openlifu

openlifu is a toolbox for planning and controlling focused ultrasound treatments. It generally replicates the functionality developed in the MATLAB open-TFUS toolbox.

Installation

Requirements

Python 3.10-3.12 on Windows or Linux.

Create Virtual Environment

Windows:

C:\Users\<uname>\AppData\Local\Programs\Python\Python311\python.exe -m venv env
.\env\Scripts\activate

Linux:

python3.11 -m venv env

Install project (editable)

With this repo as the working directory:

Basic mode

pip install -e .

Dev mode

pip install -e '.[dev]'

Installing Meshroom

If you are using openlifu.nav.photoscan to reconstruct meshes from photo collections, then you will need to set up Meshroom 2025.1.0.

Ubuntu

Download and Extract

1. Download Meshroom 2025.1.0 for Linux from https://github.com/alicevision/Meshroom/releases/tag/v2025.1.0.

2. Extract the downloaded archive:

   tar -xvf Meshroom-2025.1.0-Linux.tar.gz

Add Meshroom to PATH

Temporary (Current Session) Run:

export PATH="<path-to-meshroom>/Meshroom-2025.1.0-Linux:$PATH"

Replace <path-to-meshroom> with the actual path where Meshroom was extracted.

Permanent (Persistent Across Sessions) For Bash users:

echo 'export PATH="<path-to-meshroom>/Meshroom-2025.1.0-Linux:$PATH"' >> ~/.bashrc
source ~/.bashrc

Windows

Download and Extract

1. Download Meshroom 2025.1.0 for Windows from https://github.com/alicevision/Meshroom/releases/tag/v2025.1.0.
2. Extract the downloaded archive to a directory of your choice.

Add Meshroom to PATH

1. Open Edit environment variables for your account from the Start menu.
2. In the Environment Variables window, under User variables, select Path and click Edit.
3. Click New, and add the path to the folder containing Meshroom.exe.
4. Click OK to save the changes.

Enable GPU Acceleration

To ensure Meshroom uses your NVIDIA GPU:

1. Open NVIDIA Control Panel.
2. In the left sidebar under 3D Settings, click Manage 3D settings.
3. Go to the Program Settings tab.
4. Click Add, then browse to and select Meshroom.exe from the folder where you extracted Meshroom.
5. Under Select the preferred graphics processor for this program, choose High-performance NVIDIA processor.
6. Click Apply.

Getting Sample Data

A sample database for testing and examples is maintained in the openlifu-sample-database repository. Its files are tracked with Git LFS, so first install Git LFS.

Then check out the tagged version of the sample database that is compatible with this version of openlifu:

git clone --depth 1 --branch openlifu-v0.20.0 https://github.com/OpenwaterHealth/openlifu-sample-database.git
cd openlifu-sample-database
git lfs pull

Disclaimer

CAUTION - Investigational device. Limited by Federal (or United States) law to investigational use. The system described here has not been evaluated by the FDA and is not designed for the treatment or diagnosis of any disease. It is provided AS-IS, with no warranties. User assumes all liability and responsibility for identifying and mitigating risks associated with using this software.