Oxygen vacancy distributions and dynamics directly control the operation of solid-oxide fuel cells and are intrinsically coupled with magnetic, electronic and transport properties of oxides. For understanding the atomistic mechanisms involved during operation of the cell it is highly desirable to know the distribution of vacancies on the unit-cell scale. Here, we develop an approach for direct mapping of oxygen vacancy concentrations based on local lattice parameter measurements by scanning transmission electron microscopy. The concept of chemical expansivity is demonstrated to be applicable on the subunit-cell level: local stoichiometry variations produce local lattice expansion that can be quantified. This approach was successfully applied to lanthanum strontium cobaltite thin films epitaxially grown on substrates of different symmetry, where polarized neutron reflectometry revealed a strong difference in magnetic properties. The different vacancy content found in the two films suggests the change in oxygen chemical potential as a source of distinct magnetic properties, opening pathways for structural tuning of the vacancy concentrations and their gradients.