Sleep-An Open-Source Python Software for Visualization, Analysis, and Staging of Sleep Data

Description

:class:Sleep is a flexible graphical user interface for visualization, analysis and scoring of polysomnographic sleep data. Sleep is built on top of the VisPy library, which provides GPU-based fast and high-level visualization. Sleep is freely available (​http://visbrain.org/sleep) and comes with sample datasets and an extensive documentation.

The main features of Project Sleep are:

1. Graphical User Interface (GUI) - Modular and responsive
2. Hypnogram (Real-time computation of sleep statistics, export high-quality hypnogram figure)
3. Display (spectrogram, polysomnographic data, Topographic map)
4. Signal processing (Filtering, Bipolarization)
5. Semi-automatic events detections
6. Load standard electro-physiological files (.txt, .csv, .hyp or raw data)

URL:

1. ​http://visbrain.org/sleep
2. ​https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5613192/

Project Anatomy

Community: The lead developer and the contributors

Leadership: EtienneCmb - ​https://github.com/EtienneCmb

Forking: Fork your own copy at this address ​https://github.com/EtienneCmb/visbrain/blob/master/docs/sleep.rst, for which you will need a GitHub account.

Communication: There are a couple of ways for communicating with Project !Sleep developers, one is their support chat rooms about their website and their separate projects. Sleep chat room is accessible from: ​https://gitter.im/visbrain-python/Sleep?utm_source=share-link&utm_medium=link&utm_campaign=share-link

Roadmaps:

To do goals:

• Run detections on non down-sampled signals
• Improve detections integration (New detection axis?)

In progress:

• lazy loading and loading file improvements
• Improve loading and specially down-sampling (data hypnogram save and load hypnogram data)
• Automatic scoring based on machine learning :
  • Compute features
  • Trained the classifier
  • Provide an already trained classifier (channel problem?)
  ,based on the detections
  • Perform spindles / KCs / slow waves on a central electrodes
  • Perform REM on EOG electrode / MT on EMG
  • PerformPeaks on ECG
  • Compute frequency band power by epochs of 30 sec
  • Create a probability vector

Releases:

1.METHODS ARTICLE Front. Neuroinform., 21 September 2017 | ​https://doi.org/10.3389/fninf.2017.00060 Sleep: An Open-Source Python Software for Visualization, Analysis, and Staging of Sleep Data - Etienne Combrisson1,2*†, Raphael Vallat3*†, Jean-Baptiste Eichenlaub4, Christian O'Reilly5, Tarek Lajnef1,6, Aymeric Guillot2, Perrine M. Ruby3‡ and Karim Jerbi

2. Front Neuroinform. 2017; 11: 60. Published online 2017 Sep 21. doi: 10.3389/fninf.2017.00060 , PMCID: PMC5613192, PMID: 28983246, Sleep: An Open-Source Python Software for Visualization, Analysis, and Staging of Sleep Data

Etienne Combrisson,1,2,*† Raphael Vallat,3,*† Jean-Baptiste Eichenlaub,4 Christian O'Reilly,5 Tarek Lajnef,1,6 Aymeric Guillot,2 Perrine M. Ruby,3,‡ and Karim Jerbi1,‡

Repositories

The main repository of !Sleep is: ​https://github.com/EtienneCmb/visbrain/blob/master/docs/sleep.rst , where you can download the source code, clone it to desktop, or even make your own fork.

Packaging:

Different packages for PyGaze, including Windows, Linux and Mac OS X packages can be found at the downloads page of PyGaze: ​http://www.pygaze.org/downloads/

Upstream/downstream:

So far, from 2013 when it was originaly published, PyGaze has 12 contibutors, and it is open for contributing for upstream, after of course your pull request is revised and approved.

Version Control:

version 0.6.0 (07-09-2017) - Latest version control

Trackers:

You can see commits and verified changes at this link: ​https://github.com/esdalmaijer/PyGaze/commits/master

Project Evaluation

Fieldtrips

Github: ​https://github.com/EtienneCmb/visbrain/blob/master/docs/sleep.rst

Openhub: / (!Sleep is not listed here)

Source Forge: / (!Sleep is not listed here)

Evaluation

Licensing: New BSD License (3-Clause BSD License), Copyright (c) 2007–2017 The Visbrain developers.

Language: Python software built on top of NumPy, VisPy, !PyQt4.

Activity: Active

Number of contributors: There are two contributors: Raphael Vallat and Christian O Reilly. They are listed on these pages: ​https://raphaelvallat.github.io/ and ​https://bluebrain.epfl.ch/page-143249-en.html

Size:

Issue tracker: If you found a bug to report, a patch or a request feature you can submit an issue here: ​https://github.com/EtienneCmb/visbrain/issues

New contributor: If you want to be a contributor to PyGaze one way is through the GitHub page, where you can make your own fork and pull request and wait for an approval.

Community norms: You can report an issue through the forum page , help to fix it by forking in the GitHub repository and commit fixes and if you prefer to work via different channels (contact form, or via carrier pigeon), that’s fine too.

User base: Their user base are the developers and the contributors: ​http://www.pygaze.org/contributors/