I have recently been working on a project where I analyse segmentations of brain tissue. My question is one that I thought would be very simple. The images are binary and I have been able to measure the sphericity (by first performing a distance transform watershed to make sure touching structures get seperated and to make sure they all get a different color for the sphericity measurement) of the nuclei using MorpholibJ. However, there is also some linear structures in the 3D data, which I would like to exclude by choosing a threshold value for the sphericity and only keeping structures that have a sphericity above this value. This has proven to be much harder than I expected however, so I would like to know if anyone knows a plugin that is capable of doing this.
Thanks in advance