General Information

biopeaks is a straightforward graphical user interface for feature extraction from electrocardiogram (ECG), photoplethysmogram (PPG) and breathing biosignals. It processes these biosignals semi-automatically with sensible defaults and offers the following functionality:

• processes files in the open biosignal formats EDF, OpenSignals (Bitalino) as well as plain text files (.txt, .csv, .tsv)
• interactive biosignal visualization
• biosignal segmentation
• benchmarked, automatic extrema detection (R-peaks in ECG, systolic peaks in PPG, exhalation troughs and inhalation peaks in breathing signals) with signal-specific, sensible defaults
• automatic state-of-the-art artifact correction for ECG and PPG extrema
• manual editing of extrema
• extraction of instantaneous features: (heart- or breathing-) rate and period, as well as breathing amplitude
• .csv export of extrema and instantaneous features for further analysis (e.g., heart rate variability)
• automatic analysis of multiple files (batch processing)

Installation

biopeaks can be installed from PyPI:

pip install biopeaks

Alternatively, on Windows, download biopeaks.exe and run it. Running the executable does not require a Python installation.

You can find more details on the installation here.

Documentation

Have a look at the user guide to get started with biopeaks.

Contributors welcome!

Improvements or additions to the repository (documentation, tests, code) are welcome and encouraged. Spotted a typo in the documentation? Caught a bug in the code? Ideas for improving the documentation, increase test coverage, or adding features to the GUI? Get started with the contributor guide.

Citation

Please refer to the biopeaks paper in The Journal of Open Source Software.

Changelog

Have a look at the changelog to get an overview of what has changed throughout the versions of biopeaks.