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I've been searching for an answer to my question, but my Google-Fu isn't quite up to scratch to figure out what is likely a pretty simple question.

Anyways, I'm looking to improve my hair on my character models in Blender Internal. I am looking to use alpha maps to make hair strands appear nicer and rounder while conserving on polygons (as I'm trying to eventually do models for games and animations in a cartoony-stylistic approach, a low poly count is vital to me).

I was wondering if anyone knew how to have a colour map and an alpha map work together. For example; I want one map where all my strands are on top of eachother on a texture like this:

enter image description here

Where he has all of his locks of hair on the same spot of the texture so that all the strands go with the grain.

And then I also want a separate map like this:

enter image description here

Where I can control the alpha of each individual hair.

How can I do this?

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I wouldn't do it that way since the pixels counts are so different between the two images BUT if you wanted to, you do have the ability to have more than one UV map - so where you normally reference the default UVMap in the Data panel of the Properties editor, you would use one map for the color image and then add a new one for unwrapping to use the alpha map.

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