Publication: open source animal tracking and closed-loop stimulation

Buccino, Lepperød, Dragly et al (Journal of Neural Engineering, 2018)

Open source modules for tracking animal behavior and closed-loop stimulation based on Open Ephys and Bonsai. 

Methods that combine monitoring neural activity, behavioral tracking, and targeted manipulation of neurons in closed-loop are powerful tools. However, commercial systems that allow these types of experiments are usually expensive and rely on non-standardized data formats and proprietary software which may hinder user-modifications for specific needs. In order to promote reproducibility and data-sharing in science, transparent software and standardized data formats are an advantage.Based on the Open Ephys system (www.open-ephys.org) we developed multiple modules to include real-time tracking and behavior-based closed-loop stimulation. Combining the open source software Bonsai (bonsai-rx.org) for analyzing camera images in real time with the newly developed modules in Open Ephys, we acquire position information, visualize tracking, and perform tracking-based closed-loop stimulation experiments. To analyze the acquired data we provide an open source file reading package in Python. The system robustly visualizes real-time tracking and reliably recovers tracking information recorded from a range of sampling frequencies (30–1000 Hz). We recorded place cell and grid cell activity in the hippocampus and in the medial entorhinal cortex and used the system for closed-loop optogenetic stimulation of entorhinal grid cells. 

Wiki page on github containing a detailed guide on how to set up the system:

Open source modules for tracking animal behavior and closed-loop stimulation based on Open Ephys and Bonsai

Alessio Paolo Buccino^1,5, Mikkel Elle Lepperød^1,2,4, Svenn-Arne Dragly^1,3, Philipp Häfliger^1,5, Marianne Fyhn^1,2 and Torkel Hafting^1,2,4

Journal of Neural Engineering, Volume 15, Number 5 
Special Issue on Open Source Tools in Systems Neuroscience