QuantUS-UTC

QuantUS is an open-source quantitative analysis tool designed for ultrasonic tissue characterization (UTC) and contrast enhanced ultrasound (CEUS) imaging analysis. This repository contains all code behind the UTC features of the software.

Overview

In general, QuantUS provides an ultrasound system-independent platform for standardized, interactive, and scalable quantitative ultrasound research. QuantUS follows a two-tier architecture that separates core functionality in the backend from user interaction support in the frontend. The software is compatible on Mac OS X, Windows, and Linux.

This repository supports UTC analysis on 2D RF and IQ data by computing spectral parameters (i.e. midband fit, spectral slope, spectral intercept) using the sliding window method within a region of interest (ROI), generating parametric maps. Additionally, it also includes implementations for calculating the attenuation coefficient, Nakagami parameters, backscatter coefficient, effective scatterer diameter, and effective scatterer concentration. However, validation studies are required to confirm the accuracy of these additional parameters.

The UTC feature of QuantUS also supports a CLI for scalable batch processing. More information and an example can be found in scCanonUtc.ipynb and terasonUtc.ipynb. The CLI is accessible through QuantUS's pip-accessible backend.

For more information, see our documentation.

Requirements

• Python

Environment

First, download Python3.11.8 (non-Conda version) from the Python website. Once installed, note its path. We will refer to this path as $PYTHON below.

Next, complete the following steps. Note lines commented with # Unix should only be run on MacOS or Linux while lines commented with # Windows should only be run on Windows.

git clone https://github.com/TUL-Dev/QuantUS.git
cd QuantUS
$PYTHON -m pip install virtualenv
$PYTHON -m virtualenv .venv
source .venv/bin/activate # Unix
.venv\Scripts\activate # Windows cmd
sudo apt-get update & sudo apt-get install python3-dev # Linux
pip install -r requirements.txt

Following this example, this environment can be accessed via the source .venv/bin/activate command from the repository directory on Unix systems, and by .venv\Scripts\activate on Windows.

Building

After configuring a Python virtual environment, finish preparing QuantUS to be run using the following commands:

# Using Python virtual env (Mac/Linux)
chmod +x saveQt.sh
./saveQt.sh

# Using Python virtual env (Windows)
ren saveQt.sh saveQt.bat
.\saveQt.bat

Running

Mac/Linux

source .venv/bin/activate
python main.py

Windows

call .venv\scripts\activate.bat
python main.py

Sample Data

This folder contains minimal sample data required to get started with UTC. Note that since phantom data must be collected using identical transducer settings as the images they're compared to, we do not recommend using phantoms from this folder for analysis on custom data.

Reference Phantom Dataset

(in progress)