This directory contains OmeroPy scripts which use the OmeroScripts API. All scripts ("*.py") present in the directory will be automatically distributed with all binary builds.
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()
If you would like to provide your own scripts for others to install into their OMERO installations, please see http://openmicroscopy.org/info/scripts