biotop: picking peaks in physiological data

A simple GUI for human-assisted semiautomatic ECG and respiration preprocessing.

Purpose ECG analysis of real-world data can be tricky, especially when there are lots of artefacts. Automated pipelines exist but the results can often not be inspected, and not manually adjusted.

The current script allows you to import, view and explore ECG and respiratory data. You can run automated peak detection which you can then inspect and modify manually. The results are saved in a JSON file format.

Prerequisites

• Python 3.X

Prerequisite packages are installed automatically using the following:

python3 -m pip install biotop

Usage

For ECG analysis:

biotop

For respiration analysis:

respire

Basic GUI controls

• Hold down shift while moving the mouse : Snap to closest maximum
• Mouse scroll wheel up/down : Scroll back and forth in time
• Ctrl key + Mouse scroll wheel up/down : Zoom in/out in time
• Mouse left button double click : Insert peak (or zoom in if not zoomed in enough)
• Mouse right button single click : Remove peak
• Mouse middle button click : Insert marker for invalid region
• Mouse middle button double click : Remove invalid region
• Keyboard keys:
  • z toggles between micro and macro zoom (make sure the window has focus)
  • a shows the entire signal
  • Left/right arrow keys scroll through the signal slowly
  • PageDown/PageUp keys browse through the signal a full window at a time

Development

Install latest development version:

pip install --upgrade "biotop @ git+https://github.com/florisvanvugt/biotop"

Wishlist

• Show a window when waiting for peak autodetection to complete
• Make sure y axis labels remain visible even for greater zoom