[Insight-users] Centerline

[chans at cs.uh.edu]

Hi,

I am a newbie to ITK. I have a confocal image of zebrafish
vasculature(stack.tif, MIP.tif). My aim is to model zebrafish vessel using
parametric model such as ellipse.

I have a segmented image(segmentedStack.tif), which I have obtained by doing
median filtering, followed by thresholding.

I wish to extract the centerline for this data and compute radius in tangent
and normal direction at each centerline point. With this information, I
would like to fit an ellipse to each centerline point.

My concerns are following
1. I tried to extract centerline using 3d thinning, it gave me very noisy
centerline.
2. Is there a way, I can improve segmentation and fill holes in the vessel,
to get a better centerline.
3. May be there is some other method, which would be more suitable for my
kind of data.

I am really stuck here, any help would be greatly appreciated.

All the data is here http://www2.cs.uh.edu/~chans/image/data/



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