liana.ds.vicari_2024

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liana.ds.vicari_2024#

liana.ds.vicari_2024()#

Load a single spatial multimodal analysis (SMA) slide from Vicari et al., 2024.

The slide comes from a murine Parkinson’s disease model, in which one hemisphere was subjected to unilateral 6-hydroxydopamine-induced lesions while the other remained intact. Vicari, M., Mirzazadeh, R., Nilsson, A. et al. Spatial multimodal analysis of transcriptomes and metabolomes in tissues. Nat Biotechnol 42, 1046-1050 (2024). https://doi.org/10.1038/s41587-023-01937-y

Return type:

MuData

Returns:

Returns a MuData object with three modalities of the same slide: mod['rna'] with log1p-transformed 10X Visium counts, mod['msi'] with total-ion-count-normalised MALDI-MSI peaks, and mod['ct'] with the Tangram cell type proportions of the RNA modality. The MSI observations are not aligned to the Visium spots; aligning them is part of the corresponding tutorial.

Examples

This downloads ~165MB into scanpy.settings.datasetdir on first call, so it is not run here:

import liana as li

mdata = li.ds.vicari_2024()
rna, msi, ct = mdata.mod["rna"], mdata.mod["msi"], mdata.mod["ct"]
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