Installation and quickstart

Install from PyPI

pip install pyXenium

Install from source

git clone https://github.com/hutaobo/pyXenium
cd pyXenium
pip install -e ".[dev]"

Install the docs toolchain

pip install -e ".[docs]"

This installs the Sphinx-based documentation stack used by Read the Docs and local builds.

First examples

Xenium I/O

from pyXenium.io import read_xenium

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

Canonical multimodal loading

from pyXenium.multimodal import load_rna_protein_anndata

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

Multimodal workflow CLI

pyxenium multimodal validate-renal-ffpe-protein /path/to/xenium_export
pyxenium multimodal renal-immune-resistance-pilot /path/to/xenium_export

Build the docs locally

sphinx-build -b html docs docs/_build/html -W --keep-going

The docs should build without relying on MkDocs or GitHub Pages.