# 3scan-skeleton 3D Image Skeletonization Tools REQUIREMENTS: python > 3 https://www.python.org/downloads/ miniconda http://conda.pydata.org/miniconda.html and then use conda to install the following packages *scipy *numpy *skfmm - (conda install -c pranathi scikit-fmm=0.0.8) *networkx *skimage *matplotlib Input must be a binary array with z in its first dimension Thinning is cythonized for fast execution and pyximport is used to automatically build and use cythonized function (reference - http://docs.cython.org/src/reference/compilation.html) This repository contains programs needed to obtain a 3D skeleton using python 3 and quantify the skeletonized array to statistics with the help of function present in metrics.segmentStats To use import functions of this repo follow runscripts.getMetrics program To view the 3D volume (input or skeleton output) and save *mlab.contour3d(anynpynonbooleanarray) *mlab.options.offscreen = True *mlab.savefig("arrayName.png") Install nosetests to run tests in 3scan-skeleton/skeleton folder under the name submodule_tests *conda install nose *pip install nose nosetests -xs path to + "3scan-skeleton/skeleton/" To run tests with coverage *conda install coverage nosetests -sxv --with-coverage --cover-package=3scan-skeleton/tests