Complete Neural Signal Analysis Toolbox is an open-source research toolbox for EEG analysis, neural signal processing, electrophysiology, human cortical organoid signal analysis, multichannel time-series analysis, spectral analysis, entropy and complexity measures, nonlinear dynamics, fractal analysis, topology, graph theory, geometry, quantum-inspired methods, and neural-state manifold dynamics.
This repository is intended for researchers, developers, students, computational neuroscientists, neurotechnology builders, signal-processing engineers, brain-computer interface researchers, human cortical organoid researchers, government research groups, academic labs, and open-source scientific software users working with neural recordings, EEG data, organoid electrophysiology, multichannel time-series data, nonlinear neural dynamics, feature extraction, and advanced mathematical methods for neural systems.
Browse the folders to see the full method library and experimental tools.
The current no-code GUI and integrated web application are documented here:
GUI/neuro_signal_importer_analyzer/README.md
Start with that README if you want the latest drag-and-drop workflow, automatic installation checks, HTML/FastAPI frontend, neural-signal conversion backend, variable-electrode support, integrated NeuroMouse workbench, live replay, offline analysis, and comparison workflows.
Recommended launch:
cd GUI/neuro_signal_importer_analyzer
python3 run_neuro_signal_app.pyThe launcher checks whether the software and required Python libraries are installed, installs missing dependencies only when needed, starts the local app server, and opens the browser interface.
Use the GUI folder above for the current end-to-end interface. It is designed for users who want to load neural recordings, convert files, analyze data, open NeuroMouse visualizations, run live replay, and compare datasets without writing code.
Each folder contains methods for a different analysis area, including spectral analysis, entropy, nonlinear dynamics, fractal analysis, topology, geometry, quantum-inspired analysis, and neural-state manifold dynamics.
Researchers can use this repository as a reference toolbox, method library, educational resource, or starting point for reproducible neural signal analysis, EEG analysis, human cortical organoid signal analysis, electrophysiology workflows, computational neuroscience, and AI-assisted neural data analysis.
The GUI/web app documentation lives in GUI/neuro_signal_importer_analyzer/README.md. In brief, the current interface supports:
- Drag-and-drop neural signal files and folders
- Automatic installation and library checks
- Flexible conversion into a standardized neural-signal format
- Variable electrode/channel counts and channel names
- EEG, ECoG/iEEG-style, MEA-style, and human cortical organoid electrophysiology workflows
- Offline analysis and feature extraction
- Live replay of prerecorded recordings
- Group and dataset comparison workflows
- Integrated NeuroMouse workbench for interactive visualization
- Backend-generated NeuroMouse datasets instead of demo data
- Output folders with converted files, metadata, provenance, quality reports, and analysis products
The toolbox and GUI are designed around flexible neural signal workflows. Depending on the available modules and project setup, the repository can be used with:
- EEG files and recordings
- ECoG/iEEG-style recordings
- MEA and organoid electrophysiology recordings
- Human cortical organoid neural signal recordings
- Multichannel time-series matrices
- Folder-based datasets
- Table-based datasets
- Spreadsheet-style data layouts
- Custom neural signal data structures
- Feature tables and analysis exports
- Experimental neural recordings
- Data exported from external acquisition systems
- EEG analysis
- Neural signal processing
- Human cortical organoid signal analysis
- Organoid electrophysiology
- Electrophysiology analysis
- Brain-signal analysis
- Multichannel time-series analysis
- Signal analysis and signal processing
- Spectral analysis and time-frequency analysis
- Entropy and complexity analysis
- Nonlinear dynamics and chaos
- Fractal and multifractal analysis
- Topological data analysis
- Graph theory and network neuroscience
- Geometry, manifolds, and curvature
- Quantum-inspired information analysis
- Neural-state and manifold dynamics
- AI-assisted neural data analysis
- Computational neuroscience
- Brain-computer interface research
- Neuroinformatics
- Reproducible scientific software
| Folder / Area | Description |
|---|---|
GUI/neuro_signal_importer_analyzer/ |
Current no-code GUI/web app. See its README for detailed usage, installation, NeuroMouse integration, conversion, live replay, and comparison workflows. |
Data_Loading_and_Variable_Assigning_files/ |
Data loading, variable assignment, signal preparation, and analysis setup. |
Dynamical_Systems/ |
Dynamical systems, nonlinear dynamics, chaos, Lyapunov methods, attractor reconstruction, nonlinear coupling, and chaos control. |
Entropy/ |
