Generating single-cell gene expression profiles for high-resolution spatial transcriptomics based on cell boundary images

Abstract

In spatially resolved transcriptomics, Stereo-seq facilitates the analysis of large tissues at the single-cell level, offering subcellular resolution and centimeter-level field-of-view. Our previous work on StereoCell introduced a one-stop software using cell nuclei staining images and statistical methods to generate high-confidence single-cell spatial gene expression profiles for Stereo-seq data. With advancements allowing the acquisition of cell boundary information, such as cell membrane/wall staining images, we updated our software to a new version, STCellbin. Using cell nuclei staining images, STCellbin aligns cell membrane/wall staining images with spatial gene expression maps. Advanced cell segmentation ensures the detection of accurate cell boundaries, leading to more reliable single-cell spatial gene expression profiles. We verified that STCellbin can be applied to mouse liver (cell membranes) and Arabidopsis seed (cell walls) datasets, outperforming other methods. The improved capability of capturing single-cell gene expression profiles results in a deeper understanding of the contribution of single-cell phenotypes to tissue biology. Availability & Implementation The source code of STCellbin is available at https://github.com/STOmics/STCellbin.