Spatial transcriptome (ST) technology is a revolutionary method that enables the analysis of gene expression while preserving spatial location information, providing a powerful tool for revealing tissue structure and function. ST technologies have captured considerable attention in the research community, especially after being named Method of the Year 2020 by Nature Methods. Over these years, an array of ST technologies has emerged, enabling transcriptome analysis at the multi-cellular, single-cellular, or sub-cellular level while preserving spatial location information. These technologies can be broadly classified into two types: next-generation sequencing-based spatial transcriptomes (sST) and image-based spatial transcriptomes (iST). While sSTs allow whole transcriptome analysis, conventional methods such as 10X Visium and slide-seq are impeded by limited spatial resolution and low mRNA capture rates.

With the continuous development and diversification of spatial transcriptome technologies, the effective selection and use of appropriate analysis tools have become a challenge. To address this issue, we have developed the Spatial Transcriptome Analysis Hub (STASH), a comprehensive, systematic, and user-friendly database of spatial transcriptome analysis tools. STASH collects and categorizes the 260 tools currently available and provides a wealth of information and features to help researchers quickly find the right tool for their needs. Furthermore, we have conducted a trend analysis of the tools in the database to highlight the current state and direction of spatial transcriptome research, which could help researchers develop better tools. STASH is a resource worthy of attention and use that will facilitate the spatial analysis of transcriptome data.