1. Presentation

1.1. Quick description

Visbrain is an open-source Python 3 package, distributed under the 3-Clause BSD license and is dedicated to brain signals visualization. It is under heavy development and many functionalities are frequently added to the package, such as bug fixing, documentation improvements etc.

Visbrain use VisPy to render graphics. Taken from their website :

VisPy is a high-performance interactive 2D/3D data visualization library leveraging the computational power of modern Graphics Processing Units (GPUs) through the OpenGL library to display very large datasets.

1.2. Structure

Visbrain is mainly divided into two branches :

  • Modules : essentially designed for beginner users, modules comes with a graphical user interface (GUI) for interactions between plotted elements and parameters.
  • Objects : objects are elementary bricks i.e. one visualization purpose per object. It’s mainly designed for advanced users since objects are much more modular. See the Objects documentation and the API visbrain.objects
Module name Description
Brain Visualizations involving a MNI brain
Sleep Visualize and score polysomnographic data
Signal Visualize multi-dimensional datasets
Topo Topographic representations
Figure Figure layout

The visbrain structure is summarized below.

_images/visbrain_structure.png

Structure and hierarchy used in visbrain

2. Installation

2.1. Dependencies

Package Version Purpose
NumPy >= 1.13 Scientific computing
SciPy
Mathematics, science, and engineering
Matplotlib >= 1.5.5 Colors and colormaps integration
VisPy >= 0.5.2 Graphics rendering
PyQt5
Graphical User Interface components
Pillow
Screenshots and image file format support

PyQt5 can be installed using either pip install pyqt5 or conda install pyqt. We also strongly recommend to install pandas and pyopengl :

pip install pandas PyOpenGL PyOpenGL_accelerate

2.2. Regular installation

Run the following command in a terminal :

pip install visbrain

2.3. Develop mode

If you want to install visbrain in develop mode :

git clone https://github.com/EtienneCmb/visbrain.git visbrain/
cd visbrain/
python setup.py develop