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.
Scripts are separated into several categories, one per directory.
---------------- | --------------------- |
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