stlearn.ReadSeqFish

stlearn.ReadSeqFish(count_matrix_file: Union[str, Path], spatial_file: Union[str, Path], library_id: Optional[str] = None, scale: float = 1.0, quality: str = 'hires', field: int = 0, spot_diameter_fullres: float = 50, background_color: ['black', 'white'] = 'white') → AnnData[source]

Read SeqFish data

Parameters:

  • count_matrix_file – Path to count matrix file.

  • spatial_file – Path to spatial location file.

  • library_id – Identifier for the visium 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’]

  • field – Set field of view for SeqFish data

  • spot_diameter_fullres – Diameter of spot in full resolution

  • background_color – Color of the backgound. Only black or white is allowed.

Return type:

AnnData