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Stereopy
Stereopy
  • Installation
  • Usage Principles
  • Tutorials (Multi-sample)
    • Quick Start (Multi-sample)
    • Batch QC
    • Batch Effect
    • Comparative Analysis
    • Time Series Analysis
    • 3D Cell-cell Communication
    • 3D Gene Regulatory Network
    • ST-Gears
  • Tutorials
    • Basic Workflow
      • Quick Start (Square Bin)
      • Quick Start (Cell Bin)
      • Input & Output
      • Format Conversion
      • Work with AnnData
    • Data Preprocessing
      • Gaussian Smoothing
      • scTransform
    • Annotation
      • SingleR
    • Cell Analysis
      • Cell-Cell Communication
      • Cell Co-occurrence
      • Cell Community Detection
    • Gene Analysis
      • Spatial Hotspot
      • Gene Regulatory Network
    • Cell Fate Inference
      • Trajectory Analysis
      • RNA Velocity
    • Image Processing
      • Tissue Segmentation
      • Cell Segmentation
      • Cell Correction
    • Interactive Visualization
      • High Resolution Matrix Export
    • Performance Optimization
      • Clustering by GPU
      • Performance
  • API
    • IO: io
      • stereo.core.StereoExpData
      • stereo.core.ms_data.MSData
      • stereo.io.read_gef_info
      • stereo.io.read_gem
      • stereo.io.read_gef
      • stereo.io.read_h5ad
      • stereo.io.read_ann_h5ad
      • stereo.io.read_stereo_h5ad
      • stereo.io.read_seurat_h5ad
      • stereo.io.anndata_to_stereo
      • stereo.io.stereo_to_anndata
      • stereo.io.write_h5ad
      • stereo.io.write_mid_gef
      • stereo.io.update_gef
      • stereo.io.read_h5ms
      • stereo.io.write_h5ms
      • stereo.core.ms_data.MSData.integrate
      • stereo.core.ms_data.MSData.to_integrate
      • stereo.core.ms_data.MSData.to_isolated
    • StPipeline: tl
      • stereo.core.StPipeline
      • stereo.core.StPipeline.cal_qc
      • stereo.core.StPipeline.filter_cells
      • stereo.core.StPipeline.filter_genes
      • stereo.core.StPipeline.filter_coordinates
      • stereo.core.StPipeline.filter_by_clusters
      • stereo.core.StPipeline.filter_marker_genes
      • stereo.core.StPipeline.filter_by_hvgs
      • stereo.core.StPipeline.raw_checkpoint
      • stereo.core.StPipeline.sctransform
      • stereo.core.StPipeline.normalize_total
      • stereo.core.StPipeline.log1p
      • stereo.core.StPipeline.scale
      • stereo.core.StPipeline.disksmooth_zscore
      • stereo.core.StPipeline.quantile
      • stereo.core.StPipeline.highly_variable_genes
      • stereo.core.StPipeline.pca
      • stereo.core.StPipeline.neighbors
      • stereo.core.StPipeline.spatial_neighbors
      • stereo.core.StPipeline.umap
      • stereo.core.StPipeline.leiden
      • stereo.core.StPipeline.louvain
      • stereo.core.StPipeline.phenograph
      • stereo.core.StPipeline.find_marker_genes
      • stereo.core.StPipeline.spatial_hotspot
      • stereo.core.StPipeline.batches_integrate
      • stereo.core.StPipeline.gaussian_smooth
      • stereo.core.StPipeline.annotation
      • stereo.core.StPipeline.adjusted_rand_score
      • stereo.core.StPipeline.silhouette_score
      • stereo.algorithm.single_r.SingleR.main
      • stereo.algorithm.batch_qc.BatchQc.main
      • stereo.algorithm.paste.Paste.main
      • stereo.algorithm.paste.pairwise_align
      • stereo.algorithm.paste.center_align
      • stereo.algorithm.get_niche.GetNiche.main
      • stereo.algorithm.gen_ccc_micro_envs.GenCccMicroEnvs.main
      • stereo.algorithm.cell_cell_communication.CellCellCommunication.main
      • stereo.algorithm.regulatory_network_inference.RegulatoryNetworkInference.main
      • stereo.algorithm.co_occurrence.CoOccurrence.main
      • stereo.algorithm.community_detection.CommunityDetection.main
      • stereo.algorithm.time_series_analysis.TimeSeriesAnalysis.main
      • stereo.algorithm.dendrogram.Dendrogram.main
      • stereo.algorithm.st_gears.StGears.main
      • stereo.algorithm.st_gears.StGears.stack_slices_pairwise_rigid
