions: upcoming NEUBIAS meeting, tagathon

    and training sessions.

  • GBI hackathon in April/May (TBD)

    • Also: Okinawa, Bangalore, Sydney
  • JRS: Upcoming IDR presentations at Cambridge & ASCB

B. Other releases/upgrades:

• Figure

  • Workshop at SMS next week

• iViewer

  • board with cards considered for [iviewer

    1.0</u>](https://trello.com/b/n0uYFFOB/iviewer-10) (date to beconfirmed but before end of year)

• Website

  • Hosting of training materials

  • Forum posts re: docs. Relationship between website and docs.

    Content / styling.

  • Naming, de-wiki-fication

  • Balaji: proper doc review (point-by-point)

• Sysadmin

  • Web deployments with public users needing periodic restart (too

    many threads)

  • https://trello.com/c/DC5CB4Ty/106-bug-omeroweb-processes-threads

C. Glencoe Update (Chris)

• BF: OIR discussion with Olympus. Needs testing against entire suite.

• omero-ms : working with masks. First pass almost done. Will open

  design issue for proposals.

1. AOB

• [Proposal for the removal of Java 7

  support</u>](https://docs.google.com/document/d/1L_aSP1B0TNTny75Xvua6DPLLOt68jnJTF8GEHj1y4Ug/edit)(Roger)

  • Please add feedback / comments to doc by end of November

1. Upcoming Epics and teams

• History - CVS -> SVN -> private Git -> Public Git ->

  Github -> Snoopy -> Devspace

• Problem: size & complexity of software stack, big problems, complex

  decisions etc.

• Horizontal teams -> Vertical teams

• Gatekeeping: conflict between deadlines and good open-source

  commits.

• Now:

  • Cambridge December training

  • IDR prod44 release (datasets and notebooks)

• Next:

  • Upcoming IDR Datasets

  • ROIs & features

• Gatekeeping:

  • Training materials -> public

  • IDR submission knowledge transfer

  • Coordination between Now/Next priorities

• Adjustments:

  • Standup template - No PRs?

  • Trello boards - by component instead of release version? Use

    github issues?

• WM: main todo till Cambridge? Probably not code focused

  • JM: heavy preparation that is not strictly code. Get material

    ready, testing burden

  • Balaji: apart from server/infrastructure, also things to be done

    in terms of users expectations

  • WM: can’t filter by tags in webclient. Priority? JM: depends on

    the criticality of the issue.

  • SL: pb of webclient coupled to the server at the moment. JM: can

    schedule a milestone release if needed.

  • JRS: puts the now team in charge of making these decisions

    responding to the training or community needs.

  • @@JAM: put slides publicly

• Petr: where are the PRs????

  • JRS: create sections for now/next in tomorrow’s standup

  • Roger/Riad: use feature branches as a way to solve this problem?

• Balaji: what about adjusting for the annual leave with this

  construction

  • JAM: existence of team deadlines should allow people to raise

    flags early

• Balaji: how to prevent divergence in the near-future?

  • JAM: define the responsibilities for merging/rebasing.

    Management cost associated to keeping 2 lines synchronized.

  • Idea of keeping 5.4 stable included. Idea: try to keep test

    server running as long as possible - prevent serverredeployment as habit to try and stabilize developmentefforts.

• Petr: teams established? JAM: teams thought through with epics

  coming up.

  • JRS: open proposal. Open for comments/feedback.

• MTC: discouraged to take random PRs to focus on teamwork?

  • Josh: separation between functional testing and code review. At

    some point some feature branch will need a review across theboard.

  • Encourage discussing an issue i.e. design issues

• Balaji: no UI/usability in Next.

  • JAM: motivated by upcoming Cambridge training. Trade off made

    initially for the upcoming month. Discussion of theconstitution might need to happen again in 2018 incl. changesof priorities.

  • JRS: hiring
• JRS: cF. team organization during FS, permissions, …