dynamo.tl.scc(adata, min_cells=100, spatial_key='spatial', e_neigh=30, s_neigh=6, resolution=None, copy=False)[source]

Spatially constrained clustering (scc) to identify continuous tissue domains.

  • adata (AnnData) – A normalized AnnData object.

  • min_cells (int) – Minimal number of cells the gene expressed. Defaults to 100.

  • spatial_key (str) – The key in .obsm corresponding to the spatial coordinate of each bucket. Defaults to “spatial”.

  • e_neigh (int) – The number of nearest neighbor in gene expression space. Defaults to 30.

  • s_neigh (int) – The number of nearest neighbor in physical space. Defaults to 6.

  • resolution (Optional[float]) – The resolution parameter of the leiden clustering algorithm. Defaults to None.

  • copy (bool) – Whether to return a new deep copy of adata instead of updating adata object passed in arguments. Defaults to False.

Return type:



An updated AnnData object with cluster info stored in .obs[scc_e_{a}_s{b}] if copy is set to be true.