Spatial transcriptomics
Xenium data analysis
Single-cell and subcellular spatial transcriptomics, analyzed end to end, from segmentation and cell typing to spatial niches and figures.
What Xenium measures
Xenium is an imaging-based, in situ platform. Gene-specific probes are imaged cycle by cycle directly in the tissue section, so every transcript is located with subcellular precision. Panels range from a few hundred genes to around 5,000, and the same section can be stained for morphology afterwards, which makes it straightforward to tie gene expression back to histology.
Strengths
- Single-cell and subcellular resolution across whole tissue sections
- Works with FFPE and fresh frozen tissue
- High sensitivity for targeted genes, including low-expressed markers
- Morphology stains and post-run H&E on the same section
- Panels can be customized with add-on genes
How we can help with Xenium data
Panel and study design
Choosing panels, add-on genes, controls and section layout so the experiment can answer your question.
QC and segmentation
Transcript quality filtering, negative-control checks and segmentation refinement using nuclear and membrane stains.
Cell typing
Clustering, marker-based annotation and reference mapping to single-cell atlases.
Spatial analysis
Neighbourhoods and niches, cell–cell proximity, spatially variable genes and ligand–receptor context.
Histology integration
Registering Xenium data to H&E or immunofluorescence and relating expression to tissue regions.
Figures and reporting
Publication-quality figures, methods text and reproducible Python or R notebooks.
Related technologies
Working with Xenium data?
Tell us about your samples, panel and question. The first consultation is free.