Find 3d branch points - Remove smaller branches

Hello all,

I want to remove small branches from this skeleton of a vessel, and to be left with just the main binary centerline. To do this I want to set a minimum branch length on the centrelines. But to do this I need to find the branch points...

BWMORPH works in 2D to find branch point/ end point locations, but this is a 3D skeleton...

Many thanks,

Will

[Sean de Wolski]

Out of curiosity, how did you come up with the 3-dimensional skeleton?

[William]

http://uk.mathworks.com/matlabcentral/fileexchange/43400-skeleton3d

Answer 1

[Sean de Wolski]

I don't have time right now to implement it, but you should be able to use bwlookup with a 3x3x3 lookup table to identify the branch points.

The algorithm would be: is the middle pixel connected two more than three or more pixels on the periphery of the 3x3x3 box. If it is, then it's a branch point.

[William]

Not sure how to define a lookup table... something like...?

f = @(x) (sum(x(:)) >= 3);
lut = makelut(f,3)
branch_point = bwlookup(skeleton, lut)

[William]

Found a premade function called Skel2Graph3D which you can define a threshold branch length and then convert it back into a skeleton with Graph2Skel3D.