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Skimage Regionprops Feature Extraction

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Use this skill to extract deterministic morphology and intensity features from a toy image with `scikit-image` `regionprops_table`.

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  • Added September 8, 2026
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Scanned September 8, 2026

npx -y skills add ma-compbio-lab/SkillFoundry --skill skimage-regionprops-feature-extraction --agent claude-code

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SKILL.md
# scikit-image Regionprops Feature Extraction

Use this skill to extract deterministic morphology and intensity features from a toy image with `scikit-image` `regionprops_table`.

## What it does

- creates a reproducible grayscale toy image with three bright ellipse-like objects
- thresholds and labels connected components locally
- summarizes per-object morphology and intensity features into compact JSON
- keeps the output stable enough for smoke tests and starter workflows

## When to use it

- You need a local `feature-extraction` starter in the scikit-image ecosystem.
- You want a minimal handoff point before building larger imaging or phenotype-analysis pipelines.

## Example

```bash
./slurm/envs/scientific-python/bin/python \
  skills/imaging-and-phenotype-analysis/skimage-regionprops-feature-extraction/scripts/run_skimage_regionprops_features.py \
  --threshold 0.35 \
  --out scratch/skimage-regionprops/summary.json
```

## Verification

- Skill-local tests: `python3 -m unittest discover -s skills/imaging-and-phenotype-analysis/skimage-regionprops-feature-extraction/tests -p 'test_*.py'`
- Asset regeneration: `./slurm/envs/scientific-python/bin/python skills/imaging-and-phenotype-analysis/skimage-regionprops-feature-extraction/scripts/run_skimage_regionprops_features.py --out skills/imaging-and-phenotype-analysis/skimage-regionprops-feature-extraction/assets/toy_regionprops_summary.json`

## Notes

- This is a starter for the taxonomy leaf `feature-extraction`.
- The image is synthetic and deterministic; it is intended for scaffolding and verification rather than biological interpretation.

Files in this skill

  • SKILL.md1.6 KB
  • assets/README.md140 B
  • assets/toy_regionprops_summary.json1.1 KB
  • examples/README.md395 B
  • metadata.yaml1.2 KB
  • refs.md370 B
  • scripts/run_skimage_regionprops_features.py4.4 KB
  • tests/README.md159 B
  • tests/test_run_skimage_regionprops_features.py2.2 KB

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