Code and other assets from the brain hack for functional transcranial ultrasound.

• Python 3.13 or higher
• uv - Fast Python package installer

1. Install uv (if not already installed):

   curl -LsSf https://astral.sh/uv/install.sh | sh

2. Clone the repository:

   git clone https://github.com/yourusername/transcranial-ultrasound.git
   cd transcranial-ultrasound

3. Create a virtual environment and install dependencies:

   uv venv
   source .venv/bin/activate  # On Windows: .venv\Scripts\activate
   uv pip install -r requirements.txt

• 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, 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.

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