Spatial transcriptomics atlas of inflammatory bowel disease to guide implementation in research consortiums and clinical trials.

Using over 100 intestinal tissue sections from non-diseased controls and patients with ulcerative colitis or Crohn's disease across multiple inflammatory bowel disease consortia, we construct a spatially resolved atlas containing over three million cells and systematically evaluate two imaging-based spatial transcriptomics platforms. Here we show that CosMx tends to achieve higher detection efficiency than Xenium across commercially available panels in both ulcerative colitis and Crohn's disease, whereas Xenium shows reduced performance associated with tissue type, block quality, and panel size. CosMx identifies regulatory T cell associated biology in both disease subtypes, which we validate using independent laboratory experiments and multi-plex spatial multi-omics. CosMx's data quality remains stable across variation in fixation time and sectioning procedures, supporting its operational feasibility for multi-center studies. This study establishes a technical and biological benchmark for the application of single-cell-resolved spatial transcriptomics in gastrointestinal tissue, enabling more reliable application of spatial technologies in translational inflammatory bowel disease research.