Posted by
Tiago Ferreira-2 on
Apr 01, 2014; 4:41pm
URL: http://imagej.273.s1.nabble.com/color-pixel-for-Strahler-order-tp5007132p5007169.html
Hi Gabriel,
On Apr 1, 2014, at 08:54, Gabriel Landini <
[hidden email]> wrote:
> The number of branches of order 1 should be the same as the number of end
> points at the start of the skeleton, or am I missing something obvious?
>
> How is it possible to have 128 branches of order 1 with only 67 end points?
I'm definitely not an expert, but I think this has to do with our expectation of
what a branch is and how a branch is defined in a topographic skeleton, that
tries to be graph-theoretic representation of the arbor.
Looking at the snapshot Ignatio posted on the top of the documentation[1] page:
http://fiji.sc/images/b/be/Analyze_skeleton_09_13_2009.pngAll the skeletons have more branches than tips (e.g, the largest has 9 end-points
and 15 branches). This is because branches are defined as all segments of slab
voxels (i.e., voxels with exactly 2 neighbors) flanked by either a end-point voxel
_or_ a junction voxel. So, the total number of branches in a skeletonized structure
would be the sum of segments of slab voxels connecting:
1) End-point to End-point
2) Junction to End-point
3) Junction to Junction
This is at least, the way I see it, at least in in the context of AnalyzeSkeleton.
But hopefully someone more knowledgable will be able to discuss this better.
Would you like to have junction-to-junction segments subtracted from the
definition of "branch"?
All the real measurements in Strahler Analysis[2] are done by AnalyzeSkeleton,
mainly using the "prune" option that was implemented in BoneJ[3].
If you suspect there is something wrong, we'd have to look at the code by
Ignacio Arganda-Carreras and Michael Doube. But in case I've missed something
obvious (I'm notorious for that), if you want to post your test image, I can
have a look at it and compare the results.
-tiago
[1]
http://fiji.sc/AnalyzeSkeleton[2]
http://fiji.sc/Strahler_Analysis[3]
http://bonej.org/analyseskeleton--
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