Kicad CaPuLeT PCB Update

An open-source system to integrate Calcium-imaging, Pupillometry, and Locomotion-estimated Tracking (CaPuLeT) in head-fixed mice

Designed by members of the Pégard and Rodríguez-Romaguera Labs at the University of North Carolina at Chapel Hill, CaPuLeT allows researchers to capture locomotion, pupil dynamics, and body kinematics simultaneously. Our system relies on CMOS cameras, an infrared camera placed at eye-level to capture pupil size and an additional camera to record body kinematics. Our system is capable of capturing locomotion, or the mouse's movement across time, as our wheel system is attached to a mounted rotary encoder. For more information, refer to Ortiz-Juza et al, 2024 [1].

Graphic User Interface (GUI)

The CaPuLeT MATLAB graphical user interface (GUI) allows users to trigger and manage the cameras and LEDs driven by an Arduino microcontroller with a custom shield. Within CaPuLeT, users can track locomotion, pupil-size, and in vivo calcium imaging data in real-time.

Behavioral and Imaging Data Collected:

• IR Camera → Pupil Dynamics (Dilation and Constriction)
• Additional Camera → Body Kinematics (Body and Tail Movement)
• Rotary Encoder → Locomotion (Speed and Acceleration)
• Multi-Photon Microscope → Neuronal Activity (Intracellular Calcium Concentration)

Custom Arduino Printed Circuit Board Shield:

The head-fixation wheel system is driven and controlled by an Arduino Mega 2560 microcontroller board, with a custom printed circuit board (PCB) Arduino shield with built-in resistance, interactive feedback LEDs, real-time clock compatibility, and screw hole terminals. The printed circuit board shield expands the capabilities of the microcontroller board and allows for greater stability than a conventional solderless circuit board. The Arduino shield allows users to interface with each of the components of the CaPuLeT GUI.

Commercially Available and Custom Made Parts

The following component list details the manufacturer, part number, and quantity of each item required. This version of the component list contains a color coded key which provides an additional layer of support when building the system.

This document outlines the design of each of the custom pieces and the file types found within this repository that can be used to replicate the system. More details regarding the specifications of the custom parts can be found here. The following spreadsheet outlines the total cost of the system.

Here is a list of the manufacturers we purchased materials from:

• McMaster-Carr
• Pololu
• Thorlabs
• SparkFun
• Digikey
• Amazon
• FLIR
• The Imaging Source
• SYSRACKS

Here is a list of companies you can purchase custom parts from, if not fabricated in-house:

• eMachineShop (CNC Machining)
• Ponoko (Laser Cutting)
• Craftcloud3d (3-D Printing)
• JBL PCB (PCB Printing / Soldering)

Step-by-Step Building Guide

A fully functioning system requires users to build the following elements from the materials purchased:

• Locomotion Wheel
• Headplate Fixation System
• IR / UV LEDs

Additionally, the following commercial materials need to modified to be used within our system:

• Rotary Encoder
• GPIO Cable
• Hirose Cable
• Overhead Speaker
• Ambient Noise Fan
• Red LED Strips

This following guide provides a step-by-step walkthrough for building and modifying each of the required components. This document includes diagrams and explanations for assembling each of the final components of the build.

Software Installation Guide and Dependencies

Following this installation guide will ensure that your system will be able to run the set of MATLAB scripts and Arduino IDE sketches we have provided. Our system is run primarily on MATLAB's interface. While other software is used to first initialize components, such as Arduino IDE for the rotary encoder and Spinnaker SDK for the cameras, the subsequent input signals and data acquisition steps are performed exclusively with MATLAB.

Required Software and Applications:

• MATLAB R2022a
• Arduino IDE
• Spinnaker SDK
• DeepLabCuts

Our MATLAB scripts are based on MATLAB R2022a, a previous version of the software application. Running our scripts on a more recent version of the application will result in a number of errors. After downloading MATLAB R2022a, you will need to download a number of toolboxes and add-ons.

Base Toolboxes:

• Data Acquisition Toolbox
• Image Acquisition Toolbox
• Image Processing Toolbox
• Statistics and Machine Learning Toolbox

Additional Toolbox Support Packages:

• Data Acquisition Toolbox Support Package for National Instruments NI-DAQmx Devices
• Image Acquisition Toolbox Support Package for GenICam Interface
• Image Acquisition Toolbox Support Package OS Generic Video Interface
• Image Acquisition Toolbox Support Package for Point Grey Hardware
• Image Acquisition Toolbox Support Support Package for GigE Vision Hardware
• MATLAB Support Package for Arduino Hardware

Finally, users will need to download the following drivers to generate a connection between their computer system and an external hardware device. In our case, we need to download two drivers to interface with the additional camera used in our system.

Driver Requirements:

• USB3 Driver
• DMK 22BUC03 Driver
• Spinnaker SDK USB3 Vision Cameras Driver
• IC Matlab Plugin for Matlab (Version 3.4.0.58)

Library Requirements:

• DS3231 Library

Contact

Further information and requests for resources should be directed to and will be fulfilled by the lead contact and corresponding author, Jose Rodriguez-Romaguera (jose_rodriguezromaguera@med.unc.edu). Example pupillometric and locomotion data is available upon request to the technical contact and corresponding author, Nicolas C. Pégard (pegard@unc.edu).

Citation

If you replicate this system in your own labs or use parts of our designs and code, we kindly ask that you please cite Ortiz-Juza et al, 2024 [1].

[1] Ortiz-Juza, M. M., Tormes-Vaquerano, J., Hegel, S. M., Curtis, V. R., Alghorazi, R. A., Miller, N. W., McTaggart, E. M., Pégard, N. C., & Rodriguez-Romaguera, J. (2024). Protocol for an open-source system to integrate calcium imaging, pupillometry, and locomotion-estimated tracking in head-fixed mice. STAR Protocols, 5(4), 103331. https://doi.org/10.1016/j.xpro.2024.103331