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We will deliver the first organ-scale, subcellular-resolution 3D kidney atlases of 10 different disease models, comprising complete 3D reconstructions of hundreds of intact nephrons per tissue with nephron-specific cytometry and co-segmented peritubular capillaries. This breakthrough combines thick-tissue small-molecule labeling, tissue clearing, high-throughput lightsheet imaging, and AI-driven reconstructions to overcome the central blind-spot in nephrology: the inability to study whole nephrons continuously in situ. Current nephrology research relies on studying glomeruli or partial tubular patches through 2D sectioning-based assays or small volume 3D snapshots. This obscures critical relationships within nephrons, between neighboring nephrons, and with the microvasculature. Our platform captures nephron trajectories across millimeters of tissue — 100X greater sampling than existing methods — while preserving cellular detail and spatial relationships. We have already demonstrated feasibility by completely segmenting 1000 whole nephrons in 3D from a single, healthy kidney tissue slab—two orders of magnitude beyond any published result. Our innovative approach treats each nephron as a statistical unit, enabling robust population-level analyses across multiple disease models. The atlases will feature comprehensive whole-nephron cytometry, quantifying cellular loss per segment (proximal tubules, thin limbs, distal tubules, etc.) alongside whole-nephron morphological measurements (length, diameters, tortuosity, glomerular volumes) and frequency of pathology (atrophy/hypertrophy, cyst burden, atubular glomeruli). Critically, we will generate quantitative maps of nephron-capillary interfaces, revealing local contact sites, vascular rarefaction, and damage gradients unavailable with current technologies. This paradigm shift transforms nephrology from anecdotal, sparsely sampled 2D analyses to population-level, anatomically faithful, and quantifiable 3D measurements. For the first time, researchers will be able to capture large-scale alterations in nephron geometry, compare cell counts between cortical and juxtamedullary nephrons, track disease trajectories through tubular epithelial cell loss and proliferation, and directly correlate nephron pathology such as geometrical deformities, tubular atrophy or cyst formation with adjacent microvascular disruptions. We will create openly accessible reference atlases with raw volumes, segmentation, and standardized analyses enabling direct cross-disease comparisons. Beyond nephrology, our computational methods will be generalizable to other organs with tubular/glandular architecture. This project fundamentally redefines how kidney disease is mapped, quantified, and ultimately treated—establishing a new class of 3D assays that unlock previously intractable questions such as nephron-nephron and nephron-vascular relationships in disease progression.
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