ArticlePlant physiology2015
Root system markup language: toward a unified root architecture description language.
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Article in Plant physiology, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 48 papers.
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48 citing papers in PubMed.
- Root system architecture reorganization under decreasing soil phosphorus lowers root system conductance of Zea mays.Annals of botany · 2025Article
- Genetic analysis of common bean (Phaseolus vulgaris L.) genotypes for root traits, yield components and seed yield.Journal of applied genetics · 2025Article
- Growth Cost and Transport Efficiency Tradeoffs Define Root System Optimization Across Varying Developmental Stages and Environments in Arabidopsis.bioRxiv : the preprint server for biology · 2025Article
- VRoot: A VR-Based application for manual root system architecture reconstruction.Plant phenomics (Washington, D.C.) · 2025Article
- High-throughput phenotyping of wheat root angle and coleoptile length at different temperatures using 3D-printed equipment.BMC plant biology · 2025Article
- Seedling root system adaptation to water availability during maize domestication and global expansion.Nature genetics · 2024Article
- OPIA: an open archive of plant images and related phenotypic traits.Nucleic acids research · 2024Article
- The State of the Art in Root System Architecture Image Analysis Using Artificial Intelligence: A Review.Plant phenomics (Washington, D.C.) · 2024Review
- A Field-to-Parameter Pipeline for Analyzing and Simulating Root System Architecture of Woody Perennials: Application to Grapevine Rootstocks.Plant phenomics (Washington, D.C.) · 2024Article
- Lysinibacillus spp.: an IAA-producing endospore forming-bacteria that promotes plant growth.Antonie van Leeuwenhoek · 2023Article
- Phenotypic quantification of root spatial distribution along circumferential direction for field paddy-wheat.PloS one · 2023Article
- 3D U-Net Segmentation Improves Root System Reconstruction from 3D MRI Images in Automated and Manual Virtual Reality Work Flows.Plant phenomics (Washington, D.C.) · 2023Article
- High-throughput and automatic structural and developmental root phenotyping on Arabidopsis seedlings.Plant methods · 2022Article
- Phenotyping and modeling of root hydraulic architecture reveal critical determinants of axial water transport.Plant physiology · 2022Article
- Holm oak decline is determined by shifts in fine root phenotypic plasticity in response to belowground stress.The New phytologist · 2022Article
- Identifying Developmental Patterns in Structured Plant Phenotyping Data.Methods in molecular biology (Clifton, N.J.) · 2022Article
- Analysis of Plant Root Gravitropism.Methods in molecular biology (Clifton, N.J.) · 2022Article
- TopoRoot: a method for computing hierarchy and fine-grained traits of maize roots from 3D imaging.Plant methods · 2021Article
- Genomic prediction and QTL mapping of root system architecture and above-ground agronomic traits in rice (Oryza sativa L.) with a multitrait index and Bayesian networks.G3 (Bethesda, Md.) · 2021Article
- Root phenotyping: important and minimum information required for root modeling in crop plants.Breeding science · 2021Article
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Authors and funding
12 authors.
