Challenges and opportunities for quantifying roots and rhizosphere interactions through imaging and image analysis

A scanner system for high-resolution quantification of variation in root growth dynamics of Brassica rapa genotypes

(2014) Michael O. Adu et al.   JOURNAL OF EXPERIMENTAL BOTANY

Understanding the genetic control and physiological traits associated with rhizosheath production by barley (Hordeum vulgare)

(2014) Timothy S. George et al.   NEW PHYTOLOGIST

LEGO® Bricks as Building Blocks for Centimeter-Scale Biological Environments: The Case of Plants

(2014) Kara R. Lind et al.   PLoS One

Plant roots use a patterning mechanism to position lateral root branches toward available water

(2014) Y. Bao et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Disentangling who is who during rhizosphere acidification in root interactions: combining fluorescence with optode techniques

(2014) Marc Faget et al.   Frontiers in Plant Science

Can root electrical capacitance be used to predict root mass in soil?

(2013) R. C. Dietrich et al.   ANNALS OF BOTANY

Quantitative imaging of rhizosphere pH and CO2 dynamics with planar optodes

(2013) Stephan Blossfeld et al.   ANNALS OF BOTANY

Root cortical aerenchyma inhibits radial nutrient transport in maize (Zea mays)

(2013) Bo Hu et al.   ANNALS OF BOTANY

Root–root interactions: extending our perspective to be more inclusive of the range of theories in ecology and agriculture using in-vivo analyses

(2013) Marc Faget et al.   ANNALS OF BOTANY

Matching roots to their environment

(2013) Philip J. White et al.   ANNALS OF BOTANY

Steep, cheap and deep: an ideotype to optimize water and N acquisition by maize root systems

(2013) Jonathan P. Lynch   ANNALS OF BOTANY

A rapid, controlled-environment seedling root screen for wheat correlates well with rooting depths at vegetative, but not reproductive, stages at two field sites

(2013) M. Watt et al.   ANNALS OF BOTANY

Exploring the interacting effect of soil texture and bulk density on root system development in tomato (Solanum lycopersicum L.)

(2013) Saoirse R. Tracy et al.   ENVIRONMENTAL AND EXPERIMENTAL BOTANY

How Conserved Are the Bacterial Communities Associated With Aphids? A Detailed Assessment of the Brevicoryne brassicae (Hemiptera: Aphididae) Using 16S rDNA

(2013) E. L. Clark et al.   ENVIRONMENTAL ENTOMOLOGY

The Impact of Beneficial Plant-Associated Microbes on Plant Phenotypic Plasticity

(2013) Chooi-Hua Goh et al.   JOURNAL OF CHEMICAL ECOLOGY

High resolution synchrotron imaging of wheat root hairs growing in soil and image based modelling of phosphate uptake

(2013) Samuel D. Keyes et al.   NEW PHYTOLOGIST

Light Sheet Tomography (LST) for in situ imaging of plant roots

(2013) Zhengyi Yang et al.   OPTICS EXPRESS

Spatio-temporal mapping of local soil pH changes induced by roots of lupin and soft-rush

(2013) Nicole Rudolph et al.   PLANT AND SOIL

Quantifying the effect of soil moisture content on segmenting root system architecture in X-ray computed tomography images

(2013) Susan Zappala et al.   PLANT AND SOIL

An online database for plant image analysis software tools

(2013) Guillaume Lobet et al.   Plant Methods

Root hair length and rhizosheath mass depend on soil porosity, strength and water content in barley genotypes

(2013) Rebecca E. Haling et al.   PLANTA

Distribution of microbial- and root-derived phosphatase activities in the rhizosphere depending on P availability and C allocation – Coupling soil zymography with 14C imaging

(2013) Marie Spohn et al.   SOIL BIOLOGY & BIOCHEMISTRY

Cell to whole-plant phenotyping: the best is yet to come

(2013) Stijn Dhondt et al.   TRENDS IN PLANT SCIENCE

Plant growth-promoting rhizobacteria and root system functioning

(2013) Jordan Vacheron et al.   Frontiers in Plant Science

Root traits for infertile soils

(2013) Philip J. White et al.   Frontiers in Plant Science

What are the implications of variation in root hair length on tolerance to phosphorus deficiency in combination with water stress in barley (Hordeum vulgare)?

