Say there are 3 circles: red, blue, black.
I only want the black circle to remain. How can I remove the red and blue circles?
ImageMagick will do it. Just shell out to this command:
convert circles.png -channel black -white-threshold 10% circles2.png
You didn't say what to do with green. This script takes the easy way out and wipes out green as well. Actually, it wipes out anything not black.
The RMagick libary lets you drive imagemagick with Ruby. Sadly, it's not working in my distro, so I can't prepare an example for you. However, using system or backtick to shell out to the command works just fine.