You could also try a program like Snap-it. It will let you capture an image and automatically change color A to color B of your choice, color C to D etc... as long as you have set it up in the preferences.
This idea is handy if there are a lot of captures (20, 50, 100, 500) to make and several color changes to make on them and you don't feel like editing them all in a photo-editing program.
However, if it's just something simple, do it the way dragon2309 said. If you have photoshop, for example, you could set up an action to change color A to B etc.. and then run that action on the batch of captured images.