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

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

The Plant Phenome Journal · 16 Feb 2026 · 10.1002/ppj2.70065

Abstract

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.

Code and data availability

The paper's Data Availability Statement explicitly deposits the authors' analysis scripts on GitHub (danforthcenter/plantcv-4-paper), which directly reproduces this paper's phenotyping analyses.

Codepublic

erest. DATA AVA I L A B I L I T Y S TAT E M E N T Links to code, tutorials, documentation, and other resources are available on the PlantCV homepage at https://plantcv.org. PlantCV source code is available on GitHub at https:// github.com/danforthcenter/plantcv. Scripts used for analyses in this paper are available on GitHub at https://github.com/danforthcenter/plantcv-4-paper.O RC I D HaleySchuhl https://orcid.org/0000-0002-8825-8297 KeelyE. Brown https://orcid.org/0000-0002-5371-5830 ParagK. Bhatt https://orcid.org/0000-0002-0396-6412 DominikSchneider https://orcid.org/0000-0002-5846-5033 Anna L. Casto https://orcid.org/0000-0002-9597-0514 Lucia Acosta-Gamboa https://orcid.org/0000-0001-77

Open resource ↗danforthcenter/plantcv-4-paper · pdf-raw-page:15 lines:1-97

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