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This is how I do red-green Anaglyphs in Photoshop:
1. Open left image convert to greyscale, then to CMYK. (I use actions
for this).
It's also possible to use 'desaturate' but is not as good conversion.
2. Copy the whole image (select all) and paste it into the Y and C
channel.
3. Delete the contents of the other channels.
4. Create a new layer and repeat steps 1-3 for the right image, pasting
it into Y and M channel.
5. Put on your glasses, set the layer mode to Darken (is it in the
English version?) and move on of the layers until you adjusted the
anaglyph correctly.
You can also use Multiply mode, but that will give you not a
green-red-grey, but a green-red-brownish picture.
Who has a better way?
Cheers, Peter
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