Electron backscattered diffraction (EBSD) has been employed to study a polycrystalline nickel superalloy containing a complex non-metallic agglomerate under thermal loading. Heterogeneous distributions of elastic strains are observed near the inclusion due to its complex geometry and these have been quantified. Lattice rotations were also related to geometrically necessary dislocation (GND) density (View the MathML source), indicating the development of localized plasticity arising from the mismatch in thermal expansivity between the Ni polycrystal and the inclusion. A crystal plasticity finite-element (CPFE) model which explicitly represents the full detail of the complex microstructure was developed to interpret the experimental measurements, and good quantitative and qualitative agreement has been obtained. However, a limitation of the EBSD technique when investigating polycrystal systems is that full-field, transgranular strain measurement remains difficult due to the necessity to reference a lattice spacing within a grain for strain calculation. An inverse reference shifting methodology has been developed using CPFE modeling to overcome this problem, thereby allowing like-for-like and grain-by-grain strain comparisons to be made. The method, in conjunction with high-resolution EBSD, shows promise for the determination of full-field strains and rotations in polycrystalline materials, and provides key information for fatigue nucleation in these material systems.