The correlation between the structural and optical properties of Si nanocrystals embedded in SiO2 is the key factor to understand their emission mechanism. However, there is a great difficulty in imaging Si nanocrystals in SiO2 and measuring their size distribution because of the lack of contrast in electron microscopy. We have used here a new method for imaging Si nanocrystals by using high resolution electron microscopy in conjunction with conventional electron microscopy in dark field conditions. Regarding the optical properties, the band-gap energies and photoluminescence have been measured by direct and independent methods. The results have allowed experimental determination, for the first time in this material, of the experimental Stokes shift between absorption and emission as a function of crystallite size. The experimental band-gap versus size correlates well with the most accurate theoretical predictions. Moreover, the photoluminescence energy emission versus crystallite size shows a parallel behaviour to that of band-gap energy. Consequently, the experimental Stokes shift is independent of nanocrystal size and is found to be 0.26±0.03 eV. This value is almost twice the energy of the Si-O vibration (0.134 eV). These results suggest that the dominant emission of Si nanocrystals passivated with SiO2 is a fundamental transition spatially located at the Si-SiO2 interface and with the assistance of a local Si-O vibration.