DOI: 10.1101/482349Nov 28, 2018Paper

Real-time markerless video tracking of body parts in mice using deep neural networks.

BioRxiv : the Preprint Server for Biology
Brandon ForysTimothy H Murphy


Markerless and accurate tracking of mouse movement is of interest to many biomedical, pharmaceutical, and behavioral science applications. The additional capability of tracking body parts in real-time with minimal latency opens up the possibility of manipulating motor feedback, allowing detailed explorations of the neural basis for behavioral control. Here we describe a system capable of tracking specific movements in mice at a frame rate of 30.3 Hz. To achieve these results, we adapt DeepLabCut - a robust movement-tracking deep neural network framework - for real-time tracking of body movements in mice. We estimate paw movements of mice in real time and demonstrate the concept of movement-triggered optogenetic stimulation by flashing a USB-CGPIO controlled LED that is triggered when real time analysis of movement exceeds a pre-set threshold. The mean time delay between movement initiation and LED flash was 93.44 ms, a latency sufficient for applying behaviorally-triggered feedback. This manuscript presents the rationale and details of the algorithms employed and shows implementation of the system using behaving mice. This system lays the groundwork for a behavior-triggered 'closed loop' brain-machine interface with optogenetic...Continue Reading

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