129Xenon Image Processing Pipeline (XIPline)

XIPline application is developed at the CPIR.

Table of contents:

1. Running the Application

2. Usage

3. Acknowledgments

4. Updates

Setup

Developer Mode (Recommended)

To customize the application, the user will need MATLAB version R2023b or newer.

Clone XIPline to your local directory.

git clone https://github.com/aboodbdaiwi/XIPline.git

Start by adding the local folder to the MATLAB path and execute the XIPline.mlapp file.

When implementing new features, or debugging, we recommend using the debugging MATLAB script XIPline_Code_Script.m. This script can run the entire application but without the graphical user interface (GUI).

Set up XIPline folder (this step is automatically done when you run XIPline.mlapp)

1. Download the XIPline folder.

2. Unzip the folder and place it directly in the C:\ drive without renaming or moving it.

3. This directory includes all required components:

   • AI segmentation models
   • Offline reconstruction scripts

These components are essential for image reconstruction, registration, and segmentation.

Set up Python

1. Install Python 3.10.2.

2. Add the Python path to the environment variables.

3. Navigate to C:\XIPline\python_path.txt and change the Python path to your local location.

Note: If you're having problems with the auto-segmentation, please take a look at issue #3 for potential solutions.

For GE offline recon: Waveform Files

Add waveform files in the C:\XIPline\GE\waveforms folder. Please refer to User_Manual.pdf document for more detailed steps.

Usage

These are a few analysis demos (please refer to the user's manual for step-by-step guide on performing all analysis)

1 - Installation demo (Please refer to the instructions above for the latest version)

2 - Calibration Analysis demo

3 - Ventilation Analysis demo

4 - Diffusion Analysis demo

5 - Gas Exchange Analysis demo

6 - Developer Mode demo

Acknowledgments:

Author: Abdullah S. Bdaiwi

Work email: abdullah.bdaiwi@cchmc.org

Personal email: abdaiwi89@gmail.com

Website: CPIR

If you use this software, please cite:

Bdaiwi AS, Willmering MM, Plummer JW, et al. 129Xe Image Processing Pipeline: An open-source, graphical user interface application for the analysis of hyperpolarized 129Xe MRI. Magn Reson Med. 2024;1–18. https://doi.org/10.1002/mrm.30347

Updates:

Task	Date
XIPline is compatible with Windows, macOS, and Linux	Aug 18, 2026
Batch Processing for Vent, Diff, and GX in one go	Aug 16, 2026
Setup XIPline folder automatically	June 22, 2026
Update Diffusion analysis (add SNR rules and exclude noisy points)	May 16, 2026
Add denosing methods option	Jan 13, 2026
Add FV VDP method	Jan 13, 2026
Update Vent AI segmentation model	Jan 01, 2026
Update Diffusion Analysis (SNR, healthy ref, report)	Dec 11, 2025
Update AI segmentation model for Diffusion Analysis	Oct 20, 2025
Add new ventilation analysis report	July 17, 2025
Add offline reconstruction for 2D spiral Philips ventilation images	July 17, 2025
Add ANTs and manual registration for ventilation analysis	July 17, 2025
Remove Python requirement for AI segmentation models	July 17, 2025
Update AI segmentation models	May 20, 2025

Analysis Report Examples: