Change image rendering settings and channel names using the Command Line Interface (CLI)¶
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.
- Data: example images from
- IDR data idr0021.
- Rendering plugin for OMERO
- Rendering yml files defining the various rendering parameters, such as the channel color, channel name and minimum and maximum values.
- 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.
- Shellscript for batch modification of rendering settings of images
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.
$ pip install omero-cli-render
On your local machine, open a terminal
Activate the virtual environment where
omero-pyis installed or add it to
$ export PATH=/opt/omero/server/venv3/bin:$PATH
$IDbelow 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
Verify the change in the browser.
To change the rendering of images in two Datasets, run:
$ omero render set Dataset:$ID1 Dataset:$ID2 renderingdef2.yml
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.