Summary: We use mirror symmetry, quantum geometry and modularity properties of elliptic curves to calculate the refined free energies in the Nekrasov-Shatashvili limit on non-compact toric Calabi-Yau manifolds, based on del Pezzo surfaces. Quantum geometry here is to be understood as a quantum deformed version of rigid special geometry, which has its origin in the quantum mechanical behaviour of branes in the topological string B-model. We will argue that, in the Seiberg-Witten picture, only the Coulomb parameters lead to quantum corrections, while the mass parameters remain uncorrected. In certain cases we will also compute the expansion of the free energies at the orbifold point and the conifold locus. We will compute the quantum corrections order by order on , by deriving second order differential operators, which act on the classical periods.