I started TrakEM2: register/edit/analyze/3D model terabytes of images. For scientific image processing -mostly neuroscience, mostly electron microscopy images, but also other fields and imaging techs.

http://repo.or.cz/w/trakem2.git

http://www.ini.uzh.ch/~acardona/trakem2.html

It's based off ImageJ. And yes it is in Java, with plenty of jython scripting on top.