Index _ | A | B | C | D | E | F | G | H | I | K | L | M | N | O | P | R | S | T | V | W | X | Y _ __init__() (AxisStrengthConfig method) (ContourGmiConfig method) (ContourGmiDataset method) (ContourGmiResult method) (GmiModuleConfig method) (GmiModuleResult method) (HistoSegLazySlideConfig method) (MechanostressCohortResult method) (MechanostressConfig method) (MechanostressResult method) (PolarityConfig method) (ProteinMicroEnv method) (TumorStromaGrowthConfig method) (XeniumImage method) (XeniumSlide method) A adata (ProteinMicroEnv attribute) add_contours_from_geojson() (in module pyXenium.contour) aggregate_multi_sample_study() (in module pyXenium.multimodal) aggregate_structure_image_features() (in module pyXenium.multimodal) alignment_csv_path (XeniumImage attribute) amp (HistoSegLazySlideConfig attribute) analyze() (ProteinMicroEnv method) anchor_merge_correlation (GmiModuleConfig attribute) angle_col (AxisStrengthConfig attribute) annotate_joint_cell_states() (in module pyXenium.multimodal) annotation_col (TumorStromaGrowthConfig attribute) assign_tiles_to_histoseg_structures() (in module pyXenium.multimodal) axes (XeniumImage attribute) axis (MechanostressConfig attribute) axis_strength_by_radius (MechanostressResult attribute) AxisStrengthConfig (class in pyXenium.mechanostress) B batch_size (HistoSegLazySlideConfig attribute) bootstrap_fraction (ContourGmiConfig attribute) bootstrap_repeats (ContourGmiConfig attribute) build_contour_feature_table() (in module pyXenium.contour) build_contour_gmi_dataset() (in module pyXenium.gmi) build_gmi_effect_graph() (in module pyXenium.gmi) build_kdtree_full() (ProteinMicroEnv method) build_spatho_manifest() (in module pyXenium.multimodal) build_spatial_graph() (ProteinMicroEnv method) build_spatial_niches() (in module pyXenium.multimodal) build_spatialperturb_handoff() (in module pyXenium.perturb) C cache_dir (SpatialPerturbBridgeConfig attribute) cci_topology_analysis() (in module pyXenium.cci) cell_axes (MechanostressResult attribute) cell_group_path (SpatialPerturbBridgeConfig attribute) cell_id_col (PolarityConfig attribute) (TumorStromaGrowthConfig attribute) cell_polarity (MechanostressResult attribute) cell_query (AxisStrengthConfig attribute) classify_tumor_stroma_growth() (in module pyXenium.mechanostress) cluster_key (ProteinMicroEnv attribute) compare_contour_cell_composition() (in module pyXenium.contour) compare_contour_de() (in module pyXenium.contour) compare_contour_transcript_de() (in module pyXenium.contour) compare_programs_with_embeddings() (in module pyXenium.multimodal) component_summary() (XeniumSlide method) compute_ane_density() (in module pyXenium.mechanostress) compute_cell_polarity() (in module pyXenium.mechanostress) compute_distance_expression_coupling() (in module pyXenium.mechanostress) compute_pathway_activity_matrix() (in module pyXenium.pathway) compute_rna_protein_discordance() (in module pyXenium.multimodal) config (ContourGmiDataset attribute) (MechanostressResult attribute) contour_coordinate_space (HistoSegLazySlideConfig attribute) contour_geojson (ContourGmiConfig attribute) (HistoSegLazySlideConfig attribute) contour_id_key (ContourGmiConfig attribute) (HistoSegLazySlideConfig attribute) contour_images (XeniumSlide attribute) contour_key (ContourGmiConfig attribute) (HistoSegLazySlideConfig attribute) contour_label_col (ContourGmiConfig attribute) contour_pixel_size_um (ContourGmiConfig attribute) (HistoSegLazySlideConfig attribute) ContourGmiConfig (class in pyXenium.gmi) ContourGmiDataset (class in pyXenium.gmi) ContourGmiResult (class in pyXenium.gmi) coordinate_shuffle (ContourGmiConfig attribute) copy_with() (AxisStrengthConfig method) (ContourGmiConfig