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 into anndata.AnnData.uns ['spatial']['{sample_id}']['metadata']['source_image_path'].

  • base_dir (Union[PathLike, str, None]) – Directory where to download the data. If None, use scanpy._settings.ScanpyConfig.datasetdir.

Return type

AnnData

Returns

Spatial anndata.AnnData.