wsidata.agg_wsi

agg_wsi(slides_table, feature_key, tile_key='tiles', agg_key=None, agg_by=None, wsi_col=None, store_col=None, pbar=False, error='raise')

Aggregate feature from a whole slide image.

Parameters:

slides_table: pd.DataFrame

The table of slides, including information of whole slide image and .zarr paths and metadata.

Backed file path to the SpatialData file is optional, by default the same directory as the whole slide image.

feature_key: str

The feature key on which aggregation should be run on.

tile_key: str

The tile key.

agg_key: str

The output aggregation key in the varm slot.

agg_by: str or array of str

The keys that have been used to aggregate the features.

wsi_col: str

The column name of the whole slide image paths.

store_col: str

The column name of the backed file.

pbar: bool, default: False

Whether to show progress bar.

error: str

Whether to raise error when file not existed.

Returns:

AnnData

The aggregated feature space.