A Matlab based software for analysis of video data of rodents (rats or mice) engaged in string pulling

In the string pulling task for rodents (rats or mice), they pull a vertical string to obtain food reward attached to the end of the string. This task is elegant because rodents require little training and it lends to kinematic analysis of body, head, arm, and hand movements. Using this task with control and experimental animals such as animal models of neurological or spinal cord diseases, one can investigate sensorimotor physiology and pathophysiology as well as test the efficacy of therapeutic drugs in the recovery of sensorimotor function. This software facilitates the analysis of video data of rodents pulling strings and provide kinematic measures of body, head, and hand movements as well as allows whole-body analysis of string pulling motion sequence.

Representative bout of string pulling sequence of a mouse and examples of a subset of analysis. From left to right, 1) tracked hands, ears, nose, and body of the mouse, 2) path of hands, 3) instantaneous speed determined using optical flow, and 4) and 5) show running standard deviation and average of the image sequence respectively

Clone the github repository and then run the following file in the main folder to start the software string_pulling_behavior_analytics.m

Important Note: Use a minimum screen resolution of 1920x1080 for optimal viewing of the GUI window

Matlab Toolbox dependencies

1. Signal processing
2. Image processing
3. Statistics and Machine Learning
4. Computer vision system

Please visit the wiki page https://github.com/samsoon-inayat/string_pulling_mouse_matlab/wiki/Home

Please visit the following page on Open Science Framework to download video files and processed data for 5 C57BL6 and 5 Swiss Webster Albino mice. https://osf.io/gmk9y/

Developed by Samsoon Inayat (Imaging Scientist), Labs of Drs. Majid Mohajerani and Ian Whishaw at the University of Lethbridge, Alberta, Canada

Contributors: Surjeet Singh and Arashk Ghasroddashti

Please see license file

[https://github.com/samsoon-inayat/string_pulling_mouse_matlab/blob/master/LICENSE]

Please report any issues here

https://github.com/samsoon-inayat/string_pulling_mouse_matlab/issues

Inayat, S., S. Singh, A. Ghasroddashti, Qandeel, P. Egodage, I. Q. Whishaw and M. H. Mohajerani (2019). "A toolbox for automated video analysis of rodents engaged in string-pulling: Phenotyping motor behavior of mice for sensory, whole-body and bimanual skilled hand function." bioRxiv: 2019.2012.2018.881342. https://doi.org/10.1101/2019.12.18.881342

Inayat, S. (2020). string_pulling_mouse_matlab, GitHub: String Pulling Behavioral Analytics, A Matlab-based toolbox for characterizing behavior of rodents engaged in string-pulling, https://github.com/samsoon-inayat/string_pulling_mouse_matlab, v4.0, aa7eb6c.