Storing Pixel Coordinates with movements of mechanical stage.

I have a mechanical stage under the camera that moves along x-y axis, I want the movements of the stage to be able to see a pixel location like [749,114] and then the mechanical stage shifts that point to the very center.

I use this to find pixel coordinates BW = roipoly('example.png'); [x,y] = find(BW);

Do I need to save every x,y coordinate in the image as a variable linked with a movement in the stage controller that centers it? Would the function need to store the roughly 4,000 pixel values with their linked stage movement?

Any ideas are appreciated, I'll send bitcoin for a really good answer :)