Space Ranger

Primary analysis

Space Ranger is the 10X Genomics pipeline designed to analyze spatial gene expression data generated by Visium systems. It begins with processing microscope images of tissue sections to ensure proper alignment and stitching. Next, it demultiplexes and aligns raw sequencing data to a reference genome, generating feature-barcode matrices. The software then performs counting of unique molecular identifiers (UMIs) associated with each gene in each spatial spot. Following this, the software maps the sequencing data to spatial coordinates on the tissue image. It ouputs a repertory notably containing the gene per spot counts matrix, the spatial positions, a web summary of QC metrics, a preliminary default statistical analysis, and a cloupe file for visualization in Loupe Browser. This module is usually performed by the platform that owns the 10x Genomics Visium system, such as UCAGenomiX.