stlearn.add.positions

stlearn.add.positions(adata: anndata._core.anndata.AnnData, position_filepath: Union[pathlib.Path, str] = None, scale_filepath: Union[pathlib.Path, str] = None, quality: str = 'low', copy: bool = False) → Optional[anndata._core.anndata.AnnData][source]

Adding spatial information into the Anndata object

Parameters

  • adata – Annotated data matrix.

  • position_filepath – Path to tissue_positions_list file.

  • scale_filepath – Path to scalefactors_json file.

  • quality – Choosing low or high resolution image.

  • copy – Return a copy instead of writing to adata.

Returns

  • Depending on copy, returns or updates adata with the following fields.

  • **imagecol and imagerow** (adata.obs field) – Spatial information of the tissue image.