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Script Sharing

Scripts: Plugins for OMERO, allowing you to add functionality to OMERO

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.pyAnalysisCorrelate image channel intensities AllAlex Herbertaherbert
Colocalisation Analyser.pyAnalysisAssess colocalisation of image channels AllAlex Herbertaherbert
Batch_Image_Export.pyExportZip images for download AllOME teamCore
Make_Movie.pyExportMake movie from image AllOME teamCore
Movie_Figure.pyFigureMake figure from movie frames AllOME teamCore
Movie_ROI_Figure.pyFigureMake figure of zoomed ROIs in movie AllOME teamCore
ROI_Split_Figure.pyFigureMake figure of zoomed ROIs AllOME teamCore
Split_View_Figure.pyFigureMake split view figure of images AllOME teamCore
Thumbnail_Figure.pyFigureMake figure of multiple thumbnails AllOME teamCore
Check_original.pyFixingCheck DropBox imports AllPierre PouchinPPouchin
Rename_Images.pyFixingReplaces names AllPierre PouchinPPouchin
Restore_colors.pyFixingFix colors for LIF and LSM files AllPierre PouchinPPouchin
Restore_date.pyFixingFix acquisition date AllPierre PouchinPPouchin
Populate_ROI.pyImportGenerate ROIs from Plate measurements AllOME teamCore
Check Images.pyImportValidate converted pixel data AllAlex Herbertaherbert
Image size.pyImportCheck file size AllAlex Herbertaherbert
Channel_Offsets.pyUtilGenerate new images with x,y,z shifts AllOME teamCore
Combine_Images.pyUtilMerge images or Z-stacks to extra dimensions AllOME teamCore
Dataset_To_Plate.pyUtilConvert Dataset of images to Plate AllOME teamCore
Images_From_ROIs.pyUtilMake new image cropped to ROI, now including tiled big images AllOME teamCore
Move_Annotations.pyUtilMove Annotations from SPW Images to their parent Wells AllOME teamCore
New_Images_From_ROIs.pyUtilAdapted new images from ROIs allowing cropping through entire T or Z stack AllAlex Herbert & OME teamExample scripts
Dataset_To_Well.pyUtilConvert a Dataset of Images to Fields in a Well AllDamir Sudardsudar

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.

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:

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 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 util_scripts/ 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

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