CartoScope: democratized, harmonized, and scalable ecosystem for subcellular spatial omics exploration

Subcellular spatial omics technologies now generate vast datasets that capture tissue organization at microscopic resolution. However, biological discovery has lagged behind data production due to fragmentation across platforms, reliance on binning or imperfect cell segmentation, and high computational barriers that limit accessibility for experimental biologists. Here we present CartoScope for democratized, scalable, and segmentation-independent exploration and analysis of subcellular omics data. CartoScope efficiently renders multi-resolution spatial omics data on demand through an interactive web interface, enabling multi-layered visualization of genes, transcriptional programs, and inferred cell types over histological images at molecular resolution. Beyond visualization, CartoScope supports interactive analysis of user-defined regions-of-interest (ROIs), including region-specific cell type composition analysis and differential gene expression analyses stratified by cell type or spatial context. The CartoScope ecosystem integrates a backend harmonization pipeline and a public data repository, currently hosting over 320 datasets spanning 16 technologies and 28 tissue types, with an architecture designed for continuous expansion and scalable integration of future datasets. Through representative applications, including cross-technology benchmarking and cellular, subcellular, and multicellular analysis of transcriptomic heterogeneity across development and disease, we demonstrate that CartoScope enables rapid biological discovery, hypothesis testing, and insight sharing within minutes of web-based operation.