Guillaume LobetPhytoSYSTEMS, Université de Liège, 4000 Liege, Belgium (G.L.);Centre for Plant Integrative Biology, School of Biosciences, University of Nottingham, Sutton Bonington LE12 5RD, United Kingdom (M.P.P.);Virtual Plants, Inria, Cirad, Institut National de la Recherche Agronomique, 34095 Montpellier, France (J.D., C.P., C.G.);Institut de Biologie Computationnelle, F-34095 Montpellier, France (C.P.);Earth and Life Institute, Université Catholique de Louvain, 1348 Louvain-la-Neuve, Belgium (X.D., M.J., F.M.);Institut für Bio- und Geowissenschaften: Agrosphäre, Forschungszentrum Jülich, D-52425 Julich, Germany (M.J., A.S.);Computational Science Center, University of Vienna, 1090 Vienna, Austria (D.L.);Biochemistry and Plant Molecular Physiology, Unité Mixte de Recherche 5004 Centre National de la Recherche Scientifique/Institut National de la Recherche Agronomique/SupAgro-M/UM2, Institut de Biologie Intégrative des Plantes, 34060 Montpellier cedex 1, France (P.N.); andSchool of Computer Science, University of Nottingham, Nottingham NG8 1BB, United Kingdom (T.P.P.).ORCID http://orcid.org/0000-0002-5883-4572
Michael P PoundPhytoSYSTEMS, Université de Liège, 4000 Liege, Belgium (G.L.);Centre for Plant Integrative Biology, School of Biosciences, University of Nottingham, Sutton Bonington LE12 5RD, United Kingdom (M.P.P.);Virtual Plants, Inria, Cirad, Institut National de la Recherche Agronomique, 34095 Montpellier, France (J.D., C.P., C.G.);Institut de Biologie Computationnelle, F-34095 Montpellier, France (C.P.);Earth and Life Institute, Université Catholique de Louvain, 1348 Louvain-la-Neuve, Belgium (X.D., M.J., F.M.);Institut für Bio- und Geowissenschaften: Agrosphäre, Forschungszentrum Jülich, D-52425 Julich, Germany (M.J., A.S.);Computational Science Center, University of Vienna, 1090 Vienna, Austria (D.L.);Biochemistry and Plant Molecular Physiology, Unité Mixte de Recherche 5004 Centre National de la Recherche Scientifique/Institut National de la Recherche Agronomique/SupAgro-M/UM2, Institut de Biologie Intégrative des Plantes, 34060 Montpellier cedex 1, France (P.N.); andSchool of Computer Science, University of Nottingham, Nottingham NG8 1BB, United Kingdom (T.P.P.).
Julien DienerPhytoSYSTEMS, Université de Liège, 4000 Liege, Belgium (G.L.);Centre for Plant Integrative Biology, School of Biosciences, University of Nottingham, Sutton Bonington LE12 5RD, United Kingdom (M.P.P.);Virtual Plants, Inria, Cirad, Institut National de la Recherche Agronomique, 34095 Montpellier, France (J.D., C.P., C.G.);Institut de Biologie Computationnelle, F-34095 Montpellier, France (C.P.);Earth and Life Institute, Université Catholique de Louvain, 1348 Louvain-la-Neuve, Belgium (X.D., M.J., F.M.);Institut für Bio- und Geowissenschaften: Agrosphäre, Forschungszentrum Jülich, D-52425 Julich, Germany (M.J., A.S.);Computational Science Center, University of Vienna, 1090 Vienna, Austria (D.L.);Biochemistry and Plant Molecular Physiology, Unité Mixte de Recherche 5004 Centre National de la Recherche Scientifique/Institut National de la Recherche Agronomique/SupAgro-M/UM2, Institut de Biologie Intégrative des Plantes, 34060 Montpellier cedex 1, France (P.N.); andSchool of Computer Science, University of Nottingham, Nottingham NG8 1BB, United Kingdom (T.P.P.).ORCID http://orcid.org/0000-0002-8214-6411
Christophe PradalPhytoSYSTEMS, Université de Liège, 4000 Liege, Belgium (G.L.);Centre for Plant Integrative Biology, School of Biosciences, University of Nottingham, Sutton Bonington LE12 5RD, United Kingdom (M.P.P.);Virtual Plants, Inria, Cirad, Institut National de la Recherche Agronomique, 34095 Montpellier, France (J.D., C.P., C.G.);Institut de Biologie Computationnelle, F-34095 Montpellier, France (C.P.);Earth and Life Institute, Université Catholique de Louvain, 1348 Louvain-la-Neuve, Belgium (X.D., M.J., F.M.);Institut für Bio- und Geowissenschaften: Agrosphäre, Forschungszentrum Jülich, D-52425 Julich, Germany (M.J., A.S.);Computational Science Center, University of Vienna, 1090 Vienna, Austria (D.L.);Biochemistry and Plant Molecular Physiology, Unité Mixte de Recherche 5004 Centre National de la Recherche Scientifique/Institut National de la Recherche Agronomique/SupAgro-M/UM2, Institut de Biologie Intégrative des Plantes, 34060 Montpellier cedex 1, France (P.N.); andSchool of Computer Science, University of Nottingham, Nottingham NG8 1BB, United Kingdom (T.P.P.).
