9-Axis IMU Intan Sync Toolbox

Author: Hongyu Chang Date: 2026/03/01

This repository is organized as a small toolbox for collecting 9-axis IMU data with an Arduino Mega, sending a TTL sync pulse to an Intan system, and logging the IMU stream to a computer with Python.

The active toolbox now has one supported Arduino sketch and one supported Python logger:

• arduino/imu_intan_sync_toolbox/imu_intan_sync_toolbox.ino
• python/read_imu.py

Legacy experiments that are not part of the supported workflow are kept under archive/.

Folder Layout

• arduino/imu_intan_sync_toolbox/ Arduino sketch for the MPU9250 + Intan TTL sync workflow.
• python/read_imu.py Python logger that starts the Arduino stream, reads binary packets, and saves a CSV file.
• python/requirements.txt Python dependency list.
• 3D_printing_parts/ 3D design files for mounting the IMU as part of an electrophysiology headstage assembly.
• archive/ Older notebook, legacy Arduino sketches, legacy Python logger, and unrelated servo test material.

Hardware

This toolbox assumes:

• Arduino Mega
• MPU9250 IMU
• Intan digital input for the sync pulse

Default wiring for the Arduino Mega:

• MPU9250 VCC -> 3.3V
• MPU9250 GND -> GND
• MPU9250 SDA -> pin 20
• MPU9250 SCL -> pin 21
• Arduino pin 13 -> Intan digital input
• Arduino GND -> Intan GND

Important:

• Verify your Intan digital input voltage compatibility before directly wiring the Arduino sync pin.
• Use a level shifter if your recording setup requires it.
• A shared ground between Arduino and Intan is required for reliable TTL synchronization.

Reference for the Arduino-side IMU implementation:

• based on hideakitai/MPU9250
• based on arnefmeyer/IMUReaderPlugin
• https://github.com/hideakitai/MPU9250.git
• https://github.com/arnefmeyer/IMUReaderPlugin.git

3D Printing Parts

The folder 3D_printing_parts/ contains the mechanical design files for incorporating the IMU into the ephys headstage setup.

Included files:

• mouse_cam_base_final_withgyro_wall_2.5mm.stl
• mouse_cam_base_final_withgyro_wall.stl
• mouse_cam_base_final_withgyro_wall.ipt
• mouse_cam_base_final_withgyro-base_10deg.ipt

File types:

• .stl files are ready for slicing and 3D printing.
• .ipt files are Autodesk Inventor part files for editing the design.

Design purpose:

• provide a base that incorporates the IMU into the headstage assembly
• support integration with the electrophysiology headstage hardware
• make the IMU mounting reproducible across experiments

Practical note:

• Use the .stl files for printing the current version.
• Use the .ipt files if you need to modify the geometry for a different headstage, cable routing, wall thickness, or sensor placement.

Arduino Behavior

The sketch:

• reads the MPU9250 at a fixed target rate of 100 Hz
• emits a 1 ms TTL pulse on Arduino pin 13
• sends one binary IMU packet for each sample
• includes arduino_millis and sample_index in every packet

The default packet fields are:

• arduino_millis
• sample_index
• accel_x/y/z_g
• gyro_x/y/z_dps
• mag_x/y/z_mg
• roll/pitch/yaw_deg
• linear_accel_x/y/z_g

Supported serial commands:

• s start streaming and reset the sample counter
• x stop streaming
• p send one test TTL pulse
• i print sketch information
• c run sensor calibration and print calibration values

IMU Calibration

Before recording, you can calibrate the IMU by opening the serial monitor or a serial terminal and sending:

c

During calibration, the Arduino sketch prints these instructions:

# Accel/gyro calibration will start in 5 seconds.
# Keep the IMU still on a flat surface.
# Magnetometer calibration will start in 5 seconds.
# Move the IMU in a figure-eight pattern until complete.

Recommended calibration workflow:

• Place the IMU flat on a stable surface.
• Send the c command.
• Do not touch the IMU during the accelerometer and gyroscope calibration step.
• When prompted for magnetometer calibration, move the IMU through a broad figure-eight motion until the routine finishes.
• Save the printed calibration values if you want a record of that session.

Setup

1. Arduino library

Install the MPU9250 Arduino library by hideakitai in the Arduino IDE or Arduino CLI.

2. Python environment

Install Python dependencies:

pip install -r python/requirements.txt

3. Upload the Arduino sketch

Upload:

arduino/imu_intan_sync_toolbox/imu_intan_sync_toolbox.ino

Logging Data

Example command on Windows:

python python/read_imu.py --port COM5 --output-dir data

Optional: stop automatically after a fixed duration:

python python/read_imu.py --port COM5 --output-dir data --duration-seconds 600

The logger will:

• open the serial port
• wait for the Arduino to reboot
• stop any old stream
• start a fresh stream
• align to the IMU packet header
• save data as CSV in the chosen output folder

The output CSV contains:

• computer receive time in UTC
• computer Unix time in seconds
• Arduino timestamp and sample index
• all IMU channels from the packet

Synchronizing With Intan

For each IMU packet, the Arduino sends one TTL pulse on pin 13. Record that digital input in Intan and align the Intan pulse train with the CSV sample_index and arduino_millis columns.

This gives you:

• a hardware sync event recorded by Intan
• the corresponding IMU sample number in the computer log

Notes

• If you need a different sampling rate, edit SAMPLE_RATE_HZ in the Arduino sketch.
• If you need a different sync pin, edit SYNC_PIN in the Arduino sketch.
• The archive/ folder is kept only for reference and is not part of the supported toolbox workflow.