Change image rendering settings and channel names using the Command Line Interface (CLI)

Description

This chapter will show how to change rendering settings on images using the Command Line Interface (CLI).

This action is typically done after a successful import of images.

We will show:

• How to change rendering settings of large amount of images on the CLI in a repeatable manner.

Resources

• Documentation:

  • https://docs.openmicroscopy.org/latest/omero/users/cli/installation.html

  • https://docs.openmicroscopy.org/omero/latest/users/cli/index.html

• Data: example images from

  • IDR data idr0021.

• Rendering plugin for OMERO

  • https://pypi.org/project/omero-cli-render/

• Rendering yml files defining the various rendering parameters, such as the channel color, channel name and minimum and maximum values.

  • https://github.com/ome/training-scripts/blob/master/maintenance/preparation/renderingdef.yml

  • https://github.com/ome/training-scripts/blob/master/maintenance/preparation/renderingdef2.yml

• Rendering mapping file has two columns, in the left-hand one there are the images to be rendered and in the right-hand side column points to the appropriate ​renderingdef.yml​ for that image.

  • https://github.com/ome/training-scripts/blob/master/maintenance/preparation/renderingMapping.tsv

• Shellscript for batch modification of rendering settings of images

  • https://github.com/ome/training-scripts/blob/master/maintenance/scripts/apply_rnd_settings_as.sh

Setup

Rendering plugin installation

• Go to the environment where you installed your OMERO.cli as specified under - https://docs.openmicroscopy.org/latest/omero/users/cli/installation.html.

• Activate the virtual environment.

• Run:

  $ pip install omero-cli-render
  

Step-by-step

1. On your local machine, open a terminal

2. Activate the virtual environment where omero-py is installed or add it to PATH e.g.:

   $ export PATH=/opt/omero/server/venv3/bin:$PATH
   

3. The variable $ID​ below is the ID of the ​selected Dataset. To change the rendering of images in one Dataset, run:

   $ ​omero render set Dataset:$ID local_path/to/renderingdef.yml
   

4. Verify the change in the browser.

5. To change the rendering of images in two Datasets, run:

   $ omero render set Dataset:$ID1 Dataset:$ID2 renderingdef2.yml
   

6. Modify the rendering settings in batch using a shellscript such as apply_rnd_settings_as.sh which uses ​HQL ​to find the Images IDs in OMERO and deliver them to the omero-cli-render​ plugin. The script reads the Datasets in which the Images are located in OMERO are listed from a​ renderingMapping.tsv ​​file, such as renderingMapping.tsv. Go to the folder where the script is located. Then run the bash script with the default parameters:

   $ ​sh apply_rnd_settings.sh
   

   The script could be run by a facility manager on behalf of other users.