Setup

Setting up scripts for OMERO.web has to be done by an administrator of your server. Please contact them if the scripts are not present or in a different version as the one presented in this guide, and redirect them to this page.

The scripts menu is located in the top-right part of the OMERO.web client, on the left of the search bar. Please refer to the script documentation for more information.

Installing the scripts

The Key-value pairs scripts have been updated in 2023 to enable them to annotate all the common object type in OMERO.web:

  • Image

  • Dataset

  • Project

  • Well

  • Run/Acquisition

  • Plate

  • Screen

Check that the version of the currently installed scripts are of 2.0.0 and higher.

If not, you can find the scripts here and follow these instructions to install them.

Configuring the Export script

Note that the Export script can be fine tuned to your specific OMERO.web installation. For that, open the script and find the global parameter named “WEBCLIENT_URL”, and set it to the URL of your webclient, without forgetting to add the http/https protocol in front:

https://your-omeroweb-adress.org/webclient

This will allow the script to return a link for the created .csv for a direct downloading. If not configured, the .csv can be found as an attachment of the first parent object passed in parameter of the export script (the file is attached regardless of whether the URL is set or not).

This can be done with the OMERO CLI:

> omero script list
(out)  ...
       1234 | /omero/KV-pairs_scripts/KeyVal_to_csv.py
       ...
> omero script edit 1234