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cellpose-cell-segmentation

80 / 100 · Low risk

Fine to try.

By stanfish06/skillquarium (GitHub) · media · 12 stars · scanned at commit f748ea9

DL cell/nucleus segmentation for fluorescence and brightfield microscopy with Cellpose 4's Cellpose-SAM and CellposeDINO models. Handles grayscale, multichannel, 2D, and 3D images and outputs label masks for morphology and tracking. Use scikit-image watershed for rule-based segmentation; use Cellpose when learned generalization is needed.

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/'cellpose-cell-segmentation' ] || [ -L ~/.agents/skills/'cellpose-cell-segmentation' ]; then echo 'A skill folder named cellpose-cell-segmentation already exists — not replacing it' >&2; false; else d=$(mktemp -d) && git clone --quiet --filter=blob:none --no-checkout 'https://github.com/stanfish06/skillquarium' "$d" && git -C "$d" checkout --quiet 'f748ea91aa51ce8fc42c27c809dba73a8377b1d5' -- 'skills/cellpose-cell-segmentation' && mkdir -p ~/.agents/skills && cp -R "$d"/'skills/cellpose-cell-segmentation' ~/.agents/skills/'cellpose-cell-segmentation' && 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/'cellpose-cell-segmentation' ~/.claude/skills/'cellpose-cell-segmentation' (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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