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Computer-aided data acquisition, analysis, and interpretation are rapidly gaining traction in numerous facets of research. One of the subsets of this field, image processing, is most often implemented for post-processing material microstructural characterization data to understand better and predict materials’ features, properties, and behaviors at multiple scales. However, to tackle the ambiguity of multi-component materials analysis, spectral data can be used in combination with image processing. The current study introduces a novel Python-based image and data processing method for in-depth analysis of energy dispersive spectroscopy (EDS) elemental maps to analyze multi-component agglomerate size distribution, the average area of each component, and their overlap. The framework developed in this study is applied to examine the interaction of Cerium Oxide (CeO x ) and Palladium (Pd) particles in the membrane electrode assembly (MEA) of an Anion-Exchange Membrane Fuel Cell (AEMFC) and to investigate if this approach can be correlated to cell performance. The study also performs a sensitivity analysis of several parameters and their effect on the computed results. The developed framework is a promising method for semi-automatic data processing and can be further advanced towards a fully automatic analysis of similar data types in the field of clean energy materials and broader.