Strain, as an easy and clearly defined concept in continuum mechanics, has no direct counterpart in atomistic models. Existing methods, relying on the concept of atomic coordination number, do not provide a complete description of volumetric and deviatoric strains across metallic nanocrystalline microstructures. To overcome those limitations a new method is proposed: the Voronoi Cell deformation (VCD) fully accounts for the local geometry and provides a description of the strain field independent of the atomic coordination. As a typical case of study, a large atomic cluster of 200 Al grains (ca 2 million atoms) and overall size of 33 cubic nanometres was considered.