scvi.data.smfish

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

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

Parameters
save_path : strstr (default: 'data/')

Location to use when saving/loading the data.

use_high_level_cluster : boolbool (default: True)

If True, use higher-level agglomerate clusters. The resulting cell types are “Astrocytes”, “Endothelials”, “Inhibitory”, “Microglias”, “Oligodendrocytes” and “Pyramidals”.

run_setup_anndata : boolbool (default: True)

If true, runs setup_anndata() on dataset before returning

Return type

AnnDataAnnData

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()