Accelerating 2D image processing

I am beginning a project where we need to accelerate the processing of 2d astronomy images. Basically, we need to load a base image’s pixels and process the image against calibration images that need to be subtracted from it (from a pixel level point of view). There are a couple of other issues in dealing with the image pixels and they can be solved readily if we had a way to use shaders. I have googled the hell out of the keywords you can imagine here and have found very little which is surprising. We need to use the GPU to accelerate the loading and manipulating of all of these images and it would be great if we could use jogl or java 2d to create an app that can do this - if it could run arbitrary shaders against the images then that would be just perfect. Any help here would be greatly appreciated.

http://www.gpgpu.org/

Although the precion gurantees you get with shaders aren’t as strict as on a CPU, so if you need 100% accuracy instead of speed you might be better off doing it on the CPU.