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README.md

OMERO User Scripts

Installation

  1. Change into the scripts location of your OMERO installation

     cd OMERO_DIST/lib/scripts
    
  2. Clone the repository with a unique name (e.g. "gdsc")

     git clone https://github.com/aherbert/omero-user-scripts.git gdsc
    
  3. Update your list of installed scripts by examining the list of scripts in OMERO.insight or OMERO.web, or by running the following command

     path/to/bin/omero script list
    
  4. The ImageJ analysis scripts require additional configuration. The scripts need to know where to locate the ImageJ program and ImageJ must have the correct plugins installed.

    Additional steps for headless execution of ImageJ on UNIX platforms are also required.

    Further details are available in the INSTALL file.

Upgrading

  1. Change into the repository location cloned into during installation

     cd OMERO_DIST/lib/scripts/UNIQUE_NAME
    
  2. Update the repository to the latest version

     git pull --rebase
    
  3. Update your list of installed scripts by examining the list of scripts in OMERO.insight or OMERO.web, or by running the following command

     path/to/bin/omero script list
    

Developer Installation

  1. Fork omero-user-scripts in your own GitHub account

  2. Change into the scripts location of your OMERO installation

     cd OMERO_DIST/lib/scripts
    
  3. Clone the repository

     git clone git@github.com:YOURGITUSER/omero-user-scripts.git YOUR_SCRIPTS
    
  4. The ImageJ analysis scripts require additional configuration. Further details are available in the INSTALL file.

Adding a script

  1. Choose a naming scheme for your scripts. The name of the clone (e.g. "YOUR_SCRIPTS"), the script name, and all sub-directories will be shown to your users in the UI, so think about script organization upfront.

    a. If you don't plan to have many scripts, then you need not have any sub-directories and can place scripts directly under YOUR_SCRIPTS.

    b. Otherwise, create a suitable sub-directory. Examples of directories in use can be found in the official scripts repository.

  2. Place your script in the chosen directory:

  • If you have an existing script, simply save it.
  • Otherwise, copy Example.txt and edit it in place. (Don't use git mv)
  1. Add the file to git, commit, and push.

Testing your script

  1. List the current scripts in the system

     path/to/bin/omero script list
    
  2. List the parameters

     path/to/bin/omero script params SCRIPT_ID
    
  3. Launch the script

     path/to/bin/omero script launch SCRIPT_ID
    
  4. See the developer documentation for more information on testing and modifying your scripts.

Legal

See LICENSE

About

This section provides machine-readable information about your scripts. It will be used to help generate a landing page and links for your work. Please modify all values on each branch to describe your scripts.

Repository name

GDSC OMERO User Scripts repository

Minimum version

4.4

Maximum version

5.0

Owner(s)

Alex Herbert

Institution

Genome Damage and Stability Centre, University of Sussex

URL

http://www.sussex.ac.uk/gdsc/intranet/microscopy/omero/scripts

Email

a.herbert@sussex.ac.uk

Description

Example script repository to be cloned, modified, and extended.

The scripts contain examples of utility scripts and image analysis using ImageJ.

The following scripts are available:

  • Check Images : Check the final frame of an image contains pixel data. Used to validate data import completed
  • New Images From ROIs : Allows cropping an image, optionally through the z/t stack, using ROIs
  • Image Size : Produce a report showing the size of images including archives
  • Correlation Analyser : Produces a report of an all-vs-all channel correlation
  • Coloclisation Analyser : Uses the Confined Displacement Algorithm (CDA) to determine if the correlation between two channels is significant. This is done by comparison with random images created by shifting the pixels within a confined region
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