Is it possible to calculate arc lengths in image stacks when the voxel dimensions are anisotropic?

Hello, Using (with great appreciation) Skeleton3D and Skel2Graph3D I have skeletonized 3D image stacks of vasculature. Part of the output from Skel2Graph3D is a list of linear indices for each branch. I am struggling to find a way to convert these values into the branch length when my voxel dimensions are anisotropic. I would greatly appreciate any suggestions on how to tackle this problem. In case it helps, I have attached the voxel indices from a 1024x1024x462 image stack where the voxel dimensions are 0.4x0.4x1 micron.

Thank you!

Answer 1

[John D'Errico]

I don't see the problem. Convert the linear indices back into subscripts.

help ind2sub

Then scale by the respective size of a voxel in each dimension. That effectively gives you a set of ordered points in (x,y,z). Now arc length is trivial, at least if you will compute the piecewise linear arc length. If you want the length of a smooth curvilinear arc that passes through those points, you can use my arclength tool, as found on the file exchange. (It can also compute a piecewise linear arclength in n-dimensions, if that is painful for you.)

Answer 2

[NCramer]

Thanks for the speedy reply... The ind2sub, scaling and arclength tool work beautifully!