scanpy.datasets.visium_sge¶
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scanpy.datasets.visium_sge(sample_id='V1_Breast_Cancer_Block_A_Section_1', *, include_hires_tiff=False)¶ Processed Visium Spatial Gene Expression data from 10x Genomics. Database: https://support.10xgenomics.com/spatial-gene-expression/datasets
- Parameters
- sample_id : {‘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’}
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 :
boolbool(default:False) Download and include the high-resolution tissue image (tiff) in
adata.uns["spatial"][sample_id]["metadata"]["source_image_path"].
- sample_id : {‘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’}
- Return type
- Returns
Annotated data matrix.