Hi, I wrote some time ago: http://dip4fish.blogspot.fr/2014/05/construct-graph-from-skeleton-image-of.html
http://dip4fish.blogspot.fr/2014/06/graph-again.html http://dip4fish.blogspot.fr/2015/11/prune-iteratively-leaves-of-toy-graph.html https://gist.github.com/jeanpat/aac681d6b56932941281 hope this help 2017-05-18 9:12 GMT+02:00 Juan Nunez-Iglesias <jni.s...@gmail.com>: > Hi YXDragon! > > Coincidentally, I have been working on a package to do just that, which I > have imaginatively-called “skan” (for SKeleton ANalysis). It runs lightning > quick using Numba, and works with n-D skeletons. It’s available on pip (pip > install skan) and conda-forge (conda install -c conda-forge skan). The > source code is on github (github.com/jni/skan). > > The interface is a little fiddly currently but you should be able to > figure it out. The functions you want are skan.csr.skeleton_to_csgraph > (produces a pixel-to-pixel graph in scipy.sparse.csr_matrix format) and > skan.csr.summarise (produces a pandas DataFrame with nodes and arcs, > including coordinates in the image, arc distances, and euclidean > distances). You just need to provide the skeleton. > > I hope this helps! Feedback on the API is much appreciated! > > Juan. > > PS: Oh yeah, you might want to look at my Numba post, which described part > of the development of this library: https://ilovesymposia.com/2016/12/20/ > numba-in-the-real-world/ > > On 18 May 2017, 1:08 PM +1000, imag...@sina.com, wrote: > > Hi everyone: > I saw the newest version, require the networkx module. I find some > function to find shortest path from image. But I want to know if there is a > method to build a network from a skeleton image(2D/3D with arcs and nodes). > I wrote one, but in python. it runs very slowly... > yxdragon-imagepy > _______________________________________________ > scikit-image mailing list > scikit-image@python.org > https://mail.python.org/mailman/listinfo/scikit-image > > > _______________________________________________ > scikit-image mailing list > scikit-image@python.org > https://mail.python.org/mailman/listinfo/scikit-image > > -- http://dip4fish.blogspot.fr/ Dedicated to Digital Image Processing for FISH, QFISH and other things about the telomeres.
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