Analysis of anatomical multi-cellular structures from spatial omics data using sosta

Abstract Spatial omics technologies enable high-resolution, large-scale quantification of molecular features while preserving the spatial context within tissues. Existing analysis methods largely focus on spatial arrangements of single cells, whereas biological function often emerges from multicellular arrangements. Here, we introduce structure-based analysis of spatial omics data, which focuses on the direct analysis of multicellular, anatomical structures. We illustrate this type of analysis using two publicly available datasets and provide sosta, an open-source Bioconductor package for broad community use. Competing Interest Statement The authors have declared no competing interest. Footnotes This revision contains major updates to our manuscript. - We reorganized the manuscript to improve comprehensibility, especially in the "Design and Implementation" section. - We added a systematic comparison against other methods for spatial omics structure reconstruction. - We clarified multiple parts in the results sections and added additional results.