Visual Behavior Control System

A comprehensive system for delivering high-frequency visual stimuli and analyzing behaviors of Drosophila (fruit flies). This controller allows precise timing of visual stimuli coordinated with hardware control for behavioral experiments.

Features

• High-frequency video stimulus delivery with precise timing
• Hardware control via Arduino:
  • LED control (ON/OFF, timed, pulsing)
  • Air pump and valve control
  • Odor valve control
  • Shock pulse delivery
• Interactive command interface with:
  • Real-time commands
  • Command series execution (chaining multiple commands)
  • Command shortcuts
  • Protocol creation and playback
• Detailed experimental logging
• Customizable stimuli
• Timing precision with dynamic ISI adjustments

Requirements

Hardware

• Arduino board (Arduino Uno recommended)
• A computer with dual monitors (recommended for visual stimulus presentation)
• Customized hardware setup with:
  • LEDs connected to Arduino
  • Solenoid valves (optional)
  • Air pump (optional)
  • Shock delivery system (optional)

Software

• Python 3.6+
• Required Python packages (see below)

Installation

1. Clone this repository:

   git clone https://github.com/yourusername/visual-behavior.git
   cd visual-behavior
   

2. Set up your environment:

   Option A: Using Conda (recommended)

   Create and activate a new conda environment:

   conda create -n visual-behavior python=3.9
   conda activate visual-behavior
   

   Install the required packages from requirements.txt:

   pip install -r requirements.txt
   

   Or with conda for packages available in conda-forge:

   conda install -c conda-forge --file requirements.txt
   pip install moviepy==1.0.3  # Specific version required
   

   Option B: Using pip

   Install the required Python packages:

   pip install -r requirements.txt
   

3. Connect Arduino with appropriate firmware loaded.

Quick Start

1. Navigate to the controller directory:

   cd controller_2_1_1
   

2. Run the default configuration:

   python play.py
   

3. Use the interactive command interface to control stimuli.

Custom Configuration

Edit the play.py file to customize your experiment setup:

from StimulationAssistant import StimController

player = StimController(
    video_dir='path/to/your/video/files',
    stim_name='r/v',  # Customize stimulus naming
    stimulus='20',    # Default stimulus to use
    LED_retention=2000,  # LED retention time in ms
    video_retention=1000,  # Video retention time in ms
    # Add other parameters as needed
)

player.start_journey()

Command Reference

The system provides numerous commands for interactive control:

• v - Deliver a single video stimulus
• v[number] - Deliver video stimulus multiple times (e.g., v5 for 5 times)
• r - Toggle red LED on/off
• rX - Turn on LED for X seconds (e.g., r5 for 5 seconds)
• p - Deliver LED pulses
• t - Coordinated LED and video stimulation
• stim or r/v - Update stimulus value
• pump - Toggle air pump on/off
• air - Toggle air valve open/closed
• odor_a - Toggle odor A valve open/closed
• odor_b - Toggle odor B valve open/closed
• shock - Toggle shock pulses on/off
• trig - Send trigger signal
• isiX - Wait for X seconds (e.g., isi5 for 5 seconds)
• load - Run available local protocol files
• h or help - Show help information
• q - Quit the program

Advanced Commands

• Command chaining with > operator: r5 > isi2 > p
• Command repetition with parentheses and *: (r2 > isi1) * 5
• Command shortcuts: test_odor <- pump:on > odor_a:on > isi5 > odor_a:off > pump:off

Folder Structure

• controller_2_1_1/ - Main controller code
  • StimulationAssistant.py - Core controller class
  • stimfunc.py - Helper functions for stimulation
  • play.py - Example configuration
• looming_videos/ - Default location for video stimuli
• Jail/ - Default location for log files

Troubleshooting

• Arduino connection issues: Make sure the Arduino is properly connected and has the correct firmware loaded.
• Serial port errors: Try restarting the program. If the error persists, check your Arduino connection.
• Video playback issues: Ensure the video path is correctly set and video files are in the proper format.
• Performance problems: Try closing other resource-intensive applications to ensure smooth video playback.