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Review
. 2025 Dec;26(12):828-846.
doi: 10.1038/s41576-025-00845-y. Epub 2025 May 14.

Cell-type deconvolution methods for spatial transcriptomics

Lucie C Gaspard-Boulinc #  1   2   3 , Luca Gortana #  1   2   3 , Thomas Walter  1   2   3 , Emmanuel Barillot  1   2   3 , Florence M G Cavalli  4   5   6
Affiliations
Review

Cell-type deconvolution methods for spatial transcriptomics

Lucie C Gaspard-Boulinc et al. Nat Rev Genet. 2025 Dec.

Abstract

Spatial transcriptomics is a powerful method for studying the spatial organization of cells, which is a critical feature in the development, function and evolution of multicellular life. However, sequencing-based spatial transcriptomics has not yet achieved cellular-level resolution, so advanced deconvolution methods are needed to infer cell-type contributions at each location in the data. Recent progress has led to diverse tools for cell-type deconvolution that are helping to describe tissue architectures in health and disease. In this Review, we describe the varied types of cell-type deconvolution methods for spatial transcriptomics, contrast their capabilities and summarize them in a web-based, interactive table to enable more efficient method selection.

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Conflict of interest statement

Competing interests: The authors declare no competing interests.

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