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bioRxiv · 10.1101/2025.09.18.677135

Differential colocalization of cell-type pairs in single-cell spatial omics with DC-SPOMIC

Chang, J.·Perez, A. E.·Molina, P.·Tian, L.·Plevritis, S.
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Abstract

MotivationSpatial omics studies compare cell-cell organization across samples, but most methods model between-sample variability while treating sample-level spatial estimates as error-free. Overlooking within-sample uncertainty can distort inference in heterogeneous cohorts, motivating methods that explicitly quantify and propagate this uncertainty into cohort-level analyses. ResultsWe present PANORAMIC, a hierarchical framework for spatial colocalization analysis that uses edge-corrected neighborhood enrichment to estimate local cell-type colocalization, spatial bootstrapping to quantify within-sample uncertainty, and multilevel random-effects meta-analysis to propagate this uncertainty across samples, patients, and conditions. In simulations, PANORAMIC improved recovery of within-sample uncertainty and between-sample heterogeneity relative to naive estimators across diverse spatial settings and progressive data degradation. Applied to a colorectal cancer tissue microarray profiled by multiplexed immunofluorescence imaging, PANORAMIC identified stronger B- and T-cell colocalization in tumors with Crohns-like reaction than in tumors with diffuse inflammatory infiltration, together with tighter higher-order immune organization consistent with immune aggregates. These results show that propagating within-sample spatial uncertainty can improve cohort-level inference in spatial omics studies. Availability and ImplementationPANORAMIC is released as an open-source R package at https://github.com/plevritis-lab/panoramic. Contact[sylvia.plevritis@stanford.edu]

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Chang, J., Perez, A. E., Molina, P., Tian, L., Plevritis, S.. 2025-09-21. Differential colocalization of cell-type pairs in single-cell spatial omics with DC-SPOMIC. https://doi.org/10.1101/2025.09.18.677135

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