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Plantcv plant phenotyping starter

Skill ma-compbio-lab/SkillFoundry/skills/agriculture-food-and-plant-science/plantcv-plant-phenotyping-starter

A framework for discovering, compiling, and validating reusable skills for scientific agents.

Install
npx -y skills add ma-compbio-lab/SkillFoundry --skill plantcv-plant-phenotyping-starter

Assembled from the repository path, not quoted from the project. Check it against their README if it does not work.

SKILL.md

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PlantCV Plant Phenotyping Starter

Use this skill to generate a tiny synthetic plant image, segment it with PlantCV, and summarize simple morphology-style phenotyping measurements.

What it does

  • Builds a small deterministic RGB image containing one synthetic plant-like region.
  • Uses PlantCV HSV conversion plus binary thresholding to produce a foreground mask.
  • Reports foreground area, bounding box, and a simple saturation-based phenotype summary.

When to use it

  • You need a runnable starter for Plant phenotyping.
  • You want a local segmentation and mask-summary example before scaling to real greenhouse or field images.

Example

slurm/envs/plant-science/bin/python skills/agriculture-food-and-plant-science/plantcv-plant-phenotyping-starter/scripts/run_plantcv_plant_phenotyping.py \
  --image-out scratch/plantcv/toy_plant.png \
  --mask-out scratch/plantcv/toy_plant_mask.png \
  --out scratch/plantcv/toy_plant_summary.json

Verification

  • Skill-local tests: python3 -m unittest discover -s skills/agriculture-food-and-plant-science/plantcv-plant-phenotyping-starter/tests -p 'test_*.py'
  • Repository smoke: python3 -m unittest tests.smoke.test_phase30_empty_domain_seed_skills -v

Keep looking

Skills are one crate of 328,083. Ordering is by how many stacks a row turns up in, so the top of any crate is what has actually been picked rather than what has the most stars.