pyXenium#
Nine canonical sections for Xenium I/O, multimodal analysis, CCI, pathway topology, contour geometry, GMI inference, mechanostress analysis, and external workflow bridges.
pyXenium is a Python toolkit for 10x Genomics Xenium organized around nine major sections:
pyXenium.io, pyXenium.multimodal, pyXenium.cci,
pyXenium.pathway, pyXenium.contour, pyXenium.gmi,
pyXenium.mechanostress, the external AI pathology bridge via spatho,
and the Perturb-seq handoff bridge via pyXenium.perturb.
This site keeps those sections visible first, then maps them to tutorials, guides,
workflows, and API pages.
pyXenium’s nine-feature overview connects Xenium data loading, multimodal spatial analysis, topology-aware biology, contour-native inference, mechanostress analysis, and optional external workflow bridges.#
Version & Build#
Current repository version:
0.4.5Package index: PyPI
Documentation site: Read the Docs latest
Canonical build status: GitHub Actions CI
Releases: GitHub releases
Changelog: RTD changelog
License: GNU AGPL v3.0 only
Maintained by:
SPATHO AB
Nine core sections#
Load Xenium exports, recover partial bundles, round-trip XeniumSlide, and export compat stores.
Work with the canonical pyXenium.multimodal surface for RNA + protein preparation and joint analysis.
Walk through topology-native cell-cell interaction analyses and compare Atera breast benchmark outputs.
Connect pathway topology scoring to cell-state programs on the same Xenium study.
Generate HistoSeg-backed annotations, contour-level transcript summaries, and boundary-aware density profiles.
Build contour pseudo-bulk matrices and run GMI main-effect, interaction, and validation workflows.
Compute fibroblast axis strength, tumor-stroma growth patterning, and cell polarity from Xenium morphology.
Call the external spatho workflow on Xenium cases structured by pyXenium XeniumSlide.
Generate handoff specs for Perturb-seq reference projection with the external SpatialPerturb CLI.
Documentation entry points#
Install pyXenium, set up the docs environment, and run your first Xenium workflow.
Browse notebook-style walkthroughs for all nine sections, including the optional external bridges.
Read focused guides for Xenium I/O, multimodal preparation, contour analysis, and contour GMI inference.
Run packaged renal and Atera workflows with standardized artifact bundles and report-ready outputs.
Browse curated autosummary pages for the canonical pyXenium namespaces and the SpatialPerturb bridge helpers.
Track documentation, branding, and package-level changes.
Feature areas#
pyXenium.io: Xenium artifact loading, partial export recovery, XeniumSlide store I/O, and slide export.pyXenium.multimodal: canonical RNA + protein loading, immune-resistance scoring, joint analyses, and packaged multimodal workflows.pyXenium.cci: topology-native cell-cell interaction analysis primitives.pyXenium.pathway: pathway topology analysis and pathway activity scoring.pyXenium.contour: GeoJSON contour import and contour-aware density profiling around polygon annotations.pyXenium.gmi: contour-level GMI modeling for sparse main-effect and interaction discovery in spatial transcriptomics.pyXenium.mechanostress: morphology-derived mechanical stress states from cell/nucleus boundaries and tumor-stroma context.AI-Driven Spatial Pathologist via
spatho: optional external AI pathology review workflow built on pyXenium’sXeniumSlidecase structure, not a pyXenium runtime dependency.pyXenium.perturb: SpatialPerturb Bridge for optional Perturb-seq reference projection onto Xenium tissue through the externalSpatialPerturbpackage.