Xavier DrayePhytoSYSTEMS, Université de Liège, 4000 Liege, Belgium (G.L.);Centre for Plant Integrative Biology, School of Biosciences, University of Nottingham, Sutton Bonington LE12 5RD, United Kingdom (M.P.P.);Virtual Plants, Inria, Cirad, Institut National de la Recherche Agronomique, 34095 Montpellier, France (J.D., C.P., C.G.);Institut de Biologie Computationnelle, F-34095 Montpellier, France (C.P.);Earth and Life Institute, Université Catholique de Louvain, 1348 Louvain-la-Neuve, Belgium (X.D., M.J., F.M.);Institut für Bio- und Geowissenschaften: Agrosphäre, Forschungszentrum Jülich, D-52425 Julich, Germany (M.J., A.S.);Computational Science Center, University of Vienna, 1090 Vienna, Austria (D.L.);Biochemistry and Plant Molecular Physiology, Unité Mixte de Recherche 5004 Centre National de la Recherche Scientifique/Institut National de la Recherche Agronomique/SupAgro-M/UM2, Institut de Biologie Intégrative des Plantes, 34060 Montpellier cedex 1, France (P.N.); andSchool of Computer Science, University of Nottingham, Nottingham NG8 1BB, United Kingdom (T.P.P.) xavier.draye@uclouvain.be.
Christophe GodinPhytoSYSTEMS, Université de Liège, 4000 Liege, Belgium (G.L.);Centre for Plant Integrative Biology, School of Biosciences, University of Nottingham, Sutton Bonington LE12 5RD, United Kingdom (M.P.P.);Virtual Plants, Inria, Cirad, Institut National de la Recherche Agronomique, 34095 Montpellier, France (J.D., C.P., C.G.);Institut de Biologie Computationnelle, F-34095 Montpellier, France (C.P.);Earth and Life Institute, Université Catholique de Louvain, 1348 Louvain-la-Neuve, Belgium (X.D., M.J., F.M.);Institut für Bio- und Geowissenschaften: Agrosphäre, Forschungszentrum Jülich, D-52425 Julich, Germany (M.J., A.S.);Computational Science Center, University of Vienna, 1090 Vienna, Austria (D.L.);Biochemistry and Plant Molecular Physiology, Unité Mixte de Recherche 5004 Centre National de la Recherche Scientifique/Institut National de la Recherche Agronomique/SupAgro-M/UM2, Institut de Biologie Intégrative des Plantes, 34060 Montpellier cedex 1, France (P.N.); andSchool of Computer Science, University of Nottingham, Nottingham NG8 1BB, United Kingdom (T.P.P.).
