Figure 6. BonePit program – a computational tool for morphometric analysis of bone matrix resorption.

Stacked images of calcein-stained dentine substrates are loaded into BonePit algorithm (A), developed in MATLAB. The program applies a Gaussian filter to reduce noise and changes the colour representation to identify more easily pit regions. The contours of a single pit were then manually drawn in each stack and compiled into a mask (B). Finally, every point in the mask is connected to the neighbouring points creating a 3D reconstruction mesh of the resorption pit (C).