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 |