We report on numerical simulations of quantum-dot heterostructures derived from experimental high-resolution transmission electron microscopy results. A real sample containing large InGaN islands with size of ten of nm and non-uniform In content is analyzed. The three-dimensional models for the quantum dots have been directly extrapolated from experimental results by a numerical algorithm. We show electromechanical, continuum k·p, empirical tight-binding and optical calculations for these realistic structures, which present a very good agreement if compared with experimental measurements, implying that the use of realistic structures can provide significant improvements into the modeling and the understanding of quantum-dot nanostructures.