DOE OSTI · 3363101
PlantCV v4: Image analysis software for high‐throughput plant phenotyping
Abstract
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.
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Schuhl, Haley [Donald Danforth Plant Science Center, St. Louis, MO (United States); et al.] (ORCID:0000000288258297), Brown, Keely E. [Donald Danforth Plant Science Center St. Louis Missouri USA] (ORCID:0000000253715830), Sheng, Hudanyun [Donald Danforth Plant Science Center St. Louis Missouri USA], Bhatt, Parag K. [Donald Danforth Plant Science Center St. Louis Missouri USA] (ORCID:0000000203966412), Gutierrez, Jorge [Donald Danforth Plant Science Center St. Louis Missouri USA], Schneider, Dominik [Compact Plants Phenomics Center Washington State University Pullman Washington USA] (ORCID:0000000258465033), Casto, Anna L. [Donald Danforth Plant Science Center St. Louis Missouri USA] (ORCID:0000000295970514), Acosta‐Gamboa, Lucia [Donald Danforth Plant Science Center St. Louis Missouri USA] (ORCID:0000000177041845), Ballenger, Joe G. [Donald Danforth Plant Science Center St. Louis Missouri USA], Barbero, Fabio [Faculty of Science and Engineering Maastricht University Maastricht The Netherlands] (ORCID:0009000136263000), Braley, Jackson [Donald Danforth Plant Science Center St. Louis Missouri USA], Brown, Autumn M. [Donald Danforth Plant Science Center St. Louis Missouri USA] (ORCID:0000000182510773), Chavez, Leonardo [Donald Danforth Plant Science Center St. Louis Missouri USA] (ORCID:000000033914993X), Cunningham, Shannon [Arkansas Biosciences Institute Arkansas State University Jonesboro Arkansas USA], Dilhara, Malinda [Department of Computer Science University of Colorado Boulder Colorado USA], Dimech, Adam M. [Agriculture Victoria, Department of Energy Environment and Climate Action Bundoora Victoria Australia] (ORCID:0000000305331354), Duenwald, Joseph G. [Donald Danforth Plant Science Center St. Louis Missouri USA] (ORCID:0009000688190970), Fischer, Annika [Donald Danforth Plant Science Center St. Louis Missouri USA] (ORCID:0009000929168046), Gordon, Jared M. [Donald Danforth Plant Science Center St. Louis Missouri USA], Hendrikse, Chloe [Donald Danforth Plant Science Center St. Louis Missouri USA] (ORCID:0009000256859319), Hernandez, Gabriela L. [Donald Danforth Plant Science Center St. Louis Missouri USA] (ORCID:0009000952278278), Hodge, John G. [Department of Plant Biology, Ecology and Evolution Oklahoma State University Stillwater Oklahoma USA] (ORCID:0000000307931871), Huber, Martina [Plant Ecophysiology, Institute of Environmental Biology Utrecht University Utrecht The Netherlands] (ORCID:0000000296700460), Hurr, Brandon M. [Syngenta Crop Protection AG Basel Switzerland] (ORCID:0000000325764544), Jarolmasjed, Sanaz [Donald Danforth Plant Science Center St. Louis Missouri USA], Jimenez, Karina Medina [Arkansas Biosciences Institute Arkansas State University Jonesboro Arkansas USA] (ORCID:0000000243057854), Kenney, Samuel [Donald Danforth Plant Science Center St. Louis Missouri USA] (ORCID:0009000760219169), Konkel, Grant [Donald Danforth Plant Science Center St. Louis Missouri USA; Collegiate School of Medicine and Bioscience St. Louis Missouri USA], Kutschera, Alexander [RAYN Growing Systems Middleton Wisconsin USA] (ORCID:0000000332181371), Lama, Sunita [Donald Danforth Plant Science Center St. Louis Missouri USA] (ORCID:0009000544870555), Lohbihler, Matthew [Serotonin Software Technologies, Inc. Markham Ontario Canada], Lorence, Argelia [Arkansas Biosciences Institute Arkansas State University Jonesboro Arkansas USA] (ORCID:0000000198448820), Luebbert, Collin [Donald Danforth Plant Science Center St. Louis Missouri USA] (ORCID:0000000286655950), Ly, Nathaniel [Donald