I am trying to count the number of pores in a 3D stack of a soil column. I have a binary image and I want to filter out pores less than 4 voxels. For some reason, both the object counter and particle analyzer in Bonej are showing only 11 particles in my image which is incorrect. Can anyone assist me with this? My voxel size is 0.35 * 0.35 * 0.625mm(z-axis).
I also wanted to make sure if removing anything less than 4 voxels, in my case, will eliminate all the pores<0.75mm(which is my intention).
I have uploaded 50 slices out of my stack for reference, can anyone please help me count the white pores in the 3D?
Any kind of help will be greatly appreciated!
Sumancropped stack.tif (7.3 MB)