An Algorithm for Automatic Tracking of Rat Whiskers

All mammals, apart from humans and primates, have facial ‘whiskers’. Rodents are "whisker specialists" and have more than 30 whiskers on each side of their face, which they use to gather tactile sensory data on their near surroundings. Many rodents (including rats, discussed here) actively move their whiskers back and forth in a behaviour known as ‘whisking’. In attempting to understand this sensory system (and its neural underpinnings), there is a strong need for automatic tracking of these whisker movements. Tracking all individual whiskers (more than 60) is a very difficult task (into which research is ongoing [1,2]). Here, we introduce an unsupervised algorithm for detection of the ‘mean angular position’ (MAP [3]) of the whiskers on each side of the face during active whisking from high speed greyscale video recordings of freely behaving animals. The core of the algorithm is a geometrical image transform which aids in finding the whiskers and calculating the whisker angles at their root. The only manual input required is to mark two points in the first video frame.