This article describes the size control synthesis of silicon quantum dots with simple microemulsion techniques. The silicon nanocrystals are small enough to be in the strong confinement regime and photoluminesce in the blue region of the visible spectrum and the emission can be tuned by changing the nanocrystal size. The silicon quantum dots were capped with allylamine either a platinum catalyst or UV-radiation. An extensive purification protocol is reported and assessed using 1H NMR to produce ultra pure silicon quantum dots suitable for biological studies. The highly pure quantum dots were used in cellular uptake experiments and monitored using confocal microscopy. The results showed that the amine terminated silicon nanocrystals accumulated in lysosome but not in nuclei and could be used as bio-markers to monitor cancer cells over long timescales.