Plant Phenomics: Fundamental Bases, Software and Hardware Platforms, and Machine Learning

Seed-per-pod estimation for plant breeding using deep learning

(2018) L.C. Uzal et al.   COMPUTERS AND ELECTRONICS IN AGRICULTURE

Photochemical activity changes accompanying the embryogenesis of pea (Pisum sativum) with yellow and green cotyledons

(2018) Galina Smolikova et al.   FUNCTIONAL PLANT BIOLOGY

The ‘PhenoBox’, a flexible, automated, open-source plant phenotyping solution

(2018) Angelika Czedik-Eysenberg et al.   NEW PHYTOLOGIST

The use of plant models in deep learning: an application to leaf counting in rosette plants

(2018) Jordan Ubbens et al.   Plant Methods

Deep Learning: Individual Maize Segmentation From Terrestrial Lidar Data Using Faster R-CNN and Regional Growth Algorithms

(2018) Shichao Jin et al.   Frontiers in Plant Science

Genetics and Physiology of the Nuclearly Inherited Yellow Foliar Mutants in Soybean

(2018) Devinder Sandhu et al.   Frontiers in Plant Science

Aerial Images and Convolutional Neural Network for Cotton Bloom Detection

(2018) Rui Xu et al.   Frontiers in Plant Science

Field-Based Scoring of Soybean Iron Deficiency Chlorosis Using RGB Imaging and Statistical Learning

(2018) Geng Bai et al.   Frontiers in Plant Science

Application of light detection and ranging and ultrasonic sensors to high-throughput phenotyping and precision horticulture: current status and challenges

(2018) André F. Colaço et al.   Horticulture Research

The adoption of automated phenotyping by plant breeders

(2018) Lana Awada et al.   EUPHYTICA

Deep phenotyping: deep learning for temporal phenotype/genotype classification

(2018) Sarah Taghavi Namin et al.   Plant Methods

On-The-Go Hyperspectral Imaging Under Field Conditions and Machine Learning for the Classification of Grapevine Varieties

(2018) Salvador Gutiérrez et al.   Frontiers in Plant Science

Growth kinetics and mathematical modeling of Synechocystis sp. PCC 6803 under flashing light

(2018) Levi Straka et al.   BIOTECHNOLOGY AND BIOENGINEERING

From plant genomes to phenotypes

(2017) Marie Bolger et al.   JOURNAL OF BIOTECHNOLOGY

Differential coupling of gibberellin responses byRht-B1csuppressor alleles andRht-B1bin wheat highlights a unique role for the DELLA N-terminus in dormancy

(2017) Karel Van De Velde et al.   JOURNAL OF EXPERIMENTAL BOTANY

Highlighting the differential role of leaf paraheliotropism in two Mediterranean Cistus species under drought stress and well-watered conditions

(2017) Giacomo Puglielli et al.   JOURNAL OF PLANT PHYSIOLOGY

High light acclimation of Chromera velia points to photoprotective NPQ

(2017) Erica Belgio et al.   PHOTOSYNTHESIS RESEARCH

Automated Identification of Northern Leaf Blight-Infected Maize Plants from Field Imagery Using Deep Learning

(2017) Chad DeChant et al.   PHYTOPATHOLOGY

Non-destructive, high-content analysis of wheat grain traits using X-ray micro computed tomography

(2017) Nathan Hughes et al.   Plant Methods

Panicle-SEG: a robust image segmentation method for rice panicles in the field based on deep learning and superpixel optimization

(2017) Xiong Xiong et al.   Plant Methods

Genetic Architecture and Molecular Networks Underlying Leaf Thickness in Desert-Adapted Tomato Solanum pennellii

(2017) Viktoriya Coneva et al.   PLANT PHYSIOLOGY

Constitutive down-regulation of SiSGR gene is related to green millet in Setaria italica

(2017) L. Cheng et al.   RUSSIAN JOURNAL OF PLANT PHYSIOLOGY

UAV-Based Thermal Imaging for High-Throughput Field Phenotyping of Black Poplar Response to Drought

(2017) Riccardo Ludovisi et al.   Frontiers in Plant Science

Editorial: Plant Phenotyping and Phenomics for Plant Breeding

(2017) Gustavo A. Lobos et al.   Frontiers in Plant Science

PlantCV v2: Image analysis software for high-throughput plant phenotyping

(2017) Malia A. Gehan et al.   PeerJ

Plant phenomics: an overview of image acquisition technologies and image data analysis algorithms

(2017) Fernando Perez-Sanz et al.   GigaScience

Computer vision and machine learning for robust phenotyping in genome-wide studies

(2017) Jiaoping Zhang et al.   Scientific Reports

Systematic Phenomics Analysis Deconvolutes Genes Mutated in Intellectual Disability into Biologically Coherent Modules

(2016) Korinna Kochinke et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Machine learning and data mining in complex genomic data—a review on the lessons learned in Genetic Analysis Workshop 19

