RootGraph: a graphic optimization tool for automated image analysis of plant roots

Highlight The method presented analyses root scans automatically, distinguishes primary from lateral roots, and quantifies a broad range of traits for individual primary roots and their associated lateral roots.

[1]  Xavier Draye,et al.  An automated image-processing pipeline for high-throughput analysis of root architecture in OpenAlea , 2013 .

[2]  Jinhai Cai,et al.  Robust Filtering-Based Thinning Algorithm for Pattern Recognition , 2012, Comput. J..

[3]  Bas J Zwaan,et al.  Genotype×environment interaction QTL mapping in plants: lessons from Arabidopsis. , 2014, Trends in plant science.

[4]  Rosie Jones,et al.  Learning to Extract Entities from Labeled and Unlabeled Text , 2005 .

[5]  R. Fildes.  Journal of the Royal Statistical Society (B): Gary K. Grunwald, Adrian E. Raftery and Peter Guttorp, 1993, “Time series of continuous proportions”, 55, 103–116.☆ , 1993 .

[6]  C. Bustamante,et al.  High-throughput two-dimensional root system phenotyping platform facilitates genetic analysis of root growth and development. , 2012, Plant, cell & environment.

[7]  G. Scoles,et al.  Inheritance of resistance to covered smut in barley and development of a tightly linked SCAR marker , 2002, Theoretical and Applied Genetics.

[8]  A. Eshel,et al.  Plant roots : the hidden half , 1991 .

[9]  Baskar Ganapathysubramanian,et al.  Analysis of Maize (Zea mays L.) Seedling Roots with the High-Throughput Image Analysis Tool ARIA (Automatic Root Image Analysis) , 2014, PloS one.

[10]  A. Hills,et al.  EZ-Rhizo: integrated software for the fast and accurate measurement of root system architecture. , 2009, The Plant journal : for cell and molecular biology.

[11]  R. Gerlai.  Phenomics: fiction or the future? , 2002, Trends in Neurosciences.

[12]  Victor O. Sadras,et al.  A water-centred framework to assess the effects of salinity on the growth and yield of wheat and barley , 2010, Plant and Soil.

[13]  Johannes E. Schindelin,et al.  Fiji: an open-source platform for biological-image analysis , 2012, Nature Methods.

[14]  Loïc Pagès,et al.  A Novel Image-Analysis Toolbox Enabling Quantitative Analysis of Root System Architecture1[W][OA] , 2011, Plant Physiology.

[15]  J. Masle,et al.  High soil strength: mechanical forces at play on root morphogenesis and in root:shoot signaling , 2002 .

[16]  R. MacCurdy,et al.  Three-Dimensional Root Phenotyping with a Novel Imaging and Software Platform1[C][W][OA] , 2011, Plant Physiology.

[17]  A. Price,et al.  Upland rice grown in soil-filled chambers and exposed to contrasting water-deficit regimes: II. Mapping quantitative trait loci for root morphology and distribution , 2002 .

[18]  D. A. Rose,et al.  Root development and function , 2004, Plant Growth Regulation.

[19]  Jose Crossa,et al.  From Genotype × Environment Interaction to Gene × Environment Interaction , 2012, Current genomics.

[20]  A. Schnepf,et al.  Recovering Root System Traits Using Image Analysis Exemplified by Two-Dimensional Neutron Radiography Images of Lupine1[C][W][OPEN] , 2013, Plant Physiology.

[21]  S. Sabatini,et al.  SCARECROW is involved in positioning the stem cell niche in the Arabidopsis root meristem. , 2003, Genes & development.

[22]  E. Blumwald,et al.  Na+ transport in plants , 2007, FEBS letters.

[23]  Karl J Niklas,et al.  On the Vegetative Biomass Partitioning of Seed Plant Leaves, Stems, and Roots , 2002, The American Naturalist.

[24]  M. Drew,et al.  COMPARISON OF THE EFFECTS OF A LOCALISED SUPPLY OF PHOSPHATE, NITRATE, AMMONIUM AND POTASSIUM ON THE GROWTH OF THE SEMINAL ROOT SYSTEM, AND THE SHOOT, IN BARLEY , 1975 .

[25]  Mathieu Javaux,et al.  Root System Markup Language: Toward a Unified Root Architecture Description Language1[OPEN] , 2015, Plant Physiology.

[26]  P. Benfey,et al.  Imaging and Analysis Platform for Automatic Phenotyping and Trait Ranking of Plant Root Systems1[W][OA] , 2010, Plant Physiology.

[27]  Richard L. Church,et al.  Finding shortest paths on real road networks: the case for A* , 2009, Int. J. Geogr. Inf. Sci..

[28]  Jinhai Cai,et al.  Handwriting Recognition - Soft Computing and Probabilistic Approaches , 2003, Studies in Fuzziness and Soft Computing.

[29]  Ching Y. Suen,et al.  A fast parallel algorithm for thinning digital patterns , 1984, CACM.

[30]  R. H. Dowdy,et al.  Automated image analyses for separating plant roots from soil debris elutrated from soil cores , 1998, Plant and Soil.

[31]  Alastair H. Fitter,et al.  Characteristics and Functions of Root Systems , 2002 .

[32]  Christophe Jourdan,et al.  IJ_Rhizo: an open-source software to measure scanned images of root samples , 2013, Plant and Soil.

[33]  Pankaj Kumar,et al.  Root phenotyping by root tip detection and classification through statistical learning , 2014, Plant and Soil.

[34]  P. Gregory,et al.  Root Development and Function. , 1988 .

[35]  L. Saker,et al.  Nutrient Supply and the Growth of the Seminal Root System in Barley I. THE EFFECT OF NITRATE CONCENTRATION ON THE GROWTH OF AXES AND LATERALS , 1973 .

[36]  Tony Pridmore,et al.  High-Throughput Quantification of Root Growth Using a Novel Image-Analysis Tool1[C][W] , 2009, Plant Physiology.

[37]  E. J. Morton,et al.  Non-invasive imaging of roots with high resolution X-ray micro-tomography , 2003, Plant and Soil.

[38]  Dennis Shasha,et al.  Nitrogen economics of root foraging: Transitive closure of the nitrate–cytokinin relay and distinct systemic signaling for N supply vs. demand , 2011, Proceedings of the National Academy of Sciences.

[39]  John Gorham,et al.  Upland rice grown in soil-filled chambers and exposed to contrasting water-deficit regimes. I. Root distribution, water use and plant water status , 2002 .

[40]  R. Furbank,et al.  Plant phenomics: from gene to form and function , 2009 .

[41]  Jinhai Cai,et al.  3D Reconstruction, Modelling and Analysis of in Situ Root System Architecture , 2013 .

[42]  D. Rubin,et al.  Maximum likelihood from incomplete data via the EM - algorithm plus discussions on the paper , 1977 .

[43]  Jinhai Cai,et al.  Surface fitting for individual image thresholding and beyond , 2013, IET Image Process..

[44]  Guohua Xu,et al.  Auxin distribution is differentially affected by nitrate in roots of two rice cultivars differing in responsiveness to nitrogen. , 2013, Annals of botany.

[45]  B. Ney,et al.  A simplified conceptual model of carbon/nitrogen functioning for QTL analysis of winter wheat adaptation to nitrogen deficiency , 2006, Theoretical and Applied Genetics.

[46]  N. Manikanda Boopathi,et al.  Phenotypic and genotypic analysis of drought-resistance traits for development of rice cultivars adapted to rainfed environments , 2008 .

[47]  Michael P. Pound,et al.  RootNav: Navigating Images of Complex Root Architectures1[C][W] , 2013, Plant Physiology.