• ImageJ and the Fiji distribution
• Python derivatives like Jython for ImageJ scripting and NumPy/SciPy for numeric/array processing
• There are a ton of other scripting language choices but seems like python covers this well enough. I don’t want the brain damage of Clojure.

Other stuff to learn? I’ll have to pick up an editor and source management tool as well. The benefit of all this? Any code I write should be faster, more easily redistributable, and there is a large support community. The disadvantage? I have to assemble all these piece-parts to get something equivalent to MatLab, so more time d&*king around with software which is time taken away from research focus. And the Matlab universe has a pretty good support community too, so not clear I am trading up there. Certainly the ImageJ/Jython/NumPy path is “cooler” along a certain dimension, but do I care?