From 497dd6db4436f1bce75c8d1ea2fa3a5b267557c0 Mon Sep 17 00:00:00 2001
From: Lukas Heumos <lukas.heumos@posteo.net>
Date: Wed, 9 Sep 2026 18:31:37 +0200
Subject: [PATCH] Show one Xenium tutorial covering SpatialData and squidpy

Squidpy's Xenium notebook reads the dataset with spatialdata-io into a
SpatialData object and then runs quality control, clustering and spatial
statistics, so it covers both packages. It replaces the SpatialData reading
notebook, which it supersedes.
---
 .../tutorials/spatialdata-xenium/icon.svg     | 108 ------------------
 .../tutorials/spatialdata-xenium/meta.yaml    |  20 ----
 .../tutorials/squidpy-xenium/icon.svg         |  80 +++++++++++++
 .../tutorials/squidpy-xenium/meta.yaml        |  23 ++++
 4 files changed, 103 insertions(+), 128 deletions(-)
 delete mode 100644 tutorial-registry/tutorials/spatialdata-xenium/icon.svg
 delete mode 100644 tutorial-registry/tutorials/spatialdata-xenium/meta.yaml
 create mode 100644 tutorial-registry/tutorials/squidpy-xenium/icon.svg
 create mode 100644 tutorial-registry/tutorials/squidpy-xenium/meta.yaml

diff --git a/tutorial-registry/tutorials/spatialdata-xenium/icon.svg b/tutorial-registry/tutorials/spatialdata-xenium/icon.svg
deleted file mode 100644
index 728efc5..0000000
--- a/tutorial-registry/tutorials/spatialdata-xenium/icon.svg
+++ /dev/null
@@ -1,108 +0,0 @@
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diff --git a/tutorial-registry/tutorials/spatialdata-xenium/meta.yaml b/tutorial-registry/tutorials/spatialdata-xenium/meta.yaml
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index 0ba3e9a..0000000
--- a/tutorial-registry/tutorials/spatialdata-xenium/meta.yaml
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-name: Reading Xenium data with SpatialData
-description: |
-  Read a 10x Genomics Xenium experiment and explore transcripts, cell boundaries and morphology images.
-link: https://spatialdata.scverse.org/en/stable/tutorials/notebooks/notebooks/examples/technology_xenium.html
-image: icon.svg
-primary_category: Spatial
-order: 5
-modality:
-  - spatial
-  - RNA
-tags:
-  - data structures
-  - preprocessing
-  - visualization
-packages:
-  - spatialdata
-  - spatialdata-io
-authors:
-  - LucaMarconato
-  - giovp
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diff --git a/tutorial-registry/tutorials/squidpy-xenium/meta.yaml b/tutorial-registry/tutorials/squidpy-xenium/meta.yaml
new file mode 100644
index 0000000..b8cede0
--- /dev/null
+++ b/tutorial-registry/tutorials/squidpy-xenium/meta.yaml
@@ -0,0 +1,23 @@
+name: Analyze Xenium data with SpatialData and squidpy
+description: |
+  Read a Xenium dataset with spatialdata-io, then run quality control, clustering and spatial statistics with squidpy.
+link: https://squidpy.readthedocs.io/en/latest/notebooks/tutorials/tutorial_xenium.html
+image: icon.svg
+primary_category: Spatial
+order: 5
+modality:
+  - spatial
+  - RNA
+tags:
+  - quality control
+  - preprocessing
+  - visualization
+packages:
+  - squidpy
+  - spatialdata
+  - spatialdata-io
+  - scanpy
+  - anndata
+authors:
+  - LLehner
+  - giovp