PlantCV

PlantCV is an open-source tool for automated plant phenotyping. It measures plant morphological traits from images — shape, size, color distribution, and more.

Input formats

.png, .jpg, .jpeg, .tiff

Analysis types

Type	Description
Morphology	Combined shape and color analysis (recommended)
Shape only	Area, perimeter, convexity, solidity, eccentricity
Color only	Color histogram, dominant colors, color distribution

Parameters

Parameter	Range	Default	Description
Binary threshold	0–255	128	Threshold for foreground/background separation
Min object area	Pixels	100	Minimum plant area to detect (filters noise)
ROI restriction	Toggle	Off	Limit analysis to a specific region of interest

Outputs

Output	Format	Description
Plant traits	JSON	Measurements: area, perimeter, height, width, color metrics
Binary mask	PNG	Foreground/background segmentation mask
Annotated overlay	PNG	Original image with analysis overlay

Presets

Preset	Description
Full Morphology + Color	Complete analysis with all measurements
Shape Only	Shape metrics without color analysis

Compute requirements

Resource	Requirement
GPU	None — CPU only
Duration	~30 seconds per image

SpikeInterface — Spike Sorting

SExtractor — Source Extraction