stlearn.read_old_st

stlearn.read_old_st(count_matrix_file: PathLike[str] | str | Iterator[str], spatial_file: int | str | bytes | PathLike[str] | PathLike[bytes], image_file: str | Path | None = None, library_id: str = 'OldST', scale: float = 1.0, quality: str = 'hires', spot_diameter_fullres: float = 50) → AnnData[source]

Read Old Spatial Transcriptomics data

Parameters:

  • count_matrix_file – Path to count matrix file.

  • spatial_file – Path to the spatial location file.

  • image_file – Path to the tissue image file

  • library_id – Identifier for the library. Can be modified when concatenating multiple adata objects.

  • scale – Set scale factor.

  • quality – Set quality that convert to stlearn to use. Store in anndata.obs[‘imagecol’ & ‘imagerow’]

  • spot_diameter_fullres – Diameter of spot in full resolution

Return type:

AnnData