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I had this scene:

enter image description here

Then I broke it into these two render layers:

enter image description here enter image description here

Normally I use an alpha over node to combine render layers, but the transparency and overlapping doesn't allow that in this case. Here are the results of "alpha over" with "one over two" and "two over one".

enter image description here enter image description here

Is there a better way to combine these render layers to get the original back? Or have I broken a rule for what can actually live on separate layers?

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  • $\begingroup$ You can combine this using masks in a photo editing program, or by drawing a mask and using it in the compositor. Otherwise, I would probably prefer to render out the two myelin for both axons together, and the both neurons without the covers as your two render layers. $\endgroup$ – TLousky Sep 27 '15 at 13:45
  • $\begingroup$ Are you sure your suggestion for different layers would work? So far, the only way I've been able to recombine them is when the neuron and the myelin are on the same layer as each other (e.g. a neuron/myelin pair per render layer) $\endgroup$ – ajwood Sep 27 '15 at 14:07
  • $\begingroup$ From your first image it doesn't seem like there are any areas where the neurons are above the myelin, which is why I think you can have all the myelin in one layer, and the neurons in another, then combine them with alpha over. $\endgroup$ – TLousky Sep 27 '15 at 14:09
  • $\begingroup$ What about the bit sticking out the end of the cross-section? $\endgroup$ – ajwood Sep 27 '15 at 14:21
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    $\begingroup$ Right, that bit is gonna cause a problem. You can always separate it into a different object and use the object ID mask to perform any post processes on it without affecting the myelin. $\endgroup$ – TLousky Sep 27 '15 at 14:24
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Render your layers with Z pass:
Passes

Combine them using Z Combine node from Color tab: Node editor

On Z Combine node check "Use Alpha" checkbox if needed.

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