Scripting

The ImageJ ecosystem supports scripting in many languages. Which scripting system you’re using depends on which application you’re running.

Which scripting system?

There are two distinct scripting systems in the ImageJ ecosystem:

The original ImageJ (1.x) ships its own scripting support: the ImageJ macro language plus a few other script languages. For this system, see the ImageJ developer documentation on the original ImageJ website. SciJava #@ script parameters are not part of the original ImageJ.

 Fiji ships the SciJava scripting framework: a cross-language system with #@ parameters, the #@script directive, the #!Lang shebang, a unified Script Editor, and many supported languages. The rest of this section covers SciJava scripting.

Terminology

These pages use the following terms consistently:

• ImageJ — the original ImageJ 1.x application.
• ImageJ2 — the ImageJ2 libraries upon which Fiji is built.
• Fiji — the Fiji distribution (ImageJ + ImageJ2 + curated plugin set + Jaunch-based launcher).
• SciJava scripting — the cross-language scripting framework shared by ImageJ2 and Fiji.
• ImageJ ecosystem — all of the above, plus other ImageJ-flavored applications.

Getting started

• Read the Scripting basics page for an introduction to writing SciJava scripts.
• Read the ImageJ2 tutorial notebooks for runnable examples.
• Press the [ key in Fiji 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.

Supported languages

Many different languages are supported. The following table summarizes the possibilities.

Recommended options

Other options

Script parameters

There is a universal script parameter notation available across all SciJava scripts for declaring inputs and outputs. This approach is preferred to using 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: 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 menus, the following must apply:

1. The script file is saved in the Fiji/scripts or the Fiji/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.

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 Fiji/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 Fiji/scripts/File directory will add it to the File menu.

The menu path, label, icon, and other module metadata can also be set from within a script using the #@script directive.

If you aren’t able to find your script, you can always use the search bar 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/).

Fiji looks for scripts in subfolders of ./scripts/ as it is already described in the previous section, and for jars in ./jars/. The original ImageJ recognizes plugins and scripts in ./plugins/.

Running scripts in headless mode

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