pyXenium.multimodal

load_rna_protein_anndata	Load a Xenium RNA + protein dataset into an AnnData object.
rna_protein_cluster_analysis	Joint RNA/protein analysis for Xenium AnnData objects.
protein_gene_correlation	Compute spatial correlation between protein intensity and transcript density.
ProteinMicroEnv	Microenvironment analysis for protein heterogeneity within an RNA cluster.
annotate_joint_cell_states	Annotate joint RNA/protein classes and subtypes using hierarchical rules.
compute_rna_protein_discordance	Compute marker-, state-, and pathway-level RNA/protein discordance scores.
build_spatial_niches	Build spatial niches from local composition of joint cell states.
score_immune_resistance_program	Score decoupled immune-resistance programs and ablations.
score_contour_boundary_programs	Score contour-level tumor boundary ecology programs.
HistoSegLazySlideConfig	Configuration for HistoSeg-anchored LazySlide image feature analysis.
run_histoseg_lazyslide_structure_workflow	Run a HistoSeg structure-to-H&E feature workflow with optional LazySlide.
histoseg_contours_to_image_table	Convert HistoSeg/pyXenium contour geometries from Xenium um to H&E pixels.
assign_tiles_to_histoseg_structures	Assign image tiles to HistoSeg structures using tile centroids.
aggregate_structure_image_features	Aggregate tile-level image features by HistoSeg structure.
export_for_stgpt	Write a lightweight pyXenium-to-stGPT handoff bundle.
import_stgpt_embeddings	Read stGPT embeddings and optionally attach cell embeddings to AnnData.
compare_programs_with_embeddings	Compare pyXenium interpretable program scores with external embeddings.
build_spatho_manifest	Build a SPatho-facing manifest without importing or running SPatho.
aggregate_multi_sample_study	Aggregate per-sample immune-resistance pilot outputs into cohort tables.
run_validated_renal_ffpe_smoke
run_renal_immune_resistance_pilot
run_contour_boundary_ecology_pilot