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Physiological Data Preprocessing
Simulate physiological signals
Electrodermal Activity (EDA/GSR)
Cardiac activity (ECG)
Respiration (RSP)
Electromyography (EMG)
Photoplethysmography (PPG/BVP)
Electrooculography (EOG)
Electrogastrography (EGG)
Physiological Data Analysis
Event-related
Interval-related
Miscellaneous
Heart Rate Variability (HRV)
ECG Delineation
Signal Processing
Complexity (Entropy, Fractal Dimensions, …)
Signal Decomposition
Signal Power Spectrum Density (PSD)
Statistics
Popularity
Notes
Authors
Core team
Contributors
Installation
1. Python
Windows
Winpython
Miniconda or Anaconda
Mac OS
2. NeuroKit
Get Started
Get familiar with Python in 10 minutes
Setup
Variables
Variables and data types
Lists and dictionnaries
Basic indexing
Indexing starts from 0
Control flow (if and else)
For loops
Functions
Packages
Lists
vs.
vectors (arrays)
Conditional indexing
Dataframes
Reading data
Next steps
Where to start
Examples
Try the examples in your browser
1. Analysis Paradigm
a) Event-related paradigm
b) Interval-related paradigm
2. Biosignal Processing
a) Custom processing pipeline
3. Heart rate and heart cycles
a) Detecting components of the cardiac cycle
b) Looking closer at heart beats
4. Electrodermal activity
a) Extracting information in EDA
5. Respiration rate and respiration cycles
a) Extracting Respiration Rate Variability metrics
6. Muscle activity
Simulate Artificial Physiological Signals
Cardiac Activity (ECG)
Respiration (RSP)
Electromyography (EMG)
Electrodermal Activity (EDA)
Customize your Processing Pipeline
The Default NeuroKit processing pipeline
Building your own
process()
function
Changing the processing parameters
Customize even more!
Event-related Analysis
The Dataset
Find Events
Process the Signals
Create Epochs
Extract Event Related Features
Plot Event Related Features
Important remarks:
Interval-related Analysis
The Dataset
Process the Signals
Extract Features
Optional: Segmenting the Data
Analyze Electrodermal Activity (EDA)
Extract the cleaned EDA signal
Locate Skin Conductance Response (SCR) features
Decompose EDA into Phasic and Tonic components
Quick Plot
Analyze Respiratory Rate Variability (RRV)
Download Data and Extract Relevant Signals
Analyse RRV
See documentation for full reference
ECG-Derived Respiration (EDR) Analysis
Download ECG Data
Extraction of ECG Features
Analyse EDR
Extract and Visualize Individual Heartbeats
Extract the cleaned ECG signal
Extract R-peaks location
Segment the signal around the heart beats
Advanced Plotting
Custom colors and legend
Interactivity
How to create epochs
One signal with multiple event markings
One subject with multiple data files
Complexity Analysis of Physiological Signals
Basic Concepts
Definitions
Time-delay embedding
Embedding Parameters
Entropy as measures of Complexity
Shannon Entropy (ShEn)
Approximate Entropy (ApEn)
Sample Entropy (SampEn)
Fuzzy Entropy (FuzzyEn)
Multiscale Entropy (MSE)
Detrended Fluctuation Analysis (DFA)
Analyze Electrooculography EOG data (eye blinks, saccades, etc.)
Explore the EOG signal
Clean the signal
Detect and visualize eye blinks
Fit a function to a signal
Fit a linear function
Non-linear curves
Resources
Recording good quality signals
Recording
Signal quality
Artifacts and Anomalies
What software for physiological signal processing
Software
vs.
programming language (packages)
GUI
vs.
code
Matlab
vs.
Python
vs.
R
vs.
Julia
Additional Resources
General Neuroimaging
ECG
EDA
EEG
Functions
ECG
PPG
HRV
RSP
EDA
EMG
EEG
Signal Processing
Events
Data
Epochs
Statistics
Complexity
Miscellaneous
Benchmarks
Benchmarking of ECG Preprocessing Methods
Introduction
Databases
Glasgow University Database
MIT-BIH Arrhythmia Database
MIT-BIH Normal Sinus Rhythm Database
Concanate them together
Study 1: Comparing Different R-Peaks Detection Algorithms
Procedure
Results
Conclusion
Study 2: Normalization
Procedure
Results
Conclusion
References
Datasets
ECG
(1000 hz)
ECG - pandas
(3000 hz)
Event-related
(4 events)
Resting state
(5 min)
Resting state
(8 min)
Contributing
Understanding NeuroKit
1. readthedocs
Example
2. The code on Github
Example
3. The code on YOUR machine
Python directory
Windows
Mac
Example
Contributing guide
NeuroKit’s style
Structure and code
Run code checks
Avoid Semantic Errors
Development workflow
How to use GitHub to contribute
Step 1: Fork it
Step 2: Clone it
Step 3: Find it and fix it
Step 4: Commit it and push it
Step 4: Create pull request
Step 5: Let’s do it
Useful reads
What’s next?
Ideas for first contributions
Look for
“good first contribution”
issues
Improving documentation
Adding tests
Adding examples and tutorials
How to write
Where to add the files
NeuroKit
Docs
»
Resources
Edit on GitHub
Resources
¶
Contents:
Recording good quality signals
What software for physiological signal processing
Additional Resources
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