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This is how you apply colour, the paradigm shift comes when you realise consecutive frames can be use to "stabilize" the autostereogram

On the left is a single colour stereogram. RGB (0.5, 0, 0.5) 

On the right is the same stereogram but it's colour is mainly distributed between left and right. RGB (1,0,0) & (0, 0, 1)...(i have included 1 matched pixel to help with alignment) 

In the distributed stereogram your eyes will fight for dominance but if you swap the location of left and right on each consecutive frame you will negate this....we used a simple gif animator to test this. But if you stay very still and stare long enough you will see the effect.

The trick would be to distribute the colour in such a way that the image can't be seen(well) outside of the parallel and crossed modes.