Question

I am attempting to fill holes in a binary image. The image is rather large so I have broken it into chunks for processing.

When I use the scipy.ndimage.morphology.binary_fill_holes functions, it fills larger holes that belong in the image. So I tried using scipy.ndimage.morphology.binary_closing, which gave the desired results of filling small holes in the image. However, when I put the chunks back together, to create the entire image, I end up with seamlines because the binary_closing function removes any values from the border pixels of each chunk.

Is there any way to avoid this effect?

Answer 1

Operations that involve information from neighboring pixels, such as closing will always have trouble at the edges. In your case, this is very easy to get around: just process subimages that are slightly larger than your tiling, and keep the good parts when stitching together.