method) (GmiModuleConfig method) (MechanostressConfig method) (PolarityConfig method) (TumorStromaGrowthConfig method) coupling_genes (MechanostressConfig attribute) cv_metrics (ContourGmiResult attribute) D de_within_cluster() (ProteinMicroEnv method) device (HistoSegLazySlideConfig attribute) discover_gmi_modules() (in module pyXenium.gmi) distance_expression_coupling (MechanostressResult attribute) dtype (XeniumImage attribute) E ebic_gamma (ContourGmiConfig attribute) effect_graph_edges (GmiModuleResult attribute) effect_graph_nodes (GmiModuleResult attribute) er_threshold (AxisStrengthConfig attribute) errors (MechanostressCohortResult attribute) estimate_cell_axes() (in module pyXenium.mechanostress) eta (ContourGmiConfig attribute) exclude_coordinate_spatial_features (ContourGmiConfig attribute) expand_contours() (in module pyXenium.contour) expansion_correlation (GmiModuleConfig attribute) expansion_spatial_lag_correlation (GmiModuleConfig attribute) export_for_stgpt() (in module pyXenium.multimodal) export_xenium_to_slide_zarr() (in module pyXenium.io) F feature_count (ContourGmiConfig attribute) feature_metadata (ContourGmiDataset attribute) files (ContourGmiResult attribute) (GmiModuleResult attribute) (MechanostressCohortResult attribute) (MechanostressResult attribute) force_reinstall_gmi (ContourGmiConfig attribute) G generate_barrier_contour_shells() (in module pyXenium.contour) generate_contour_shells() (in module pyXenium.contour) generate_xenium_explorer_annotations() (in module pyXenium.contour) GmiModuleConfig (class in pyXenium.gmi) GmiModuleResult (class in pyXenium.gmi) groupby (AxisStrengthConfig attribute) groups (ContourGmiResult attribute) H he_image_key (HistoSegLazySlideConfig attribute) he_source_path (HistoSegLazySlideConfig attribute) heterogeneity (ContourGmiResult attribute) heterogeneity_min_contours (ContourGmiConfig attribute) histoseg_contours_to_image_table() (in module pyXenium.multimodal) HistoSegLazySlideConfig (class in pyXenium.multimodal) I image_to_xenium_affine (XeniumImage attribute) image_xy_to_xenium_pixel_xy() (XeniumImage method) image_xy_to_xenium_um_xy() (XeniumImage method) images (XeniumSlide attribute) import_stgpt_embeddings() (in module pyXenium.multimodal) include_boundary_programs (HistoSegLazySlideConfig attribute) include_pathomics (ContourGmiConfig attribute) include_prediction_benchmark (HistoSegLazySlideConfig attribute) include_rna (HistoSegLazySlideConfig attribute) include_spatial_features (GmiModuleConfig attribute) include_wta_programs (HistoSegLazySlideConfig attribute) infer_level_downsamples() (XeniumImage method) inner_rim_um (ContourGmiConfig attribute) inspect_wsi() (XeniumSlide method) install_gmi (ContourGmiConfig attribute) install_requirement (SpatialPerturbBridgeConfig attribute) interaction_effects (ContourGmiResult attribute) K keypoints_validation (XeniumImage attribute) L lambda_min_ratio (ContourGmiConfig attribute) layer (ContourGmiConfig attribute) level_chunk_shapes() (XeniumImage method) levels (XeniumImage attribute) load_anndata_from_partial() (in module pyXenium.io) load_rna_protein_anndata() (in module pyXenium.multimodal) load_xenium_gene_protein() (in module pyXenium.io) local_k (AxisStrengthConfig attribute) M main_effects (ContourGmiResult attribute) max_features_per_module (GmiModuleConfig attribute) max_iter (ContourGmiConfig attribute) max_tiles (HistoSegLazySlideConfig attribute) MechanostressCohortResult (class in pyXenium.mechanostress) MechanostressConfig (class in pyXenium.mechanostress) MechanostressResult (class in pyXenium.mechanostress) metadata (XeniumImage attribute) (XeniumSlide attribute) method (TumorStromaGrowthConfig