In this work, we propose an experimental approach allowing for the identification and the subsequent quantification of nanoparticles crystallographic facets, based on 3D data obtained using Transmission Electron Microscopy (TEM). The particle shape and faceting can be determined using Electron Tomography (ET) combined with High-Resolution TEM (HR-TEM). The quantitative analysis of faceting is carried out on the particles 3D model using a geometrical approach that automatically detects planar regions on particle boundaries. In order to check the reliability of our approach, we analysed palladium particles confined inside or located at the outer surface of a mesoporous silica shell (Pd@SiO 2 ) after an annealing treatment at 250°C under H 2 for 12 h. From the materials perspective, the aim of the current work is to investigate the encapsulation effect of silica (SiO 2 ) shells on the change in morphology and faceting of palladium NPs during such annealing treatment.