I want to get the branching coordinates from a computer-generated image like this one:

Generated tree

After SkeletonTransform and Pruning, I get:


I would like to develop an algorithm that automatically detect and give coordinates of branching points (I could do it manually but really time consuming).


Edit: I already tried MorphologicalBranchPoints with poor results...

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    $\begingroup$ "I already tried MorphologicalBranchPoints with poor results..." Can you be specific about what you got and what you want instead? $\endgroup$ – Szabolcs Feb 18 '19 at 14:48
  • $\begingroup$ @ Szabolcs It was more about a careful selection of thinning and skeletonize options. The result with MorphologicalBranchPoints wasn't good then. $\endgroup$ – Valacar Feb 18 '19 at 15:08
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    $\begingroup$ Added another update. $\endgroup$ – Szabolcs Feb 18 '19 at 15:09

Use MorphologicalBranchPoints.

im = Binarize@Import["https://i.stack.imgur.com/O0AMj.png"]

skel = Pruning[Thinning[im], 20];

HighlightImage[skel, MorphologicalBranchPoints[skel]]

enter image description here

Another possibility is to use

skel1 = Pruning[Thinning[im, Method -> "MedialAxis"], 10];

as a start then smoothen the result using

skel2 = Thinning@Dilation[skel1, 5]

so that MorphologicalBranchPoints would not give false results.

HighlightImage[skel2, MorphologicalBranchPoints[skel2]]

enter image description here

| improve this answer | |
  • $\begingroup$ Great ! Thanks a lot. $\endgroup$ – Valacar Feb 18 '19 at 15:09

I notice there's a faint pink background that seems like a natural boundary. I've highlighted it to showcase this:

enter image description here

We can extract this curve and use it as the original boundary:

im = Import["https://i.stack.imgur.com/7Ck2S.png"];
mask = FillingTransform[Thinning[Binarize[ColorReplace[im, White -> Black, .055], 0]], CornerNeighbors -> True]

enter image description here

And the simply call MorphologicalBranchPoints:

skel = Thinning[mask];
HighlightImage[skel, MorphologicalBranchPoints[skel], 1]

enter image description here

| improve this answer | |
  • $\begingroup$ This is really clean! $\endgroup$ – Valacar Feb 19 '19 at 9:24
  • $\begingroup$ by the way I think it's Thinning[mask] in this case, isn't it? $\endgroup$ – Valacar Feb 19 '19 at 12:26
  • $\begingroup$ @Valacar Yes. I made the correction, thank you. $\endgroup$ – Chip Hurst Feb 19 '19 at 12:36

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