A system for tracking whisker kinematics and whisker shape in three dimensions

• Published in: PLoS computational biology 2020, Vol.16 (1), p.e1007402-e1007402
• Main Authors: Petersen, Rasmus S, Colins Rodriguez, Andrea, Evans, Mathew H, Campagner, Dario, Loft, Michaela S E
• Format: Article
• Language: English
• Subjects: Algorithms; Animals; Biology and Life Sciences; Biomechanical Phenomena - physiology; Cameras; Curve fitting; Curves; Engineering and Technology; Experimental psychology; Graphical user interface; High speed; Imaging, Three-Dimensional - methods; Kinematics; Male; Measurement methods; Medicine and Health Sciences; Mice; Mice, Inbred C57BL; Neurosciences; Physical Sciences; Research and Analysis Methods; Sensorimotor system; Social Sciences; Software; Three dimensional imaging; Vibrissae; Vibrissae - diagnostic imaging; Vibrissae - physiology; Video data
• ISSN: 1553-7358; 1553-734X; 1553-7358
• DOI: 10.1371/journal.pcbi.1007402

Quantification of behaviour is essential for biology. Since the whisker system is a popular model, it is important to have methods for measuring whisker movements from behaving animals. Here, we developed a high-speed imaging system that measures whisker movements simultaneously from two vantage points. We developed a whisker tracker algorithm that automatically reconstructs 3D whisker information directly from the 'stereo' video data. The tracker is controlled via a Graphical User Interface that also allows user-friendly curation. The algorithm tracks whiskers, by fitting a 3D Bezier curve to the basal section of each target whisker. By using prior knowledge of natural whisker motion and natural whisker shape to constrain the fits and by minimising the number of fitted parameters, the algorithm is able to track multiple whiskers in parallel with low error rate. We used the output of the tracker to produce a 3D description of each tracked whisker, including its 3D orientation and 3D shape, as well as bending-related mechanical force. In conclusion, we present a non-invasive, automatic system to track whiskers in 3D from high-speed video, creating the opportunity for comprehensive 3D analysis of sensorimotor behaviour and its neural basis.