You can indeed use Jython to call ImageJ. See the Jython scripting page on the Fiji wiki for an overview and lots of example code. One easy way to get started from within ImageJ is to use the Script Editor. You can then invoke your Jython scripts from the command line using the ImageJ launcher [instructions]. Or you can run them via the jython
executable by adding the needed Java libraries to the classpath.
But beware: this does not provide total integration between Python libraries and Java ones. The problem is that many Python libraries are backed by C code, making them accessible only from CPython, and not from Jython. For example, the very popular SciPy and NumPy libraries cannot be called directly from Jython code.