← All skills

cellpose-cell-segmentation

80 / 100 · Low risk

Fine to try.

By BioTender-max/awesome-bio-agent-skills (GitHub) · design · 219 stars · scanned at commit 8cbdd18

DL cell/nucleus segmentation for fluorescence and brightfield microscopy. Pre-trained models (cyto3, nuclei, tissuenet) and a generalist flow-based algorithm segment cells without retraining. Outputs label masks for morphology and tracking. Use scikit-image watershed for rule-based; Cellpose when DL generalization across staining 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=$(mktemp -d) && git clone --quiet --filter=blob:none --no-checkout 'https://github.com/BioTender-max/awesome-bio-agent-skills' "$d" && git -C "$d" checkout --quiet '8cbdd18837aa6296c4e77616a03b323bd69b57b1' -- 'skills/sciagent/cellpose-cell-segmentation' && mkdir -p ~/.agents/skills && cp -R "$d"/'skills/sciagent/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.

Badge for your README

The badge for BioTender-max/awesome-bio-agent-skills shows the score of its lowest-scoring skill.

[![SkillTrust](https://zalavijaysinh.github.io/skilltrust/badges/BioTender-max/awesome-bio-agent-skills.svg)](https://zalavijaysinh.github.io/skilltrust/repos/BioTender-max/awesome-bio-agent-skills/)

Score history