> ## Documentation Index
> Fetch the complete documentation index at: https://docs.biom.science/llms.txt
> Use this file to discover all available pages before exploring further.

# PlantCV — Plant Phenotyping

> Automated plant morphology, shape, and color analysis.

# 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 |