How to get the skeleton of a binary particle.

[Zachary Pincus]

> Then this is simply a connected component :)
> 
> You can do morphological thinning
> (see http://homepages.inf.ed.ac.uk/rbf/HIPR2/thin.htm or http://microboone-docdb.fnal.gov/cgi-bin/RetrieveFile?docid=732&version=1&filename=12-11-09-CAnderson-CVCenterlineExtraction.pdf )
> using simple operations, most of which should be either in sckits.image or easily implementable from numpy
> 

Also, CellProfiler has good skeletonization routines, amongst others:
https://svn.broadinstitute.org/CellProfiler/trunk/CellProfiler/cellprofiler/cpmath/
It's built on top of scipy.ndimage where practical, and with extensions written in cython otherwise. Check out cpmorphology.py for the skeletonization stuff. (The cpmath is pretty stand-alone from the rest of the package.)

Zach