Most of the Moose tools now use the MSE file format as an interchange format. By the way, if you are interested in writing your own visualisations or analysis tools it is probably worthwhile looking at MSE, reading this format is so much more convenient than parsing source code.
In Java it was always relatively easy to create MSE files. Among many other things, iPlasma can read Java source code and export to MSE. That said, iPlasma has so many interesting features itself that oftentimes no export to an external tool is necessary.
For C# the story was different and for one reason or another no tool existed that could create MSE files for C#. This has changed now. As a student project at the University of Lugano such a tool was written and, thanks to Michele Lanza, then donated for general use. I've made a few improvements and put the code into this Bitbucket repository.