The self-absorption problem in the x-ray fluorescence (XRF) imaging community is a long-lasting and grand challenge to achieve quantitative analysis. Accurate correction is of broad interest in many disciplines, including material science, environmental science, and biology. The researchers desire to obtain a 3D structure with accurate material compositions or trace element distributions from complex 3D specimens with multi-components. We will present a generalized absorption correction method, which works broadly for 2D and 3D imaging. With the developed method, we reveal internal 3D elemental composition in a mixed ionic-electronic conductor (MIEC), which has important applications in energy conversion and catalysis, whose material functionality is intimately tied to diffusion and phase-separation at grain boundaries. By performing accurate quantification of 3D concentration over an unprecedented number of grains (i.e. a total of 340 grains), we unveil deep insights on the complex phase transformation at the grain boundaries and the mechanistic model for producing the so-called emergent phases, which plays a critical role in achieving high transport properties of the MIEC material system.