Posted by
Tiago Ferreira-2 on
Apr 02, 2014; 3:44pm
URL: http://imagej.273.s1.nabble.com/color-pixel-for-Strahler-order-tp5007132p5007180.html
Hi Gabriel,
On Apr 2, 2014, at 04:39, Gabriel Landini <
[hidden email]> wrote:
> Thanks for the follow up. Maybe we are talking different things
Hopefully we are :)
> Yes there are more "branches" than "endpoints" in most skeletons, but I am not
> talking about "any branches", but "order 1 branches" only.
>
> Isn't what the table shows? Those would disappear after the first pass of
> hierarchical pruning.
The table simply reports the properties of the remaining skeleton upon a pruning cycle.
Thus, "order 1 branches" are listed under the "# End-points" column in row 1, "order 2"
in row 2, etc...
As I've mentioned, the "# Branches" column just reports the count of _all_ slab segments,
and its logged (together with "# Junctions") just so that users can monitor the progressive
pruning. Is this what is causing misunderstandings?
> But as I said earlier, I am not sure what is exactly the plugin doing.
Did you look at the code annotations[1] and the script page[2]?
Running it with ImageJ in debug mode was not useful?
The relevant code that is called is the pruneEndBranches() method by Michael Doube:
https://github.com/mdoube/BoneJ/blob/master/src/org/doube/skeleton/AnalyzeSkeleton.java#L472I'll try to describe what the script does:
1) Skeletonizes the arbor using Ignacio's library[3][4]
2) Calls the pruneEndBranches() method[5] to eliminate terminal branches
3) Keeps track of the properties of the remaining skeleton using AnalyzeSkeleton_[6][7]
4) Iterates previous steps until no junction pixels are detected, or until the "max n. of
interactions" specified in the dialog prompt is reached
5) For each iteration, the AnalyzeSkeleton_ properties[7][8] of the pruned skeleton are
logged to the "Strahler table"
6) If debug mode is active, each pruned skeleton is added to a new slice of an ImageStack
> but that count does not match the labelled Strahler pictures I have seen.
Which images? The toy arbor in [2]? You will have to be more specific, as it is very hard
for me to materialize it into a concrete criticism that I can address. Perhaps we should
be working on a common image? (e.g., a region of the ddaC sample image in Fiji?) and a
reproducible example?
-tiago
Links:
[1]
https://github.com/tferr/Scripts/blob/master/Morphometry/Strahler_Analysis.bsh[2]
http://fiji.sc/Strahler_Analysis[3]
https://github.com/fiji/fiji/blob/master/src-plugins/Skeletonize3D_/src/main/java/Skeletonize3D_/Skeletonize3D_.java[4]
http://fiji.sc/Skeletonize3D[5]
https://github.com/fiji/fiji/blob/master/src-plugins/AnalyzeSkeleton_/src/main/java/skeleton_analysis/AnalyzeSkeleton_.java#L605[6]
https://github.com/fiji/fiji/blob/master/src-plugins/AnalyzeSkeleton_/src/main/java/skeleton_analysis/AnalyzeSkeleton_.java[7]
http://fiji.sc/AnalyzeSkeleton[8]
http://fiji.sc/javadoc/skeleton_analysis/AnalyzeSkeleton_.html--
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