I have a stack of image slices of a cylindrical soil sample. The resolution of the image in the x and y-axis is 0.35*0.35 mm. The Z-axis resolution is 0.625 mm (slice thickness). I am using the local thresholding method to separate the pores from the rest portion of the soil. However, I see that the roots are also considered as pores because of their similar attenuation coefficients. I have a lot of fine roots. How can I exclude them from being segmented as a pore?
I have included a tiff file which I want to segment (may be using auto local thresholding- Sauvola). Black region are the pore/air spaces while the grey constitute the soil matrix. However, I am finding it hard to eliminate everything except the pores. Dark greys represent the roots and these are also segmented as a pore which I don’t want.