In order to make an anaglyph you need two slightly off-set images. These can be produced using 3D software applications (Bryce, 3D Studio Max) or they can downloaded from a camera or pair of cameras. If you are downloading images from cameras, it is absolutely critical that you keep track of which image is for the left eye and which is for the right eye. You can figure this out later, but it is a very tedious process and prone to error. I recommend placing all left-eye images in one folder (called Left) and all the right-eye images in another folder (called Right).
If you are using cameras it is likely that the image file names don't sync up properly - the left-right pairs have different, unrelated file-names. If you are working with a large number of images, it's worth your time right now to go through and rename all of the images so that you can tell which pairs go together. I recommend a naming system that goes something like this: 01l, 01r, 02l, 02r... and so on where the number indicates the images go together as a pair and the r/l indicates which eye the image is. This system is good because it lets you put all the images into a single folder without the order getting confused.
Now that you have that done, it's time to start working in Adobe Photoshop. For this demo, I'll be using version 7.0.
Repeat these steps for the second image. You should now have a 3-layer image, with layers "left", "right" and "background."
Now you need to align the layers properly. to do this, go to the top layer and select the Opacity drop-down menu. Slide the bar until it reads around 50%.
The focus is roughly in the circle (added for emphasis)
You don't want any parts of the image to have information from only one picture, because that hurts the eyes and messes up the symmetry. So the next step is to return the top layer to 100% Opacity. Now deselect the eye next to the layer for the bottom image layer . There will be two white boarders from where you have moved your image in order to line them up. You need to get rid of these boarders. To do this, use the select tool and select the portion of your image that is inside of these white boarders.
Now go to Edit > Crop. This will resize your image so that both eyes take up the entire field.
Now it is time to remove the appropriate colors from the left and right eye. Make the bottom layer visible again by clicking on the eye icon next to the layer. This should make both eyes visible again. Let's start with the right eye. The best way to remember this is Right red. Make sure the right eye image is selected and go to Image > Adjustments > Levels... (Control-L) This will open the following box. Drop down the top menu and select the Red channel (Control-1).
Now, at the bottom where it says Output Levels (Tab four times to get there): change the 255 to 0 and click OK. This should change your layer to a green-blue color (cyan).
Now select the left layer. and open the Level... dialog box again (Control-L). Select the Green Layer (Control-2) change the Output Level to 0 (Tab four times). Select the Blue Layer (Control-3) and change the Output Level to 0 (Tab four times). Click OK. This should turn the top layer to bright red. Your layers should now look like this:
The final step is to select the top layer (left or right) and in the box where it currently says Normal change it to Screen.
Go to Save Image As (Control-Shift-S) and save it as a jpeg (or tiff or whatever kind of file you need). Voila! Your own anaglyph image.
Open Right Image
Open Left Image
Select New Image
Change top transparency to 50%
Move top layer to align focus
Replace 100% opacity for top layer
Make bottom layer invisible
Crop out empty space
Make bottom layer visible
Select Right Layer
Tab, Tab, Tab, Tab
Select Left Layer
Tab, Tab, Tab, Tab
Tab, Tab, Tab, Tab
Change top layer from Normal to Screen