Danforth Plant Science Center St. Louis Missouri USA; Cell, Molecular and Developmental Biology Purdue University West Lafayette Indiana USA] (ORCID:0009000764204001), Manching, Heather K. [Department of Crop and Soil Sciences North Carolina State University Raleigh North Carolina USA] (ORCID:0000000263486808), Marrano, Annarita [Department of Biology University of Massachusetts Boston Massachusetts USA] (ORCID:0000000195602706), Meerdink, Susan [School of Earth, Environment, and Sustainability University of Iowa Iowa City Iowa USA] (ORCID:0000000178590248), Miklave, Nicholas M. [Department of Biology University of Louisiana at Lafayette Lafayette Louisiana USA] (ORCID:0009000919024946), Mudrageda, Pavan [Donald Danforth Plant Science Center St. Louis Missouri USA; School of Molecular & Cellular Biology University of Illinois Urbana‐Champaign Illinois USA], Murphy, Katherine M. [Donald Danforth Plant Science Center St. Louis Missouri USA] (ORCID:0000000288914274), Peery, J. David [Donald Danforth Plant Science Center St. Louis Missouri USA; Department of Computer Science University of North Carolina Chapel Hill North Carolina USA] (ORCID:0000000201923427), Pierik, Ronald [Plant Ecophysiology, Institute of Environmental Biology Utrecht University Utrecht The Netherlands] (ORCID:0000000253206817), Polydore, Seth [Donald Danforth Plant Science Center St. Louis Missouri USA] (ORCID:0000000277797367), Robey, Caleb [Department of Electrical & Computer Engineering University of Florida Gainesville Florida USA], Rogers, Tess [Donald Danforth Plant Science Center St. Louis Missouri USA] (ORCID:0009000407197333), Schultz, Tyler J. [Department of Electrical & Computer Engineering University of Florida Gainesville Florida USA] (ORCID:0009000407388754), Seigel, Eliza [Donald Danforth Plant Science Center St. Louis Missouri USA] (ORCID:0009000547933267), Srivastava, Dhiraj [Donald Danforth Plant Science Center St. Louis Missouri USA] (ORCID:0009000408735332), Summerer, Stephan [ALSIA Centro Ricerche Metapontum Agrobios Bernalda Italy] (ORCID:0000000215059473), Sumner, Josh [Donald Danforth Plant Science Center St. Louis Missouri USA] (ORCID:0000000233999063), Teng, Chong [Donald Danforth Plant Science Center St. Louis Missouri USA] (ORCID:0000000198986442), Thompson, Adriane E. [Donald Danforth Plant Science Center St. Louis Missouri USA; Grinnell College Grinnell Iowa USA] (ORCID:0000000288535856), Tovar, Jose C. [Donald Danforth Plant Science Center St. Louis Missouri USA] (ORCID:0000000225042018), van Daalen, Tim [Wageningen Plant Research Wageningen University & Research Wageningen The Netherlands] (ORCID:0009000303081969), Watson, Mark [Plant Breeding Center University of California Davis California USA] (ORCID:000900016607880X), Wheeler, John J. [Donald Danforth Plant Science Center St. Louis Missouri USA] (ORCID:0000000265174701), Wilson, Mark C. [Donald Danforth Plant Science Center St. Louis Missouri USA], Ying, Kaitlyn R. [Donald Danforth Plant Science Center St. Louis Missouri USA; Cell, Molecular and Developmental Biology Purdue University West Lafayette Indiana USA], Zare, Alina [Department of Electrical & Computer Engineering University of Florida Gainesville Florida USA] (ORCID:0000000248477604), Zhou, Yutai [Department of Electrical & Computer Engineering University of Florida Gainesville Florida USA], Gehan, Malia A. [Donald Danforth Plant Science Center St. Louis Missouri USA] (ORCID:0000000232382627), Fahlgren, Noah [Donald Danforth Plant Science Center St. Louis Missouri USA] (ORCID:0000000255974537). 2026-02-16. PlantCV v4: Image analysis software for high‐throughput plant phenotyping. https://doi.org/10.1002/ppj2.70065
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