pyXenium.contour#
The contour tutorials collect the workflows that turn Xenium Explorer annotations, HistoSeg-derived structures, and contour shells into spatial biology.
Basic Atera Contour Workflow
Generate HistoSeg-backed Atera breast contours, import Xenium Explorer annotations, expand boundaries, and profile shell-based marker densities.
S1-S5 Breast Contour Application
Aggregate Atera breast cancer cell groups into five contour classes, run transcript-level contour DEG, compare cell composition, and profile barrier-aware boundary density curves.
Boundary Ecology Tutorial
Combine contour-specific H&E patches with spatial transcriptomics to score tumor-boundary programs, match controls, and rank biological hypotheses.