liana.ds.yao_2023

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liana.ds.yao_2023#

liana.ds.yao_2023()#

Load the WB_MERFISH_animal2_coronal slide of the whole mouse brain atlas from Yao et al., 2023.

The data was generated with MERFISH, which profiles the expression of more than 1,000 genes at subcellular spatial resolution. Yao, Z., van Velthoven, C.T.J., Kunst, M. et al. A high-resolution transcriptomic and spatial atlas of cell types in the whole mouse brain. Nature 624, 317-332 (2023). https://doi.org/10.1038/s41586-023-06808-9

The object is the CELLxGENE release of the dataset (https://cellxgene.cziscience.com/collections/0cca8620-8dee-45d0-aef5-23f032a5cf09).

Return type:

AnnData

Returns:

Returns the AnnData object as released on CELLxGENE: ~4M cells; ~1.1k genes indexed by Ensembl ID (with symbols in var['gene_name']), cell type annotations in obs, and the spatial coordinates in obsm['spatial'].

Examples

This downloads ~1GB into scanpy.settings.datasetdir on first call, so it is not run here:

import liana as li

adata = li.ds.yao_2023()

It is the dataset used in the inflow and LRIC tutorials.

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