I just stumbled across a tool called ‘MeVisLab’, just recently at version 2.1, that offers a GUI-based development environment for medical image processing and visualization in a variety of ways.
MeVisLab represents a powerful, modular framework for the development of image processing algorithms and visualization and interaction methods, with a special focus on medical imaging.
Besides basic image processing and visualization modules, MeVisLab includes advanced medical imaging algorithms for segmentation, registration, and quantitative morphological and functional image analysis.
It seems very pipeline oriented, allowing you to match various filter and segmentation algorithms together to achieve a wide spectrum of results. Perhaps most impressively, the entire software is freely available from their website compiled with a variety of compilers, making it available to extend with plugins developed in just about any modern environment.
