xregi 0.3.4

A package for automatic 2D/3D registration of X-ray and CT images

This is a python package for registering x-ray images and CT scans. It is based on the xReg, a C++ library for medical image registration, and synthex, a python package for synthetic x-ray imaging.

Third-party libraries

Before you start, please make sure you have all the dependencies installed. The following libraries are required:

• Total Segmentator
• xReg
• SyntheX

Install TotalSegmentator

total segmentator can be installed through pip

pip install TotalSegmentator

Install xReg

xReg is a C++ library for medical image registration. It is used as the backend of xregi. To install xReg, please follow the instructions in the README.md of xreg On other environments, such as Windows, MacOS and Ubuntu，you may need to install xreg aside according to your system. The detailed information can be found at the Building section in the README.md of xreg.

Install SyntheX

Synthex will be installed along with xregi. If you want to install it separately, here is the installation for SyntheX:

git clone https://github.com/arcadelab/SyntheX.git
cd /SyntheX
conda install .

Xregi Installation Guide

Install through pip

On ubuntu 20.04, simply install this package using pip

pip install xregi

Install from source

On ubuntu 20.04, download the source code and install it under xregi path

git clone https://github.com/shez12/xregi
git checkout master

Fetch the source data and example images from here or

#download data.zip
wget --load-cookies /tmp/cookies.txt "https://docs.google.com/uc?export=download&confirm=$(wget --quiet --save-cookies /tmp/cookies.txt --keep-session-cookies --no-check-certificate 'https://docs.google.com/uc?export=download&id=1wjrxNE6B0pX3IooGxwC_cjf4n8MhxU1p' -O- | sed -rn 's/.*confirm=([0-9A-Za-z_]+).*/\1\n/p')&id=1wjrxNE6B0pX3IooGxwC_cjf4n8MhxU1p" -O data.zip && rm -rf /tmp/cookies.txt

#unzip data.zip
cd Downloads/
unzip data.zip

Usage

Before using xregi, you need to move the data folder to xregi directory.

mv data xregi/

xregi supports command line interactions and API. To use the API,

import xregi

reg_ = Registration2D3D().load()

reg_.solve()

...

Contributors

Jiaming (Jeremy) Zhang, MSE in Robotics, Johns Hopkins University

Zhangcong She, MSE in Mechanical Engineering, Johns Hopkins University

Benjamin D. Killeen, PhD in Computer Science, Johns Hopkins University