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 (
PathLike[str] |str|None) – Directory where to download the data. If None, usesscanpy.settings.datasetdir.
- Return type:
- Returns:
anndata.AnnDataSpatial AnnData object.