IJ2 is out
 Sec. 16: Plugins Up Part III: Extending IJ Sec. 18: Command Line 

17 Scripting in Other Languages

Support for other languages is possible in ImageJ using Fiji↑ and its powerful editor. Fiji adds extra support for BeanShell, Clojure, Python and Ruby. The following documents will introduce you to the advanced scripting capabilities of Fiji:
  1. The extensive tutorial on scripting Fiji with Jython by Albert Cardona:
  2. Dedicated tutorials on the Fiji webpage:

Fiji Script Editor

Fiji features a more powerful script editor than ImageJ’s built-in Editor↓. The Fiji editor is an invaluable help when writing scripts in any of Fiji’s supported languages, including the ImageJ macro language. The editor features full undo support, syntax highlighting, tabs, bookmarks and several other tools that simplify scripting workflows in ImageJ. For more information visit Fiji’s editor website at http://fiji.sc/wiki/index.php/Script_Editor.
figure images/FijiScriptEditor.png
Figure 10 The Fiji Script Editor (ImageJA 1.44m). The Fiji Editor is an advanced text editor, supporting BeanShell, Jython, JRuby and other scripting languages. It does not support Function Finder… [F]↓ but selecting a built-in macro function and running ToolsOpen Help on Macro Functions… retrieves the documentation for the selected function.
Scripting in Other Languages↑, Running ImageJ From the Command Line↓, IJ_ED, a plugin by Jérôme Mutterer that binds jEdit to ImageJ
 Sec. 16: Plugins Up Part III: Extending IJ Sec. 18: Command Line