This summer, the OpenBehavior project team is focusing on creating documentation for setting up and using three valuable video analysis tools in neuroscience research. These tools often lack straightforward, in-lab setup guides, so we want to make them more accessible.
First, we will provide a step-by-step guide on how to set up a Linux PC for pose estimation using the (SLEAP) software package. Many labs currently rely on cloud-based platforms like Colab, which can be time-consuming and frustrating when jobs die in the cloud. By setting up a local, in-lab option, researchers can streamline this process and get faster and more reliable access to their results. We aim to make the hardware and software setup involved easier to understand, making this powerful tool more accessible to neuroscientists.
Second, we will document the process of using Bonsai to record synchronized video files with precise timestamps and behavioral data from operant tasks. While Bonsai offers an initial (tutorial) on synchronization, our documentation will provide more detailed instructions for integrating commonly used MedPC systems with Bonsai. This will enable seamless alignment of behavioral events with corresponding video recordings.
Third, we will explain how to use ArUco markers for real-time rodent tracking using Bonsai to trigger task events and optogenetic stimulation. We will also show how to extract key movement parameters from recorded videos using these markers. This marker-based approach offers a valuable alternative to full pose estimation and may be enough for many researchers interested in understanding how movement variability influences their neural or behavioral outcomes. The application of ArUco markers in operant studies was recently highlighted in a paper published by eNeuro and in a recent OpenBehavior blog post.
This work is being carried out by the OpenBehavior research team, including Mark Laubach (Professor of Neuroscience at American University and Principal Investigator), Kevin Chavez Lopez (a rising third-year PhD student at American University), Jason Blackmer (a neuroscience and data science double major at American University), and Ray Shen (a student from Montgomery Blair High School).
Stay tuned for updates on our progress, which will be shared throughout the summer of 2025.