Planarian ManuscriptΒΆ This section contains methods used in planarian manuscript with step-by-step description. Sampling Design Sampling Sample fixation Stereo-seq Data preprocessing Stereo-seq Analysis Workflow Image registration Cell boundary detection DNB aggregation Cell clustering 3D alignment 3D mesh building Downstream Analysis SPC clustering Spatial gradient gene profiling Spatial pattern clustering Potential PCGs detection Principal component analysis of PCGs Cell-cell connection analysis Cell colocation estimation Micro-environment estimation Visualization 3D projection plot Data availability Index