3D length determination through image stack


I have a stack of 2D images of rock core sample. I am interested in determining the length of linear feature in propagating in 3D. When I go through the whole stack of images I can see that linear feature displacement. But I am interested in its length quantification in 3D.

Right now, I was trying to first segment that linear feature from whole image based on Trainable Weka Segmentation. After segmenting this linear feature I was trying to run Skeletonisation 3D and then Analyze Skeleton. But the result of analyze skeleton doesn’t include the length of that feature for the whole stack. I am not sure what operations to perform to determine this.

Does anybody has any idea regarding this problem?

What do you mean by “the length of that feature”? AnalyzeSkeleton provides with the length of all branches of the skeletons in the image.


Suppose I have 100 images of a cylindrical core taken throughout its length at fix gap. I want to determine the length of one feature that is present in all of 100 images along the stack of images. I tried using Analyze skeleton but I am not able to determine the complete length.

Do you mean the 2D length of one skeleton on each slice?


No. I mean 3D length that encompass whole stack of slices.

I see, so, if I understood well, your only problem is how to identify the specific skeleton in the image from which you want to measure the length. Is that right? In that case, you can use the AnalyzeSkeleton option “Display labeled skeletons” so you know which ID corresponds to which skeleton in both the tables and the result images.


I will try that and see if I am getting desired results or not. Thank you

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