Skip to main content

OMERO scripts

Project description

https://travis-ci.org/ome/omero-scripts.svg https://badge.fury.io/py/omero-scripts.svg

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

Testing

Integration tests under test/ require an OMERO server with scripts installed. The tests are run by Travis for open PRs using omero-test-infra to deploy OMERO via Docker containers.

To run tests locally:

# All tests $ python setup.py test

# Single test in a single file $ python setup.py test -t test/integration/test_util_scripts.py -k test_dataset_to_plate

Project details


Download files

Download the file for your platform. If you're not sure which to choose, learn more about installing packages.

Files for omero-scripts, version 5.6.0
Filename, size File type Python version Upload date Hashes
Filename, size omero-scripts-5.6.0.tar.gz (76.5 kB) File type Source Python version None Upload date Hashes View hashes

Supported by

Elastic Elastic Search Pingdom Pingdom Monitoring Google Google BigQuery Sentry Sentry Error logging AWS AWS Cloud computing DataDog DataDog Monitoring Fastly Fastly CDN DigiCert DigiCert EV certificate StatusPage StatusPage Status page