Mapping biology in space: from spatial transcriptomics platforms to analytical tools and databases

Spatial transcriptomics (ST) has become a key technology for interrogating gene expression within spatial context, providing spatially resolved insights into tissue architecture and microenvironmental organization. Rapid advances in experimental platforms and analytical methods, however, have resulted in challenges for technology selection, methodological comparison, and data interpretation. In this review, we present a systematic summary of 594 ST analysis tools spanning 77 ST technologies (as of September 2025). We outline the complete analytical workflow and discuss major analytical tasks, including data preprocessing, denoising and imputation, spatial pattern and domain identification, cellular composition, trajectory analysis, cell-cell communication, and spatial multi-omics integration. For each task, we summarize representative methodological principles and emphasize platform-dependent considerations arising from differences in spatial resolution and detection efficiency. We further highlight how analytical applications of ST data have enabled biomedical discoveries by revealing spatial heterogeneity, tissue organization, and context-dependent cellular interactions. Furthermore, we develop SpatialToolDB (https://www.spatialtooldb.yelab.site/), a systematically curated, categorized, and continuously updated platform that integrates the ST technologies, analytical methods, and related databases covered in this review, facilitating informed tool selection and method comparison. We also discuss development trends and future directions of spatial-omics technologies and analytical tools, including advances in spatial technologies, AI-driven computation, benchmarking and standardization, and improved experimental validation for mechanistic and predictive spatial biology. Together, this review and SpatialToolDB provide a data-driven foundation for selecting ST platforms and analytical strategies tailored to diverse biological and translational research applications.