ArticlePlant physiology2013
RootNav: navigating images of complex root architectures.
Article in Plant physiology, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 97 papers.
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Who cites it
97 citing papers in PubMed.
- Roots of wheat and rice maintain gravitropic setpoint angles.Journal of experimental botany · 2026Article
- Root system architecture and drought adaptation: emerging tools and genetic insights.Frontiers in plant science · 2026Review
- Transcription factor-promoter interactions forbioRxiv : the preprint server for biology · 2025Article
- RPT: An integrated root phenotyping toolbox for segmenting and quantifying root system architecture.Plant biotechnology journal · 2025Article
- Identification of phenotypic and transcriptomic signatures underpinning maize crown root systems.Plant phenomics (Washington, D.C.) · 2025Article
- Research on Fine-Grained Phenotypic Analysis of Temporal Root Systems - Improved YoloV8seg Applied for Fine-Grained Analysis of In Situ Root Temporal Phenotypes.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2025Article
- High-throughput phenotyping of wheat root angle and coleoptile length at different temperatures using 3D-printed equipment.BMC plant biology · 2025Article
- Defense-related callose synthase PMR4 promotes root hair callose deposition and adaptation to phosphate deficiency in Arabidopsis thaliana.The Plant journal : for cell and molecular biology · 2024Article
- Automated seminal root angle measurement with corrective annotation.AoB PLANTS · 2024Article
- An ecotype-specific effect of osmopriming and melatonin during salt stress in Arabidopsis thaliana.BMC plant biology · 2024Article
- Beneficial Effects of Phosphite inPlants (Basel, Switzerland) · 2024Article
- Defying gravity: WEEP promotes negative gravitropism in peach trees by establishing asymmetric auxin gradients.Plant physiology · 2024Article
- Evaluation of drought-tolerant varieties based on root system architecture in cotton (Gossypium hirsutum L.).BMC plant biology · 2024Article
- Article
- Reproducible growth ofScience advances · 2024Article
- Improved Transformer for Time Series Senescence Root Recognition.Plant phenomics (Washington, D.C.) · 2024Article
- Semantic segmentation of plant roots from RGB (mini-) rhizotron images-generalisation potential and false positives of established methods and advanced deep-learning models.Plant methods · 2023Article
- A method of cotton root segmentation based on edge devices.Frontiers in plant science · 2023Article
- High-throughput and automatic structural and developmental root phenotyping on Arabidopsis seedlings.Plant methods · 2022Article
- Genetic variation underlying differential ammonium and nitrate responses in Arabidopsis thaliana.The Plant cell · 2022Article
37 more citing papers are in PubMed but not listed here.
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Authors and funding
6 authors.
Funding
Abstract
We present a novel image analysis tool that allows the semiautomated quantification of complex root system architectures in a range of plant species grown and imaged in a variety of ways. The automatic component of RootNav takes a top-down approach, utilizing the powerful expectation maximization classification algorithm to examine regions of the input image, calculating the likelihood that given pixels correspond to roots. This information is used as the basis for an optimization approach to root detection and quantification, which effectively fits a root model to the image data. The resulting user experience is akin to defining routes on a motorist's satellite navigation system: RootNav makes an initial optimized estimate of paths from the seed point to root apices, and the user is able to easily and intuitively refine the results using a visual approach. The proposed method is evaluated on winter wheat (Triticum aestivum) images (and demonstrated on Arabidopsis [Arabidopsis thaliana], Brassica napus, and rice [Oryza sativa]), and results are compared with manual analysis. Four exemplar traits are calculated and show clear illustrative differences between some of the wheat accessions. RootNav, however, provides the structural information needed to support extraction of a wider variety of biologically relevant measures. A separate viewer tool is provided to recover a rich set of architectural traits from RootNav's core representation.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.