Documentation of toolbox physio

physio is a python toolbox to analyse physiological signals : respiration and ECG (electrocardiogram).

Authors

physio is developped by Samuel Garcia, Valentin Ghibaudo and Jules Granget.

This toolbox is used by the CMO team in the Centre de recherche en Neurosciences de Lyon (CRNL)

Manuscript

This work has been published at eNeuro : https://www.eneuro.org/content/10/10/ENEURO.0197-23.2023

Features

• respiration cycle detection

• respiration cycle features (amplitude, duration, volumes, …)

• simple preprocessing on signals: filtering with SciPy and smoothing

• ECG peak detection

• ECG/HRV metrics (time domain and frequency domain)

• RespHRV: a new approach to compute cycle-by-cycle metrics

• cyclic deformation machinery: a simple stretcher of any signal to a cycle template

• simple readers for Micromed and BrainVision using Neo

• “auto-magic” parameters for different species (human, rat)

Contents:

• Physio package overview
• Getting started tutorial
• Respiration tutorial
• ECG tutorial
• Cyclic Deformation Tutorial
• RespHRV Tutorial
• Cardio-respiratory synchronization
• Handling parameters
• API
• Release notes

Installation

Installation from pypi (releases only):

pip install physio

Installation from (github) sources (more up-to-date):

pip install https://github.com/samuelgarcia/physio/archive/main.zip

Installation with local clone of sources (for dev mode):

git clone https://github.com/samuelgarcia/physio.git
cd physio
pip install -e .

Update local sources:

cd physio
git pull origin main

Indices and tables

• Index

• Module Index

• Search Page