Image processing software development for the biosciences: Indicators of neurodegenerative disease revealed through animal behaviour

Project Summary

A multi-disciplinary project developing image analysis software for objective, non-invasive assessment of animal behaviour. In particular, the project will focus on developing a piece of usable software to process videos to quantify changes in patterns of mouse locomotion and whisker movements resulting from neurodegenerative disorders such as Motor Neuron Disease, Huntingdon's Disease and ageing.

Project Aims and Objectives

Being able to monitor disease progression and the effects of drug administration is the key to describing and monitoring chronic disease. Animal models are employed to observe these effects, but they are intrusive and often involve making in-situ recordings from the target organ. Generating measurable behavioural models would reduce animal numbers in experiments and increase longitudinal studies of disease progression; however, existing custom-made programmes that automatically measure behaviours tend to be expensive commercially and cannot be applied more generally. Grant et al. (2013, Behavioural Brain Research) found that locomotion and whisker movements were both affected in a mouse model of Motor Neuron Disease (MND). They were able to accurately measure the disruption of whisker movements, and found that deficits were strongly correlated to muscular atrophy and facial nucleus decline in diseased mice. They suggested, therefore, that whisker movements are a strong behavioural measure of movement disorders, such as MND, especially as they can be non-invasively observed and accurately measured. This PhD will develop this behavioural model further, by developing image processing and tracking techniques to precisely measure locomotion and whisking behaviours; it aims:
i) to characterise locomotion and whisker movement declines in a range of movement disorders, including Motor Neuron Disease, Huntington’s Disease, Cerebellar Ataxia, Neural Development Disorders, Aging and Smoking.
ii) to develop an open-source toolbox of suitable behavioural measures for locomotion and whisker movements, by applying skills in image processing and signal analysis. The end product will be a piece of usable software for users to apply to a range of movement disorders.

Specific Requirements of the Project

Candidates must have good software development skills and a strong motivation for research. Expertise of developing image analysis algorithms would be desirable, with an interest in animal behavior.
• Qualifications
A high grade undergraduate degree (first class or upper second) in Computer Science with an interest in biological applications
An MSc level would be desirable for this post, either in Computational Neuroscience or Computer Science using image processing techniques
• Skills
Knowledge of software development and programming, including C/C++/Java, OpenCV and Matlab
Experience of designing experiments and running statistical analyses, in Matlab, r, or SPSS
Developing image analysis algorithms would be beneficial

Please quote the studentship reference number SE2014RG7 in your application.