Hi

It's certainly doable. The SilverStripe GD class is just a wrapper around the PHP GD functionality (http://php.net/manual/en/ref.image.php). You can do a lot using these functions. If you're doing per-pixel operations, prepare for a performance hit though (at least when processing larger images).
You can create a subclass of the SilverStripe GD class where you implement the desired functionality. Then create a subclass of the Image class and override generateFormattedImage (to use your custom GD class instead of the default one). You can also implement different custom generate methods to use them in your templates (http://doc.silverstripe.com/doku.php?id=recipes:customising_image).