Journal article
PlantCV v4: Image analysis software for high‐throughput plant phenotyping
Plant phenome journal, Vol.9(1), e70065
12/2026
DOI: 10.1002/ppj2.70065
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. Plant physical and physiological characteristics are the result of the interaction between genetics and the environment, which is a dynamic process. To better understand how plants interact with and respond to the environment, imaging and image analysis can be used to quantitatively measure plant characteristics at larger spatial and higher temporal scales than can be feasible through manual work. PlantCV is an open‐source Python‐based software that provides tools for measuring plants from image datasets. In this work, we demonstrate new features of PlantCV and how they are used to analyze plant image data. New features include support for new data types from specialized camera systems, higher flexibility and ease of use, and leaf‐level morphological measurement capabilities. PlantCV provides a modular and flexible system for measuring plants using image data for a wide array of experimental contexts in plant science research and agricultural applications.
Details
- Title: Subtitle
- PlantCV v4: Image analysis software for high‐throughput plant phenotyping
- Creators
- Haley Schuhl - Donald Danforth Plant Science CenterKeely E. Brown - Donald Danforth Plant Science CenterHudanyun Sheng - Donald Danforth Plant Science CenterParag K. Bhatt - Donald Danforth Plant Science CenterJorge Gutierrez - Donald Danforth Plant Science CenterDominik Schneider - Washington State UniversityAnna L. Casto - Donald Danforth Plant Science CenterLucia Acosta-Gamboa - Donald Danforth Plant Science CenterJoe G. Ballenger - Donald Danforth Plant Science CenterFabio Barbero - Maastricht UniversityJackson Braley - Donald Danforth Plant Science CenterAutumn M. Brown - Donald Danforth Plant Science CenterLeonardo Chavez - Donald Danforth Plant Science CenterShannon Cunningham - Arkansas Biosciences InstituteMalinda Dilhara - University of Colorado BoulderAdam M. Dimech - Agriculture VictoriaJoseph G. Duenwald - Donald Danforth Plant Science CenterAnnika Fischer - Donald Danforth Plant Science CenterJared M. Gordon - Donald Danforth Plant Science CenterChloe Hendrikse - Donald Danforth Plant Science CenterGabriela L. Hernandez - Donald Danforth Plant Science CenterJohn G. Hodge - Oklahoma State UniversityMartina Huber - Utrecht UniversityBrandon M. Hurr - Syngenta (Switzerland)Sanaz Jarolmasjed - Donald Danforth Plant Science CenterKarina Medina Jimenez - Arkansas Biosciences InstituteSamuel Kenney - Donald Danforth Plant Science CenterGrant Konkel - Donald Danforth Plant Science CenterAlexander Kutschera - RAYN Growing Systems Middleton Wisconsin USASunita Lama - Donald Danforth Plant Science CenterMatthew Lohbihler - JDA Software (Canada)Argelia Lorence - Arkansas Biosciences InstituteCollin Luebbert - Donald Danforth Plant Science CenterNathaniel Ly - Purdue University West LafayetteHeather K. Manching - North Carolina State UniversityAnnarita Marrano - University of Massachusetts BostonSusan Meerdink - University of IowaNicholas M. Miklave - University of Louisiana at LafayettePavan Mudrageda - University of Illinois Urbana-ChampaignKatherine M. Murphy - Donald Danforth Plant Science CenterJ. David Peery - University of North Carolina at Chapel HillRonald Pierik - Utrecht UniversitySeth Polydore - Donald Danforth Plant Science CenterCaleb Robey - University of FloridaTess Rogers - Donald Danforth Plant Science CenterTyler J. Schultz - University of FloridaEliza Seigel - Donald Danforth Plant Science CenterDhiraj Srivastava - Donald Danforth Plant Science CenterStephan Summerer - Centro Ricerche FIATJosh Sumner - Donald Danforth Plant Science CenterChong Teng - Donald Danforth Plant Science CenterAdriane E. Thompson - Grinnell CollegeJose C. Tovar - Donald Danforth Plant Science CenterTim van Daalen - Wageningen University & ResearchMark Watson - University of California, DavisJohn J. Wheeler - Donald Danforth Plant Science CenterMark C. Wilson - Donald Danforth Plant Science CenterKaitlyn R. Ying - Purdue University West LafayetteAlina Zare - University of FloridaYutai Zhou - University of FloridaMalia A. Gehan - Donald Danforth Plant Science CenterNoah Fahlgren - Donald Danforth Plant Science Center
- Resource Type
- Journal article
- Publication Details
- Plant phenome journal, Vol.9(1), e70065
- DOI
- 10.1002/ppj2.70065
- ISSN
- 2578-2703
- eISSN
- 2578-2703
- Publisher
- Wiley
- Grant note
- Defense Advanced Research Projects AgencyDepartment of EnergyEmerging Frontiers Office: 1921724 Division of Biological Infrastructure: 2120153 Biological and Environmental Research: DE-SC0018072, DE-SC0023142 United States Department of Agriculture: 2019-67021-29926, 2022-67021-36467, 2022-67013-36129, 2021-67013-33778, 2020-67034-31901 Directorate for Technology, Innovation and Partnerships: 2347188, 2346101 Division of Undergraduate Education: 2121293 DARPANational Institute of Food and AgricultureBiological Technologies Office: HR001118C01327 National Science Foundation
We would like to thank the PlantCV users and community. This work is supported by the Donald Danforth Plant Science Center, USDA-NIFA (2019-67021-29926 and 2022-67021-36467 to N.F. and M.A.G.; 2022-67013-36129 and 2021-67013-33778 to M.A.G.; and 2020-67034-31901 to A.L.C.), DOE (DE-SC0018072 to N.F and M.A.G. and DE-SC0023142 to M.A.G.), NSF (2121293, 2120153, 2346101, 2347188, and 1921724 to N.F. and M.A.G.), the Taylor Geospatial Institute, and the Wells Fargo IN2 program. This work was supported by Defense Advanced Research Projects Agency Advanced Plant Technologies (DARPA-APT and HR001118C01327). We thank the Plant Growth Facility (RRID:SCR_024902) and the Phenotyping Core Facility (RRID:SCR_019049) at the Donald Danforth Plant Science Center for plant growth and image collection, respectively. The views, opinions, and /or findings expressed are those of the authors and should not be interpreted as representing the official views or policies of the Department of Defense of the US Governments. A.M. has recently joined the European Research Council Executive Agency (ERCEA) as a scientific officer. The information and views set out in this article are those of the author and do not necessarily reflect the official opinion of the European Commission and ERCEA.
- Language
- English
- Electronic publication date
- 02/16/2026
- Date published
- 12/2026
- Academic Unit
- School of Earth, Environment, and Sustainability
- Record Identifier
- 9985139296402771
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