attribute) microenv_predict_from_comp() (ProteinMicroEnv method) min_abs_anchor_coefficient (GmiModuleConfig attribute) min_cells_per_contour (ContourGmiConfig attribute) min_feature_prevalence (ContourGmiConfig attribute) min_library_size (ContourGmiConfig attribute) min_stability_frequency (GmiModuleConfig attribute) model (HistoSegLazySlideConfig attribute) module_enrichment (GmiModuleResult attribute) module_features (GmiModuleResult attribute) module_interactions (GmiModuleResult attribute) module_prefix (GmiModuleConfig attribute) module_scores (GmiModuleResult attribute) module_spatial_autocorr (GmiModuleResult attribute) mpp (HistoSegLazySlideConfig attribute) multiscale_shapes() (XeniumImage method) N n_lambda (ContourGmiConfig attribute) negative_label (ContourGmiConfig attribute) neighbor_composition_global() (ProteinMicroEnv method) neighbor_enrichment_from_comp() (ProteinMicroEnv method) normalize_protein() (ProteinMicroEnv method) O obs_xy (ProteinMicroEnv attribute) offset_norm_threshold (PolarityConfig attribute) orientation_summary (MechanostressResult attribute) outer_rim_um (ContourGmiConfig attribute) output_dir (ContourGmiResult attribute) (GmiModuleResult attribute) (HistoSegLazySlideConfig attribute) (MechanostressCohortResult attribute) (MechanostressResult attribute) (SpatialPerturbBridgeConfig attribute) P pathway_topology_analysis() (in module pyXenium.pathway) penalty (ContourGmiConfig attribute) pixel_size_um (XeniumImage attribute) plot_spatial() (ProteinMicroEnv method) point_sources (XeniumSlide attribute) points (XeniumSlide attribute) polarity (MechanostressConfig attribute) polarity_summary (MechanostressResult attribute) PolarityConfig (class in pyXenium.mechanostress) positive_label (ContourGmiConfig attribute) predictions (ContourGmiResult attribute) prepared_h5ad (SpatialPerturbBridgeConfig attribute) program_library (HistoSegLazySlideConfig attribute) prompt_review_status (HistoSegLazySlideConfig attribute) prompt_set_name (HistoSegLazySlideConfig attribute) prompt_source (HistoSegLazySlideConfig attribute) protein_gene_correlation() (in module pyXenium.multimodal) protein_moransI() (ProteinMicroEnv method) protein_norm_obsm (ProteinMicroEnv attribute) protein_obsm (ProteinMicroEnv attribute) ProteinMicroEnv (class in pyXenium.multimodal) provenance (ContourGmiDataset attribute) R r_lib_path (ContourGmiConfig attribute) radii_um (AxisStrengthConfig attribute) random_seed (ContourGmiConfig attribute) random_state (ProteinMicroEnv attribute) read_slide() (in module pyXenium.io) read_xenium() (in module pyXenium.io) reference_datasets (SpatialPerturbBridgeConfig attribute) relative_prompt_axes (HistoSegLazySlideConfig attribute) render_contour_gmi_report() (in module pyXenium.gmi) render_gmi_module_report() (in module pyXenium.gmi) render_mechanostress_report() (in module pyXenium.mechanostress) results (MechanostressCohortResult attribute) ring_density() (in module pyXenium.contour) rna_markers (HistoSegLazySlideConfig attribute) rna_protein_cluster_analysis() (in module pyXenium.multimodal) roi_geojson_path (SpatialPerturbBridgeConfig attribute) rscript (ContourGmiConfig attribute) run_atera_breast_contour_gmi() (in module pyXenium.gmi) run_contour_boundary_ecology_pilot() (in module pyXenium.multimodal) run_contour_gmi() (in module pyXenium.gmi) run_coordinate_shuffle_control (ContourGmiConfig attribute) run_histoseg_lazyslide_structure_workflow() (in module pyXenium.multimodal) run_label_permutation_control (ContourGmiConfig attribute) run_mechanostress_cohort() (in module pyXenium.mechanostress) run_mechanostress_workflow() (in module pyXenium.mechanostress) run_renal_immune_resistance_pilot() (in module