pyXenium.mechanostress

pyXenium.mechanostress is the canonical beta surface for morphology-derived mechanical stress analysis in Xenium data. It converts cell and nucleus boundaries into fibroblast axis strength, tumor-stroma growth patterning, and cell polarity outputs.

AxisStrengthConfig	Configuration for axial orientation and ANE density analysis.
TumorStromaGrowthConfig	Configuration for tumor-stroma growth pattern classification.
PolarityConfig	Configuration for cell/nucleus centroid polarity analysis.
MechanostressConfig	Configuration for the integrated mechanostress workflow.
MechanostressCohortResult	Per-sample mechanostress results and cohort-level artifact paths.
MechanostressResult	Computed mechanostress tables, summary metadata, and artifact paths.
estimate_cell_axes	Estimate per-cell axial orientation and elongation ratio from boundary vertices.
summarize_axial_orientation	Summarize global and local axial orientation coherence.
compute_ane_density	Compute Aligned Neighbour Energy density across radius-based neighborhoods.
classify_tumor_stroma_growth	Classify tumor cells as infiltrative or expanding from tumor-stroma geometry.
summarize_tumor_growth	Summarize infiltrative and expanding tumor fractions.
compute_distance_expression_coupling	Compute gene-wise Spearman coupling to tumor-stromal distance.
compute_cell_polarity	Compute cell polarity from cell and nucleus centroid offsets.
summarize_cell_polarity	Summarize polarized cell fractions and offset magnitudes.
run_mechanostress_cohort	Run the mechanostress workflow across sample directories and write cohort summaries.
run_mechanostress_workflow	Run the integrated mechanostress workflow on a XeniumSlide object or Xenium export path.
write_mechanostress_artifacts	Write the fixed mechanostress artifact set to disk.
render_mechanostress_report	Render a compact markdown report for mechanostress outputs.
validate_hnscc_mechanostress_outputs	Validate HNSCC tumor-stroma reference outputs or compare recomputed outputs.
validate_suzuki_luad_mechanostress_outputs	Validate Suzuki LUAD/TSU ER and ANE reference outputs or compare recomputed outputs.