Trabecular connectivity

Hello All,

I was looking at the documentation for Purify and Connectivity.

I notice purify doc mentions that connectivity assumes no cavities in the image.

Currently, I am using this on microCT images of mouse Tibia. I threshold imagjes and use clear outside to to leave on trabecular segment behind. I then apply purify and then connectivity.
This a snapshot of purified segment.

As you can see the middle is empty, which fits with original scan image.

I was wondering if this is a problem.


Not at all. A topological cavity is distinct from a topological hole (or handle). Your space is a hole, not a cavity. A cavity is best thought of as a disconnected particle or bubble of background floating in a sea of foreground. A hole on the other hand is best thought of as a space that penetrates right through the foreground, like the space in the middle of a ring on your finger, the hole in a doughnut or as I teach my anatomy students, the mouth-to-anus tube of the gastrointestinal tract. Try drawing a single pixel of white background right in the middle of a trabecula (i.e. your new white pixel must not touch any other white pixels), and run Connectivity again, then run Purify and Connectivity again, and see the effect of (and on) your isolated white pixel. Compare this with the same experiment where you draw a line of background right through the middle of a trabecula.