plantcv-plant-phenotyping-starter

Name: plantcv-plant-phenotyping-starter
Author: ma-compbio-lab

36stars5forks

How to install plantcv-plant-phenotyping-starter?

ma-compbio-lab/skillfoundry/plantcv-plant-phenotyping-starter

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

Installs into the current project.

Summary

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

Files · 1

SKILL.md

1	# PlantCV Plant Phenotyping Starter
2
3	Use this skill to generate a tiny synthetic plant image, segment it with `PlantCV`, and summarize simple morphology-style phenotyping measurements.
4
5	## What it does
6
7	- Builds a small deterministic RGB image containing one synthetic plant-like region.
8	- Uses `PlantCV` HSV conversion plus binary thresholding to produce a foreground mask.
9	- Reports foreground area, bounding box, and a simple saturation-based phenotype summary.
10
11	## When to use it
12
13	- You need a runnable starter for `Plant phenotyping`.
14	- You want a local segmentation and mask-summary example before scaling to real greenhouse or field images.
15
16	## Example
17
18	```bash
19	slurm/envs/plant-science/bin/python skills/agriculture-food-and-plant-science/plantcv-plant-phenotyping-starter/scripts/run_plantcv_plant_phenotyping.py \
20	--image-out scratch/plantcv/toy_plant.png \
21	--mask-out scratch/plantcv/toy_plant_mask.png \
22	--out scratch/plantcv/toy_plant_summary.json
23	```
24
25	## Verification
26
27	- Skill-local tests: `python3 -m unittest discover -s skills/agriculture-food-and-plant-science/plantcv-plant-phenotyping-starter/tests -p 'test_*.py'`
28	- Repository smoke: `python3 -m unittest tests.smoke.test_phase30_empty_domain_seed_skills -v`

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