The two mentioned software packages for modelling tissue growth in three dimensions are:
BioDynamo: A C++ based project that aims to become a general platform for computer simulations of growth in biological tissue, not just brain tissue. Build to scale up to large simulations, it can handle large networks and includes genetic circuits within cells as well as cell migration, extracellular chemical gradients, and axon/dendrite formation [1].
CX3D is a Java software environment for modeling the development of large realistic neural networks such as the neocortex, in a physical 3D space. In CX3D, neurons arise by the replication and migration of precursors, which mature into cells able to extend axons and dendrites. The software also includes simulations of the extracellular environment and allows for the diffusion of extracellular signaling molecules, as well as the physical interactions of the many developing neurons [2].
References
[1] Bauer, Roman, Lukas Breitwieser, Alberto Di Meglio, Leonard Johard, Marcus Kaiser, Marco Manca, Manuel Mazzara, Fons Rademakers, Max Talanov, and Alexander Dmitrievich Tchitchigin. 2017. “The BioDynaMo Project: Experience Report.” In Advanced Research on Biologically Inspired Cognitive Architectures, edited by Vallverdú Jordi, Mazzara Manuel, Talanov Max, Distefano Salvatore and Lowe Robert, 117-125. Hershey, PA, USA: IGI Global
[2] Zubler, F. and R. Douglas (2009). A framework for modeling the growth and development of neurons and networks. Front Comput Neurosci 3: 25