Full-Field LED Visual Stimulator

An open-source, high-precision visual stimulation platform designed for visual neuroscience, sensory physiology, and human psychophysics. The system delivers temporally agile, multi-chromatic optical stimulation (e.g., Green for M-cones/rods and UV for S-cones, or custom multi-spectral arrays) with sub-millisecond precision.

LEDstim_antiphase_2hz.MOV

Example stimulus: 2 Hz antiphase (Green / UV) sinusoidal flicker.

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Key Capabilities

• High-Resolution Temporal Modulation: 16-bit Phase-Correct carrier PWM (~7.68–10 kHz) combined with hardware-interrupt pacing (Timer3 CTC ISR) eliminates visible digital stepping and software loop jitter.
• Rich Stimulus Battery: Native microsecond-timed generation of sinusoidal flickers, Gaussian white noise (with Central Limit Theorem PRNG), contrast-switching adaptation sequences, exponential frequency chirps, and stepped luminance pulses.
• Quantitative Radiometric Calibration: End-to-end MATLAB calibration pipeline mapping raw duty cycles to linearized lookup tables (LUTs) and calculating exact photoreceptor isomerisation rates ($R^*/\text{photoreceptor/s}$).
• Flexible Form Factors: Supports both 200mm full-field panel enclosures (with magnetic diffusion clamping) and miniature wearable mounts for Pupil Labs Neon eye-tracking glasses.
• Reactive Experiment Orchestration: Full integration with Bonsai for closed-loop, state-dependent, adaptive psychometric staircase, and LabStreamingLayer (LSL) multi-modal recording.

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System Architecture

graph LR
    subgraph Host Software
        Bonsai[Bonsai Reactive Workflows]
        LSL[LabStreamingLayer / LabRecorder]
        MATLAB[MATLAB Calibration Suite]
    end

    subgraph Microcontroller Firmware
        MCU[Arduino Leonardo / Teensy 4.1]
        T1[Timer1: 16-bit PWM]
        T3[Timer3: CTC Interrupt Pacing]
        LUT[PROGMEM Gamma LUT]
    end

    subgraph Hardware & Optics
        Driver[Multi-Channel Driver Stage]
        LEDs[Dual-Channel LED Arrays]
        Enclosure[Magnetic Diffusion Enclosure / Glasses]
        Sensors[Photodiode / Power Meter / Eye Tracker]
    end

    Bonsai -- Serial ASCII (115200) --> MCU
    MATLAB -. Offline Calibration .-> LUT
    MCU --> T1 & T3
    T3 --> LUT --> T1
    T1 --> Driver --> LEDs --> Enclosure
    Enclosure -. Optical Feedback .-> Sensors
    Sensors --> LSL

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Quickstart Guide

1. Flash the Firmware

1. Open ArduinoCode/StimulusControlViaSerial_Leonardo_v8/StimulusControlViaSerial_Leonardo_v8.ino in the Arduino IDE.
2. Select Arduino Leonardo as your board and choose the corresponding COM port.
3. Click Upload.

2. Connect Hardware & Verify

1. Connect your LED driver to the designated MCU pins (PWM: Pins 9 & 10; Indicators: Pins 4 & 5).
2. Open the Serial Monitor at 115200 baud.
3. Send a test sinusoidal flicker:

   s, 3000, 2.0, 0.0, 0.5, 0.8, 0.8
   

   (Runs a 3-second, 2 Hz antiphase flicker on Channels A and B at 80% contrast).

3. Launch Experimental Workflows

Open Bonsai and load one of the pre-built visual stimulation workflows from BonsaiCode/ (e.g., LEDstimulation_normal.bonsai or ManualMethodOfAdjustment.bonsai).

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Documentation Index

Comprehensive guides, schematics, and technical specifications are available in the docs/ directory:

Section	Description
1. Hardware	Circuit & Driver • Custom PCBs • Panel Enclosure • Wearable Glasses • Bill of Materials
2. Firmware	Architecture & Hardware Timers • Serial API Reference • Firmware Variants
3. Calibration	Calibration Guide • Gamma LUT Pipeline • Photoreceptor Calculations
4. Experimental Workflows	Bonsai Setup • Stimulation Paradigms • Integration & Multi-Modal Sync
5. Reference	Performance Characteristics, Switching Dynamics & Thermal Notes

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Repository Structure

├── ArduinoCode/                  # Microcontroller firmware (Leonardo v8, DDS, Teensy 4.1, IMU)
├── BonsaiCode/                   # Main Bonsai visual reactive workflows & stimulus CSVs
├── BonsaiForHumanExperiments/    # Dedicated human psychophysics Bonsai workflows
├── Calibration/                  # MATLAB scripts for radiometry, gamma LUTs & opsin calculations
├── Hardware/                     # CAD files (.stp, .stl, .ipt), KiCad PCB designs & driver schematics
│   ├── Enclosure/                # Baseplate CAD & 3D printed magnetic diffusion clamps
│   ├── glasses/                  # Pupil Labs Neon glasses boom arm & miniature diffuser
│   ├── LED_board/                # KiCad dual-channel LED array PCB
│   └── LED_board_humans/         # KiCad 3-colour LED array PCB (WIP redesign with layout improvements)
├── HumanExpAnalysis/             # MATLAB scripts for IMU movement and behavioural analysis
├── LabRecorderFiles/             # Multi-modal LabStreamingLayer (LSL) recording configurations
└── docs/                         # Modular technical documentation

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License & Attribution

Developed for scientific research applications. If you use this platform in your research, please cite this repository.