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 workflow. PlantCV currently supports the analysis of standard RGB color images (aka "VIS"), standard grayscale images (e.g. near-infrared, "NIR"), thermal infrared images, and grayscale images from chlorophyll fluorescence imaging systems ("PSII"). 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.
At the Danforth Center we refer to our saturation pulse 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.
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:
- Installing PlantCV
- Updating PlantCV
- Frequently Asked Questions
- General Approaches to Image Analysis with PlantCV
- Using Jupyter Notebooks with PlantCV
- Summary of Output Measurements and Database Structure
Also see our tutorials for more detailed overviews of using PlantCV for specific tasks:
- VIS/RGB Image Processing
- Near-Infrared 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
We have added interactive documentation (the link takes up to a few minutes to load so be patient please), so you can test out workflows and even upload your own images to test on.
If you are interested in contributing to PlantCV, please see:
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.