This paper focuses on the important role of open-source software in the development of a fully-automatic and accurate registration system for images of Quadrature Tomographic Microscopy. The system is correspondence-based, using the framework provided by open-source RGRL(Rensselear Generalized Registration Library). The library implements several well-known techniques and the ability to mix-and-match techniques for components of the framework allows testing of ideas and
development of the robust system in a timely fashion.