simple-VS

A comprehensive visual stimulus presentation system for neuroscience experiments, designed to coordinate visual stimulation with various data acquisition devices.

Overview

This system enables precise control and synchronization of:

• Visual stimulus presentation on calibrated displays
• Two-photon microscope triggering
• Eye-tracking camera control
• Body-tracking camera control
• TTL signal collection for post-hoc data synchronization

Installation

1. Clone the repository:

   git clone [repository-url]

2. Create and activate a conda environment using the provided environment file:

   conda env create -f simple-vs_env.yaml
   conda activate simple-vs

3. Hardware setup:

   • Connect your National Instruments/PCO DAQ device
   • Configure your display monitor
   • Connect your tracking cameras and microscope triggers

Features

• Multiple experiment paradigms:
  • Retinotopy mapping
  • Texture analysis
  • Locally sparse noise
  • Dynamic battery
  • Simple orientation
  • Custom experiments via extensible base classes
• Flexible configuration via YAML files for:
  • Monitor settings and calibration
  • Experiment parameters
  • Data saving preferences
• Robust data acquisition (DAQ) support:
  • National Instruments
  • PCO
  • Other DAQ systems via extensible interfaces

Dependencies

• psychopy - Visual stimulus presentation
• nidaqmx - National Instruments DAQ interface
• numpy - Numerical computations
• pyaml - Configuration file parsing
• h5py - Data storage
• pandas - Data analysis and logging

Project Structure

• BaseExperiment.py - Core experiment infrastructure
• *Experiment.py files - Specific experiment implementations
• *DAQ.py files - Data acquisition interfaces
• *_config.yaml files - Configuration templates

Usage

1. Configure your experiment parameters in the appropriate YAML file
2. Set up your monitor configuration in monitor_config.yaml
3. Configure data saving preferences in save_settings_config.yaml
4. Run your experiment using the corresponding runner script (e.g., run_TEX_experiment.py)

Example Usage

Running a Texture Experiment

1. Edit texture_FB-VGG_config.yaml to set your desired parameters:

   name: texture_FB-VGG
   experiment_delay: 5
   # ... other parameters

2. In main.py, uncomment the desired experiment (current manual selection process):

   # Comment out other experiments and uncomment:
   experiment = TextureExperimentFBVGG(
       experiment_id=experiment_id,
       mouse_id=mouse_id,
       daq=daq,
       monitor_config_filename='monitor_config.yaml',
       save_settings_config_filename='save_settings_config.yaml',
       exp_config_filename='texture_FB-VGG_config.yaml',
       debug=bool_DEBUG
   )

3. Run the experiment:

   python main.py

Running a Retinotopy Experiment

1. Configure retinotopy_config.yaml
2. In main.py, uncomment the RetinotopyExperiment section
3. Run:

   python main.py

Note: The current experiment selection process requires manually editing main.py to uncomment the desired experiment. Future versions may implement a command-line argument or configuration-based selection system.

Contributing

This project is maintained by the Visual Neuroscience Group at UBC. For questions or contributions, please contact the repository maintainers.