(2012) L.K. Brown et al.   ANNALS OF BOTANY

Quantifying the impact of soil compaction on root system architecture in tomato (Solanum lycopersicum) by X-ray micro-computed tomography

(2012) Saoirse R. Tracy et al.   ANNALS OF BOTANY

Soil strength and macropore volume limit root elongation rates in many UK agricultural soils

(2012) Tracy A. Valentine et al.   ANNALS OF BOTANY

High-throughput root phenotyping screens identify genetic loci associated with root architectural traits in Brassica napus under contrasting phosphate availabilities

(2012) Lei Shi et al.   ANNALS OF BOTANY

Advanced phenotyping offers opportunities for improved breeding of forage and turf species

(2012) Achim Walter et al.   ANNALS OF BOTANY

Quantitative Imaging with Fluorescent Biosensors

(2012) Sakiko Okumoto et al.   Annual Review of Plant Biology

Manipulating the soil microbiome to increase soil health and plant fertility

(2012) Jacqueline M. Chaparro et al.   BIOLOGY AND FERTILITY OF SOILS

GiA Roots: software for the high throughput analysis of plant root system architecture

(2012) Taras Galkovskyi et al.   BMC PLANT BIOLOGY

Estimating root-soil contact from 3D X-ray microtomographs

(2012) S. Schmidt et al.   EUROPEAN JOURNAL OF SOIL SCIENCE

GROWSCREEN-Rhizo is a novel phenotyping robot enabling simultaneous measurements of root and shoot growth for plants grown in soil-filled rhizotrons

(2012) Kerstin A. Nagel et al.   FUNCTIONAL PLANT BIOLOGY

Integrated genetic and computation methods for in planta cytometry

(2012) Fernán Federici et al.   NATURE METHODS

A new tool for analysis of root growth in the spatio-temporal continuum

(2012) Paramita Basu et al.   NEW PHYTOLOGIST

Aluminium tolerance of root hairs underlies genotypic differences in rhizosheath size of wheat (Triticum aestivum) grown on acid soil

(2012) Emmanuel Delhaize et al.   NEW PHYTOLOGIST

Recovering the dynamics of root growth and development using novel image acquisition and analysis methods

(2012) D. M. Wells et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Spatial distribution and phenotypic variation in root cortical aerenchyma of maize (Zea mays L.)

(2012) Amy L. Burton et al.   PLANT AND SOIL

RootScan: Software for high-throughput analysis of root anatomical traits

(2012) Amy L. Burton et al.   PLANT AND SOIL

Quantitative Analysis of Lateral Root Development: Pitfalls and How to Avoid Them

(2012) J. G. Dubrovsky et al.   PLANT CELL

High-throughput two-dimensional root system phenotyping platform facilitates genetic analysis of root growth and development

(2012) RANDY T. CLARK et al.   PLANT CELL AND ENVIRONMENT

OsMYB2P-1, an R2R3 MYB Transcription Factor, Is Involved in the Regulation of Phosphate-Starvation Responses and Root Architecture in Rice

(2012) X. Dai et al.   PLANT PHYSIOLOGY

Transparent Soil for Imaging the Rhizosphere

(2012) Helen Downie et al.   PLoS One

New Lens Offers Scientist A Brighter Outlook

(2012) A. Saini   SCIENCE

Integrated genomics, physiology and breeding approaches for improving drought tolerance in crops

