Crystalline TiO2 nanoparticles were produced by scalable flame spray pyrolysis of organometallic solutions. A protocol is presented for the optimized functionalization of these particles with fluorescein isothiocyanate (FITC), an important biomedical dye via a lysine linker. The pH, stoichiometry and time for lysine reaction were determined for highest dye loading and minimized degree of polylysine formation. Acidic reaction conditions, low lysine concentration and short reaction times were found to meet this aim. The resulting particles were used for imaging single neurons, showing high fluorescence emission and ability for the particles to diffuse into small neuron structures such as dendrites.