Describing the shapes of 3D objects


I have a tissue structure, which changes shape over a time course. In particular, it becomes more concave. I am trying to find a measure that would be sensitive to this shape change. I have been looking into different options, but my head is spinning… Can I work on the 8-bit mask or do I need to generate a some kind of a mesh first? I have tried something called 3D convex hull (3D image suite), but it is extremely slow (even though my stack is small) so I have stopped it before I even saw the output. And I do not know what to do with the output to get the measures I would need. This was under the 3D manager, but also separately under the 3D analysis, but I do not know what is the difference. Then I also ran into something called 3D shape (Kristopher Sheets), which allows to measure Convexity3D, but I cannot find the path to open it after I have dropped the .jar. (I think It becomes mixed up with another plugin under the same name that provides different measures). Can someone point me to the right direction?