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.
python3 -m pip install biobabel
Install latest development version from Github:
python -m pip install --upgrade "biobabel @ git+https://github.com/florisvanvugt/biobabel"
https://biobabel.readthedocs.io/
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)
Install locally:
pip install .
and editable:
pip install -e .
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!