So I am trying to create a binary mask for a stack - that i’l eventually convert to a mesh. However I’m having some issue getting the binary mask to accurately resemble the original images.
The main problem is that at the outer edge the threshold seems to ‘smooth over’ the outer columns of the image (as can be seen in the second image), where as the threshold needs to be more like the one in the third image (but as you can see adjusting the threshold deselects the bulk of the image).
So I just wonder if there is a way to overcome this, I have tried using the erosion and dilation tools, post thresholding however have had little success.
Is it possible to create separate binary masks for different parts of the images or something similar?