spatialdata_io.dbit#
- spatialdata_io.dbit(path=None, anndata_path=None, barcode_position=None, image_path=None, dataset_id=None, border=True, border_scale=1)#
Read DBiT experiment data (Deterministic Barcoding in Tissue)
This function reads the following files:
'.h5ad'
: Counts matrix.'barcode_list'
: Barcode file.'tissue_lowres_image.png'
: Histological image | Optional.
- Parameters:
path (Optional[str | Path] (default:
None
)) – Path to the directory containing the data.anndata_path (Optional[str] (default:
None
)) – path to the counts and metadata file.barcode_position (Optional[str] (default:
None
)) – path to the barcode coordinates file.dataset_id (Optional[str] (default:
None
)) – Dataset identifier to name the constructedSpatialData
elements. If not given, filename is used as dataset_idimage_path (Optional[str] (default:
None
)) – path to the low resolution image. It expect the image to be correctly cropped and transformed.border (bool (default:
True
)) – Value passed internally to _xy2edges() If True, the square is shrinked toward its center, leaving an empty border.border_scale (float (default:
1
)) – Value passed internally to _xy2edges() The factor by which the border is scaled. The default is 1. It corresponds to a border length of (0.125 * length of the square’s edge)
- Return type:
SpatialData
- Returns: