STtools: A Comprehensive Software Pipeline for Ultra-high Resolution Spatial Transcriptomics Data.


While there are many software pipelines for analyzing spatial transcriptomics data, few can process ultra high-resolution datasets generated by emerging technologies. There is a clear need for new software tools that can handle sub-micrometer resolution spatial transcriptomics data with computational scalability without compromising its resolution. We developed STtools, a software pipeline that provides a versatile framework to handle spatial transcriptomics datasets with various resolutions, such as the ones produced by Seq-Scope (<1μm), Slide-seq (10μm) and VISIUM (100μm). It automatically processes raw FASTQ files and runs downstream analyses at several folds higher resolution than existing methods. It also generates various visualizations including transcriptome density, cell type mapping, marker gene highlighting, and subcellular architectures. STtools is publically available for download at


Spatial Transcriptomics


Xi, Jingyue
Lee, Jun Hee
Kang, Hyun Min
Jun, Goo