transcranial-ultrasound

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transcranial-ultrasound

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Functional ultrasound through the skull

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// repository documentation

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# Transcranial Functional Ultrasound

Code and other assets from the [brain hack](https://brainhack.vercel.app) for functional transcranial ultrasound.

## Getting Started

### Prerequisites

- Python 3.13 or higher
- [uv](https://github.com/astral-sh/uv) - Fast Python package installer

### Installation

1. **Install uv** (if not already installed):
   ```bash
   curl -LsSf https://astral.sh/uv/install.sh | sh
   ```

2. **Clone the repository**:
   ```bash
   git clone https://github.com/yourusername/transcranial-ultrasound.git
   cd transcranial-ultrasound
   ```

3. **Create a virtual environment and install dependencies**:
   ```bash
   uv venv
   source .venv/bin/activate  # On Windows: .venv\Scripts\activate
   uv pip install -r requirements.txt
   ```

## Repository Structure

- `data` contains scan data for a cross-section of a human skull.
- `imaging` contains an implementation of image reconstruction via beamforming. The implementation is taken from [NeurotechDevKit](https://github.com/agencyenterprise/neurotechdevkit), with minor modifications to improve speed. We thank `NeurotechDevKit` for their robust beamforming implementation.
- `notebooks` contains various Jupyter notebooks used in image reconstruction experiments.
- `skull-attenuation-analysis` contains data and analysis code for an experiment quantifying attenuation of signals through the skull.
- `skull-propagation` contains a notebook for simulating skull propagation through the skull in 2D
- `syringepump` contains code to control a syringe pump and pump fluid through an artificial vein at a controlled rate.
- `utils` contains various code we wrote to assist with wave simulations, beamforming, and other tasks.

## Dependencies

We use `jwave` and `kwave` for wave simulations, and standard libraries (`jax`, `matplotlib`, `numpy`, `pandas`, `scipy`) for scientific computing and data manipulation.

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