Dear experienced BoneJ-users and developers,
first of all I want to say how happy I was when I found the Thickness option of the BoneJ2 plugin. It seems like it is a tool that I have been looking for for a long time.
I want the determine the pore sizes of a collagen network. As the pores are connected, I figures that Thickness should be the plugin to use and went for the Trabecular spacing option. I have a 3D stack, which I segmented to make it binary and I rescaled it to make it isotropic. I then ran the thickness plugin and obtained the trabecular spacing map. I understood, that from the histogram I should then get the distribution of pores - meaning how many pores have a given pore diameter. I am interested in this pore size distribution not only of a single z-slice, but of the whole z-stack, so I ran the histogram on the stack. That is when I realised, that how the trabecular spacing image is set up (with showing the fitted bubble in every z to which it extends) the pores will be counted multiple times - as often as they appear in different z planes. That would mean that large pores are counted more often than little ones, as they span more z planes.
I wondered if it is also possible to export an image that shows the fitted bubble only in the z plane where it has its maximum diameter. Running a histogram on such an image-stack, would then give the real amount of pores of a given diameter. Or if there is any other way to quantify the number of pores in a 3D volume.
Additionally, I would like to know if there is a way to obtain the volume that is created by pores of a given diameter in such an open network.
Can anyone help me with this and has suggestions?
All the best and thank you