We want to color our EM density map , so we need mask different part of the map in order to distinguish them with different colors. Unfortunately, the sample is not irregular shape , we could not use "shape" to mask volume as usually. Could anyone give some suggestion?

We also use Amira for 3D rendering. We think the rendering in amira is just the mask, so we want solve the problem the mask the irregular shape with amira , have anyone done with it?