I want to calculate the apico-basal angle of individual cells in a 3D object e.g. an acini structure (See attached).
I understand that once I’ve generated nucleus-centrosome vectors I need to generate a normal vector with which to calculate an angle. In 2D monolayer cultures this would be the vector perpendicular to the culture surface. How do I go about detecting the surface of the structure in 3D to generate appropriate normal vectors and how would I then define the correct vector for each cell in my structure?