Abstract Advances in spatial omics technologies have brought opportunities to dissect tissue microenvironment, while also posing more requirements and challenges for computational methods. Here we developed a package SOAPy to systematically dissect spatial architecture, dynamics and communication from spatial omics data. Specifically, it provides analysis methods for multiple spatial-related tasks, including spatial domain, spatial expression tendency, spatiotemporal expression pattern, cellular co-localization, multi-cellular niches, and ligand-receptor-mediated and spatial-constrained cell communication. Applying SOAPy on different spatial omics technologies and diverse biological fields has demonstrated its power on elucidation of biological questions about tumors, embryonic development, and normal physiological structures. Overall, SOAPy is a universal tool for spatial omics analysis, providing a foundation for continued investigation of the microenvironment.

SOAPy: a Python package to dissect spatial architecture, dynamics and communication