scmorph.qc.qc_images_by_dissimilarity

scmorph.qc.qc_images_by_dissimilarity(adata, qcadata, filter=True, threshold=0.05, **kwargs)

Perform QC of datasets using unsupervised, kNN-based distance filtering

Parameters:

adata AnnData

Single-cell data

qcadata AnnData

Image-level data

filter bool (default: True)

Whether to return filtered or unfiltered (i.e. only annotated) adatas

threshold float (default: 0.05)

Threshold for removal

Return type:

tuple[AnnData, AnnData]

Returns:

Tuple of single-cell and image-level adatas