Skip to content

cneves/scripts

 
 

Folders and files

NameName
Last commit message
Last commit date

Latest commit

 
 
 
 
 
 
 
 
 

Repository files navigation

OMERO Core Scripts

This directory contains OMERO scripts which use the OMERO.scripts API. All scripts (e.g. "*.py") present in the directory will be automatically distributed with all binary builds. Which file-endings will be detected and how they will be launched are both configured centrally in the server. ".py", ".jy", and ".m" (MATLAB) files should all be detected by default starting with OMERO 5.

Categories

Scripts are separated into several categories, one per directory.

In the directory should be scripts which ...
analysis_scripts crunch images to produce numerical results and similar tasks
export_scripts take one or more images as an input, and produce a representation for exchange
figure_scripts take one or more images as an input, and produce a summary representation
hcs_scripts work with screens/plates/wells rather than just images
import_scripts are run on images after import for extra processing
processing_scripts create new images from existing images or other data
setup_scripts are executed once, often by administrators, to configure OMERO itself
util_scripts perform other miscellaneous tasks like cleaning up or optimizing OMERO itself

Scripts which would like to rely on other scripts can use:

import omero.<sub_dir>.<script_name>

For this to work, the official script in question must be properly importable, i.e.:

def run():
    client = omero.scripts.client(...)

if __name__ == "__main__":
    run()

OMERO User Scripts

If you would like to provide your own scripts for others to install into their OMERO installations, please see http://openmicroscopy.org/info/scripts

Packages

No packages published

Languages

  • Python 100.0%