Thalamo-cortical loop

the repository for thalamo-cortical loop modelling

🧠 Cortical Column Simulation (NEURON + Python)

We model the thalamo-cortical loop using the NEURON neurosimulator. We model excitatory and inhibitory neurons and visualise there activities.

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📁 Project contents

File	Description
cortical_column.py	Main script of the simulation: imports all submodules and runs simulation and does visualisation.
create_HHNeuron_group.py	Defines Neuron class HHNeuron (Hodgkin-Huxley) and groups of neurons creation functions.
connect_functions.py	Contains functions of neurons connection: connect_exc (excitatory projections) and connect_inh (inhibitory).
create_connections.py	Setup synaptic connections between all neuronal groups (thalamus, cortical layers).
thalamus_stimulation.py	Exeternal stimulation of neurons of thalamus via NetStim.
visualization.py	Results visualisation: membraine potentials, spike times, heatmaps etc.

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🧠 Biological components

• TCR (Thalamocortical relay cells) — thalamus excitatory neurons

• nRT (nucleus Reticularis Thalami) — thalamus inhibitory neurons

• Cortical layers:

  • L2/3 SyppyrRS
  • L2/3 SyppyrFRB
  • L4 Spinstel
  • L5 TuftRS
  • L5 TuftIB
  • L6 NontuftRS

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⚙️ Dependencies

• Python 3.8+
• NEURON
• numpy
• matplotlib

Installation of dependencies:

pip install numpy matplotlib

NEURON installation: official documents.

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🚀 Run

Run the main script:

python cortical_column.py

The results visualisation are presented as graphs: spike-times, membraine potentials.

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📊 Options

• Modelling neurons and their groups HH-neurons
• Excitatory and inhibitory neurons
• External stimulation NetStim
• Record and analysis of spikes
• Flexible setup of weights and delays and parameters of synapses
• Visualisation of neurons activities

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📎 Examples

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