Code for automatic lung and airway segmentation and evaluation. Visit Project Drive!
- AirwaySegmentationAuto_v2: Macaques version.
- Lungs_Segmentation: Include Hu, labeleize and morpholical filter for macaques lung segmentation.
- SpeedImageCalc: Calculation of Hessian features
- Checkers: Additional functions
- Externals: ImageJ/ITK Filters
- Libs: Dicom utilities
- Propagator: Fast Marching algorithm for airway segmentation
- Registration: Registration filters
- Utilities: Help's filters used by the rest of projects
- R
- Waterfalls code.
- Java
- Batch mode scripts.
- Similitude evaluation
- ImageJ plugings to open MMWKS images(.hdr, .img) and ITK files(.mhd,.raw).
- Python
- Batch mode filters.
- Manual thresholding tissue classification
- Help's functions
- Manual and automatic
In order to complile the code sucessfully the following packages must be installed before:
- g++/gcc (Compiler)
- git-core
- git-svan
- libfontconfig-dev
- libgl1-mesa-dev
- libglu1-mesa-dev
- libncurses5-dev
- libosmesa6-dev
- libx11-dev
- libxrender-dev
- libxt-dev
- make
- python-dev
- python-numpy
- subversion
- libbz2-dev
The libraries set could be installed in one step by running the following line:
sudo apt-get install g++ gcc git-core git-svn libfontconfig-dev libgl1-mesa-dev libglu1-mesa-dev libncurses5-dev libosmesa6-dev libx11-dev libxrender-dev libxt-dev make python-dev python-numpy subversion libbz2-dev
In this version is necessary to perform the compilation in two phases. A first compilation to install the dependecies CMake TLS_SECOND_STEP (compilation option unchecked) and second one with CMake TLS_SECOND_STEP checked.
@article{Gordaliza2018,
doi = {10.1038/s41598-018-28100-x},
issn = {2045-2322},
journal = {Sci. Rep.},
keywords = {Biomedical engineering,Computer science,Experimental models of disease,Infectious,disease epidemiology},
month = {dec},
number = {1},
publisher = {Nature Publishing Group},
title = {{Unsupervised CT Lung Image Segmentation of a Mycobacterium Tuberculosis Infection Model}},
url = {http://www.nature.com/articles/s41598-018-28100-x},
volume = {8},
year = {2018}
}