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  • Installation and quickstart
  • Tutorials
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Section Navigation

  • pyXenium.io
    • pyXenium.io.read_xenium
    • pyXenium.io.write_xenium
    • pyXenium.io.read_slide
    • pyXenium.io.load_anndata_from_partial
    • pyXenium.io.export_xenium_to_slide_zarr
    • pyXenium.io.load_xenium_gene_protein
    • pyXenium.io.XeniumSlide
    • pyXenium.io.XeniumImage
  • pyXenium.multimodal
    • pyXenium.multimodal.load_rna_protein_anndata
    • pyXenium.multimodal.rna_protein_cluster_analysis
    • pyXenium.multimodal.protein_gene_correlation
    • pyXenium.multimodal.ProteinMicroEnv
    • pyXenium.multimodal.annotate_joint_cell_states
    • pyXenium.multimodal.compute_rna_protein_discordance
    • pyXenium.multimodal.build_spatial_niches
    • pyXenium.multimodal.score_immune_resistance_program
    • pyXenium.multimodal.score_contour_boundary_programs
    • pyXenium.multimodal.HistoSegLazySlideConfig
    • pyXenium.multimodal.run_histoseg_lazyslide_structure_workflow
    • pyXenium.multimodal.histoseg_contours_to_image_table
    • pyXenium.multimodal.assign_tiles_to_histoseg_structures
    • pyXenium.multimodal.aggregate_structure_image_features
    • pyXenium.multimodal.export_for_stgpt
    • pyXenium.multimodal.import_stgpt_embeddings
    • pyXenium.multimodal.compare_programs_with_embeddings
    • pyXenium.multimodal.build_spatho_manifest
    • pyXenium.multimodal.aggregate_multi_sample_study
    • pyXenium.multimodal.run_validated_renal_ffpe_smoke
    • pyXenium.multimodal.run_renal_immune_resistance_pilot
    • pyXenium.multimodal.run_contour_boundary_ecology_pilot
  • pyXenium.cci
    • pyXenium.cci.cci_topology_analysis
  • pyXenium.pathway
    • pyXenium.pathway.pathway_topology_analysis
    • pyXenium.pathway.compute_pathway_activity_matrix
  • pyXenium.contour
    • pyXenium.contour.add_contours_from_geojson
    • pyXenium.contour.build_contour_feature_table
    • pyXenium.contour.compare_contour_cell_composition
    • pyXenium.contour.compare_contour_de
    • pyXenium.contour.compare_contour_transcript_de
    • pyXenium.contour.expand_contours
    • pyXenium.contour.generate_barrier_contour_shells
    • pyXenium.contour.generate_contour_shells
    • pyXenium.contour.generate_xenium_explorer_annotations
    • pyXenium.contour.ring_density
    • pyXenium.contour.smooth_density_by_distance
    • pyXenium.contour.summarize_contour_composition
    • pyXenium.contour.summarize_contour_topology
  • pyXenium.gmi
    • pyXenium.gmi.ContourGmiConfig
    • pyXenium.gmi.ContourGmiDataset
    • pyXenium.gmi.ContourGmiResult
    • pyXenium.gmi.GmiModuleConfig
    • pyXenium.gmi.GmiModuleResult
    • pyXenium.gmi.build_contour_gmi_dataset
    • pyXenium.gmi.run_contour_gmi
    • pyXenium.gmi.run_atera_breast_contour_gmi
    • pyXenium.gmi.build_gmi_effect_graph
    • pyXenium.gmi.discover_gmi_modules
    • pyXenium.gmi.score_gmi_modules
    • pyXenium.gmi.render_gmi_module_report
    • pyXenium.gmi.render_contour_gmi_report
  • pyXenium.mechanostress
    • pyXenium.mechanostress.AxisStrengthConfig
    • pyXenium.mechanostress.TumorStromaGrowthConfig
    • pyXenium.mechanostress.PolarityConfig
    • pyXenium.mechanostress.MechanostressConfig
    • pyXenium.mechanostress.MechanostressCohortResult
    • pyXenium.mechanostress.MechanostressResult
    • pyXenium.mechanostress.estimate_cell_axes
    • pyXenium.mechanostress.summarize_axial_orientation
    • pyXenium.mechanostress.compute_ane_density
    • pyXenium.mechanostress.classify_tumor_stroma_growth
    • pyXenium.mechanostress.summarize_tumor_growth
    • pyXenium.mechanostress.compute_distance_expression_coupling
    • pyXenium.mechanostress.compute_cell_polarity
    • pyXenium.mechanostress.summarize_cell_polarity
    • pyXenium.mechanostress.run_mechanostress_cohort
    • pyXenium.mechanostress.run_mechanostress_workflow
    • pyXenium.mechanostress.write_mechanostress_artifacts
    • pyXenium.mechanostress.render_mechanostress_report
    • pyXenium.mechanostress.validate_hnscc_mechanostress_outputs
    • pyXenium.mechanostress.validate_suzuki_luad_mechanostress_outputs
    • pyXenium.mechanostress.AxisStrengthConfig
    • pyXenium.mechanostress.TumorStromaGrowthConfig
    • pyXenium.mechanostress.PolarityConfig
    • pyXenium.mechanostress.MechanostressConfig
    • pyXenium.mechanostress.MechanostressCohortResult
    • pyXenium.mechanostress.MechanostressResult
    • pyXenium.mechanostress.estimate_cell_axes
    • pyXenium.mechanostress.summarize_axial_orientation
    • pyXenium.mechanostress.compute_ane_density
    • pyXenium.mechanostress.classify_tumor_stroma_growth
    • pyXenium.mechanostress.summarize_tumor_growth
    • pyXenium.mechanostress.compute_distance_expression_coupling
    • pyXenium.mechanostress.compute_cell_polarity
    • pyXenium.mechanostress.summarize_cell_polarity
    • pyXenium.mechanostress.run_mechanostress_cohort
    • pyXenium.mechanostress.run_mechanostress_workflow
    • pyXenium.mechanostress.write_mechanostress_artifacts
    • pyXenium.mechanostress.render_mechanostress_report
    • pyXenium.mechanostress.validate_hnscc_mechanostress_outputs
    • pyXenium.mechanostress.validate_suzuki_luad_mechanostress_outputs
  • pyXenium.perturb
  • API reference
  • pyXenium.pathway

pyXenium.pathway#

pathway_topology_analysis

Compute pathway-level topology in two coordinated views: gene-topology aggregate and activity point cloud.

compute_pathway_activity_matrix

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