For easy access to use EMBL cluster for calculation using ImageJ, I tested using Jsch, a pure SSH2 implementation in Java (http://www.jcraft.com/jsch).

I made a ImageJ launcher that runs server-side ImageJ on local desktop (see GitHub repository ServerIJ). X should be ready for hosting the GUI. For further development, interface will be more boring as only some fields to input name of shell script and some options (path name to image files, macro or scripts) will be what you will see.