Paper

PlantCV v4: Image analysis software for high-throughput plant phenotyping

Barbero, Fabio, Marrano, Annarita, Pierik, Ronald, Seigel, Eliza, Wheeler, John J., Srivastava, Dhiraj, Bhatt, Parag K., Teng, Chong, Schneider, Dominik, Casto, Anna L., Manching, Heather K., Gutierrez, Jorge, Lama, Sunita, Kenney, Samuel, Lohbihler, Matthew, Zhou, Yutai, Thompson, Adriane E., Medina Jimenez, Karina, Wilson, Mark C., Jarolmasjed, Sanaz, Robey, Caleb, Sheng, Hudanyun, Ballenger, Joe G., Murphy, Katherine M., Zare, Alina, Luebbert, Collin, Brown, Keely E., Ly, Nathaniel, van Daalen, Tim, Tovar, Jose C., Chavez, Leonardo, Kutschera, Alexander, Hendrikse, Chloe, Ying, Kaitlyn R., Konkel, Grant, Brown, Autumn M., Dimech, Adam M., Gordon, Jared M., Duenwald, Joseph G., Hodge, John G., Schultz, Tyler J., Schuhl, Haley, Fahlgren, Noah, Hurr, Brandon M., Mudrageda, Pavan, Fischer, Annika, Sumner, Josh, Meerdink, Susan, Lorence, Argelia, Dilhara, Malinda, Summerer, Stephan, Peery, J. David, Polydore, Seth, Gehan, Malia A., Cunningham, Shannon, Braley, Jackson, Huber, Martina, Rogers, Tess, Watson, Mark, Miklave, Nicholas M., Hernandez, Gabriela L., Acosta-Gamboa, Lucia

2025

Overview

PlantCV is an open-source Python project aimed at developing tools to address a range of image-based, plant phenotyping questions. PlantCV has been used for more than 10 years to automate trait collection from image data and the newest release, PlantCV version 4, continues to lower the barrier to entry for users without substantial coding experience through extensive example use-case tutorials and simplified installation. In addition to usability, we document added functionality since the release of PlantCV v2, including support for more image types such as fluorescence, thermal, and hyperspectral data. Finally, we describe the development of a new subpackage focused on morphological trait measurements like leaf angle, and demonstrate its utility as compared to more manual methods of data collection. PlantCV is an open-source, open-development, Python-based software package that has a new release for improved functionality and usability to make image analysis flexible and easier for researchers without a coding background. PlantCV is now capable of handling new data types that are relevant to researchers, such as thermal and hyperspectral, and has built in functionality for extracting information from these image types. The software project aims to lower the barrier to entry into image analysis for researchers by providing numerous, versioned, interactive tutorials that cover most common use cases, particularly in plant science.

• Publisher: Cold Spring Harbor Laboratory
• Subject: Plant Biology