Quantifying disease-associated renal tubular remodeling is challenging because tubular appearances are heterogeneous. We introduce TuMAP (Tubular Morphotype-Aware Pathomics), a pipeline combining (1) dual-view foundation-model representations and provisional morphotype annotation, (2) compositional and within-morphotype pathomics, and (3) patient-level statistical inference. From 456,158 tubules in 358 PAS-stained kidney biopsy slides, TuMAP identified eight image-based morphotypes, seven of which showed stable subsampling assignments. Across 219 patients in six diagnostic groups, diabetic nephropathy (DN) and tubulointerstitial nephritis/acute tubular injury (TIN/ATI) each differed from minimal change disease in seven morphotype proportions, while IgA nephropathy differed in six. DN showed reduced nuclear solidity and increased eccentricity across all eight morphotypes. Area-normalized nuclear density exposed additional within-morphotype differences. TuMAP provides a framework for separating changes in tubular morphotype composition from phenotypic differences within morphotypes.

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