It takes about 1 day to run the whole process (I'm using Gforce 1080), so you may just want to check this video which shows the outcome:

If you really want to run it by your self, run files in this order:

• 3d_pattern_generation.ipynb
• segmentation3d.ipynb (could take several hours depending on your GPU)
• skeletonization.ipynb
• skeleton_analysis.ipynb (If you are not running on windows system, you need to recompile .mod files in the 'biophsical mods' folder using NERUON)

Here is an comparison of the segemntation and original image