C# Wheel Encoder Plugin

Overview

This document describes the C# wheel encoder plugin, specifically the aind-behavior-amt10-encoder library, used for acquiring rotary encoder data from the running wheel on Neuropixel and Mesoscope experimental rigs at the Allen Institute. This plugin provides Bonsai nodes for reading and interacting with AMT10 quadrature encoders.

Note: This plugin is not used for SLAP2 rigs, which utilize HARP for wheel encoder communication.

Important Disclaimer: This documentation is provided for transparency and to fully describe the experimental setup. The aind-behavior-amt10-encoder and the associated hardware configuration are highly specific to the Allen Institute's experimental rigs and are not intended for general use outside of this specific context.

Purpose

The primary purpose of this plugin within the Allen Institute's setup is to:

  • Provide real-time access to wheel position and speed from AMT10 encoders.
  • Offer a standardized interface within Bonsai workflows for these specific digital wheel encoders.
  • Facilitate synchronization of behavioral data (running) with neural recordings and visual stimuli, which is critical for experiments such as sensory-motor oddballs.

Hardware and Communication Architecture

The system relies on a specific hardware and software chain:

  1. AMT10 Encoder: A digital rotary encoder measures the wheel's rotation.
  2. LS7366R Quadrature Counter Chip: This chip interfaces directly with the encoder.
  3. Arduino: An Arduino board, running custom firmware (LS7366R_quadrature_counter.ino), reads data from the LS7366R chip.
  4. Serial Communication: The Arduino sends the encoder data over a serial (USB) connection.
  5. C# (Bonsai Nodes): The aind-behavior-amt10-encoder library provides Bonsai nodes (e.g., AMT10EncoderSource) that communicate with the Arduino via this serial connection, parsing the data to make it available within Bonsai workflows.

This architecture allows C# applications, primarily Bonsai workflows, to access and utilize the wheel encoder data.

Source Code

  • Repository Link: https://github.com/AllenNeuralDynamics/aind-behavior-amt10-encoder

  • Key Files/Modules:

    • src/Aind.Behavior.Amt10Encoder/: Contains the C# source code for the Bonsai nodes.
    • reference/LS7366R_quadrature_counter.ino: The Arduino firmware.
    • reference/AMT10_quadrature_encoder.py: Python reference implementation of the communication protocol.

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