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:

N/A

Upstream/downstream:

So far, from when it was originaly published, Sleep has two developers, 2 contributors and these people helped in developing Project Sleep: Karim Jerbi, Christian O'Reilly, David Meunier, Dmitri Altukchov, Tarek Lajnef, Perrine Ruby, JB Einchenlaub, kevroy314, Annalisa Pascarella, Thomas Thiery, Yann Harel, Anne-Lise Saive, Golnush Alamian

Version Control:

version v0.3.8 - Latest version control

Trackers:

You can see commits and verified changes at this link: ​https://github.com/EtienneCmb/visbrain/graphs/commit-activity

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: N/A

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 Sleep 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 GithHub issue page , help to fix it by forking in the GitHub repository and commit fixes.

User base: N/A