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bio-spatial-transcriptomics-spatial-visualization

85 / 100 · Low risk

Fine to try.

By lilinji/GeneTind-Life-Skills (GitHub) · data · 17 stars · scanned at commit 908229c

Plots spatial transcriptomics expression, clusters, and annotations on tissue using Squidpy and Scanpy. Use when choosing the plotter and spot size by platform fork (sc.pl.spatial / sq.pl.spatial_scatter with real scalefactors and capture diameter for spot/capture data like Visium and Slide-seq, versus molecule/segmentation overlays for imaging/FOV data like Xenium, MERFISH, and CosMx); getting the histology coordinate-frame transform right (micron<->pixel, scalefactors) so points land on the i…

Works with any agent that supports SKILL.md skills.

What this skill can do

Install

Paste this into your terminal. It downloads exactly the version we scanned, not whatever is newest.

if [ -e ~/.agents/skills/'bio-spatial-transcriptomics-spatial-visualization' ] || [ -L ~/.agents/skills/'bio-spatial-transcriptomics-spatial-visualization' ]; then echo 'A skill folder named bio-spatial-transcriptomics-spatial-visualization already exists — not replacing it' >&2; false; else d=$(mktemp -d) && git clone --quiet --filter=blob:none --no-checkout 'https://github.com/lilinji/GeneTind-Life-Skills' "$d" && git -C "$d" checkout --quiet '908229c955510a1841b216e8bf58f6b22818d4dc' -- 'skills/bio-spatial-transcriptomics-spatial-visualization' && mkdir -p ~/.agents/skills && cp -R "$d"/'skills/bio-spatial-transcriptomics-spatial-visualization' ~/.agents/skills/'bio-spatial-transcriptomics-spatial-visualization' && rm -rf "$d"; fi

Codex reads ~/.agents/skills directly. For Claude Code, Cursor, Copilot, Gemini CLI, Antigravity or OpenCode, also link it. For Claude Code: ln -s ~/.agents/skills/'bio-spatial-transcriptomics-spatial-visualization' ~/.claude/skills/'bio-spatial-transcriptomics-spatial-visualization' (other agents: ~/.cursor/skills, ~/.copilot/skills, ~/.gemini/skills, ~/.gemini/config/skills, ~/.config/opencode/skills). Or install through the finder skill, which does both.

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