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hutaobo merged 2 commits into from
Jun 12, 2026
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docs: trim repetitive feature list in README header #6

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docs: replace nine-feature overview figure with new SVG
hutaobo Jun 12, 2026
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docs: trim repetitive feature list in README header
hutaobo Jun 12, 2026
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10 changes: 3 additions & 7 deletions README.md
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Expand Up @@ -5,7 +5,7 @@
<h1 align="center">pyXenium</h1>

<p align="center">
nine feature areas for Xenium I/O, multimodal analysis, CCI, pathway topology, contour geometry, GMI inference, mechanostress analysis, and external workflow bridges.
Load, analyze, and interpret 10x Genomics Xenium spatial data in one Python toolkit.
</p>

<p align="center">
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</p>

<p align="center">
<img src="https://raw.githubusercontent.com/hutaobo/pyXenium/main/docs/_static/figures/pyxenium-nine-feature-overview.png" alt="pyXenium nine-feature overview figure" width="960">
<img src="https://raw.githubusercontent.com/hutaobo/pyXenium/main/docs/_static/figures/pyxenium-nine-feature-overview.svg" alt="pyXenium nine-feature overview figure" width="960">
</p>

<p align="center">
<em>Figure 1. pyXenium summarizes Xenium I/O, multimodal analysis, spatial topology, contour-aware inference, mechanostress analysis, and external workflow bridges in one submission-ready overview.</em>
</p>

pyXenium is a Python toolkit for **10x Genomics Xenium** organized around nine major sections.
pyXenium is organized around nine major sections, each with a canonical entry point:

| Section | Canonical entry | Start here |
| --- | --- | --- |
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2 changes: 1 addition & 1 deletion docs/index.md
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</div>
</div>

```{figure} _static/figures/pyxenium-nine-feature-overview.png
```{figure} _static/figures/pyxenium-nine-feature-overview.svg
:alt: pyXenium nine-feature overview figure
:class: pyxenium-overview-image
:figclass: pyxenium-overview-figure
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2 changes: 1 addition & 1 deletion docs/user-guide/nine-feature-overview.md
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# Nine-feature overview

```{figure} ../_static/figures/pyxenium-nine-feature-overview.png
```{figure} ../_static/figures/pyxenium-nine-feature-overview.svg
:alt: pyXenium nine-feature overview figure
:class: pyxenium-overview-image
:figclass: pyxenium-overview-figure
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