FlyLimbTracker: An active contour based approach for leg segment tracking in unmarked, freely behaving Drosophila

Understanding the biological underpinnings of movement and action requires the development of tools for quantitative measurements of animal behavior. Drosophila melanogaster provides an ideal model for developing such tools: the fly has unparalleled genetic accessibility and depends on a relatively compact nervous system to generate sophisticated limbed behaviors including walking, reaching, grooming, courtship, and boxing. Here we describe a method that uses active contours to semi-automatically track body and leg segments from video image sequences of unmarked, freely behaving D. melanogaster. We show that this approach yields a more than 6-fold reduction in user intervention when compared with fully manual annotation and can be used to annotate videos with low spatial or temporal resolution for a variety of locomotor and grooming behaviors. FlyLimbTracker, the software implementation of this method, is open-source and our approach is generalizable. This opens up the possibility of tracking leg movements in other species by modifications of underlying active contour models.