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bio-imaging-mass-cytometry-data-preprocessing

80 / 100 · Low risk

Fine to try.

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

Load and preprocess imaging mass cytometry (IMC) and MIBI data from raw MCD/TXT through hot-pixel removal, spillover compensation, and variance-stabilizing transformation, covering readimc/steinbock ingestion, NNLS spillover compensation (CATALYST), IMC-Denoise, and the IMC arcsinh-cofactor question. Use when starting analysis from raw MCD files, building per-channel TIFF stacks, compensating channel spillover, choosing an arcsinh cofactor, or preparing single-cell intensities for phenotyping.

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-imaging-mass-cytometry-data-preprocessing' ] || [ -L ~/.agents/skills/'bio-imaging-mass-cytometry-data-preprocessing' ]; then echo 'A skill folder named bio-imaging-mass-cytometry-data-preprocessing 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 "$d" checkout --quiet '908229c955510a1841b216e8bf58f6b22818d4dc' -- 'skills/bio-imaging-mass-cytometry-data-preprocessing' && mkdir -p ~/.agents/skills && cp -R "$d"/'skills/bio-imaging-mass-cytometry-data-preprocessing' ~/.agents/skills/'bio-imaging-mass-cytometry-data-preprocessing' && 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-imaging-mass-cytometry-data-preprocessing' ~/.claude/skills/'bio-imaging-mass-cytometry-data-preprocessing' (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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