(2012) Reyazul Rouf Mir et al.   THEORETICAL AND APPLIED GENETICS

The rhizosphere microbiome and plant health

(2012) Roeland L. Berendsen et al.   TRENDS IN PLANT SCIENCE

Stressed food – The impact of abiotic environmental stresses on crop quality

(2011) Yunxia Wang et al.   AGRICULTURE ECOSYSTEMS & ENVIRONMENT

Functional characterisation of metal(loid) processes in planta through the integration of synchrotron techniques and plant molecular biology

(2011) Erica Donner et al.   ANALYTICAL AND BIOANALYTICAL CHEMISTRY

Breeding crop plants with deep roots: their role in sustainable carbon, nutrient and water sequestration

(2011) D. B. Kell   ANNALS OF BOTANY

Real-time imaging and analysis of differences in cadmium dynamics in rice cultivars (Oryza sativa) using positron-emitting107Cd tracer

(2011) Satoru Ishikawa et al.   BMC PLANT BIOLOGY

Is There a Need for a More Sustainable Agriculture?

(2011) Tiziano Gomiero et al.   CRITICAL REVIEWS IN PLANT SCIENCES

From lab to field, new approaches to phenotyping root system architecture

(2011) Jinming Zhu et al.   CURRENT OPINION IN PLANT BIOLOGY

MicroCT for molecular imaging: Quantitative visualization of complete three-dimensional distributions of gene products in embryonic limbs

(2011) Brian D. Metscher et al.   DEVELOPMENTAL DYNAMICS

High-resolution chemical imaging of labile phosphorus in the rhizosphere of Brassica napus L. cultivars

(2011) Jakob Santner et al.   ENVIRONMENTAL AND EXPERIMENTAL BOTANY

Imaging-optode measurements of ammonium distribution in soil after different manure amendments

(2011) S. Delin et al.   EUROPEAN JOURNAL OF SOIL SCIENCE

Food vs. fuel: the use of land for lignocellulosic ‘next generation’ energy crops that minimize competition with primary food production

(2011) John Valentine et al.   Global Change Biology Bioenergy

Automated statistical method to align 2D chemical maps with 3D X-ray computed micro-tomographic images of soils

(2011) Simona M. Hapca et al.   GEODERMA

Global crop improvement networks to bridge technology gaps

(2011) M. P. Reynolds et al.   JOURNAL OF EXPERIMENTAL BOTANY

Dynamic oxygen mapping in the root zone by fluorescence dye imaging combined with neutron radiography

(2011) Nicole Rudolph et al.   JOURNAL OF SOILS AND SEDIMENTS

Three-dimensional visualization and quantification of water content in the rhizosphere

(2011) Ahmad B. Moradi et al.   NEW PHYTOLOGIST

The use of PET/CT scanning technique for 3D visualization and quantification of real-time soil/plant interactions

(2011) Amin Garbout et al.   PLANT AND SOIL

Quantifying the effect of soil compaction on three varieties of wheat (Triticum aestivum L.) using X-ray Micro Computed Tomography (CT)

(2011) Saoirse R. Tracy et al.   PLANT AND SOIL

Developing X-ray Computed Tomography to non-invasively image 3-D root systems architecture in soil

(2011) S. J. Mooney et al.   PLANT AND SOIL

High-resolution live imaging of plant growth in near physiological bright conditions using light sheet fluorescence microscopy

(2011) Alexis Maizel et al.   PLANT JOURNAL

Crop Root Behavior Coordinates Phosphorus Status and Neighbors: From Field Studies to Three-Dimensional in Situ Reconstruction of Root System Architecture

(2011) S. Fang et al.   PLANT PHYSIOLOGY

Three-Dimensional Root Phenotyping with a Novel Imaging and Software Platform

(2011) R. T. Clark et al.   PLANT PHYSIOLOGY

A Novel Image-Analysis Toolbox Enabling Quantitative Analysis of Root System Architecture

(2011) Guillaume Lobet et al.   PLANT PHYSIOLOGY

RooTrak: Automated Recovery of Three-Dimensional Plant Root Architecture in Soil from X-Ray Microcomputed Tomography Images Using Visual Tracking

(2011) S. Mairhofer et al.   PLANT PHYSIOLOGY

Automated motion estimation of root responses to sucrose in two Arabidopsis thaliana genotypes using confocal microscopy

(2011) Nathalie Wuyts et al.   PLANTA

Quantitation of Cellular Dynamics in Growing Arabidopsis Roots with Light Sheet Microscopy

(2011) Giovanni Sena et al.   PLoS One

Global food demand and the sustainable intensification of agriculture

(2011) D. Tilman et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The dynamics of oxygen concentration, pH value, and organic acids in the rhizosphere of Juncus spp.