(2016) Inke R. König et al.   BMC GENETICS

Simulation Modeling to Interpret the Captures of Moths in Pheromone-Baited Traps Used for Surveillance of Invasive Species: the Gypsy Moth as a Model Case

(2016) Josep Bau et al.   JOURNAL OF CHEMICAL ECOLOGY

High-throughput estimation of incident light, light interception and radiation-use efficiency of thousands of plants in a phenotyping platform

(2016) Llorenç Cabrera-Bosquet et al.   NEW PHYTOLOGIST

Light acclimation in the lycophyteSelaginella martensiidepends on changes in the amount of photosystems and on the flexibility of the light-harvesting complex II antenna association with both photosystems

(2016) Lorenzo Ferroni et al.   NEW PHYTOLOGIST

Pyridine nucleotide transhydrogenase PntAB is essential for optimal growth and photosynthetic integrity under low-light mixotrophic conditions in Synechocystis sp. PCC 6803

(2016) Jari Kämäräinen et al.   NEW PHYTOLOGIST

Phenomics for photosynthesis, growth and reflectance in Arabidopsis thaliana reveals circadian and long-term fluctuations in heritability

(2016) Pádraic J. Flood et al.   Plant Methods

Methods of high-throughput plant phenotyping for large-scale breeding and genetic experiments

(2016) D. A. Afonnikov et al.   RUSSIAN JOURNAL OF GENETICS

UAVs challenge to assess water stress for sustainable agriculture

(2015) J. Gago et al.   AGRICULTURAL WATER MANAGEMENT

Automated 3D reconstruction of grape cluster architecture from sensor data for efficient phenotyping

(2015) Florian Schöler et al.   COMPUTERS AND ELECTRONICS IN AGRICULTURE

Proximal hyperspectral sensing and data analysis approaches for field-based plant phenomics

(2015) K.R. Thorp et al.   COMPUTERS AND ELECTRONICS IN AGRICULTURE

Lights, camera, action: high-throughput plant phenotyping is ready for a close-up

(2015) Noah Fahlgren et al.   CURRENT OPINION IN PLANT BIOLOGY

Using machine learning techniques for evaluating tomato ripeness

(2015) Nashwa El-Bendary et al.   EXPERT SYSTEMS WITH APPLICATIONS

Multispectral airborne imagery in the field reveals genetic determinisms of morphological and transpiration traits of an apple tree hybrid population in response to water deficit

(2015) Nicolas Virlet et al.   JOURNAL OF EXPERIMENTAL BOTANY

Digital Single-Cell Analysis of Plant Organ Development Using 3DCellAtlas

(2015) Thomas D. Montenegro-Johnson et al.   PLANT CELL

Non-invasive, whole-plant imaging of chloroplast movement and chlorophyll fluorescence reveals photosynthetic phenotypes independent of chloroplast photorelocation defects in chloroplast division mutants

(2015) Siddhartha Dutta et al.   PLANT JOURNAL

Automated integrative high-throughput phenotyping of plant shoots: a case study of the cold-tolerance of pea (Pisum sativum L.)

(2015) Jan F Humplík et al.   Plant Methods

Digital imaging of root traits (DIRT): a high-throughput computing and collaboration platform for field-based root phenomics

(2015) Abhiram Das et al.   Plant Methods

Leaf Responses to Mild Drought Stress in Natural Variants of Arabidopsis

(2015) Pieter Clauw et al.   PLANT PHYSIOLOGY

RootAnalyzer: A Cross-Section Image Analysis Tool for Automated Characterization of Root Cells and Tissues

(2015) Joshua Chopin et al.   PLoS One

Can chlorophyll fluorescence be used to determine the optimal time to harvest rice seeds for long-term genebank storage?

(2015) Fiona R. Hay et al.   SEED SCIENCE RESEARCH

vitisFlower®: Development and Testing of a Novel Android-Smartphone Application for Assessing the Number of Grapevine Flowers per Inflorescence Using Artificial Vision Techniques

(2015) Arturo Aquino et al.   SENSORS

Finding Our Way through Phenotypes

(2015) Andrew R. Deans et al.   PLOS BIOLOGY

The relationship between leaf area growth and biomass accumulation in Arabidopsis thaliana

(2015) Sarathi M. Weraduwage et al.   Frontiers in Plant Science

The differential view of genotype–phenotype relationships

(2015) Virginie Orgogozo et al.   Frontiers in Genetics

High-Throughput Phenotyping of Chlamydomonas Swimming Mutants Based on Nanoscale Video Analysis

(2014) Shohei Fujita et al.   BIOPHYSICAL JOURNAL

Phenotyping and beyond: modelling the relationships between traits

(2014) Christine Granier et al.   CURRENT OPINION IN PLANT BIOLOGY

Seeing the forest through the trees: uncovering phenomic complexity through interactive network visualization

(2014) Jeremy L Warner et al.   JOURNAL OF THE AMERICAN MEDICAL INFORMATICS ASSOCIATION

Chlorophyll fluorescence emission can screen cold tolerance of cold acclimated Arabidopsis thaliana accessions