      • stereo.algorithm.st_gears.StGears.stack_slices_pairwise_elas_field
      • stereo.core.ms_pipeline.MSDataPipeLine.set_scope_and_mode
    • Plots: plt
      • stereo.plots.PlotCollection.cells_plotting
      • stereo.plots.PlotCollection.cluster_scatter
      • stereo.plots.PlotCollection.gaussian_smooth_scatter_by_gene
      • stereo.plots.PlotCollection.genes_count
      • stereo.plots.PlotCollection.highly_variable_genes
      • stereo.plots.PlotCollection.hotspot_local_correlations
      • stereo.plots.PlotCollection.hotspot_modules
      • stereo.plots.PlotCollection.interact_cluster
      • stereo.plots.PlotCollection.interact_spatial_scatter
      • stereo.plots.PlotCollection.interact_annotation_cluster
      • stereo.plots.PlotCollection.marker_genes_volcano
      • stereo.plots.PlotCollection.marker_genes_heatmap
      • stereo.plots.PlotCollection.marker_genes_text
      • stereo.plots.PlotCollection.marker_genes_scatter
      • stereo.plots.PlotCollection.spatial_scatter
      • stereo.plots.PlotCollection.spatial_scatter_by_gene
      • stereo.plots.PlotCollection.umap
      • stereo.plots.PlotCollection.batches_umap
      • stereo.plots.PlotCollection.violin
      • stereo.plots.PlotCellCellCommunication.ccc_dot_plot
      • stereo.plots.PlotCellCellCommunication.ccc_heatmap
      • stereo.plots.PlotCellCellCommunication.ccc_circos_plot
      • stereo.plots.PlotCellCellCommunication.ccc_sankey_plot
      • stereo.plots.PlotRegulatoryNetwork.auc_heatmap_by_group
      • stereo.plots.PlotRegulatoryNetwork.auc_heatmap
      • stereo.plots.PlotRegulatoryNetwork.grn_dotplot
      • stereo.plots.PlotRegulatoryNetwork.spatial_scatter_by_regulon_3D
      • stereo.plots.PlotRegulatoryNetwork.spatial_scatter_by_regulon
      • stereo.plots.PlotCoOccurrence.co_occurrence_plot
      • stereo.plots.PlotCoOccurrence.co_occurrence_heatmap
      • stereo.plots.PlotPaga.paga_plot
      • stereo.plots.PlotPaga.paga_compare
      • stereo.plots.PlotPaga.draw_graph
      • stereo.plots.PlotDendrogram.dendrogram
      • stereo.plots.ClustersGenesScatter.clusters_genes_scatter
      • stereo.plots.ClustersGenesHeatmap.clusters_genes_heatmap
      • stereo.plots.PlotTimeSeries.boxplot_transit_gene
      • stereo.plots.PlotTimeSeries.TVG_volcano_plot
      • stereo.plots.PlotTimeSeries.paga_time_series_plot
      • stereo.plots.PlotTimeSeries.fuzz_cluster_plot
      • stereo.plots.PlotTimeSeriesAnalysis.time_series_tree_plot
      • stereo.plots.PlotTimeSeriesAnalysis.ms_paga_time_series_plot
      • stereo.plots.PlotElbow.elbow
      • stereo.plots.PlotGenesInPseudotime.plot_genes_in_pseudotime
      • stereo.plots.PlotVec.plot_vec
      • stereo.plots.PlotVec.plot_time_scatter
      • stereo.plots.PlotVec3D.plot_vec_3d
      • stereo.plots.PlotMsSpatialScatter.ms_spatial_scatter
    • Image: im
      • stereo.image.pyramid.merge_pyramid
      • stereo.image.pyramid.create_pyramid
      • stereo.image.segmentation.segment.cell_seg
      • stereo.image.segmentation_deepcell.segment.cell_seg_deepcell
      • stereo.algorithm.cell_pose.Cellpose.__init__
      • stereo.image.tissue_cut.SingleStrandDNATissueCut.__init__
      • stereo.image.tissue_cut.RNATissueCut.__init__
    • Tools: tools
      • stereo.tools.cell_correct.cell_correct
      • stereo.tools.cell_cut.CellCut.cell_cut
      • stereo.tools.tissue_extraction.tissue_extraction_to_bgef
    • Utils: utils
      • stereo.utils.data_helper.merge
      • stereo.utils.data_helper.split
      • stereo.utils.cluster_bins_to_cellbins
  • Community
  • Contributing
  • Release Notes
  • References
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Interactive VisualizationΒΆ

This section shows how to perform interactive plotting and export the region of interest.

High Resolution Matrix Export
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High Resolution Matrix Export
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Cell Correction
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