Axel Rodríguez-Pérez https://axelrp.netlify.app/blog/ quarto-1.9.37 Sun, 26 Jul 2026 22:00:00 GMT Understanding Neighborhood Enrichment Analysis with Squidpy Axel R https://axelrp.netlify.app/blog/third-post/
WarningWork in progress

This site is still under development, so parts of it are rough. Check back for updates.

1 Why this notebook

Spatial transcriptomics tells you where cells sit in a tissue, not only what they express. Squidpy is one of the main Python libraries for analyzing that kind of data (the paper is here).

This guide covers one function: neighborhood enrichment analysis. It scores which pairs of cell types end up next to each other more often than you would expect by chance, which is where you start when asking about cell-cell interactions in a tissue.

The first time I ran it, I could not connect the output to anything biological. So I went digging into what the function computes, and this notebook is what came out of that.

Suggestions and questions are welcome in the comments.

2 Download the data

Following the Squidpy tutorial on analysis of Xenium data, we use a Xenium dataset of human lung cancer.

  1. Go to the dataset’s preview page.
  2. Under Output and supplemental files, download the Xenium Output Bundle (we use the full dataset).
  3. Unzip the downloaded file.
  4. Inside the unzipped folder, unzip all the .zip files as well.
# Load libraries
import spatialdata as sd
from spatialdata_io import xenium

import matplotlib.pyplot as plt
import seaborn as sns

import scanpy as sc
import squidpy as sq
/home/axel/miniconda3/envs/ne_analysis/lib/python3.12/site-packages/dask/dataframe/__init__.py:31: FutureWarning: The legacy Dask DataFrame implementation is deprecated and will be removed in a future version. Set the configuration option `dataframe.query-planning` to `True` or None to enable the new Dask Dataframe implementation and silence this warning.
  warnings.warn(
/home/axel/miniconda3/envs/ne_analysis/lib/python3.12/site-packages/xarray_schema/__init__.py:1: UserWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html. The pkg_resources package is slated for removal as early as 2025-11-30. Refrain from using this package or pin to Setuptools<81.
  from pkg_resources import DistributionNotFound, get_distribution
/home/axel/miniconda3/envs/ne_analysis/lib/python3.12/site-packages/anndata/__init__.py:44: FutureWarning: Importing read_text from `anndata` is deprecated. Import anndata.io.read_text instead.
  return module_get_attr_redirect(attr_name, deprecated_mapping=_DEPRECATED)
from pathlib import Path
import os
cwd = Path.cwd()
xenium_path = os.path.join(cwd, "data", "Xenium")
]]> Spatial Transcriptomics Xenium https://axelrp.netlify.app/blog/third-post/ Sun, 26 Jul 2026 22:00:00 GMT