Nowadays, any cutting-edge nanoscience effort includes extensive atomic-resolution electron microscopy. Recent technological advances in the field of electron microscopy have increased the spatial resolution into the sub-Ångstrom range, the energy resolution into the sub-eV range, and the sensitivity to resolve single atoms. The precision in determination of the atomic column positions is even in the range of pm (10-12m). Atomic-scale analysis plays a unique role in discovering how structures function on the nanoscale. As an example, I will present how advanced electron microscopy has been used to describe a comprehensive picture of the general light emitting mechanism of commercially available high-brightness InGaN/GaN based green light emitting diodes (LED). For the first time the local indium stoichiometry has been linked to the local electronic structure inside the quantum well (QW) structure. This challenge was addressed by application of high-resolution TEM (HRTEM), reconstruction of the exit wave (EWR), annular dark field (ADF) TEM, and Z-contrast imaging (HAADF-STEM) to characterize the atom distribution. Furthermore, valence electron energy loss spectroscopy (VEELS) has determined local band gap fluctuations. Finally, I will briefly discuss the exciting research opportunities that exist by applying experimental TEM methodologies, such as 3-D electron microscopy (electron tomography). Their application will provide critical information to help understand the nanoscale phenomena.