Calculating angles in 3D objects



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?



Hi @Darren,

The first thing you need to do is segment your acini. If they are well separated, the basic segmentation module should work well.

Then, if your structures are spheroidal, you could generate a vector for each cell towards the barycenter of the acinus the cell belong to and use this as a reference. To do this, use this group ‘Creates relationship if labels overlap’. This module will generate the vectors you need.

If your acini are too irregular you will need to extract the surface using this module: membrane ‘Boundary extraction’. After this is done, you can create relationships between your cells and the nearest boundary using rels, this module will also automatically create the vector normal to the boundary.

To better understand what each module does, hover over the icon and look at the tooltip. The documentation for each specific module will soon be available, we are working on it :wink:




Excellent, that’s covered a lot of different approaches. Thanks!