pyXenium.multimodal) run_spatial_feature_shuffle_control (ContourGmiConfig attribute) run_validated_renal_ffpe_smoke() (in module pyXenium.multimodal) run_within_label_heterogeneity (ContourGmiConfig attribute) S sample_id (MechanostressConfig attribute) sample_metadata (ContourGmiDataset attribute) sample_name (SpatialPerturbBridgeConfig attribute) score_contour_boundary_programs() (in module pyXenium.multimodal) score_gmi_modules() (in module pyXenium.gmi) score_immune_resistance_program() (in module pyXenium.multimodal) shapes (XeniumSlide attribute) slide_mpp (HistoSegLazySlideConfig attribute) smooth_density_by_distance() (in module pyXenium.contour) source_path (XeniumImage attribute) spatial_cv_folds (ContourGmiConfig attribute) spatial_feature_count (ContourGmiConfig attribute) spatial_modules (GmiModuleResult attribute) spatial_neighbor_k (GmiModuleConfig attribute) spatial_obsm (ProteinMicroEnv attribute) spatialperturb_status() (in module pyXenium.perturb) SpatialPerturbBridgeConfig (class in pyXenium.perturb) split_high_low() (ProteinMicroEnv method) stability (ContourGmiResult attribute) stroma_label (TumorStromaGrowthConfig attribute) subset() (ContourGmiDataset method) summarize_axial_orientation() (in module pyXenium.mechanostress) summarize_cell_polarity() (in module pyXenium.mechanostress) summarize_contour_composition() (in module pyXenium.contour) summarize_contour_topology() (in module pyXenium.contour) summarize_tumor_growth() (in module pyXenium.mechanostress) summary (ContourGmiResult attribute) (GmiModuleResult attribute) (MechanostressCohortResult attribute) (MechanostressResult attribute) T table (XeniumSlide attribute) table_format (HistoSegLazySlideConfig attribute) table_map() (MechanostressResult method) text_model (HistoSegLazySlideConfig attribute) text_terms (HistoSegLazySlideConfig attribute) tile_px (HistoSegLazySlideConfig attribute) to_anndata() (XeniumSlide method) to_dict() (AxisStrengthConfig method) (ContourGmiConfig method) (GmiModuleConfig method) (HistoSegLazySlideConfig method) (MechanostressConfig method) (PolarityConfig method) (TumorStromaGrowthConfig method) to_numpy_levels() (XeniumImage method) to_spatialdata() (XeniumSlide method) to_wsi_spatialdata() (XeniumSlide method) to_wsidata() (XeniumSlide method) transform_kind (XeniumImage attribute) transform_metadata() (XeniumImage method) tumor_growth_cells (MechanostressResult attribute) tumor_growth_summary (MechanostressResult attribute) tumor_label (TumorStromaGrowthConfig attribute) tumor_stroma (MechanostressConfig attribute) TumorStromaGrowthConfig (class in pyXenium.mechanostress) tune (ContourGmiConfig attribute) V validate_hnscc_mechanostress_outputs() (in module pyXenium.mechanostress) validate_suzuki_luad_mechanostress_outputs() (in module pyXenium.mechanostress) visualization_genes (ContourGmiConfig attribute) W write_figures (GmiModuleConfig attribute) write_mechanostress_artifacts() (in module pyXenium.mechanostress) write_spatial_visualizations (ContourGmiConfig attribute) write_spatialperturb_handoff() (in module pyXenium.perturb) write_xenium() (in module pyXenium.io) wsi_diagnostics() (XeniumImage method) wsi_reader (HistoSegLazySlideConfig attribute) wta_program_library (HistoSegLazySlideConfig attribute) X X (ContourGmiDataset attribute) x_col (AxisStrengthConfig attribute) (TumorStromaGrowthConfig attribute) xenium_path (SpatialPerturbBridgeConfig attribute) xenium_pixel_xy_to_image_xy() (XeniumImage method) xenium_um_to_image_xy() (XeniumImage method) XeniumImage (class in pyXenium.io) XeniumSlide (class in pyXenium.io) Y y (ContourGmiDataset attribute) y_col (AxisStrengthConfig attribute) (TumorStromaGrowthConfig attribute)
