README.md

vestibular-vr

Closed-loop VR setup for Rancz Lab

Design Document

Acquisition Prerequisites

The following need to be installed on a fresh system in order to bootstrap the Bonsai environment correctly:

• Windows 10 or greater
• Visual Studio Code (recommended for editing code scripts and git commits)
• .NET 8.0 SDK
• .NET Framework 4.7.2 Developer Pack (required for intellisense when editing code scripts)
• Git for Windows (recommended for cloning and manipulating this repository)
• Visual C++ Redistributable for Visual Studio 2012 (native dependency for OpenCV)
• FTDI CDM Driver 2.12.28 (serial port drivers for HARP devices)
• Spinnaker SDK 1.29.0.5 (device drivers for FLIR cameras, sign in required, look in the archived stable versions for 1.29.0.5)

Setting up the Bonsai environment

To set up a Bonsai environment for running vestibular-vr, use the terminal to clone the repo into a local folder:

git clone https://github.com/neurogears/vestibular-vr.git

Now navigate into vestibular-vr/bonsai folder and run the Setup.ps1 script (on Windows right-click > Run with powershell). Once all dependencies have been restored Bonsai can be launched in a local environment from the .exe in this folder.

Session settings

Experiment parameters are based on a json schema (schema.json in the repo). Implementations of this schema are defined in .yml files provided by the user that are then loaded in the main Bonsai workflow to set up experiment parameters.

Working with schemas in Visual Studio Code

To create and edit schema implementations with full autcomplete and hinting, Visual Studio Code requires some extensions to be added:

• json (ZainChen.json)
• JSON Schema Validator (tberman.json-schema-validator)
• YAML (redhat.vscode-yaml)

Creating an experiment parameter file

To create an experiment parameter file based on the schema, create a new .yml file and add a reference to the schema at the top of the file

%YAML 1.1
---
# yaml-language-server: $schema=schema.json

The schema has two main groups of properties that define global experiment parameters, and block-specific parameters respectively, e.g.:

metadata:
  animalId: plimbo
  rootPath: D:/TrialLogicTestData/
  runGain: 0.0005

blocks: [
  &blockA
  {
    stimulus: {type: "grating"},
    totalRuntime: 20,
    runThreshold: 100,
    decayTimestep: 0.1,
    runThresholdDecay: -1,
    haltProbability: 0.5,
    haltProtocol: {
      minumumDelay: 0.1,
      randomDelay: 1.5,
      haltTime: 2,
      haltGain: 0
    }
  },
  &blockB
  {
    stimulus: {type: "cloud"},
    totalRuntime: 140,
    runThreshold: 200,
    decayTimestep: 0.1,
    runThresholdDecay: -1,
    haltProbability: 0.7,
    haltProtocol: {
      minumumDelay: 0.1,
      randomDelay: 0.5,
      haltTime: 0.5,
      haltGain: 0
    }
  },
  {<<: *blockA},
  {<<: *blockB}
]

The description of each parameter's effect on the Bonsai workflow, along with its type and default values are defined within schema.json itself. Note that where a parameter is not specifically set in the .yml the value will revert the default.

Running an experiment

To run an experiment, run the Bonsai application from the local environment and open Main.bonsai. Use the property grid to select the desired experiment parameter .yml file.