Tools for

OME Users meeting
30th May 2018
Will Moore


"Tools": OMERO web apps and CLI clients

  • New app features and new apps over the last year
  • Advantages of decoupled clients
  • Testing of decoupled clients


New features in the last year:

  • Crop page to panels
  • Labels from tags
  • Add Polygons and Polylines from OMERO
  • Big (tiled) Image support
  • Last release: OMERO.figure 4.0.0, May 22nd


New features in the last year:

  • Performance improvements
  • UI improvements
  • Export ROI pixel intensity to CSV
  • Multiple viewers
  • Last release: OMERO.iviewer 0.5.0, May 22nd


3D viewer based on FPBioImage

  • August 3rd: OMERO.FPBioImage 0.2.0
    • First public release


Tool for querying data by Map Annotations

  • New feature in last year: Testing infrastructure
  • Last release: OMERO.mapr 0.2.3, May 2nd


OMERO.cli plugin for bulk saving of rendering settings.

  • Last release: cli-render 0.3.0, May 8th
$ bin/omero render set Dataset:1 settings.yml
# settings.yml
        color: "FF0000"
        label: "Red"
        min: 1
        max: 255
        active: True
        color: "00FF00"

Introducing OMERO.parade

Tool for filtering Images and Wells in webclient
using any metadata

  • Prototype presented to OME team: Feb 2018
  • Improved by Glencoe software
  • 0.1.0 Released: May 22nd, 2018

Other apps, not in active development

  • : Browse Project, Dataset Image in mobile-friendly web pages
  • OMERO.player : Web viewer that caches all planes for fast playing through Z/T

Advantages of decoupled clients
For Developers:

  • Prototypes can be developed independently, without breaking anything
  • More flexible release cycles
  • App release takes OME team ~1 hour (~1 Day for OMERO)

Advantages of decoupled clients
For Sysadmins:

  • Simpler for Users to upgrade: no server downtime
  • Easy to install. ALL apps are:
    $ pip install...
  • Only install the apps you want
  • Can install new Apps with an older OMERO.server

Advantages for Users

Integration of apps into webclient

See Linking from webclient and webclient plugin docs

Disadvantages of decoupled clients

  • Discoverability
  • More steps to install "everything"
  • Solutions:
    • Improve visibility on website and docs
    • TODO: Build an app store?!
  • "Decoupled" can mean "less well integrated"
  • For Devs: More repos and testing infrastructure to maintain
  • Solutions: Ansible, Jenkins, Docker etc.

Testing of decoupled clients

  - docker

  - git clone .omero

  - .omero/docker app

Thank you