title: Pixying Behavior: A Versatile Real-Time andPost HocAutomated Optical Tracking Method for Freely Moving and Head Fixed Animals.
abstract: Here, we describe an automated optical method for tracking animal behavior in both head-fixed and freely moving animals, in real time and offline. It takes advantage of an off-the-shelf camera system, the Pixy camera, designed as a fast vision sensor for robotics that uses a color-based filtering algorithm at 50 Hz to track objects. Using customized software, we demonstrate the versatility of our approach by first tracking the rostro-caudal motion of individual adjacent row (D1, D2) or arc whiskers (β, γ), or a single whisker and points on the whisker pad, in head-fixed mice performing a tactile task. Next, we acquired high-speed video and Pixy data simultaneously and applied the pixy-based real-time tracking to high-speed video data. With this approach, we expand the temporal resolution of the Pixy camera and track motion (post hoc) at the limit of high-speed video frame rates. Finally, we show that this system is flexible: it can be used to track individual whisker or limb position without any sophisticated object tracking algorithm, it can be used in many lighting conditions including infrared (IR); it can be used to track head rotation and location of multiple animals simultaneously. Our system makes behavioral monitoring possible in virtually any biological setting.
authors.affiliation: Neurocure Cluster of Excellence, Humboldt Universität zu Berlin, Germany; Berlin School of Mind and Brain, Humboldt Universität zu Berlin 10099, Germany.
authors.forename: Mostafa A
authors.identifier: 0000-0002-4189-5977
authors.initials: MA
authors.lastname: Nashaat
authors.affiliation: Neurocure Cluster of Excellence, Humboldt Universität zu Berlin , Germany.
authors.forename: Hatem
authors.initials: H
authors.lastname: Oraby
authors.affiliation: Neurocure Cluster of Excellence, Humboldt Universität zu Berlin, Germany; Erasmus Program, Faculdad de Biologia, Universidad de Barcelona, Barcelona 08007, Spain.
authors.forename: Laura Blanco
authors.identifier: 0000-0003-3818-5859
authors.initials: LB
authors.lastname: Peña
authors.affiliation: Neurocure Cluster of Excellence, Humboldt Universität zu Berlin , Germany.
authors.forename: Sina
authors.initials: S
authors.lastname: Dominiak
authors.affiliation: Neurocure Cluster of Excellence, Humboldt Universität zu Berlin , Germany.
authors.forename: Matthew E
authors.identifier: 0000-0001-9799-2656
authors.initials: ME
authors.lastname: Larkum
authors.affiliation: Neurocure Cluster of Excellence, Humboldt Universität zu Berlin , Germany.
authors.forename: Robert N S
authors.identifier: 0000-0002-6627-0199
authors.initials: RN
authors.lastname: Sachdev
mesh_terms: D000465:Algorithms; D000818:Animals; D001330:Electronic Data Processing; D005260:Female; D019416:Head Movements / Q000502:physiology*; D051379:Mice; D009043:Motor Activity; D012984:Software; D014110:Touch / Q000502:physiology*; D014738:Vibrissae / Q000294:innervation*; D014741:Video Recording; D014851:Wakefulness / Q000502:physiology*
keywords: behavioral analysis; closed-loop behavior; head-fixed behavior; real-time behavior; sensorimotor integration; whisker kinematics