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 PyGaze developers, one is their support forum accessible from ​http://forum.cogsci.nl/index.php?p=/categories/pygaze and the other is a contact form found at ​http://www.pygaze.org/contact/ (in case you do not want to create a forum account)

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. Behavior Research Methods, December 2014, Volume 46, Issue 4, pp 913–921 | Cite as PyGaze: An open-source, cross-platform toolbox for minimal-effort programming of eyetracking experiments - ​https://link.springer.com/article/10.3758/s13428-013-0422-2
2. Edwin S. Dalmaijer, Sebastiaan Mathôt, Stefan Van der Stigchel, 2013 - ​http://www.pygaze.org/resources/downloads/Dalmaijer_Mathot_Stigchel_2013_PyGaze_manuscript.pdf
3. Dalmaijer, E.S., Mathôt, S., & Van der Stigchel, S. (2013). PyGaze: an open-source, cross-platform toolbox for minimal-effort programming of eye tracking experiments. Behaviour Research Methods. doi:10.3758/s13428-013-0422-2

Repositories:

The main repository of PyGaze is: ​https://github.com/esdalmaijer/PyGaze , where you can download the source code, clone it to desktop, or even make your own fork. There is also a repository for PyGazeAnalizer available at: ​https://github.com/esdalmaijer/PyGazeAnalyser

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/esdalmaijer/PyGaze

Openhub: / (PyGaze is not listed here)

Source Forge: / (PyGaze is not listed here)

Evaluation

Licensing: GNU Public License (version 3)

Language: Python

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: There aren't any official releases on GitHub, you can find out the size of the packages from the download page after you download them. ​http://www.pygaze.org/downloads/

Issue tracker: There is a forum where you can write about an issue: ​http://forum.cogsci.nl/index.php?p=/categories/pygaze and there is the issue tracker on GitHub: ​https://github.com/esdalmaijer/PyGaze/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/