Xenium Python Packages

spatioloji-s

Python toolkit for image-based spatial transcriptomics (CosMx, MERFISH, Xenium). Unified data object for expression, polygons, and FOV images, plus QC, clustering, point- and polygon-based spatial statistics, and polygon-native cell-cell communication using real membrane contact geometry.

llm-sc-curator

Data-centric marker distillation for zero-shot cell-type and spatial annotation with LLMs.

cell-gps

Cell-GPS spatial topology analysis for spatial omics data.

palms

A napari-based viewer for Xenium 3.x spatial transcriptomics that records every action as a provenance graph and exports it as a replayable Jupyter notebook.

histoseg

Python toolkit for H&E image analysis, spatial contour analysis, and 3D contour reconstruction.