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Scripting

    ImageJ allows you to write scripts in several different languages.

    Getting started

    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

    • up
      bring the previously typed command.
    • down
      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\|\|Up
      move to the line above within the prompt.
    • Shift\|Down
      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:

    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”.
    Fiji-icon.png

    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.