Source code for New methods for the geometrical analysis of tubular organs, by Florent Grélard, Fabien Baldacci, Anne Vialard and Jean-Philippe Domenger, published in Medical Image Analysis (Volume 42, December 2017, Pages 89-101)
On tubular volumes:
- Orthogonal plane estimation
- Pruning algorithm using orthogonal planes
- Recentering procedure
- Curve-skeleton extraction
Algorithms implemented thanks to the DGtal Library
The main instructions on linux/unix-based systems are the following:
git clone https://github.com/fgrelard/OrthogonalPlaneBasedTools.git
cd OrthogonalPlaneBasedTools ; mkdir build ; cd build
cmake .. -DCMAKE_BUILD_TYPE=Release
makeMinimum system requirements: C++11 enabled compiler, cmake, DGtal (>= 0.9), boost (>= 1.46), Eigen (>=3.2.0)
In order to compile, the following additional libraries are necessary:
DGtal needs to be compiled with these libraries as well (checkout WITH_QGLVIEWER, WITH_EIGEN, and WITH_ITK options with CMake). Make sure WITH_QT5 is ON if your version of QGLViewer depends on QT5 (standard for Ubuntu 16.04LTS).
Note: Our code has been compiled and tested on various Unix distributions: Ubuntu 14.04LTS, Ubuntu 16.04LTS, and Debian.
Executables are located in the build directory. They all provide a self-contained description on how to use them, available with the option -h.
Examples:
./OrthogonalPlaneEstimation -h
./OrthogonalPlaneEstimation -i ../data/neurite1.volDetails:
- OrthogonalPlaneEstimation and OrthogonalPlaneEstimationWithCurve allow to estimate orthogonal planes directly from the volume and from the curve respectively.
- PruningSkeletonOrthogonalPlanes allow to remove spurious branches on an existing skeleton
- RecenterSkeletonPoints is dedicated to the recentering of an existing non-centered skeleton
- SkeletonOrthogonalPlanes is the skeletonization algorithm on tubular volumes: tracking + postprocessing (junction detection and processing).
The input format data is .vol (DGtal file format). Converters from vol to any ITK format (vol2itk) and from ITK to vol (itk2vol) are available assuming DGtal has been compiled with ITK. The data folder contains the data which has been used to generate and compare the skeletons here.
Contact at florent [dot] grelard [at] inrae [dot] fr