(2014) Anamika Mishra et al.   Plant Methods

A Review of Imaging Techniques for Plant Phenotyping

(2014) Lei Li et al.   SENSORS

Conventional and phenomics characterization provides insight into the diversity and relationships of hypervariable scarlet (Solanum aethiopicum L.) and gboma (S. macrocarpon L.) eggplant complexes

(2014) Mariola Plazas et al.   Frontiers in Plant Science

Plant phenomics and high-throughput phenotyping: accelerating rice functional genomics using multidisciplinary technologies

(2013) Wanneng Yang et al.   CURRENT OPINION IN PLANT BIOLOGY

Integrative phenomics reveals insight into the structure of phenotypic diversity in budding yeast

(2013) D. A. Skelly et al.   GENOME RESEARCH

Demonstration of Lateral IGBTs in 4H-SiC

(2013) Kuan-Wei Chu et al.   IEEE ELECTRON DEVICE LETTERS

Machine learning in cell biology – teaching computers to recognize phenotypes

(2013) Christoph Sommer et al.   JOURNAL OF CELL SCIENCE

Phenoscope: an automated large-scale phenotyping platform offering high spatial homogeneity

(2013) Sébastien Tisné et al.   PLANT JOURNAL

RootNav: Navigating Images of Complex Root Architectures

(2013) M. P. Pound et al.   PLANT PHYSIOLOGY

Field high-throughput phenotyping: the new crop breeding frontier

(2013) José Luis Araus et al.   TRENDS IN PLANT SCIENCE

A Nuclear Calcium-Sensing Pathway Is Critical for Gene Regulation and Salt Stress Tolerance in Arabidopsis

(2013) Qingmei Guan et al.   PLoS Genetics

A phenomics approach to the analysis of the influence of glutathione on leaf area and abiotic stress tolerance in Arabidopsis thaliana

(2013) Daniel Schnaubelt et al.   Frontiers in Plant Science

Machine learning and genome annotation: a match meant to be?

(2013) Kevin Y Yip et al.   GENOME BIOLOGY

A novel mesh processing based technique for 3D plant analysis

(2012) Anthony Paproki et al.   BMC PLANT BIOLOGY

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

(2012) Taras Galkovskyi et al.   BMC PLANT BIOLOGY

Field-based phenomics for plant genetics research

(2012) Jeffrey W. White et al.   FIELD CROPS RESEARCH

GlyPh: a low-cost platform for phenotyping plant growth and water use

(2012) Gustavo A. Pereyra-Irujo et al.   FUNCTIONAL PLANT BIOLOGY

Seed Fatty Acid Reduceracts downstream of gibberellin signalling pathway to lower seed fatty acid storage inArabidopsis

(2012) MINGXUN CHEN et al.   PLANT CELL AND ENVIRONMENT

SmartGrain: High-Throughput Phenotyping Software for Measuring Seed Shape through Image Analysis

(2012) T. Tanabata et al.   PLANT PHYSIOLOGY

Data mining techniques for the life sciences

(2011) G. Ya. Wiederschain   BIOCHEMISTRY-MOSCOW

Making Sense of Remotely Sensing Vegetation

(2011) Geoffrey M. Henebry   BIOSCIENCE

High-throughput phenotyping technology for maize roots

(2011) T.E. Grift et al.   BIOSYSTEMS ENGINEERING

Survival and growth of Arabidopsis plants given limited water are not equal

(2011) Aleksandra Skirycz et al.   NATURE BIOTECHNOLOGY

A growth phenotyping pipeline for Arabidopsis thaliana integrating image analysis and rosette area modeling for robust quantification of genotype effects

(2011) Samuel Arvidsson et al.   NEW PHYTOLOGIST

A novel machine-vision-based facility for the automatic evaluation of yield-related traits in rice

(2011) Lingfeng Duan et al.   Plant Methods

Accurate inference of shoot biomass from high-throughput images of cereal plants

(2011) Mahmood R Golzarian et al.   Plant Methods

Visualizing the Genetic Landscape of Arabidopsis Seed Performance

(2011) R. V. L. Joosen et al.   PLANT PHYSIOLOGY

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

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

Genes Identified by Visible Mutant Phenotypes Show Increased Bias toward One of Two Subgenomes of Maize

(2011) James C. Schnable et al.   PLoS One

Phenomics – technologies to relieve the phenotyping bottleneck

(2011) Robert T. Furbank et al.   TRENDS IN PLANT SCIENCE

Chlorophyll fluorescence imaging of plant–pathogen interactions

(2010) Stephen Alexander Rolfe et al.   PROTOPLASMA

Root phenomics of crops: opportunities and challenges

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

Thermal infrared imaging of crop canopies for the remote diagnosis and quantification of plant responses to water stress in the field

(2009) Hamlyn G. Jones et al.   FUNCTIONAL PLANT BIOLOGY

Classification of brain tumor type and grade using MRI texture and shape in a machine learning scheme

(2009) Evangelia I. Zacharaki et al.   MAGNETIC RESONANCE IN MEDICINE