Cell Segmentation Skills Index
Cell and nucleus segmentation tools for microscopy images. Covers Cellpose, SAM-based methods, StarDist, InstanSeg, and Mesmer.
npx skills add BioTender-max/awesome-bio-agent-skills --skill segmentation --agent claude-code
Same command for any agent — swap --agent for codex, cursor, copilot.
Weekly change comes from our own snapshots, not the repository page — it measures attention, not adoption.
# Cell & Nucleus Segmentation Skills Instance segmentation tools for cells and nuclei in microscopy images. Use the tool selection guide below to choose the right method, then load the corresponding skill file for detailed usage. ## Tool Selection Guide | Goal | Recommended Tool | Speed | Tested | |------|-----------------|-------|--------| | Best overall accuracy | Cellpose-SAM (v4.x) | Moderate (~310s/1024px CPU) | ✅ 955 cells | | Fastest inference | InstanSeg | **Fast** (~7s/1024px CPU) | ✅ 586 cells | | Low quality / noisy images | Cellpose 3 (image restoration) | Moderate | ✅ | | Round nuclei only | StarDist | **Fastest** (~0.5s) | ✅ 150 cells | | Whole-cell (nucleus + membrane) | Mesmer / DeepCell | Moderate | ⚠️ install issues | | Interactive annotation / 3D / tracking | micro-sam | Slow | ⚠️ Python 3.10+ | | Fully automatic, no prompts | CellSAM | Moderate | ⚠️ Python 3.10+ | > [!TIP] > Start with **Cellpose** (default in v4.x) for most tasks. It has the best > generalization. Switch to **InstanSeg** if speed matters or you need > simultaneous nuclei + cell masks. > [!WARNING] > **Environment isolation is important.** These tools have conflicting > dependencies. Cellpose/In
- Tool Selection Guide
- Available Skills
- Cellpose
- InstanSeg
- StarDist
- Mesmer / DeepCell
- SAM-Based Cell Segmentation
What does the Cell Segmentation Skills Index skill do?
Cell and nucleus segmentation tools for microscopy images. Covers Cellpose, SAM-based methods, StarDist, InstanSeg, and Mesmer.
How do I install it?
Run `npx skills add BioTender-max/awesome-bio-agent-skills --skill segmentation --agent claude-code` — it drops the skill into your project so the agent can pick it up. Swap the --agent value for codex, cursor or copilot if you use one of those.
Where does this skill come from?
From BioTender-max/awesome-bio-agent-skills, a repository with 135 stars. We read it straight from the repository tree rather than a submitted listing, so what you see here is what is actually published.
Is a popular skill a good skill?
Not necessarily. Stars measure attention, not adoption — a repository can trend for a week and be abandoned. That is why we show the weekly change from our own snapshots next to the total, instead of a single flattering number.