Entropy measures, complexity measures, multiscale entropy, sample entropy, approximate entropy, transfer entropy, entropy rate, and feature extraction. |
Fractal/ |
Fractal analysis, fractal dimension, multifractal analysis, DFA, MFDFA, Hurst exponent, and wavelet-fractal analysis. |
Geometry/ |
Manifolds, manifold learning, state-space geometry, Riemannian geometry, SPD manifolds, covariance manifolds, geodesics, curvature, and tangent-space analysis. |
Library/neural_signal_analysis/ |
Core reusable neural signal analysis library code. |
Neural Net_files/ |
Neural network, AI, machine learning, and computational modeling files. |
Quantum Analysis/ |
Quantum-inspired, density-matrix, von Neumann entropy, quantum coherence, Hermitian matrix, and positive-semidefinite analysis. |
Spectral Analysis/ |
Spectral analysis, PSD, Welch method, FFT, Lomb-Scargle, periodogram, wavelet transform, STFT, band power, coherence, and functional connectivity. |
Topology/ |
Topology, topological data analysis, persistent homology, graph theory, weighted networks, modularity, small-world networks, graph metrics, and network neuroscience. |
This toolbox may be useful for:
- EEG feature extraction
- Human cortical organoid research
- Human cortical organoid intelligence experiments
- Organoid electrophysiology analysis
- EEG biomarkers
- Neural signal analysis
- Brain-signal analysis
- Brain-computer interface signal processing
- BCI analysis
- Electrophysiology signal analysis
- AI for EEG and neural recordings
- Machine learning for neural signals
- Deep learning for EEG
- Nonlinear EEG analysis
- Neural complexity analysis
- Brain network analysis
- Functional connectivity analysis
- Time-frequency EEG analysis
- Riemannian EEG analysis
- Covariance manifold EEG analysis
- Topological neuroscience
- Fractal biomarkers
- Dynamical biomarkers
- Reproducible neural analysis
- Open-source computational neuroscience
- Research software indexing
- Academic software discovery
- No-code neural signal analysis
- GUI-based EEG analysis
- Flexible neural signal data structure support
- Beginner-friendly neural signal processing
- Current GUI README:
GUI/neuro_signal_importer_analyzer/README.md - NeuroMouse software: https://github.com/UlaYuga/NeuroMouse
- Dataset: https://zenodo.org/records/15572614
- Repository: https://github.com/soulsyrup1/Complete-Neural-Signal-Analysis
The following terms describe the scope of this repository and support discovery for GitHub search, research software indexing, academic search, neuroscience software discovery, biomedical signal processing, AI research, government research, and open-source scientific software.
Core EEG / neural signal / time-series
eeg
eeg-analysis
neural-signal-processing
signal-analysis
signal-processing
multichannel-time-series
time-series-analysis
nonlinear-time-series
biomedical-signal-processing
brain-signal-analysis
electrophysiology-analysis
human-cortical-organoid
human-cortical-organoid-intelligence
organoid-electrophysiology
organoid-neural-signals
analytic-signal
hilbert-transform
state-space-analysis
phase-space-reconstruction
delay-embedding
attractor-reconstruction
Additional SEO phrases:
EEG toolbox
EEG processing toolbox
EEG feature extraction
EEG biomarkers
neural data analysis
brain data analysis
human cortical organoid neural analysis
human cortical organoid electrophysiology
organoid intelligence signal analysis
neurophysiology signal analysis
computational neuroscience software
open-source EEG analysis
open-source neural signal processing
brain-computer interface signal processing
BCI analysis
electrophysiology analysis
neuroinformatics
neural engineering
brain dynamics
neural time-series modeling
biomedical AI
AI for EEG
machine learning for neural signals
deep learning for EEG
scientific Python neuroscience
reproducible neural analysis
Spectral / frequency / time-frequency
spectral-analysis
power-spectral-density
psd
welch-method
fast-fourier-transform
fft
lomb-scargle
periodogram
wavelet-transform
continuous-wavelet-transform
short-time-fourier-transform
stft
time-frequency-analysis
band-power
frequency-domain-analysis
spectral-entropy
spectral-centroid
spectral-edge-frequency
harmonics-detection
phase-synchronization
coherence-analysis
functional-connectivity
Additional SEO phrases:
EEG spectral analysis
neural frequency analysis
oscillatory brain activity
alpha beta gamma theta delta bands
neural oscillations
time-frequency EEG
wavelet EEG analysis
Fourier neural signal analysis
PSD brain signals
coherence connectivity analysis
phase-locking analysis
cross-frequency analysis
frequency-domain biomarkers
neural synchrony
brain network connectivity
resting-state EEG analysis
human cortical organoid spectral analysis
Entropy / complexity
entropy
entropy-measures
complexity-measures
complexity-science
multiscale-entropy
sample-entropy
approximate-entropy
transfer-entropy
kolmogorov-sinai-entropy
entropy-rate
spectral-entropy
feature-extraction
Additional SEO phrases:
EEG entropy analysis
neural complexity
brain complexity metrics
human cortical organoid complexity
organoid neural complexity
