ImageJ

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Topics Introduction Getting Started User Guides Tutorials Tips and Tricks Presentations Plugins
Techniques All Techniques Colocalization Deconvolution Registration Segmentation Stitching Tracking Visualization
Scripting Overview User input Basics of script writing How to use the Javadoc Batch processing Script Editor Auto Imports Templates Running headlessly Comparisons Toolbox Multithreading in Clojure Multithreading in JavaScript Chess in Jython
Languages BeanShell Groovy ImageJ Macro JavaScript Lisp (Clojure) MATLAB Python (Jython) R (Renjin) Ruby (JRuby) Scala

ImageJ allows you to write scripts in several different languages.

Getting started

• Read the ImageJ tutorial notebooks to learn how to write ImageJ scripts.
• Press the [ key to open the Script Editor (or ⇧ Shift-[ to open the Script Interpreter).
• Optionally, choose a template from the Templates menu to get you started.
• Otherwise, choose your language from the Language menu.
• Grab code snippets for common tasks from the Scripting toolbox.
• See Scripting comparisons for a side-by-side comparison of scripting languages.
• See Category:Scripting for a list of all scripting-related pages on this wiki.

Supported languages

ImageJ's Script Editor supports many different languages. The following table summarizes the possibilities.

Recommended options
Groovy	Groovy is a flexible and powerful scripting language, Java-like but less verbose and dynamically typed. Learn this, and using Java later (if needed) will become easier.
ImageJ Macro	The ImageJ 1.x macro language is less powerful than the other scripting languages, but is designed to be easy to learn and use.
Python (Jython)	Python is a popular choice among scientists.
JavaScript	JavaScript is a popular choice among web developers.
Ruby (JRuby)	Ruby is another popular choice among web developers.
Lisp (Clojure)	Lisp is a popular choice among computer scientists.
R (Renjin)	R is a popular choice among scientists and statisticians.
Other options
Java	You can code Java plugins in the Script Editor. This is the most difficult path, but also the most powerful.
MATLAB	ImageJ can interface bidirectionally with MATLAB. See the MATLAB Scripting page for details.
BeanShell	BeanShell is an old script language, maintained mostly for backwards compatibility. It is nearly 100% compatible with Java syntax, but so is Groovy.
Scala	Scala support is currently experimental, and has bugs.

Script parameters

There is a universal @parameter notation available across all scripts for declaring inputs and outputs. This approach is preferred to using ImageJ 1.x GenericDialog because it is totally agnostic to the user interface, allowing such scripts to run in a variety of contexts.

See the script parameters page for details.

Using an interpreter

All scripting languages use the same basic interpreter, with the following common features.

General key bindings

• ↑: bring the previously typed command.
• ↓: bring the next typed command.
• ⌅ Enter or ⏎ Return: execute the contents of the prompt.

Multiline editing and keybindings

You can enlarge the prompt by dragging the middle bar.

• ⇧ Shift+⌅ Enter: create a new line within the prompt.
• ⇧ Shift+↑: move to the line above within the prompt.
• ⇧ Shift+↓: move to the line below within the prompt.

Selecting and executing text from the screen

On selecting text, a popup offers to:

• copy
• execute
• save to a new file

Using the script editor

You can create, edit and run scripts using the built-in Script Editor. For details, please see the Script Editor documentation.

Adding scripts to the Plugins menu

For the script to appear in the ImageJ menus, the following must apply:

".txt" is not a supported script extension

1. The script file is saved in the ImageJ.app/scripts or the ImageJ.app/plugins/Scripts directory (or a subdirectory thereof).
2. The script name ends in a supported script extension. For example
   • ".groovy" for groovy,
   • ".js" for javascript,
   • ".py" for jython,
   • ".rb" for jruby,
   • ".clj" for clojure,
   • ".bsh" for beanshell, and
   • ".ijm" for ImageJ 1.x macros.
3. The script name contains a '_' (underscore) character, e.g. "MyScript_.ijm".

Replace ImageJ.app with Fiji.app

The extension will be stripped and any underscores will be turned into spaces before the script is added to the menus.

Scripts in the top-level ImageJ.app/plugins directory will appear at the bottom of the Plugins menu. Scripts can be placed in other menus by nesting subdirectories, for example placing a script in the ImageJ.app/scripts/File directory will add it to the File menu.

If you aren't able to find your script, you can always run the Command Finder to verify its location (or absence).

Commands added to the menu in the described way can be called from other scripts. Use the macro recorder to get the required code for doing so.

Adding JAR-packaged scripts to the menu

Scripts can be packaged in a JAR file for easier distribution to your colleagues and via [Update Sites]. For this purpose, example-script-collection can be used as the template Maven project.

Inside the example-script-collection jar, the scripts are in ./resources/scripts. and therefore get added to the menu when the JAR is on the classpath (i.e. in ./plugins/ or ./jars/).

ImageJ2 (and therefore Fiji) looks for scripts in subfolders of ./scripts/ as it is already described in the previous section, and for jars in ./jars/. ImageJ1 recognizes plugins and scripts in ./plugins/

Running scripts in headless mode

See the Scripting Headless page for instructions on executing scripts headlessly.