Segmenting roots from a soil

Hi all,

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.

Thanks,
Suman

SAMPLE TIFF.tif (15.4 MB)

Hi @Suman56,

Would it be possible to show us an image (tif, preferably) of the stack? Without one, it may only be clear for collegues in the same field as you to know what you mean. With an image, the whole community can put in their efforts.

1 Like

Thanks for the suggestion, I have edited the post