How to: pixel packs in an image to representative point coordinates (x,y)
Just a naive suggestion: do you know about component labeling? 

The technique is about finding chunks of "touching" pixels and assigning them a label, e.g. an integer number. You can then interrogate each chink separately, looking for the pixel that share the same label.

In MATLAB, here is the function that does it trivially: bwlabel