scispy.io.load_merscope

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scispy.io.load_merscope#

scispy.io.load_merscope(path, slide_name, vpt_outputs=None, region_name='region_0', z_layers=2, feature_key='gene')#

Load vizgen merscope data as SpatialData object

Parameters:

  • path (str) – path to folder.

  • vpt_outputs (Optional[str] (default: None)) – path to vpt folder.

  • region_name (str (default: 'region_0')) – region_name id.

  • slide_name (str) – slide_name id.

  • z_layers (int (default: 2)) – z layers to load.

  • feature_key (str (default: 'gene')) – default column for feature name in transcripts.

Return type:

SpatialData

Returns:

SpatialData object

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