Mathieu JavauxPhytoSYSTEMS, Université de Liège, 4000 Liege, Belgium (G.L.);Centre for Plant Integrative Biology, School of Biosciences, University of Nottingham, Sutton Bonington LE12 5RD, United Kingdom (M.P.P.);Virtual Plants, Inria, Cirad, Institut National de la Recherche Agronomique, 34095 Montpellier, France (J.D., C.P., C.G.);Institut de Biologie Computationnelle, F-34095 Montpellier, France (C.P.);Earth and Life Institute, Université Catholique de Louvain, 1348 Louvain-la-Neuve, Belgium (X.D., M.J., F.M.);Institut für Bio- und Geowissenschaften: Agrosphäre, Forschungszentrum Jülich, D-52425 Julich, Germany (M.J., A.S.);Computational Science Center, University of Vienna, 1090 Vienna, Austria (D.L.);Biochemistry and Plant Molecular Physiology, Unité Mixte de Recherche 5004 Centre National de la Recherche Scientifique/Institut National de la Recherche Agronomique/SupAgro-M/UM2, Institut de Biologie Intégrative des Plantes, 34060 Montpellier cedex 1, France (P.N.); andSchool of Computer Science, University of Nottingham, Nottingham NG8 1BB, United Kingdom (T.P.P.).ORCID http://orcid.org/0000-0002-6168-5467
Daniel LeitnerPhytoSYSTEMS, Université de Liège, 4000 Liege, Belgium (G.L.);Centre for Plant Integrative Biology, School of Biosciences, University of Nottingham, Sutton Bonington LE12 5RD, United Kingdom (M.P.P.);Virtual Plants, Inria, Cirad, Institut National de la Recherche Agronomique, 34095 Montpellier, France (J.D., C.P., C.G.);Institut de Biologie Computationnelle, F-34095 Montpellier, France (C.P.);Earth and Life Institute, Université Catholique de Louvain, 1348 Louvain-la-Neuve, Belgium (X.D., M.J., F.M.);Institut für Bio- und Geowissenschaften: Agrosphäre, Forschungszentrum Jülich, D-52425 Julich, Germany (M.J., A.S.);Computational Science Center, University of Vienna, 1090 Vienna, Austria (D.L.);Biochemistry and Plant Molecular Physiology, Unité Mixte de Recherche 5004 Centre National de la Recherche Scientifique/Institut National de la Recherche Agronomique/SupAgro-M/UM2, Institut de Biologie Intégrative des Plantes, 34060 Montpellier cedex 1, France (P.N.); andSchool of Computer Science, University of Nottingham, Nottingham NG8 1BB, United Kingdom (T.P.P.).
Félicien MeunierPhytoSYSTEMS, Université de Liège, 4000 Liege, Belgium (G.L.);Centre for Plant Integrative Biology, School of Biosciences, University of Nottingham, Sutton Bonington LE12 5RD, United Kingdom (M.P.P.);Virtual Plants, Inria, Cirad, Institut National de la Recherche Agronomique, 34095 Montpellier, France (J.D., C.P., C.G.);Institut de Biologie Computationnelle, F-34095 Montpellier, France (C.P.);Earth and Life Institute, Université Catholique de Louvain, 1348 Louvain-la-Neuve, Belgium (X.D., M.J., F.M.);Institut für Bio- und Geowissenschaften: Agrosphäre, Forschungszentrum Jülich, D-52425 Julich, Germany (M.J., A.S.);Computational Science Center, University of Vienna, 1090 Vienna, Austria (D.L.);Biochemistry and Plant Molecular Physiology, Unité Mixte de Recherche 5004 Centre National de la Recherche Scientifique/Institut National de la Recherche Agronomique/SupAgro-M/UM2, Institut de Biologie Intégrative des Plantes, 34060 Montpellier cedex 1, France (P.N.); andSchool of Computer Science, University of Nottingham, Nottingham NG8 1BB, United Kingdom (T.P.P.).
