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bio-imaging-mass-cytometry-interactive-annotation

85 / 100 · Low risk

Fine to try.

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

Interactive cell annotation and image QC for IMC/MIBI using napari, napari-imc, Mantis Viewer, and cytomapper, covering the pixels-to-cell-table bridge, overlaying masks to catch segmentation/spillover artifacts, inter-annotator variability as the accuracy ceiling, contrast-as-threshold, and building class-balanced ground-truth label sets. Use when manually labeling cells, generating training data for a classifier, QC-ing segmentation on the image, confirming clusters are spatially real, or cho…

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