BUFF: BUbble Flow Field

Ultrasound Simulation Framework
Examples · Report a Bug · Request a Feature

Table of Contents

1. About The Project
2. Getting Started
   • Requirements
   • Installation
3. Usage
4. Roadmap
5. Authors
6. License
7. Contact
8. Acknowledgments

About The Project

Preprint: BUbble Flow Field: a Simulation Framework for Evaluating Ultrasound Localization Microscopy Algorithms

BUFF is a comprehensive open-source simulation platform designed to validate Ultrasound Localization Microscopy (ULM) algorithms. This tool generates contrast-enhanced ultrasound images within vascular tree geometries that mimic realistic flow characteristics, facilitating the testing and validation of ULM techniques using ground truth data.

The framework is primarily implemented in MATLAB with some parts in Python. It's designed to support researchers and engineers working in areas like vector flow imaging, functional ultrasound, and super-resolution ULM.

Key Features

• Vascular Network Generation: Create complex, microvascular networks, either randomly generated or user-defined.
• Blood Flow Simulation: Fast fluid solver for realistic blood flow simulation with custom pressures and arbitrary input/output positions.
• Microbubble Dynamics: Simulate non-linear microbubble behavior with a range of point spread functions based on user-defined MB characteristics.
• Acoustic Field Simulation: Combine acoustic field simulations with MB dynamics to generate ultrasound images.
• Validation Metrics: Perform both binary and quantitative validation of ULM algorithms using built-in metrics.
• Ground Truth Generation: Ideal for objective, quantitative evaluation of localization and tracking algorithms.

BUFF was demonstrated at the Ultrasound Localization and Tracking Algorithms for Super Resolution (ULTRA-SR) Challenge at the IEEE International Ultrasonics Symposium (IUS) 2022, providing ULM images with ground truth data for evaluating localization and tracking algorithms.

Getting Started

Requirements

To use BUFF, you will need the following prerequisites:

• MATLAB (recommended version: 2021a or later)
• FieldII (simulation backend)
• Python (for specific modules)

Installation

Clone the repository:

git clone https://github.com/marcelolerendegui/buff.git

Download the backend (FieldII) and extract it:

curl -O 'https://field-ii.dk/program_code/matlab_2021/Field_II_ver_3_30_linux.tar.gz' \
  -H 'User-Agent: Mozilla/5.0 (X11; Linux x86_64)' \
  -H 'Upgrade-Insecure-Requests: 1'

mkdir -p third_party/Field_II_ver_3_30_linux
tar -xvzf Field_II_ver_3_30_linux.tar.gz -C third_party/Field_II_ver_3_30_linux/

Usage

Currently, the code is in its alpha state. While we work on adding tutorials and more documentation, here’s a basic outline to get started:

Examples

• Cyst Example
• Cross-Tube Example
• Video Example soon...
• Network Generation Example soon...
• Evaluation Example soon...

Authors

Marcelo Lerendegui	Kai Riemer

Contributors:

• Joe Hansen-Shearer joseph.hansen-shearer18@imperial.ac.uk
• Bingxue Wang bingxue.wang18@imperial.ac.uk
• Clara Rodrigo Gonzalez clara.rodrigo-gonzalez18@imperial.ac.uk

We welcome contributions to improve the platform! If you encounter any issues or have suggestions for new features, please open an issue.

License

Distributed under the MIT License. See LICENSE.txt for more information.

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Contact

• Marcelo Lerendegui: marcelo@lerendegui.com
• Kai Riemer: kr616@ic.ac.uk
• Meng-Xing Tang - mengxing.tang@imperial.ac.uk

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Acknowledgments

• FieldII
• Best-README-Template

_{BUFF was developed atULIS: Ultrasound Laboratory for Imaging and Sensing}

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