Skip to content
Branch: master
Clone or download
Permalink
Type Name Latest commit message Commit time
Failed to load latest commit information.
doc Removes requirements Nov 12, 2015
resources Adds properly downscaled version of icons for better display Nov 5, 2015
src Changes to release name Pyper Nov 12, 2015
.gitignore updates gitignore Jul 21, 2015
README.rst Adds authorship and licence Dec 7, 2015
todo.txt Updates TODO list Nov 12, 2015

README.rst

Welcome to Pyper's documentation!

Introduction

This program allows the tracking of specimen (e.g. a mouse, a rat ...) in an open field maze from pre-recorded videos or from a live feed. The live stream of frames can be generated from a USB camera or from the camera (normal or NoIR) of the Raspberry Pi. On the Raspberry Pi, a subclass of the standard PiCamera object is used to speed-up video acquisition and online processing.

The combination of recording and online position tracking allows the definition of complex behavioural experiment as the program can send a TTL pulse to an other computer upon detecting the mouse (for example: in a certain region of space).

The modules can be used interactively from the python interpreter or through the provided interfaces. This program provides both a command line interface and a graphical user interface. For the CLI, the defaults are saved to a user specific preference file.

Some basic analysis of the extracted position data is also available. Two classes are also supplied for viewing of the recorded videos or transcoding.

Example

A usage example of the software

An example of the tracking software in action.

The yellow square at the bottom right lights up when the mouse enters the predefined Region Of Interest (the yellow circle). This behaviour can easily be overwritten by the user by specifying a different function.

Documentation

For further documentation, you can compile the documentation using sphinx or alternatively, head to http://pyper.readthedocs.org/en/latest/

Authors

Charly V Rousseau1, Antonio Gonzalez2, Andrew Erskin3, Christian J Niedworok1, Troy W Margrie1.

Author information:
  • 1Margrie lab. Sainsbury Wellcome Centre for Neural Circuits and Behaviour, University College London, London, U.K.
  • 2Burdakov lab. Mill Hill Laboratory, The Francis Crick Institute, London, U.K.
  • 3Schaefer lab. Mill Hill Laboratory, The Francis Crick Institute, London, U.K.

The authors would like to thank Edward F Bracey, Nicholas Burczyk, Julia J Harris, Cornelia Schöne and Mateo Vélez-Fort for their useful comments about the interface design and the user instructions.

Licence

The software in this repository is licensed under the GNU General Public License, version 2 http://www.gnu.org/licenses/old-licenses/gpl-2.0.en.html.
The graphic assets (under resources/icons or resources/images) are distributed under a Creative commons Attribution-ShareAlike 4.0 International licence (CC BY-SA 4.0) http://creativecommons.org/licenses/by-sa/4.0/legalcode.
You can’t perform that action at this time.