nf_xpatial: A Reproducible Framework for Standardized Preprocessing and Clustering of Xenium Data

Standardized bioinformatics workflows, however, have lagged behind these developments, with most available pipelines focusing on image processing and cell segmentation. To address this gap, we present nf_xpatial, a best-practices Nextflow pipeline for the downstream analysis of 10x Genomics Xenium data.

The pipeline performs quality control, filtering, log and cell-area normalization, multi-sample integration, and both expression-driven and spatially informed clustering across systematic parameter sweeps, allowing users to evaluate and compare clustering resolutions and spatial modeling parameters within a single reproducible run. Overall, nf_xpatial streamlines the processing of Xenium data from platform outputs to integrated single-cell and spatial clustering results, providing a standardized starting point from which biologists can fine-tune parameters and proceed to hypothesis-driven spatial analyses.