Masks And Materials?

I’m modelling a neuron cell, which has axons and dendrites coming out of the main cell body.

It needs to be animated, and we are having the dendrites and axons coming out of the body, as if one cell is growing into another type of cell. The problem is when we go to texture it we have a problem, how do we show the nucleus of a cell, and not have the dendrites and axons visible as well? Are there any ways to hide or mask certain objects within other objects? Any ideas on the subject would be greatly appreciated.

You can hide parts of a mesh by assinging them to vertex groups and use mask modifier to hide them.
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You could also use boolean modifier, animated texture, animated material transparency, or mask them in compositing (render layers, material index).