(2011) Stephan Blossfeld et al.   SOIL BIOLOGY & BIOCHEMISTRY

Relationship between root structure and root cadmium uptake in maize

(2010) Tanegmart Redjala et al.   ENVIRONMENTAL AND EXPERIMENTAL BOTANY

Quantifying rhizosphere particle movement around mutant maize roots using time-lapse imaging and particle image velocimetry

(2010) A. V. Vollsnes et al.   EUROPEAN JOURNAL OF SOIL SCIENCE

Model-assisted integration of physiological and environmental constraints affecting the dynamic and spatial patterns of root water uptake from soils

(2010) Xavier Draye et al.   JOURNAL OF EXPERIMENTAL BOTANY

The X-factor: visualizing undisturbed root architecture in soils using X-ray computed tomography

(2010) S. R. Tracy et al.   JOURNAL OF EXPERIMENTAL BOTANY

Root elongation, water stress, and mechanical impedance: a review of limiting stresses and beneficial root tip traits

(2010) A. Glyn Bengough et al.   JOURNAL OF EXPERIMENTAL BOTANY

Combination of Fluorescent Reporters for Simultaneous Monitoring of Root Colonization and Antifungal Gene Expression by a Biocontrol Pseudomonad on Cereals with Flow Cytometry

(2010) Laurène Rochat et al.   MOLECULAR PLANT-MICROBE INTERACTIONS

Phenomics: the next challenge

(2010) David Houle et al.   NATURE REVIEWS GENETICS

Shovelomics: high throughput phenotyping of maize (Zea mays L.) root architecture in the field

(2010) Samuel Trachsel et al.   PLANT AND SOIL

Dynamics of soil water content in the rhizosphere

(2010) Andrea Carminati et al.   PLANT AND SOIL

The roots of a new green revolution

(2010) Griet Den Herder et al.   TRENDS IN PLANT SCIENCE

Plant growth-promoting activities of fluorescent pseudomonads, isolated from the Iranian soils

(2009) P. Abbas-Zadeh et al.   ACTA PHYSIOLOGIAE PLANTARUM

Multi-electrode 3D resistivity imaging of alfalfa root zone

(2009) Mariana Amato et al.   EUROPEAN JOURNAL OF AGRONOMY

Deep rooting and drought screening of cereal crops: A novel field-based method and its application

(2009) B.M. McKenzie et al.   FIELD CROPS RESEARCH

The use of green fluorescent protein as a tool to identify roots in mixed plant stands

(2009) Marc Faget et al.   FUNCTIONAL PLANT BIOLOGY

Root phenomics of crops: opportunities and challenges

(2009) Peter J. Gregory et al.   FUNCTIONAL PLANT BIOLOGY

The effects of dwarfing genes on seedling root growth of wheat

(2009) T. Wojciechowski et al.   JOURNAL OF EXPERIMENTAL BOTANY

Integrating pests and pathogens into the climate change/food security debate

(2009) P. J. Gregory et al.   JOURNAL OF EXPERIMENTAL BOTANY

Estimating the motion of plant root cells from in vivo confocal laser scanning microscopy images

(2009) Timothy J. Roberts et al.   MACHINE VISION AND APPLICATIONS

Growth of axile and lateral roots of maize: I development of a phenotying platform

(2009) A. Hund et al.   PLANT AND SOIL

Rhizosphere pH dynamics in trace-metal-contaminated soils, monitored with planar pH optodes

