This repository contains programs needed to obtain a 3D skeleton and quantify the skeletonized array to statistics with the help of function present in metrics.segmentStats.
Input must be a binary array with z in its first dimension.
Skeletonization on a 3D binary array is performed by iteratively removing the boundary points until a line in the center is obtained by convolving the image with structuring elements from the paper.
This function is implemented using cython for fast execution and pyximport is used to automatically build and use the function

Using mayavi is a useful way to visualize these test stacks
Install mayavi via:

conda install -c menpo mayavi=4.5.0

This version works on python 3
Versions < 4.5 don't work on python 3.x
mayavi also requires that QT4 (pyqt) is installed
This may be in conflict with matplotlib >=1.5.3, which started to use qt5. So, use mayavi and matplotlib in a separate conda environment to avoid conflicts

View the stack contours:

import mayavi as mlab
mlab.contour3d(anynpynonbooleanarray)
mlab.options.offscreen = True
mlab.savefig("arrayName.png")