Tools for
OMERO Users

OME Users meeting
30th May 2018
Will Moore

Outline

"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

OMERO.figure

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

OMERO.iviewer

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

OMERO.FPBioImage

3D viewer based on FPBioImage

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

OMERO.mapr

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-render

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
    channels:
      1:
        color: "FF0000"
        label: "Red"
        min: 1
        max: 255
        active: True
      2:
        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

• OMERO.gallery : 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

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

• Use omero-test-infra
• Docker-composed OMERO server for testing
• Testing scripts run by Travis CI on every GitHub PR
• For example: OMERO.figure .travis.yml

services:
  - docker

before_install:
  - git clone https://github.com/openmicroscopy/omero-test-infra .omero

script:
  - .omero/docker app

Thank you