Basal ganglia bottleneck paper: neuron counting and simulations

MATLAB code for the "computational bottleneck of basal ganglia output" paper:

1. Counting target neurons of the SNr using Allen Mouse Brain Projection Atlas data.
2. Example simulations of the basal ganglia's control of a cortical RNN and a superior colliculus grid model.

The folder 'Counting SNr target neurons' contains the following data sourced elsewhere:

1. XML files of six staining experiments downloaded from the Allen Mouse Brain Projection Atlas, published in Oh et al (2014) Nature.
2. An Excel file of the 295 non-overlapping brain regions used by Oh et al (2014) Nature, derived from their Supplementary Table 1.
3. An Excel file of the Blue Brain Cell Atlas neuron counts, published in Rodarie et al (2022) PLoS Computational Biology and derived from their S2 Excel file.