Re: Largest enclosed convex shape to measure eggs with appendages

Posted by Gabriel Landini on
URL: http://imagej.273.s1.nabble.com/Largest-enclosed-convex-shape-to-measure-eggs-with-appendages-tp5004483p5004487.html

On Monday 19 Aug 2013 11:20:23 Tom Kazimiers wrote:
> Therefore, I thought, it would be best to threshold first and then find
> the largest enclosed convex shape and then do the measuring on this
> shape. Now, I guess I could implement something like

Hi Tom,
If you want the length of Max Feret, you can get rid of the bits sticking out
by greyscale closing (min followed by max) radius of size 8 seems to work.
Then do an automated threshold.

Another perhaps better method is to segment as they are, make a duplicate,
erode it a bit so the bits sticking out disappear and then reconstruct the
original binary  (mask) with the eroded as seed using a procedure called
Viscous Geodesic Reconstruction (macro available in the Morphology collection
in my page). That only reconstructs the mask if the kernel can fully get into
the mask regions (so the thin parts do not get reconstructed (size 20 seems to
work).
Cheers
Gabriel

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