This is a fork of Visbrain with important modifications to the Sleep GUI making it suitable (great?) for scoring animal data, while Sleep was originally designed for human scoring.

In particular, the following features were added:

• Dissociation of 'display window' and 'scoring window', allowing one to score in short epochs while still visualizing data around the scoring window, as in standard in animal scoring. In "locked" mode, the scoring and display window are identical (as is standard for human scoring)
• Flexible definition of vigilance states (name, value in old-style hypnograms, color and order in the GUI) from a YAML file. Use by specifying the state_config_path kwarg to the Sleep object. Refer to the documentation for an exemple. The default configuration contains the following states: ['Art', 'Wake', 'REM', 'N1', 'N2', 'N3'] and their associated values: [-1, 0, 4, 1, 2, 3]
• Integration of a video player synchronized with data. Use with by specifying the video_file and video_offset kwargs to the Sleep object. Supported formats are the same as Qt's QMediaPlayer class.
• Adding a hypnogram color overlay onto signal data. This slows up state assignment quite a bit but can be deactivated in the menu.
• Adding a "click-and-drag" window to select arbitrary epochs for subsequent scoring. Life hack: if there is a rather long continuous epoch to score: click on signal to create the "click-and-drag" window, use "N" (while holding the mouse) to go to next window until you reach the end of the epoch, "close" the window where appropriate and score the whole thing at once. This will speed up dramatically scoring and hopefully make you happy.

Hopefully all this stuff will be merged to the main repo eventually. Unfortunately this all comes with no guarantee regarding maintenance and system compatibility but feel free to contribute.

Last but not least: here is the repo we use to load SpikeGLX (neuropixels) and TDT data, load a proxy to the EMG generated from LFP data, and launch the Sleep GUI: https://github.com/CSC-UW/sleepscore

Best, Tom

Visbrain

Visbrain is an open-source python 3 package dedicated to brain signals visualization. It is based on top of VisPy and PyQt and is distributed under the 3-Clause BSD license. We also provide an on line documentation, examples and datasets and can also be downloaded from PyPi.

Important links

• Official source code repository : https://github.com/EtienneCmb/visbrain
• Online documentation : http://visbrain.org
• Visbrain chat room

Installation

Dependencies

Visbrain requires :

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

User installation

Install Visbrain :

pip install -U visbrain