These files reproduce all results from Figures 4, 5 of the paper Brain-wide Maps Reveal Stereotyped Cell-Type-Based Cortical Architecture and Subcortical Sexual Dimorphism Cell 2017 https://www.sciencedirect.com/science/article/pii/S0092867417310693
You can start with main.py.
This code is only tested in Python 2.7 and Mac OS.