In light emitting diodes (LED) consisting of indium gallium nitride (InGaN) quantum wells (QWs) in a GaN matrix, the atomic In distribution inside the wells defines device performance. We analyzed samples (LED structures) with a nominal In composition of 17%. Using a comparison of experimental electron exit waves with simulations we conclude that the amount of In segregation (deviation from Poisson distribution) can be quantitatively derived from intensities with a sensitivity allowing for the detection of 1 indium atom in columns of Ga atoms.