How to Create Stereo Anaglyphs - The Basics:
Rule #1: Keep the tones in your images since white
or black will be seen equally by both eyes. You need greys to be able
to be assigned a color of cyan or red.
Working in Photoshop -
Open your Left and Right images (they must be the same magnification).
Make both images RGB (Image, Mode, RGB Color)
Select the Channels view (Window, Channels)
Go to the Left image, Red Channel and select all. Copy this Red Channel
from the Left image (Ctrl-C).
Go to the Right image, Red Channel and Paste the contents of the clipboard
into the right image's red channel (Ctrl-V).
Your anaglyph image is now together so save it under a NEW filename.
Close the other (Left) image.
View all of the channels (RGB) with you Red-Cyan anaglyph glasses.
Now is the time to fine-tune the image:
You may need to move the new Red Channel to achieve alignment and
place it into the stereo window (depth to be seen
behind the window frame, or in front of the frame,
or some of each).
You may also need to adjust the Levels and Curves of the Channels
to have both images equally prested to the eyes.
Since many stereo images are unevenly exposed, you may also need to
adjust the images for even tonal brightnesses.
Don't forget that you can select both the Green and Blue Channels
so that you can work on both of them together.