I can't help but think of ImageJ here. Except Mathematica is much more of a scripting language than Java, so much more convenient if you don't yet know if you're doing the right thing.
For ImageJ packed with scripting languages, see Fiji: http://pacific.mpi-cbg.de . Provides Javascript, Jython, JRuby, Beanshell, and Clojure, although the latter is not a scripting language despite behaving like one.
