This fork is a stripped down version of Brian Matejek's original ibex repository. It provides tools to generate skeletons from a segmentation. Additional functionalities over the original ibex include:
- Generation of skeleton edges along with nodes
- Adjacency matrix extraction
- Skeleton length calculation
- Skeleton plotting
Clone the repository.
git clone --recursive https://github.com/srujanm/ibex.git
If you are using this for parallel fiber analysis in the cerebellum repository, make sure you switch to the relevant branch. If not, proceed to the build step below.
git checkout cereb-compat
Locally build the transforms and skeletonization modules by running this command in ibex\transforms\ and ibex\skeletonization\
python setup.py build_ext --inplace
The notebook included in the repository is a great place to get started! You should run it from the directory into which you cloned ibex.