neurokit2

# NeuroKit2

## Overview

NeuroKit2 is a comprehensive Python toolkit for processing and analyzing physiological signals (biosignals). Use this skill to process cardiovascular, neural, autonomic, respiratory, and muscular signals for psychophysiology research, clinical applications, and human-computer interaction studies.

## When to Use This Skill

Apply this skill when working with:
- **Cardiac signals**: ECG, PPG, heart rate variability (HRV), pulse analysis
- **Brain signals**: EEG frequency bands, microstates, complexity, source localization
- **Autonomic signals**: Electrodermal activity (EDA/GSR), skin conductance responses (SCR)
- **Respiratory signals**: Breathing rate, respiratory variability (RRV), volume per time
- **Muscular signals**: EMG amplitude, muscle activation detection
- **Eye tracking**: EOG, blink detection and analysis
- **Multi-modal integration**: Processing multiple physiological signals simultaneously
- **Complexity analysis**: Entropy measures, fractal dimensions, nonlinear dynamics

## Core Capabilities

### 1. Cardiac Signal Processing (ECG/PPG)

Process electrocardiogram and photoplethysmography signals for cardiovascular analysis. See `references/ecg_cardiac.md` for detailed workflows.

**Primary workflows:**
- ECG processing pipeline: cleaning → R-peak detection → delineation → quality assessment
- HRV analysis across time, frequency, and nonlinear domains
- PPG pulse analysis and quality assessment
- ECG-derived respiration extraction

**Key functions:**
```python
import neurokit2 as nk

# Complete ECG processing pipeline
signals, info = nk.ecg_process(ecg_signal, sampling_rate=1000)

# Analyze ECG data (event-related or interval-related)
analysis = nk.ecg_analyze(signals, sampling_rate=1000)

# Comprehensive HRV analysis
hrv = nk.hrv(peaks, sampling_rate=1000)  # Time, frequency, nonlinear domains
```

### 2. Heart Rate Variability Analysis

Compute comprehensive HRV metrics from cardiac signals. See `references/hrv.md` for all indices and domain-specific analysis.

**Supported domains:**
- **Time domain**: SDNN, RMSSD, pNN50, SDSD, and derived metrics
- **Frequency domain**: ULF, VLF, LF, HF, VHF power and ratios
- **Nonlinear domain**: Poincaré plot (SD1/SD2), entropy measures, fractal dimensions
- **Specialized**: Respiratory sinus arrhythmia (RSA), recurrence quantification analysis (RQA)

**Key functions:**
```python
# All HRV indices at once
hrv_indices = nk.hrv(peaks, sampling_rate=1000)

# Domain-specific analysis
hrv_time = nk.hrv_time(peaks)
hrv_freq = nk.hrv_frequency(peaks, sampling_rate=1000)
hrv_nonlinear = nk.hrv_nonlinear(peaks, sampling_rate=1000)
hrv_rsa = nk.hrv_rsa(peaks, rsp_signal, sampling_rate=1000)
```

### 3. Brain Signal Analysis (EEG)

Analyze electroencephalography signals for frequency power, complexity, and microstate patterns. See `references/eeg.md` for detailed workflows and MNE integration.

**Primary capabilities:**
- Frequency band power analysis (Delta, Theta, Alpha, Beta, Gamma)
- Channel quality assessment and re-referencing
- Source localization (sLORETA, MNE)
- Microstate segmentation and transition dynamics
- Global field power and dissimilarity measures

**Key functions:**
```python
# Power analysis across frequency bands
power = nk.eeg_power(eeg_data, sampling_rate=250, channels=['Fz', 'Cz', 'Pz'])

# Microstate analysis
microstates = nk.microstates_segment(eeg_data, n_microstates=4, method='kmod')
static = nk.microstates_static(microstates)
dynamic = nk.microstates_dynamic(microstates)
```

### 4. Electrodermal Activity (EDA)

Process skin conductance signals for autonomic nervous system assessment. See `references/eda.md` for detailed workflows.

**Primary workflows:**
- Signal decomposition into tonic and phasic components
- Skin conductance response (SCR) detection and analysis
- Sympathetic nervous system index calculation
- Autocorrelation and changepoint detection

**Key functions:**
```python
# Complete EDA processing
signals, info = nk.eda_process(eda_signal, sampling_rate=100)

# Analyze EDA data
analysis = nk.eda_analyze(signals, sampling_rate=100)

# Sympathetic nervous system activity
sympathetic = nk.eda_sympathetic(signals, sampling_rate=100)
```

### 5. Respiratory Signal Processing (RSP)

Analyze breathing patterns and respiratory variability. See `references/rsp.md` for detailed workflows.

**Primary capabilities:**
- Respiratory rate calculation and variability analysis
- Breathing amplitude and symmetry assessment
- Respiratory volume per time (fMRI applications)
- Respiratory amplitude variability (RAV)

**Key functions:**
```python
# Complete RSP processing
signals, info = nk.rsp_process(rsp_signal, sampling_rate=100)

# Respiratory rate variability
rrv = nk.rsp_rrv(signals, sampling_rate=100)

# Respiratory volume per time
rvt = nk.rsp_rvt(signals, sampling_rate=100)
```

### 6. Electromyography (EMG)

Process muscle activity signals for activation detection and amplitude analysis. See `references/emg.md` for workflows.

**Key functions:**
```python
# Complete EMG processing
signals, info = nk.emg_process(emg_signal, sampling_rate=1000)

# Muscle activation detection
activation = nk.emg_activation(signals, sampling_rate=1000, method='threshold')
```

### 7. Electrooculography (EOG)

Analyze eye movement and blink patterns. See `references/eog.md` for workflows.

**Key functions:**
```python
# Complete EOG processing
signals, info = nk.eog_process(eog_signal, sampling_rate=500)

# Extract blink features
features = nk.eog_features(signals, sampling_rate=500)
```

### 8. General Signal Processing

Apply filtering, decomposition, and transformation operations to any signal. See `references/signal_processing.md` for comprehensive utilities.

**Key operations:**
- Filtering (lowpass, highpass, bandpass, bandstop)
- Decomposition (EMD, SSA, wavelet)
- Peak detection and correction
- Power spectral density estimation
- Signal interpolation and resampling
- Autocorrelation and synchrony analy