(2009) Stephan Blossfeld et al.   PLANT AND SOIL

Strategies and methods for studying the rhizosphere—the plant science toolbox

(2009) Günter Neumann et al.   PLANT AND SOIL

Plant-microbe-soil interactions in the rhizosphere: an evolutionary perspective

(2009) Hans Lambers et al.   PLANT AND SOIL

The distribution and abundance of wheat roots in a dense, structured subsoil – implications for water uptake

(2009) ROSEMARY G. WHITE et al.   PLANT CELL AND ENVIRONMENT

3D reconstruction and dynamic modeling of root architecture in situ and its application to crop phosphorus research

(2009) Suqin Fang et al.   PLANT JOURNAL

Combined MRI-PET dissects dynamic changes in plant structures and functions

(2009) Siegfried Jahnke et al.   PLANT JOURNAL

Plasticity of Arabidopsis Root Gravitropism throughout a Multidimensional Condition Space Quantified by Automated Image Analysis

(2009) T. L. Durham Brooks et al.   PLANT PHYSIOLOGY

High-Throughput Quantification of Root Growth Using a Novel Image-Analysis Tool

(2009) A. French et al.   PLANT PHYSIOLOGY

QTL Mapping in New Arabidopsis thaliana Advanced Intercross-Recombinant Inbred Lines

(2009) Sureshkumar Balasubramanian et al.   PLoS One

Soil compaction and soil management – a review

(2009) T. Batey   SOIL USE AND MANAGEMENT

Water Infiltration and Redistribution in Soil Aggregate Packings

(2009) A. Carminati et al.   VADOSE ZONE JOURNAL

When Roots Lose Contact

(2009) Andrea Carminati et al.   VADOSE ZONE JOURNAL

Integrating technologies for comparing 3D gene expression domains in the developing chick limb

(2008) Malcolm E. Fisher et al.   DEVELOPMENTAL BIOLOGY

Determination of Ammonium Turnover and Flow Patterns Close to Roots Using Imaging Optodes

(2008) Niklas Strömberg   ENVIRONMENTAL SCIENCE & TECHNOLOGY

Exploring the transport of plant metabolites using positron emitting radiotracers

(2008) Matthew R. Kiser et al.   HFSP Journal

Genotype–phenotype databases: challenges and solutions for the post-genomic era

(2008) Gudmundur A. Thorisson et al.   NATURE REVIEWS GENETICS

Neutron radiography as a tool for revealing root development in soil: capabilities and limitations

(2008) Ahmad B. Moradi et al.   PLANT AND SOIL

Root allocation in metal-rich patch by Thlaspi caerulescens from normal and metalliferous soil—new insights into the rhizobox approach

(2008) Caroline Dechamps et al.   PLANT AND SOIL

Sampling, defining, characterising and modeling the rhizosphere—the soil science tool box

(2008) Jörg Luster et al.   PLANT AND SOIL

EZ-Rhizo: integrated software for the fast and accurate measurement of root system architecture

(2008) Patrick Armengaud et al.   PLANT JOURNAL

Improved detection of soil microorganisms using fluorescence in situ hybridization (FISH) and catalyzed reporter deposition (CARD-FISH)

(2008) Thilo Eickhorst et al.   SOIL BIOLOGY & BIOCHEMISTRY

Microsensing of Water Dynamics and Root Distributions in Sandy Soils

(2008) Eran Segal et al.   VADOSE ZONE JOURNAL

Quantitative Imaging of Infiltration, Root Growth, and Root Water Uptake via Neutron Radiography

(2008) Sascha E. Oswald et al.   VADOSE ZONE JOURNAL

Changes in Soil Water Content Resulting from Root Uptake Monitored by Magnetic Resonance Imaging

(2008) A. Pohlmeier et al.   VADOSE ZONE JOURNAL

Image segmentation evaluation: A survey of unsupervised methods

(2007) Hui Zhang et al.   COMPUTER VISION AND IMAGE UNDERSTANDING