stlearn.pp.tiling

stlearn.pp.tiling(adata: anndata._core.anndata.AnnData, out_path: Union[pathlib.Path, str] = './tiling', library_id: str = None, crop_size: int = 40, target_size: int = 299, verbose: bool = False, copy: bool = False) → Optional[anndata._core.anndata.AnnData][source]

Tiling H&E images to small tiles based on spot spatial location

Parameters

  • adata – Annotated data matrix.

  • out_path – Path to save spot image tiles

  • library_id – Library id stored in AnnData.

  • crop_size – Size of tiles

  • verbose – Verbose output

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

  • target_size – Input size for convolutional neuron network

Returns

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

  • **tile_path** (adata.obs field) – Saved path for each spot image tiles