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