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The development, validation and demonstration of an automated rodent tracker and whisker detector

Hewitt, Brett Michael (2018) The development, validation and demonstration of an automated rodent tracker and whisker detector. Doctoral thesis (PhD), Manchester Metropolitan University.

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Abstract

Quantitatively assessing behaviour to measure animal behaviour and motor control is challenging because there is a lack of unobtrusive behavioural models. Some studies have suggested that measuring whisker movements might be a good, quantitative behavioural model. However, whiskers are very thin, small and move very fast; and there is not yet an automated program that can detect whiskers in a fully-intact, freely-moving animal. Therefore, this thesis develops, validates and demonstrates a novel, fullyautomated rodent tracker and a whisker annotator, that simultaneously measures locomotion and exploration behaviours as well as whisker movements. The �rst step in designing an automated rodent tracker and whisker detector, is to extract a reliable ground truth from which to compare any tracked points to. Therefore, the Manual Whisker Annotator (MWA) was designed as a validator and calibrator for the subsequent trackers and detectors. The second step is to provide a reliable body and head contour. Therefore, the Automated Rodent Tracker (ART) was developed and validated, compared to a semi-automated tracker (Ethovision) and the MWA. Finally, a fully-automated whisker detector (FAWD) was designed and validated, using two existing semi-automatic whisker trackers (BWTT and Whisk) and the MWA. FAWD incorporates a variety of image-processing algorithms, including super sampling, dilation and subtraction and frangi �ltering to reliably detect whiskers. Both ART and FAWD were also successfully demonstrated on videos collected from SOD1 mice, a model of Amyotrophic Lateral Sclerosis, from day 30 to 120. The development of this software enables whisker movements and locomotion to be tracked in a repeatable fashion, and the fully-automated nature of the software means that many videos can be collected and quickly processed with minimal user input. This thesis develops and validates a suite of behavioural software that provides robust and quantitative measures of rodent behaviour for basic research or drug discovery. Future work will be to demonstrate this software on a larger range of rodent models of neurodegeneration, to further showcase the exibility and quantitative nature of this behavioural model.

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