Welcome to the documentation for PlantCV


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 will describe use of each function and provide tutorials on how each function is used in the context of an overall image-processing pipeline. The initial releases of PlantCV have been designed for processing images from visible spectrum cameras ('VIS'), near-infrared cameras ('NIR'), and excitation imaging fluorometers ('PSII'; see note below). Development of PlantCV is ongoing---we encourage input from the greater plant phenomics community. Please post questions and comments on the GitHub issues page.

Note: At the Danforth Center we refer to our excitation imaging fluorometer (PSII) camera system as 'FLU' internally. But others have previously published on their steady-state fluorescence imaging systems (a different type of fluorescence imaging system) and referred to it as 'FLU'. We are working to make the naming changes of our functions from 'FLU' to 'PSII' to try and prevent further confusion.

Getting started

The documentation can be navigated using the sidebar table of contents. Documentation for individual PlantCV functions are listed under the headings "Package plantcv" and "Package plantcv.learn." For general information on installation, updating, and other questions, see:

Also see our tutorials for more detailed overviews of using PlantCV for specific tasks:

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


The documentation defaults to the latest version of PlantCV which is the latest commit in the master code branch. Documentation for all releases from v1.1 on are also available via the standard Read the Docs popup/pulldown menu (sidebar, bottom left).

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