aind-behavior-pirouette

A repository with source code for long-term, freely moving, electrophysiology recordings in mice.

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🔧 Prerequisites

Pre-requisites for running the project can be found here.

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🚀 Deployment

For convenience, once third-party dependencies are installed, Bonsai and python virtual environments can be bootstrapped by running:

./scripts/deploy.ps1

from the root of the repository.

⚙️ Generating settings files

The Pirouette platform is instantiated by a set of two settings files that strictly follow a DSL schema. These files are:

• rig.json
• session.json

Examples on how to generate these files can be found in the ./Examples directory of the repository. Once generated, these are the the only required inputs to run the Bonsai workflow in ./src/main.bonsai.

The workflow can thus be executed using the Bonsai CLI:

"./bonsai/bonsai.exe" "./src/main.bonsai" -p SessionPath=<path-to-session.json> -p RigPath=<path-to-rig.json>

[> ] CLI tools

The platform exposes a few CLI tools to facilitate various tasks. Tools are available via:

uv run pirouette <subcommand>

for a list of all sub commands available:

uv run pirouette -h

🔄 Regenerating schemas

DSL schemas can be modified in ./src/aind_behavior_pirouette/rig.py. Once modified, changes to the DSL must be propagated to json-schema and csharp API. This can be done by running:

uv run pirouette regenerate