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

Area of Science:

• Systems Neuroscience
• Neuroscience Research
• Experimental Systems

Background:

• Determining causal links between neural activity and behavior is a key goal in systems neuroscience.
• Existing commercial systems for neural monitoring, behavioral tracking, and closed-loop manipulation are often expensive and use proprietary formats, hindering reproducibility and data sharing.
• Open-source tools and standardized data formats are advantageous for scientific advancement.

Purpose of the Study:

• To present an open-source, low-cost, adaptable, and easy-to-set-up system for combined behavioral tracking, electrophysiology, and closed-loop stimulation.
• To enable researchers to investigate the causal relationship between neural activity and behavior.
• To promote reproducibility and data-sharing in neuroscience.

Main Methods:

• The system is based on the Open Ephys platform, incorporating new modules for real-time tracking and behavior-based closed-loop stimulation.
• Open-source Bonsai software analyzes camera images for real-time position tracking.
• Acquired electrophysiology data, including place and grid cell activity, was analyzed using an open-source Python package.

Main Results:

• The system reliably visualizes and records tracking information across various sampling frequencies (30-1000 Hz).
• Successfully combined electrophysiology with tracking modules to record hippocampal place cells and medial entorhinal cortex grid cells.
• Demonstrated closed-loop optogenetic stimulation of entorhinal grid cells using the developed system.

Conclusions:

• This expanded Open Ephys system offers a high-quality, low-cost experimental setup for neuroscience.
• The use of standardized data formats facilitates data sharing and collaboration.
• The system enhances the accessibility of advanced research tools for the neuroscience community.