loki.decompose.cell_type_decompose

loki.decompose.cell_type_decompose(sc_ad, st_ad, cell_type_col='cell_type', NMS_mode=False, major_types=None, min_percentile=5, max_percentile=95)

Performs cell type decomposition on spatial data (ST or image) with single-cell data .

Parameters:

  • sc_ad – AnnData object containing single-cell meta data.

  • st_ad – AnnData object containing spatial data (ST or image) meta data.

  • cell_type_col – The column name in sc_ad.obs that contains cell type annotations. Default is ‘cell_type’.

  • NMS_mode – Boolean flag to apply Non-Maximum Suppression (NMS) mode. Default is False.

  • major_types – Major cell types used for NMS mode. Default is None.

  • min_percentile – The lower percentile used for clipping (defaults to 5).

  • max_percentile – The upper percentile used for clipping (defaults to 95).

Returns:

The spatial AnnData object with projected cell type annotations.