stlearn.add.parsing

stlearn.add.parsing(adata: anndata._core.anndata.AnnData, coordinates_file: Union[pathlib.Path, str], copy: bool = True) → Optional[anndata._core.anndata.AnnData][source]

Parsing the old spaital transcriptomics data

Parameters

  • adata – Annotated data matrix.

  • coordinates_file – Coordinate file generated by st_spot_detector.

  • 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.