AtlasXbrowser enables spatial multi-omics data analysis through the precise determination of the region of interest

Abstract

Recent developments in novel spatial sequencing technologies allow for the incorporation of spatial information into high-throughput sequencing assays. One such method, Deterministic Barcoding in Tissue for spatial omics sequencing (DBiT-seq, abbreviated herein as DBiT), utilizes perpendicular microfluidic channels to deliver DNA barcodes across the tissue in a spatially-encoded manner, allowing for sequenced reads to be mapped back onto the 2-D coordinates of the tissue to provide spatial coordinates to cells. DBiT has been the first spatial sequencing technology developed for epigenomic assays beyond transcriptome and proteome. However, despite existing of many open-source software packages for downstream bioinformatics analysis, there is no software available for processing DBiT image data with evenly spaced channels. To facilitate the integration of DBiT spatial and sequenced data, here we proposed a new method to precisely capture the spatial information and further developed AtlasXbrowser based on the new method to extract spatial data from the image data. AtlasXbrowser is a python-based tool with GUI that requires no technical expertise to operate and enables researchers to incorporate brightfield and epifluorescence images of processed tissue samples into downstream bioinformatics analysis tools. Availability and implementationFreely available at https://github.com/atlasxomics/AtlasXbrowser.