sc3D: A Comprehensive Tool for 3D Spatial Transcriptomic Analysis

gene expression. These results show that sc3D allows reproducible reconstruction and analysis of volumetric spatial omics data across different samples and experimental platforms. Key features • 3D reconstruction: sc3D aligns serial Slide-seq arrays and interpolates between sections to generate volumetric transcriptomic datasets preserving tissue geometries. • Portable data formats: Outputs a .h5ad object storing coordinates, expression, and metadata, readable in Python or napari-sc3D-viewer. • Integrated visualization: The napari plugin enables interactive 3D exploration, virtual in situ hybridization, and gene expression profiling along developmental axes. • Spatial differential expression: Built-in functions detect regionally enriched genes and export quantitative 3D heatmaps and ranked tables.