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 : 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
Figure Figure layout

The visbrain structure is summarized below.

_images/visbrain_structure.png

Structure and hierarchy used in visbrain

2. Installation options

2.1. Dependencies

  • NumPy and SciPy (>= 1.13)
  • Matplotlib (>= 1.5.5)
  • VisPy (>= 0.5.3)
  • PyQt5
  • PyOpenGL
  • Pillow

2.2. Optional dependencies

  • Pandas & xlrd : table import / export
  • Pillow : export figures
  • Nibabel : read nifti files
  • MNE-python : alternative to read sleep data files
  • Tensorpac : compute and display phase-amplitude coupling
  • lspopt : multitaper spectrogram
  • imageio : for animated GIF export

2.3. Regular installation

In order to install Visbrain, or to update it, run the following command in a terminal :

pip install -U visbrain

2.4. 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

From here you can switch to the latest features using :

git checkout develop

If you don’t want to clone the full package, run :

pip install git+https://github.com/EtienneCmb/visbrain.git

2.5. Update visbrain

You can update visbrain using :

pip install --upgrade visbrain