The expression and spatial organization of proteins are central to tissue physiology and pathology. Although advances in imaging technologies have expanded multiplexing capabilities, challenges remain in terms of resolution, throughput, accessibility, and integrative analysis. Here we introduce pathology-oriented multiplexing (PathoPlex), a framework that integrates highly multiplexed imaging at 80 nm per pixel across 95 cycles with GPU-accelerated open-source software for pixel-level clustering of protein co-expression in formalin-fixed paraffin-embedded specimens. PathoPlex enables the profiling of over 140 antibodies per sample and allows parallel processing of at least 40 biopsies. Applied to immune-mediated kidney disease, PathoPlex identifies key protein activity clusters, while in human diabetic kidney disease it uncovers signatures of calcium-mediated tubular stress, including in patients without histological signs of disease. Moreover, tissue-based analysis reveals partial therapeutic responses to SGLT2 inhibition. Together, these findings establish PathoPlex as a robust, scalable approach for integrative disease mapping across experimental and clinical pathology.