nonlinear complexity analysis
physiological complexity
complexity biomarkers
entropy-based feature extraction
information theory neuroscience
signal irregularity
neural variability
multiscale brain dynamics
complexity science for neuroscience
biomedical entropy measures
AI-ready neural features
Dynamical systems / chaos / nonlinear methods
dynamical-systems
nonlinear-dynamics
chaos
chaos-theory
lyapunov-exponents
lyapunov-spectrum
largest-lyapunov-exponent
kaplan-yorke-dimension
correlation-dimension
false-nearest-neighbors
surrogate-data
iaaft
rosenstein-method
kantz-method
wolf-algorithm
benettin-algorithm
convergent-cross-mapping
ccm
nonlinear-coupling
chaos-control
ogy-method
pyragas-control
arnold-tongues
mode-locking
Additional SEO phrases:
nonlinear EEG analysis
chaotic neural dynamics
chaotic organoid dynamics
human cortical organoid dynamics
neural attractors
brain state-space analysis
nonlinear brain modeling
dynamical biomarkers
phase-space EEG
nonlinear neural coupling
chaos in brain signals
nonlinear systems neuroscience
neural system identification
computational dynamical neuroscience
complex systems neuroscience
dynamical systems toolbox
Fractal / multifractal
fractal-analysis
fractal-dimension
higuchi-fractal-dimension
katz-fractal-dimension
multifractal-analysis
mfdfa
detrended-fluctuation-analysis
dfa
hurst-exponent
wavelet-fractal-analysis
Additional SEO phrases:
EEG fractal dimension
neural fractal analysis
human cortical organoid fractal analysis
multifractal EEG
self-similarity brain signals
scale-free neural dynamics
long-range temporal correlations
fractal biomarkers
biomedical fractal analysis
complexity and fractals
Hurst exponent EEG
DFA brain signals
MFDFA neural signals
Topology / TDA / graphs
topology
topological-data-analysis
tda
persistent-homology
betti-numbers
rips-complex
network-science
graph-theory
graph-analysis
weighted-networks
community-detection
modularity
small-world-networks
global-efficiency
graph-metrics
network-neuroscience
Additional SEO phrases:
topological neuroscience
TDA for EEG
persistent homology brain signals
topological biomarkers
brain network analysis
graph neural signals
functional connectivity graphs
neural graph metrics
connectomics
network neuroscience toolbox
EEG network science
topology of neural dynamics
topological feature extraction
graph-based biomarkers
human cortical organoid network analysis
Geometry / manifolds / curvature
manifolds
manifold-learning
state-space-geometry
intrinsic-geometry
metric-geometry
non-euclidean-geometry
riemannian-geometry
spd-manifold
covariance-manifold
affine-invariant-metric
geodesics
geodesic-interpolation
geodesic-network
riemann-curvature
riemann-curvature-tensor
ricci-curvature
scalar-curvature
sectional-curvature
riemannian-barycenter
parallel-transport
curvature-analysis
curvature-hotspots
tangent-space
Additional SEO phrases:
Riemannian EEG analysis
covariance manifold EEG
SPD matrix signal processing
manifold-based neural analysis
human cortical organoid manifold dynamics
geometric deep learning neuroscience
neural state geometry
curvature of brain dynamics
manifold biomarkers
covariance geometry
tangent-space EEG classification
geodesic neural dynamics
brain signal manifold learning
intrinsic geometry of neural signals
Quantum-like / information-geometric
quantum-inspired
quantum-like
quantum-information
density-matrix
von-neumann-entropy
quantum-coherence
effective-rank
hermitian-matrices
positive-semidefinite
Additional SEO phrases:
quantum-inspired neural signal analysis
density matrix EEG
quantum-like cognition signals
information geometry neuroscience
von Neumann entropy brain signals
matrix-based neural features
positive semidefinite neural representations
Hermitian matrix analysis
effective rank for EEG
quantum information methods for neural recordings
human cortical organoid information geometry
The dataset associated with this project is available here:
https://zenodo.org/records/15572614
This dataset can support reproducible testing, benchmarking, neural signal analysis experiments, EEG research, time-series analysis, human cortical organoid analysis workflows, and method development.
NeuroMouse software: https://github.com/UlaYuga/NeuroMouse
NeuroMouse is integrated into the current GUI/web application workflow. See the GUI README for current details:
GUI/neuro_signal_importer_analyzer/README.md
Recommended project URL:
https://github.com/soulsyrup1/Complete-Neural-Signal-Analysis
Recommended dataset URL:
https://zenodo.org/records/15572614
Suggested citation text:
Complete Neural Signal Analysis Toolbox. Open-source neural signal analysis, EEG analysis, human cortical organoid signal analysis, electrophysiology analysis, nonlinear time-series analysis, spectral analysis, entropy analysis, fractal analysis, topology, geometry, manifold learning, and quantum-inspired analysis toolbox. https://github.com/soulsyrup1/Complete-Neural-Signal-Analysis
Complete Neural Signal Analysis Toolkit is licensed under the Creative Commons Attribution-ShareAlike 4.0 International License.
