Installation

OMERO 5.6.x

1. Set up access to the Glencoe Software provided Pageant PyPI compatible repository for use with pip. This repository acts as both a PyPI cache and datastore for Pageant packages. An example $HOME/.pip/pip.conf follows:

   [global]
   index-url = https://username:password@repo.glencoesoftware.com/repository/pageant/simple
   trusted-host = repo.glencoesoftware.com
   [search]
   index = https://username:password@repo.glencoesoftware.com/repository/pageant/pypi
   

   Note

   Credentials to access this repository are available from Glencoe Software customer support and are tied to your active Software Maintenance Agreement.

2. Add gs-population-utils repo to extra-index-url under pip.conf:

3. With your OMERO virtualenv activated, or sufficient permissions, install Pageant:

   pip install -U pageant
   

4. Enable the Pageant OMERO.web plugins:

   omero config append --set omero.web.apps '"pageant"'
   omero config append --set omero.web.apps '"gs_population_utils"'
   

5. Enable the right-click menu plugins:

   omero pageant install menu
   

6. Configure available Pageant routes. If configuration isn’t provided Pageant defaults to only Main route:

   omero config set omero.web.pageant.routes '["main", "classification", "review", "threshold"]'
   

7. Configure available Pageant thumbail shape color:

   # Solid color
   omero config set omero.web.pageant.shape_color '#ff00ff'
   # With specified opacity
   omero config set omero.web.pageant.shape_color 'rgba(255, 0, 255, 0.5)'
   

8. Configure available Pageant default channel range:

   omero config set omero.web.pageant.channel_range '[0, 600]'
   

9. Configure available Pageant default plot axis ranges:

   # Set default x range
   omero config set omero.web.pageant.x_axis_range '[400, 1600]'
   # Set default y range
   omero config set omero.web.pageant.y_axis_range '[0, 5000]'
   

10. Restart OMERO.web:

    omero web restart
    

Upgrading