Free to a good home

[Michael Doube-3]

Hi all,

I've had a plugin project stuck in an almost-ready state for about a
year (life gets in the way of these things sometimes...).

It's a skeletonizer, like Ignacio's Skeletonize3D, only
shape-preserving.  So, cylinders erode to single-pixel lines while thick
plates erode to thin plates.  In my hands, it works OK on simple test
cases, but I can see there are a few small points or corner cases it
doesn't quite handle properly yet.

I can imagine it would be happy living alongside the other skeleton
tools in Fiji, for example.

In the longer run, shape-preserving skeletonization is intended to be a
basis for branch segmentation and labelling, and will be devolved out of
BoneJ and into Fiji / ImageJ2.

So, can I request that interested people test on their own data (binary
stacks), and let me know the result?

http://bonej.org/testing/BoneJ_.jar
Menu command is Plugins > BoneJ > Shape Skeleton

The code is in the .jar and the BoneJ Github repo:
https://github.com/mdoube/BoneJ/blob/shapeSkeleton/src/org/doube/skeleton/ShapeSkeletoniser.java

Thanks,

Michael

--
Dr Michael Doube BPhil BVSc PhD MRCVS
Microscopist / Imaging Specialist
Light Microscopy Facility
Max Planck Institute of
Molecular Cell Biology and Genetics
Pfotenhauerstraße 108
01307 Dresden
Germany

Phone: [phone]