Modeling in SNT is performed through Cortex3D (Cx3D) and SciView. Cx3D was developed in 2009 as a computational modeling tool for simulating neurodevelopmental processes and is well known for generative models of cortical circuits.
The Morphonets distribution of Cx3D was modified by Kyle Harrington to be compatible with the ImageJ and Fiji ecosystem. This includes using SciView for 3D visualization, and support for image-based modeling.
 Zubler, F. & Douglas, R. A framework for modeling the growth and development of neurons and networks. Front. Comput. Neurosci. 3, 25 (2009) <PMID:19949465>.