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The dependence on serial sections is attributed to technological limitations of MTI panel size or incompatible multi-assay protocols. Although image registration can align serially sectioned MTIs, integration at the single-cell level poses a challenge due to inherent biological heterogeneity. Existing computational methods overlook both cell population heterogeneity across modalities and spatial information, which are critical for effectively completing this task. To address this problem, we first use Monte-Carlo simulations to estimate the overlap between serial 5\u03bcm-thick sections. We then introduce COEXIST, a novel algorithm that synergistically combines shared molecular profiles with spatial information to seamlessly integrate serial sections at the single-cell level. We demonstrate COEXIST necessity and performance across several applications. These include combining MTI panels for improved spatial single-cell profiling, rectification of miscalled cell phenotypes using a single MTI panel, and the comparison of MTI platforms at single-cell resolution. COEXIST not only elevates MTI platform validation but also overcomes the constraints of MTI\u2019s panel size and the limitation of full nuclei on a single slide, capturing more intact nuclei in consecutive sections and thus enabling deeper profiling of cell lineages and functional states.<\/jats:p>","DOI":"10.1371\/journal.pcbi.1013325","type":"journal-article","created":{"date-parts":[[2025,8,5]],"date-time":"2025-08-05T19:33:06Z","timestamp":1754422386000},"page":"e1013325","update-policy":"https:\/\/doi.org\/10.1371\/journal.pcbi.corrections_policy","source":"Crossref","is-referenced-by-count":2,"title":["COEXIST: Coordinated single-cell integration of serial multiplexed tissue images"],"prefix":"10.1371","volume":"21","author":[{"given":"Robert T.","family":"Heussner","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Cameron 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