Xenium data loading

Use pyXenium.io when you want low-level Xenium artifact access and pyXenium.multimodal when you want the canonical RNA + protein AnnData used by downstream joint analyses.

XeniumSlide route

from pyXenium.io import read_xenium

slide = read_xenium(
    "/path/to/xenium_export",
    as_="slide",
    prefer="zarr",
)

This route is the right choice when you want images, shapes, points, and table-level metadata together.

XeniumSlide is inspired by the data-container ideas documented by SpatialData, but pyXenium rewrites the container and on-disk slide store independently and does not require the spatialdata package for core slide I/O. The only bridge back to that ecosystem is the optional XeniumSlide.to_spatialdata() method for users who install spatialdata separately.

Canonical multimodal AnnData route

from pyXenium.multimodal import load_rna_protein_anndata

adata = load_rna_protein_anndata(
    base_path="/path/to/xenium_export",
    prefer="auto",
)

This route is the right choice when you want the package-standard RNA + protein matrix for multimodal clustering, protein-gene correlation, or immune-resistance workflows.