Philippe NacryPhytoSYSTEMS, Université de Liège, 4000 Liege, Belgium (G.L.);Centre for Plant Integrative Biology, School of Biosciences, University of Nottingham, Sutton Bonington LE12 5RD, United Kingdom (M.P.P.);Virtual Plants, Inria, Cirad, Institut National de la Recherche Agronomique, 34095 Montpellier, France (J.D., C.P., C.G.);Institut de Biologie Computationnelle, F-34095 Montpellier, France (C.P.);Earth and Life Institute, Université Catholique de Louvain, 1348 Louvain-la-Neuve, Belgium (X.D., M.J., F.M.);Institut für Bio- und Geowissenschaften: Agrosphäre, Forschungszentrum Jülich, D-52425 Julich, Germany (M.J., A.S.);Computational Science Center, University of Vienna, 1090 Vienna, Austria (D.L.);Biochemistry and Plant Molecular Physiology, Unité Mixte de Recherche 5004 Centre National de la Recherche Scientifique/Institut National de la Recherche Agronomique/SupAgro-M/UM2, Institut de Biologie Intégrative des Plantes, 34060 Montpellier cedex 1, France (P.N.); andSchool of Computer Science, University of Nottingham, Nottingham NG8 1BB, United Kingdom (T.P.P.).ORCID http://orcid.org/0000-0001-7766-4989
Tony P PridmorePhytoSYSTEMS, Université de Liège, 4000 Liege, Belgium (G.L.);Centre for Plant Integrative Biology, School of Biosciences, University of Nottingham, Sutton Bonington LE12 5RD, United Kingdom (M.P.P.);Virtual Plants, Inria, Cirad, Institut National de la Recherche Agronomique, 34095 Montpellier, France (J.D., C.P., C.G.);Institut de Biologie Computationnelle, F-34095 Montpellier, France (C.P.);Earth and Life Institute, Université Catholique de Louvain, 1348 Louvain-la-Neuve, Belgium (X.D., M.J., F.M.);Institut für Bio- und Geowissenschaften: Agrosphäre, Forschungszentrum Jülich, D-52425 Julich, Germany (M.J., A.S.);Computational Science Center, University of Vienna, 1090 Vienna, Austria (D.L.);Biochemistry and Plant Molecular Physiology, Unité Mixte de Recherche 5004 Centre National de la Recherche Scientifique/Institut National de la Recherche Agronomique/SupAgro-M/UM2, Institut de Biologie Intégrative des Plantes, 34060 Montpellier cedex 1, France (P.N.); andSchool of Computer Science, University of Nottingham, Nottingham NG8 1BB, United Kingdom (T.P.P.).
Andrea SchnepfPhytoSYSTEMS, Université de Liège, 4000 Liege, Belgium (G.L.);Centre for Plant Integrative Biology, School of Biosciences, University of Nottingham, Sutton Bonington LE12 5RD, United Kingdom (M.P.P.);Virtual Plants, Inria, Cirad, Institut National de la Recherche Agronomique, 34095 Montpellier, France (J.D., C.P., C.G.);Institut de Biologie Computationnelle, F-34095 Montpellier, France (C.P.);Earth and Life Institute, Université Catholique de Louvain, 1348 Louvain-la-Neuve, Belgium (X.D., M.J., F.M.);Institut für Bio- und Geowissenschaften: Agrosphäre, Forschungszentrum Jülich, D-52425 Julich, Germany (M.J., A.S.);Computational Science Center, University of Vienna, 1090 Vienna, Austria (D.L.);Biochemistry and Plant Molecular Physiology, Unité Mixte de Recherche 5004 Centre National de la Recherche Scientifique/Institut National de la Recherche Agronomique/SupAgro-M/UM2, Institut de Biologie Intégrative des Plantes, 34060 Montpellier cedex 1, France (P.N.); andSchool of Computer Science, University of Nottingham, Nottingham NG8 1BB, United Kingdom (T.P.P.).
Funding
No grant is acknowledged in the PubMed record.
Abstract
The number of image analysis tools supporting the extraction of architectural features of root systems has increased in recent years. These tools offer a handy set of complementary facilities, yet it is widely accepted that none of these software tools is able to extract in an efficient way the growing array of static and dynamic features for different types of images and species. We describe the Root System Markup Language (RSML), which has been designed to overcome two major challenges: (1) to enable portability of root architecture data between different software tools in an easy and interoperable manner, allowing seamless collaborative work; and (2) to provide a standard format upon which to base central repositories that will soon arise following the expanding worldwide root phenotyping effort. RSML follows the XML standard to store two- or three-dimensional image metadata, plant and root properties and geometries, continuous functions along individual root paths, and a suite of annotations at the image, plant, or root scale at one or several time points. Plant ontologies are used to describe botanical entities that are relevant at the scale of root system architecture. An XML schema describes the features and constraints of RSML, and open-source packages have been developed in several languages (R, Excel, Java, Python, and C#) to enable researchers to integrate RSML files into popular research workflow.
Indexed as
Programming LanguagesSoftwareImaging, Three-DimensionalModels, BiologicalPlant RootsWorkflow
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