Scalability and performance of current flash memories can be improved substantially by replacing the floating poly-Si gate by a layer of Si dots. This multi-dot layer can be fabricated CMOS-compatibly in very thin gate oxide by ion beam synthesis (IBS). Here, we present both experimental and theoretical studies on IBS of multi-dot layers consisting of Si nanocrystals (NCs). The NCs are produced by ultra low energy Si ion implantation, which causes a high Si supersaturation in the shallow implantation region. During post-implantation annealing, this supersaturation leads to phase separation of the excess Si from the SiO2. Till now, the study of this phase separation process suffered from the weak Z contrast between Si and SiO2 in Transmission Electron Microscopy (TEM). Here, this imaging problem is resolved by mapping Si plasmon losses with a Scanning Transmission Electron Microscopy equipped with a parallel Electron Energy Loss Spectroscopy system (PEELS-STEM). Additionally, kinetic lattice Monte Carlo simulations of Si phase separation have been performed and compared with the experimental Si plasmon maps. It has been predicted theoretically that the morphology of the multi-dot Si floating-gate changes with increasing ion fluence from isolated, spherical NCs to percolated spinodal Si pattern. These patterns agree remarkably with PEELS-STEM images. However, the predicted fluence for spinodal patterns is lower than the experimental one. Because oxidants of the ambient atmosphere penetrate into the as-implanted SiO2, a substantial fraction of the implanted Si might be lost due to oxidation. Comment: 3 pages, 2 figures, accpeted for publication in Appl. Phys. Lett