The root canal is a type of porosity, a low density space in the middle of the tooth that is of considerable interest – especially to endodontists. Ambient spaces can be binarised by threshold 0-70, but how do you separate the root canal from the surrounding space?
There are several ways to do this in CTAn custom processing, such as to first make a shrink-wrapped ROI then exclude the non-ROI space. However a simpler way to do this is to use one of the options in the "Despeckle" plugin called "remove outer objects". If white binarised objects are present both inside and outside an ambient (pore) black space, this function will remove the outer part. Note that this is run in 2D. In this case, shown in figure 4, the binarised outer space is removed leaving only the root canals and some disconnected artefact objects, which are easy to remove by another despeckle (3D sweep) operation (“remove all except the largest object”).
Figure 4. Inverse binarisation (above left) segments both the root canal and the surrounding space; the despeckle / “remove outer objects” operation removes the surrounding space, leaving the porous spaces only such as the root canal.