scvi.data.smfish

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scvi.data.smfish#

scvi.data.smfish(save_path='data/', use_high_level_cluster=True)[source]#

Loads osmFISH data of mouse cortex cells from the Linarsson lab.

Parameters:

  • save_path (str (default: 'data/')) – Location to use when saving/loading the data.

  • use_high_level_cluster (bool (default: True)) – If True, use higher-level agglomerate clusters. The resulting cell types are “Astrocytes”, “Endothelials”, “Inhibitory”, “Microglias”, “Oligodendrocytes” and “Pyramidals”.

Return type:

AnnData

Returns:

AnnData with batch info (.obs['batch']), label info (.obs['labels']), spatial info (.obs['x_coord'], .obs['y_coord'])

Examples

>>> import scvi
>>> adata = scvi.data.smfish()
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