Biological Basis of the Code

The provided code is designed to simulate the spatial organization of a neural network comprising multiple neuron types. The focus of this model is on the spatial distribution of two primary neuron types, Medium Spiny Neurons (MSNs) and Fast-Spiking Interneurons (FSNs), within a defined physical space. This setup is commonly used to emulate neural networks in the brain, such as those found in the striatum.

Key Biological Elements:

1. Medium Spiny Neurons (MSNs):

   • These neurons are the predominant cell type in the striatum, a key component of the basal ganglia, involved in motor control and various other cognitive functions.
   • The model accounts for two subtypes of MSNs: D1 and D2 receptor-expressing neurons, which are critical for processing dopaminergic signals.

2. Fast-Spiking Interneurons (FSNs):

   • FSNs are GABAergic neurons that provide inhibitory input to MSNs, playing a crucial role in the regulation of neural excitability and synchronization within the network.
   • FSNs are typically characterized by their ability to fire rapid sequences of action potentials.

3. Physical Constraints:

   • The code models a 3D spatial configuration of neurons within a defined physical volume (net.PhysicalDimensions). The neurons are distributed in space, maintaining a minimum distance from one another (limit), which reflects the biological reality of physical constraints imposed by neurite arborizations and the extracellular matrix.

4. Population Proportions:

   • The proportion of FSNs relative to MSNs is determined (net.FSpercentage), mimicking the natural biological variability in neuron types within the brain regions.

5. Spatial Randomization:

   • Neurons are initially placed at random positions within the defined space but are adjusted to ensure no two neurons are closer than a specified distance (limit). This process is biologically inspired by the physical space required for proper synaptic connectivity and to avoid overlap of neural dendrites and somas.

By integrating these biological principles, the code attempts to create a realistic spatial model of a neuronal network, enabling the study of neural interactions and network dynamics that are representative of actual brain tissue organization. This spatial setup is a foundational step used in larger simulations to explore neural connectivity and functional implications in health and disease.