Thank you for your prompt and very helpful advice. Really appreciate it. Sorry, I need to ask more as I am quite new to BoneJ. From your answer, I assume that Particle analyser can be used if I want to know how pore space are connected. Is that what you mean? In the output result of particle analyser, I think there is no result for connectivity?
And when you are saying ‘each particle’, I assume you refer to ‘sphere’ (the biggest sphere that fits in each pore space). Or are particle and sphere different? Becasue when I use particle analyser to get thickness on my example data example.tif (3.2 MB) , this is the thickness stack I got
. The data volume in this example is 150 x 150 x 150.
When I checked the result, I saw that there is only one big thickness (~38, I think that represents the big white sphere in the image) and all the rest thickness are ~2 which i think is not true.
I can see other big spheres (orange/pinkish color) in the thickness map whose diameter should be bigger than 2. That’s the reason I am confused if the particle and sphere are different. Becasue if I understand correctly, thickness of each pixel in each sphere is the diameter of that sphere.