Spatial Comparison
Xenium vs. Visium vs. Visium HD
| Feature | Xenium | Visium | Visium HD |
|---|---|---|---|
| Resolution | Subcellular (~200 nm) | Low (~55-100 μm spots) | High (near single cell) |
| Throughput | Targeted panels (100s of genes) | Whole transcriptome | Whole transcriptome |
| Tissue Type | FFPE or FF | FFPE (via CytAssist) or FF | FFPE only or FF |
| Species Support | Human, mouse, other | Human, mouse, other | Human, mouse, other |
| Panel Type | Fixed/custom RNA probes | Whole transcriptome | Whole transcriptome |
| Imaging | High-res fluorescence imaging | Brightfield (H&E) imaging + expression overlay | Brightfield (H&E) image + finer-grained overlay |
| Output Data | Spatial gene counts at subcellular resolution via imaging | Spatial gene counts per 55-100 μm spot via NGS | Spatial gene counts per ~single cell region via NGS |
| Strengths | High-res cell-level biology, rare cell types | Broad transcriptome survey | High-res transcriptomics + full gene coverage |
| Data Size | Small-to-moderate (targeted) | Large (whole transcriptome) | Very large (high-res + whole transcriptome) |
| Ideal For | Cell interactions, FFPE pathology, defined gene sets | General tissue-level trends | Cell-level spatial studies with full gene coverage |
| Turnaround Time | ~2-3 weeks | ~2-3 weeks | ~2-3 weeks |
Choosing the Right Solution
- Xenium → Best for high-resolution, targeted panels and cellular-level insights.
- Visium → Ideal for broad transcriptome coverage or exploratory tissue mapping.
- Visium HD → Combines high spatial resolution with whole-transcriptome coverage—great for single-cell-like spatial analyses in FFPE tissues.
Have questions about which platform fits your project? We’re happy to help you choose the right solution based on your tissue, species, and scientific goals.