•Binary mapping of microscopic images of two-phase systems•Measuring the integral conductivity by the analysis of binary conductivity map•Measuring the content of the conductive /non-conductive phase by the conductivity map The determination of the content of the conducting phase and the assessment of conductivity by microscopic images are interesting for rapid and non-destructive analysis of the electrophysical properties of two-phase (conductor/dielectric) samples during the atomic force microscopy. In this paper we summarized results of the analysis of the conductivity maps of the shungite surface by the method of discretization by applying a square grid with subsequent binary digital processing. Microstructure and conductivity were evaluated by measuring the average length of continuous conductive circuits isolated on the grid. A model was considered that established a unique correspondence (up to normalizing coefficients) between the length of the conductive circuits on the conductivity maps and the integral conductivity of the sample as a whole. An analytical equation was obtained that described such dependence with an accuracy of units of percent. We proposed a method for measuring the integral conductivity of a shungite samples based on an analysis of its binary conductivity map obtained by spreading resistance microscopy. This method can be used to determine the conductivity by surface conductivity mapping for shungite-like two-phase conductor/dielectric systems, and in general, for any two-phase substances where the phases differ in AFM-determined properties.