This project was developed as part of the Undergraduate Senior Thesis in
Biomedical Engineering, King Mongkut’s Institute of Technology Ladkrabang (KMITL), Thailand.
Project Title: CORTEX 4.2: A Biophysically Grounded Brain Simulation Platform for Biomedical Neural Modeling
Authors: Kongkridakorn Boonyasurat, Punnut Phoungmalai
Advisor: Prof. Dr. Chuchart Pintavirooj
The CORTEX 4.2 framework was designed to explore biologically grounded spiking neural networks and synthetic EEG generation for biomedical applications.
This open-source repository accompanies the official thesis submission and demonstration presented to the KMITL Biomedical Engineering Department, 2025.
CORTEX 4.2 is an open-source, GPU-accelerated brain simulation and neuromorphic AI framework designed for biomedical neural modeling, synthetic EEG generation, and reinforcement-learning-driven behavior. It integrates multi-compartment neuron models, astrocyte–neuron coupling, and tri-modulator (DA/ACh/NE) plasticity inside a scalable, PyTorch-based architecture.
- Biophysically grounded neurons: Conductance-based multi-compartment model (CAdEx-derived) with dendritic processing.
- Enhanced synapses 4.2: STDP + tri-modulator plasticity with dopamine, acetylcholine, and norepinephrine control.
- Astrocyte coupling: Optional Ca²⁺-mediated modulation for slow plasticity regulation.
- GPU acceleration: Fully implemented in PyTorch for real-time training and visualization.
- Regional brain architecture: Modular simulation of sensory, motor, prefrontal, hippocampal, limbic, cerebellar, and thalamic systems.
- Neuromodulation & oscillations: Built-in oscillators and dynamic modulators for realistic activity states.
- Synthetic EEG generation: Multi-scale activity exported through MNE + PyVista to 3-D cortical visualization.
- Behavioral learning: Functional testing in classic reinforcement-learning games (Pac-Man, Pong, Snake).
- Biomedical validation: EEG-like outputs, functional-connectivity matrices, power-spectral analysis, and regional correlation benchmarking.
- Open-source & educational: Licensed under Apache 2.0 for reproducible research, teaching, and neuromorphic AI prototyping.
cortex/
├── cells/ # Enhanced neurons, synapses, astrocytes
├── modulation/ # Dopamine, acetylcholine, norepinephrine, oscillators
├── regions/ # Cortical & subcortical modules (motor, limbic, PFC, etc.)
├── connectivity/ # Biological connection patterns & wiring
├── sensory/ # Spike-based visual & sensory front-ends
└── brain/ # High-level orchestration, data collection, demos
Core engine:
EnhancedNeuron42PyTorch&EnhancedSynapse42PyTorch— biologically accurate, GPU-optimized cell models.CortexBrain.py— assembles regional modules into a functional brain network.BMEDataCollector.py— logs spikes, synaptic weights, EEG spectra, and connectivity matrices.MNE_EEG_3D_Regions_Patched.py— visualizes synthetic EEG with MNE + PyVista.
Sensory Cortex (42) – Responsible for perception, input encoding, and sensory feature extraction. Influenced mainly by acetylcholine (ACh) and glutamate, enhancing attention and sensory gain.
Motor Cortex (42) – Generates movement output and supports motor learning and procedural plasticity. Modulated by dopamine (DA) and acetylcholine (ACh) to reinforce skill acquisition.
Prefrontal Cortex (42) – Governs working memory, planning, and top-down decision control. Driven by combined modulation of dopamine (DA), norepinephrine (NE), and acetylcholine (ACh).
Hippocampus (42) – Encodes episodic memory, spatial navigation, and sequential replay. Primarily shaped by dopamine (DA) and acetylcholine (ACh) activity.
Limbic / Amygdala System (42) – Processes emotion, reward, and fear conditioning. Regulated by dopamine (DA) and norepinephrine (NE) for adaptive behavioral responses.
Basal Ganglia System (42) – Implements action selection, reinforcement learning, and habit formation. Heavily dependent on dopamine (DA) signaling through D1/D2 pathways.
Cerebellum (42) – Handles coordination, timing, and predictive correction of movement. Influenced by acetylcholine (ACh) and excitatory glutamate circuits.
Thalamus System (42) – Acts as a relay and attentional gate between sensory and cortical regions. Modulated by norepinephrine (NE) and acetylcholine (ACh) to regulate arousal and focus.
Parietal Cortex (42) – Integrates spatial awareness, proprioception, and sensorimotor alignment. Modulated by ACh and NE for attention and spatial mapping.
Insula Cortex (42) – Monitors internal body states, emotion, and risk or pain evaluation. Receives modulation from norepinephrine (NE) and dopamine (DA).
Unified Neocortex (42) – Provides a generalized cortical microcircuit scaffold used by higher regions. Controlled by the tri-modulator system of dopamine (DA), acetylcholine (ACh), and norepinephrine (NE).
Clone the repository and install requirements:
git clone https://github.com/<yourusername>/CORTEX-4.2.git
cd CORTEX-4.2
pip install -r requirements.txt(For smaller environments, use the minimal requirements list if provided.)
python -m cortex.brain.pacman_3Simulates a closed-loop brain → environment → reward cycle with adaptive spiking activity and neuromodulated learning.
python -m cortex.brain.brain42_smokeChecks region integration, GPU setup, and “proof-of-life” firing activity.
python -m cortex.brain.mne_eeg_3d_regions_patchedGenerates synthetic EEG, applies inverse mapping, and renders 3-D cortical activation.
CORTEX 4.2 produces:
- Testing the Synapse, Neurons and Astrocyte agaist Allen brain.
- Showing the synthetic EEG when playing pacman game.
- PyTorch, NumPy, SciPy, Pandas
- Matplotlib, OpenCV, ImageIO
- MNE, PyVista, PyVistaQt (for EEG 3-D visualization)
- pygame (for interactive environments)
- (Optional) braincog, spikingjelly, gym for research extensions
Licensed under the Apache License 2.0 (see LICENSE) © 2025 Kongkridakorn Boonyasurat. You are free to use, modify, and distribute this software for academic or commercial purposes, provided that proper attribution is maintained.