squidpy.datasets.visium
- squidpy.datasets.visium(sample_id, *, include_hires_tiff=False, base_dir=None)[source]
Download Visium datasets from 10x Genomics.
- 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'
,'Visium_FFPE_Mouse_Brain'
,'Visium_FFPE_Mouse_Brain_IF'
,'Visium_FFPE_Mouse_Kidney'
,'Visium_FFPE_Human_Breast_Cancer'
,'Visium_FFPE_Human_Prostate_Acinar_Cell_Carcinoma'
,'Visium_FFPE_Human_Prostate_Cancer'
,'Visium_FFPE_Human_Prostate_IF'
,'Visium_FFPE_Human_Normal_Prostate'
]) – Name of the Visium dataset.include_hires_tiff (
bool
) – Whether to download the high-resolution tissue section intoanndata.AnnData.uns
['spatial']['{sample_id}']['metadata']['source_image_path']
.base_dir (
Union
[PathLike
[str
],str
,None
]) – Directory where to download the data. If None, usescanpy._settings.ScanpyConfig.datasetdir
.
- Return type:
- Returns:
: Spatial
anndata.AnnData
.