Biobabel : a unified interface for reading diverse physiology file formats

Many different file formats exist for physiology signals such as cardiac (ECG, PPG) or respiratory data. Many packages exist in Python to read these formats but they load into different data structures. This package is a wrapper of sorts for already existing tools providing a unified easy-to-use interface.

Installation

python3 -m pip install biobabel

Install latest development version from Github:

python -m pip install --upgrade "biobabel @ git+https://github.com/florisvanvugt/biobabel"

Documentation

https://biobabel.readthedocs.io/

Physiology dialects

Currently supported dialects for reading are:

• EDF through PyEDFlib
• labstreaminglayer (LSL) XDF (alpha) thanks to pyxdf
• BioPAC Acknowledge (acq) thanks to bioread
• opensignals ("OpenSignals (r)evolution" thanks to opensignalsreader
• Biosemi BDF thanks to pybdf
• Generic CSV (where CSV delimiter is automatically inferred and the time column is guessed as well)
• Brams-Bio-Box (in-house format, even though the Generic-CSV functionality should take care of this now)
• hdphysio5 thanks to hdphysio5
• TeensyECG (in-house format)

Development version

Install locally:

pip install .

and editable:

pip install -e .

Testing

To run the included tests, simply install the package and then run the following command from the root:

pytest

Support

If you have a question or would like to contribute, please see the Contributing to biobabel section.

Citation

Please cite this work if you use it:

• van Vugt, F.T. (2025). Biobabel: Python package for reading major bio/physiology data formats. https://doi.org/10.5281/zenodo.15453402

Thank you!