I want to use morphology operator for filling holes of a 3d image. The 3d image consists of 116 2-D image slices of the same size (512*512 pixels). I tried using imfill in Matlab for the 3d image but the result is not what I wanted. The small holes are filled and other holes are not filled
When I tried using imfill slice by slice the result is correct. Is there any way for filling holes in 3d images? How can I do this?
What's wrong with a for loop that uses imfill slice by slice? you stated that this works already.
Alternatively, here's an option from the file exchange: Region Growing - a recursive region growing algorithm for 2D/3D grayscale images with polygon and binary mask output.
I recently wrote https://github.com/seung-lab/fill_voids which will fill topological holes rapidly.
Alternatively, there is SciPy https://docs.scipy.org/doc/scipy/reference/generated/scipy.ndimage.binary_fill_holes.html
