stlearn.add.positions

stlearn.add.positions(adata: AnnData, position_filepath: Path | str, scale_filepath: Path | str, quality: str = 'low', copy: bool = False) → AnnData | None

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.