Overview
Processing
- 4 Cell segmentation and pre-processing
- 5 Quality Control
Cell annotation
- 6 Unsupervised clustering for cell annotation
- 7 Supervised cell annotation with a reference
Cell localisation
- 8 Cell localisation between pairs of cell types
- 9 Cell relationships relative to expected behaviour
Spatial domains
- 10 Identifying spatial domains with unsupervised clustering
Marker expression
- 11 Changes in marker expression
Classification
- 12 Finding associations between clinical variables and spatial features
Case studies
- 13 Case Study: Head and Neck Squamous Cell Carcinoma (Ferguson et al., 2022)
References
- References

References