Unless the application has an api for doing this, and you have access to a perl-callable library to use that api, the only way I could see to do this would be to do a screen-grab and then inspect the resultant bitmap.

Your problem then would be converting between the coordinate system used within the application and the screen coordinates represented in the bitmap; and that would be distinctly non-trivial.

You might also be able to use something like Pixie to obtain the color of the pixel under the cursor, but automating that would probably be quite difficult; and you still have the coordinate convertion problem to resolve.