monkeybread.util.load_merscope

monkeybread.util.load_merscope(folder='.', transcript_locations=None, paths=None)

Loads data from MERSCOPE, in accordance to the folder structure of the FFPE data release.

Parameters:

  • folder (Optional[str] (default: '.')) – A path from the current working directory to the folder containing the MERSCOPE data.

  • paths (Optional[Dict[str, str]] (default: None)) – Paths to each of the files output by MERSCOPE. Defaults are cache: 'adata.h5ad', counts: 'cell_by_gene.csv', coordinates: 'cell_metadata.csv', and transcripts: 'detected_transcripts.csv'. Default values will be filled in if an incomplete dictionary is provided.

Return type:

AnnData

Returns:

: An annotated data matrix containing spatial data from MERSCOPE.