scanpy.datasets.visium_sge

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scanpy.datasets.visium_sge#

scanpy.datasets.visium_sge(sample_id='V1_Breast_Cancer_Block_A_Section_1', *, include_hires_tiff=False)[source]#

Processed Visium Spatial Gene Expression data from 10x Genomics’ database.

Deprecated since version 1.11.0: Use squidpy.datasets.visium() instead.

The database can be browsed online to find the sample_id you want.

Parameters:
sample_id Literal['V1_Breast_Cancer_Block_A_Section_1', 'V1_Breast_Cancer_Block_A_Section_2', 'V1_Human_Heart', 'V1_Human_Lymph_Node', 'V1_Mouse_Kidney', 'V1_Adult_Mouse_Brain', 'V1_Mouse_Brain_Sagittal_Posterior', 'V1_Mouse_Brain_Sagittal_Posterior_Section_2', 'V1_Mouse_Brain_Sagittal_Anterior', 'V1_Mouse_Brain_Sagittal_Anterior_Section_2', 'V1_Human_Brain_Section_1', 'V1_Human_Brain_Section_2', 'V1_Adult_Mouse_Brain_Coronal_Section_1', 'V1_Adult_Mouse_Brain_Coronal_Section_2', 'Targeted_Visium_Human_Cerebellum_Neuroscience', 'Parent_Visium_Human_Cerebellum', 'Targeted_Visium_Human_SpinalCord_Neuroscience', 'Parent_Visium_Human_SpinalCord', 'Targeted_Visium_Human_Glioblastoma_Pan_Cancer', 'Parent_Visium_Human_Glioblastoma', 'Targeted_Visium_Human_BreastCancer_Immunology', 'Parent_Visium_Human_BreastCancer', 'Targeted_Visium_Human_OvarianCancer_Pan_Cancer', 'Targeted_Visium_Human_OvarianCancer_Immunology', 'Parent_Visium_Human_OvarianCancer', 'Targeted_Visium_Human_ColorectalCancer_GeneSignature', 'Parent_Visium_Human_ColorectalCancer'] (default: 'V1_Breast_Cancer_Block_A_Section_1')

The ID of the data sample in 10x’s spatial database.

include_hires_tiff bool (default: False)

Download and include the high-resolution tissue image (tiff) in adata.uns["spatial"][sample_id]["metadata"]["source_image_path"].

Return type:

AnnData

Returns:

Annotated data matrix.

Examples

>>> import scanpy as sc
>>> sc.datasets.visium_sge(sample_id="V1_Breast_Cancer_Block_A_Section_1")
AnnData object with n_obs × n_vars = 3798 × 36601
    obs: 'in_tissue', 'array_row', 'array_col'
    var: 'gene_ids', 'feature_types', 'genome'
    uns: 'spatial'
    obsm: 'spatial'
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