API reference#

The API reference is organized around pyXenium’s canonical namespaces rather than the legacy compatibility facade.

pyXenium.io

Xenium artifact readers, XeniumSlide store helpers, and slide export utilities.

pyXenium.multimodal

Canonical RNA + protein preparation, analysis, immune-resistance scoring, and workflows.

pyXenium.cci

Topology-native cell-cell interaction analysis.

pyXenium.pathway

Pathway topology and activity scoring.

pyXenium.contour

GeoJSON contour import and contour-aware density profiling.

pyXenium.gmi

Contour-level GMI modeling for sparse main effects, interactions, controls, and reports.

pyXenium.mechanostress

Mechanical stress state analysis from Xenium morphology and tumor-stroma geometry.

pyXenium.perturb

SpatialPerturb Bridge handoff specs for optional Perturb-seq reference projection.