Skip to content

Data Format

Note: This method requires at least the H&E high-resolution image and X and Y coordinates extracted through segmentation (see the tutorial on extracting embeddings from H&E only). Paired ST data is optional.

The method requires:

  • Image (WSI): (n_px_height, n_px_width)
  • Coordinates of cells in image space: (n_cells, 2)

If providing paired ST data, the method accepts an AnnData object. At minimum, the adata object must contain:

  • adata.obsm['spatial_px']: this should contain the X and Y coordinates of the cell/nuclei centroid in the high-resolution pixel space of the associated WSI. This is the default key expected by SpatialFusion; if your AnnData uses a different key, pass spatial_key=<your_key> to run_full_embedding (check available keys with list(adata.obsm.keys())).
  • adata.X: this should be the cell x gene matrix of raw counts (! this needs to be single-cell resolution data)
  • (optional): adata.obs['celltypes']: the annotated cell types. This is the default key; if your AnnData uses a different column name, pass celltype_key=<your_key> to run_full_embedding (check available columns with adata.obs.columns.tolist()).

SpatialFusion expects preprocessed and aligned data.