3D图像骨架化工具_python_代码_下载

# 3D Image Skeletonization Tools 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](https://drive.google.com/file/d/1kCEmfOx1mwoyggAfkYOsyRhOywfkiIU1/view?usp=sharing). This function is implemented using [cython](http://docs.cython.org/src/reference/compilation.html) 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](https://www.digitalocean.com/community/tutorials/how-to-install-the-anaconda-python-distribution-on-ubuntu-16-04) environment to avoid conflicts View the stack contours: ```import mayavi as mlab``` ```mlab.contour3d(anynpynonbooleanarray)``` ```mlab.options.offscreen = True``` ```mlab.savefig("arrayName.png")```