Welcome to the documentation for PlantCV¶

Overview¶

PlantCV is composed of modular functions in order to be applicable to a variety of plant types and imaging systems. In the following documentation we describe use of each function and provide tutorials on how each function is used in the context of an overall image-processing workflow. PlantCV currently supports the analysis of standard RGB color images (aka "VIS"), standard grayscale images (e.g. near-infrared, "NIR"), thermal infrared images, grayscale images from chlorophyll fluorescence imaging systems ("PSII"), and hyperspectral ("ENVI") images. Support for additional image types is under development. Development of PlantCV is ongoing---we encourage input from the greater plant phenomics community. Please post questions and comments on the GitHub issues page.

Getting started¶

If this is your first time using PlantCV, we recommend following this list of documentation pages to get started:

• Install PlantCV
• Use PlantCV with Jupyter Notebooks
• Get started buildling an image analysis workflow
• Run your workflow in parallel
• Use the json2csv tool to convert results files to csv
• Summary of output measurements generated by PlantCV

Other useful reference pages:

• Updating PlantCV
• Frequently Asked Questions

Tutorials¶

Check out our tutorials below or in our Tutorial Gallery to learn how to analyze different types of images:

• VIS/RGB Image Processing
• Grayscale Image Processing
• PSII Image Processing
• VIS / NIR Dual Workflows
• Multi Plant Image Processing
• Morphology Package
• Thermal Image Processing
• Hyperspectral Image Processing
• Machine Learning Tutorial
• Parallel Image Processing
• Exporting Data for Downstream Analysis

Contributing¶

If you are interested in contributing to PlantCV, please see:

• Contribution Guide
• Documentation Guide
• Code of Conduct

Versions¶

The documentation defaults to the stable version of PlantCV which is the current release version available from PyPI and Bioconda. Documentation for all releases from v1.1 on are also available via the standard Read the Docs popup/pulldown menu (bottom right corner). Select the latest version to get the most up-to-date documentation associated with the current code in GitHub.

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