Available Scripts

Whether you are writing a script or looking for a script to use, the following list provides an overview of all scripts that have been tested to work with a standard OMERO installation. Other scripts and examples, specialized for particular institutions or third-party extensions, are available from other repositories listed below. Scripts may require other software in addition to OMERO, which will be detailed in the description and should be readily available.

Name	Type	Function	OMERO Version	Attribution	Repository
Correlation Analyser.py	Analysis	Correlate image channel intensities	All	Alex Herbert	aherbert
Colocalisation Analyser.py	Analysis	Assess colocalisation of image channels	All	Alex Herbert	aherbert
Batch_Image_Export.py	Export	Zip images for download	All	OME team	Core
Make_Movie.py	Export	Make movie from image	All	OME team	Core
Movie_Figure.py	Figure	Make figure from movie frames	All	OME team	Core
Movie_ROI_Figure.py	Figure	Make figure of zoomed ROIs in movie	All	OME team	Core
ROI_Split_Figure.py	Figure	Make figure of zoomed ROIs	All	OME team	Core
Split_View_Figure.py	Figure	Make split view figure of images	All	OME team	Core
Thumbnail_Figure.py	Figure	Make figure of multiple thumbnails	All	OME team	Core
Check_original.py	Fixing	Check DropBox imports	All	Pierre Pouchin	PPouchin
Rename_Images.py	Fixing	Replaces names	All	Pierre Pouchin	PPouchin
Restore_colors.py	Fixing	Fix colors for LIF and LSM files	All	Pierre Pouchin	PPouchin
Restore_date.py	Fixing	Fix acquisition date	All	Pierre Pouchin	PPouchin
Populate_ROI.py	Import	Generate ROIs from Plate measurements	All	OME team	Core
Check Images.py	Import	Validate converted pixel data	All	Alex Herbert	aherbert
Image size.py	Import	Check file size	All	Alex Herbert	aherbert
Channel_Offsets.py	Util	Generate new images with x,y,z shifts	All	OME team	Core
Combine_Images.py	Util	Merge images or Z-stacks to extra dimensions	All	OME team	Core
Dataset_To_Plate.py	Util	Convert Dataset of images to Plate	All	OME team	Core
Images_From_ROIs.py	Util	Make new image cropped to ROI, now including tiled big images	All	OME team	Core
Move_Annotations.py	Util	Move Annotations from SPW Images to their parent Wells	All	OME team	Core
New_Images_From_ROIs.py	Util	Adapted new images from ROIs allowing cropping through entire T or Z stack	All	Alex Herbert & OME team	Example scripts
Dataset_To_Well.py	Util	Convert a Dataset of Images to Fields in a Well	All	Damir Sudar	dsudar

A note about versions - we use Github branches to manage our various development lines. Scripts for OMERO 5.3 release versions are located on our develop branch in the core repository, while the dev_5_2 branch is for OMERO 5.2.x. Since OMERO 5.2.x has entered maintenance mode, we recommend you work against the develop branch as a default.

OMERO 5 now supports jython and MATLAB scripts natively, see the OMERO 5 scripts documentation for further details.

Other places to find scripts

Below is a list of repositories on Github and elsewhere that have been submitted to the OME team. All of the included scripts and repositories can be downloaded following the instructions below in order to run the scripts locally (although some of them are intended as examples only - check the associated README). Some of the included scripts are also detailed above.

• OMERO scripts - Glencoe Software
• Example scripts - OME Team
• Fixing scripts - Pierre Pouchin
• GDSC OMERO user scripts - Alex Herbert
• QBI-Microscopy scripts - Queensland Brain Institute
• OMEROscripts - Damir Sudar

Downloading and installing scripts

The easiest way to make use of scripts is for your system administrator to upload them to the server. Once a script has been added under the lib/scripts directory, you can run them from the OMERO clients or the command line. Documentation for script developers and admins is available here. However, you will not be notified of any updates to the script, nor will you be able to automatically update them. This means that when your OMERO installation is upgraded, all your additional scripts will be lost.

Therefore, we recommend you use a Github repository to manage your scripts. If you aren't familiar with Git, you can use the Github app for your OS (available for Mac and Windows). The basic workflow is:

• Fork our omero-user-script repository or any other repository you trust (https://github.com/ome/omero-user-scripts/network/members)
• Clone it in your lib/scripts directory (cd lib/scripts; git clone git@github.com:YOURGITUSERNAME/omero-user-scripts.git YOUR_SCRIPTS )
• Save the scripts you want to use into the appropriate sub-directory in your cloned location lib/scripts/YOUR_SCRIPTS

If all you want to do is add scripts from someone else's repository to your server, you can simply clone that repository in your lib/scripts directory and the scripts within it will be added to your script list as described in the OMERO-user-script repository readme.

Developing your own scripts

The easiest way to get started developing scripts for your own site is to fork the github.com/ome/omero-user-scripts repository and clone it somewhere under lib/scripts as described above. Then go into YOUR_SCRIPTS and rename the existing script to match your needs (cd lib/scripts/YOUR_SCRIPTS; git mv Example.py util_scripts/New_function.py). Once you've done that, you can edit and test run the script and then when you're happy with it, you can save it and push it back to your fork for others to see and share.

Have a read through the documentation on using the scripting service and style guidelines for writing scripts and feel free to ask for advice.

If you are a biologist with no previous coding experience, you may find the Python for Biologists free online course helpful.

Submitting scripts back to the OME Consortium

If you have modified one of the core scripts or developed your own that you would like to contribute back to the OME Consortium, please get in touch. We can either add your repository to the list above so people can find it, or if the script is likely to have wide appeal, we can look into adding it to the core scripts that are distributed with an OMERO release.

Further information

• User guide illustrating example script functionality and how to run official scripts from OMERO.insight

• Full developer documentation on the scripting service

• Github core scripts repo - see the readme for suggested directory names for your scripts.