.. _cb_basal_ganglia:

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Striatum microcircuitry
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This Use Case is a demonstration of how the Striatum microcircuitry is created, 
and simulated. It walks you through the steps taken to place the neurons in a 
striatal volume, how the putative synapses of the microcircuitry are detected, 
and pruned. Then finally it shows how the simulation is set up and run.


**Setting up the environment:**


First the source code needs to be downloaded from the central Collab storage. 
All the required files are packed into a tar.bz2 archive that is unpacked in 
the user Collab. The files are placed in a subdirectory called 
StriatumScaffold2018.


**Placing neurons in 3D space:**


The neurons are randomly placed in a volume by using NetworkPlaceNeurons. 
This reads in configuration data stored in the file 
"config/Network-striatum-cube-v7-channels-100-15.json" where the volume is 
defined, as well as a specification of what neurons to populate the volume 
with, and parameters for how to setup the connectivity in the next step (which 
neuron types they connect to, pruning parameters etc.). The config file has 
been automatically generated by makeStratiumConfigFile.py (included in the 
tar.bz2 file). The output of the cell placement is a pickle file which is used 
in the next step.


**Creating network connectivity:**


To create the connectivity, NetworkConnect is run. It reads the pickle file 
with position data and the network configuration file, imports the morphologies 
from swc files, and then proceeds to look for close appositions between the 
axons and dendrites of these neurons. The putative connections are then pruned 
using a set of rules, to get connectivity probabilities matching experimental 
data. The resulting connectivity is saved in a HDF5 file.


**Plotting connectivity statistics:**


Network_plot_statistics reads in the HDF5 file with the connectivity data and 
computes statistical measures, such as the number of connections between neuron 
types, and the connection probability.


**Running the network simulation:**


To run the network simulation using Parallel Neuron, the mod files needs first 
to be compiled. Then, NetworkSimulate can be used to simulate the network. 
The output is stored in two files, one with spike times of the neurons, and the 
other with voltage traces.