In light emitting diodes (LED) consisting of GaN/InGaN/GaN quantum wells (QWs), the exact indium distribution inside the wells of the active region affects the performance of devices. Indium segregation can take place forming small InGaN clusters of locally varying composition. In the past, we used a local strain analysis from single HRTEM lattice images to determine the In composition inside the InGaN QWs with a resolution of 0.5 nm x 0.3 nm. Truly atomic resolution can be pursued by exploitation of intensity dependencies on the atomic number (Z) of the electron exit-wave (EW). In microscopes with sufficient sensitivity, local variations of amplitude and phase are found to be discrete with sample thickness, which allows for counting the number of atoms in each individual column of ~ 0.08 nm diameter. In QW’s of ~ 17% of average indium concentration it is possible to discriminate between pure Ga columns and columns containing 1, 2, 3, or more In atoms because phase changes are discrete and element specific. The preparation of samples with atomically flat surfaces is a limiting factor for the application of the procedure.