A Matlab-based toolbox for characterizing behavior of rodents engaged in string-pulling

Abstract
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Abstract

String-pulling by rodents is a behavior in which animals make rhythmical body, head, and bilateral forearm as well as skilled hand movements to spontaneously reel in a string. Typical analysis includes kinematic assessment of hand movements done by manually annotating frames. Here, we describe a Matlab® based software that allows whole-body motion characterization using optical flow estimation, descriptive statistics, principal component, and independent component analyses as well as temporal measures of Fano factor, entropy, and Higuchi fractal dimension. Based on image-segmentation and heuristic algorithms for object tracking, the software also allows tracking of body, ears, nose, and forehands for estimation of kinematic parameters such as body length, body angle, head roll, head yaw, head pitch, and path and speed of hand movements. The utility of the task and software is demonstrated by characterizing postural and hand kinematic differences in string-pulling behavior of two strains of mice, C57BL/6 and Swiss Webster.

Data availability

The software is available to download from https://github.com/samsoon-inayat/string_pulling_mouse_matlab. All video source and processed data is made available at the following website https://osf.io/gmk9y/?view_only=cdf229798f2d40e08b98aeadd927f1c2

The following data sets were generated

1. Samsoon Inayat
(2019) Mouse String-Pulling Data
Open Science Framework, DOI 10.17605/OSF.IO/GMK9Y.

https://osf.io/gmk9y/

Article and author information

Author details

Samsoon Inayat

Neuroscience, University of Lethbridge, Lethbridge, Canada

For correspondence
samsoon.inayat@gmail.com

Competing interests
The authors declare that no competing interests exist.

"This ORCID iD identifies the author of this article:" 0000-0003-1966-7967
Surjeet Singh

Neuroscience, University of Lethbridge, Lethbridge, Canada

Competing interests
The authors declare that no competing interests exist.
Arashk Ghasroddashti

Neuroscience, University of Lethbridge, Lethbridge, Canada

Competing interests
The authors declare that no competing interests exist.
Qandeel Qandeel

Neuroscience, University of Lethbridge, Lethbridge, Canada

Competing interests
The authors declare that no competing interests exist.
Pramuka Egodage

Neuroscience, University of Lethbridge, Lethbridge, Canada

Competing interests
The authors declare that no competing interests exist.
Ian Q Whishaw

Neuroscience, University of Lethbridge, Lethbridge, Canada

Competing interests
The authors declare that no competing interests exist.
Majid H Mohajerani

Canadian Centre for Behavioral Neuroscience, University of Lethbridge, Lethbridge, Canada

For correspondence
mohajerani@uleth.ca

Competing interests
The authors declare that no competing interests exist.

"This ORCID iD identifies the author of this article:" 0000-0003-0964-2977

Funding

Canadian Institutes of Health Research (390930)

Majid H Mohajerani

Natural Sciences and Engineering Research Council of Canada (40352)

Majid H Mohajerani

Alberta Innovates (43568)

Majid H Mohajerani

Alberta Alzheimer Research Program Grant (PAZ15010)

Majid H Mohajerani

Alberta Alzheimer Research Program Grant (PAZ17010)

Majid H Mohajerani

Alzheimer Society of Canada (43674)

Majid H Mohajerani

The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.

Ethics

Animal experimentation: All experiments were performed in strict accordance with the Canadian Council of Animal Care and were approved by the University of Lethbridge Animal Welfare Committee (Protocol 1812).

Copyright

This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.