Fig. 1: Overview of stereopy.

a Stereopy provides solutions for multi-sample analysis, including a multi-sample data container and framework, multi-sample data modules, and multi-sample interactive visualization. b Stereopy offers key analysis modules for three main multi-sample data analysis scenarios: (i) Comparative studies: Stereopy provides functions at both the cell level and gene level to infer the global and local similarity and diversity for comparative SRT datasets. DEGs: Differentially expressed genes. (ii) Temporal studies: Stereopy offers temporal trajectory analysis and spatially resolved temporal gene pattern analysis to phase the temporal variable datasets. (iii) 3D integrative studies: Stereopy enables 3D data reconstruction and 3D signaling path identification to explore regulation mechanisms. c Stereopy contributes key algorithms for the three analysis scenarios: (i) CCD algorithm detects cell communities in single/multi-sample datasets, with a focus on finding common and specific communities. (ii) TGPI algorithm identifies temporal variable gene patterns with spatial restriction, enabling the discovery of gene patterns related to development or temporal variation. (iii) NicheReg3D algorithm investigates inter- and intracellular regulation mechanisms from the 3D aspect. Source data are provided as a Source Data file.