Due to recent advances that enable real-time electrophysiological recordings in brains of awake
behaving rodents, effective methods for analyzing the large amount of behavioral data thus
generated, at millisecond resolution, are required. We describe a semiautomated, efficient method
for accurate tracking of head and mystacial vibrissae (whisker) movements in freely moving
rodents using high-speed video. By tracking the entire length of individual whiskers, we show how
both location and shape of whiskers are relevant when describing the kinematics of whisker
movements and whisker interactions with objects during a whisker-dependent task and
exploratory behavior.