Tracking Rats in Operant Conditioning Chambers Using a Versatile Homemade Video Camera and DeepLabCut

Summary

This protocol describes how to build a small and versatile video camera, and how to use videos obtained from it to train a neural network to track the position of an animal inside operant conditioning chambers. This is a valuable complement to standard analyses of data logs obtained from operant conditioning tests.

Abstract

Operant conditioning chambers are used to perform a wide range of behavioral tests in the field of neuroscience. The recorded data is typically based on the triggering of lever and nose-poke sensors present inside the chambers. While this provides a detailed view of when and how animals perform certain responses, it cannot be used to evaluate behaviors that do not trigger any sensors. As such, assessing how animals position themselves and move inside the chamber is rarely possible. To obtain this information, researchers generally have to record and analyze videos. Manufacturers of operant conditioning chambers can typically supply their customers with high-quality camera setups. However, these can be very costly and do not necessarily fit chambers from other manufacturers or other behavioral test setups. The current protocol describes how to build an inexpensive and versatile video camera using hobby electronics components. It further describes how to use the image analysis software package DeepLabCut to track the status of a strong light signal, as well as the position of a rat, in videos gathered from an operant conditioning chamber. The former is a great aid when selecting short segments of interest in videos that cover entire test sessions, and the latter enables analysis of parameters that cannot be obtained from the data logs produced by the operant chambers.

Introduction

In the field of behavioral neuroscience, researchers commonly use operant conditioning chambers to assess a wide range of different cognitive and psychiatric features in rodents. While there are several different manufacturers of such systems, they typically share certain attributes and have an almost standardized design^1,2,3. The chambers are generally square- or rectangle-shaped, with one wall that can be opened for placing animals inside, and one or two of the remaining walls containing components such as levers, nose-poke openings, reward trays, response wheels and lights....

Protocol

All procedures that include animal handling have been approved by the Malmö-Lund Ethical committee for animal research.

1. Building the video camera

NOTE: A list of the components needed for building the camera is provided in the Table of Materials. Also refer to Figure 1, Figure 2, Figure 3, Figure 4, Figur.......

Discussion

This protocol describes how to build an inexpensive and flexible video camera that can be used to record videos from operant conditioning chambers and other behavioral test setups. It further demonstrates how to use DeepLabCut to track a strong light signal within these videos, and how that can be used to aid in identifying brief video segments of interest in video files that cover full test sessions. Finally, it describes how to use the tracking of a rat’s head to complement the analysis of behaviors during operan.......

Materials

Name	Company	Catalog Number	Comments
32 Gb micro SD card with New Our Of Box Software (NOOBS) preinstalled	The Pi hut (https://thpihut.com)	32GB
330-Ohm resistor	The Pi hut (https://thpihut.com)	100287	This article is for a package with mixed resistors, where 330-ohm resistors are included.
Camera module (Raspberry Pi NoIR camera v.2)	The Pi hut (https://thpihut.com)	100004
Camera ribbon cable (Raspberry Pi Zero camera cable stub)	The Pi hut (https://thpihut.com)	MMP-1294	This is only needed if a Raspberry Pi zero is used. If another Raspberry Pi board is used, a suitable camera ribbon cable accompanies the camera component
Colored LEDs	The Pi hut (https://thpihut.com)	ADA4203	This article is for a package with mixed colors of LEDs. Any color can be used.
Female-Female jumper cables	The Pi hut (https://thpihut.com)	ADA266
IR LED module (Bright Pi)	Pi Supply (https://uk.pi-supply.com)	PIS-0027
microcomputer motherboard (Raspberry Pi Zero board with presoldered headers)	The Pi hut (https://thpihut.com)	102373	Other Raspberry Pi boards can also be used, although the method for automatically starting the Python script only works with Raspberry Pi zero. If using other models, the python script needs to be started manually.
Push button switch	The Pi hut (https://thpihut.com)	ADA367
Raspberry Pi power supply cable	The Pi hut (https://thpihut.com)	102032
Raspberry Pi Zero case	The Pi hut (https://thpihut.com)	102118
Raspberry Pi, Mod my pi, camera stand with magnetic fish eye lens and magnetic metal ring attachment	The Pi hut (https://thpihut.com)	MMP-0310-KIT