spatial-domain-detection
Installation
SKILL.md
Spatial Domain Detection
Overview
Split a tissue section into spatially coherent regions (cortical layers, tumour core vs stroma, germinal centres) from expression plus location. Each method returns one domain label per spot or cell. Output: domain labels from one or more methods, their agreement, domain marker genes and domain maps.
| Method | Data | Uses | Compute |
|---|---|---|---|
| SpaGCN | Visium / ST spots, optionally with the H&E image | Expression + spatial graph + histology colour | CPU, minutes |
| GraphST | Spots or cells up to ~30k observations | Contrastive graph embedding | GPU preferred (torch) |
| UTAG | Single-cell resolution (Xenium, MERFISH, CosMx, IMC) | Expression averaged over a radius | CPU, scales to 10^5-10^6 cells |
| Composition niches | Annotated single cells | Cell type mix of the neighbourhood | CPU; Step 7 of spatial-transcriptomics-cell-type-annotation |
Domains are clusters, not ground truth: run two methods and report where they agree.