Plant Methods

Papers
(The median citation count of Plant Methods is 4. The table below lists those papers that are above that threshold based on CrossRef citation counts [max. 250 papers]. The publications cover those that have been published in the past four years, i.e., from 2021-11-01 to 2025-11-01.)
ArticleCitations
TreeJ: an ImageJ plugin for interactive cell lineage reconstruction from static images114
The influence of water content on the longitudinal modulus of elasticity of maize stalk pith and rind tissues94
A novel method for extraction of high purity and high production Phytophthora sojae oospores84
Orchid2024: A cultivar-level dataset and methodology for fine-grained classification of Chinese Cymbidium Orchids72
Fast estimation of plant growth dynamics using deep neural networks65
A deep learning approach to track Arabidopsis seedlings’ circumnutation from time-lapse videos63
Optimized synthesis of layered double hydroxide lactate nanosheets and their biological effects on Arabidopsis seedlings60
Complementarity of Raman and Infrared spectroscopy for rapid characterization of fucoidan extracts58
Real-time monitoring of Ralstonia solanacearum infection progress in tomato and Arabidopsis using bioluminescence imaging technology51
Development of a multi-targeted real-time PCR assay for the detection of the grapevine pathogen Xylophilus ampelinus50
Targeted gene deletion with SpCas9 and multiple guide RNAs in Arabidopsis thaliana: four are better than two48
An automated method for stem diameter measurement based on laser module and deep learning47
Coconut tree modeling based on abiotic factors and modified cosserat rod theory43
Non-destructive real-time monitoring of underground root development with distributed fiber optic sensing43
Orthogonal control of gene expression in plants using synthetic promoters and CRISPR-based transcription factors40
Classification of multi-year and multi-variety pumpkin seeds using hyperspectral imaging technology and three-dimensional convolutional neural network38
The isolation strategy and chemical analysis of oil cells from Asari Radix et Rhizoma38
The semi-automated development of plant cell wall finite element models38
Estimation of cotton canopy parameters based on unmanned aerial vehicle (UAV) oblique photography36
Electrical impedance spectroscopy (EIS) in plant roots research: a review36
Determination of phosphorus compounds in plant tissues: from colourimetry to advanced instrumental analytical chemistry36
Stability investigation of air-dried olive ribo nucleic acids for metavirome studies36
A simple and efficient method to quantify the cell parameters of the seed coat, embryo and silique wall in rapeseed35
RiboPlotR: a visualization tool for periodic Ribo-seq reads33
pSIG plasmids, MoClo-compatible vectors for efficient production of chimeric double-stranded RNAs in Escherichia coli HT115 (DE3) strain31
Improved estimation of forage nitrogen in alpine grassland by integrating Sentinel-2 and SIF data31
Combination of long-term 13CO2 labeling and isotopolog profiling allows turnover analysis of photosynthetic pigments in Arabidopsis leaves31
The evaluation of different combinations of enzyme set, aligner and caller in GBS sequencing of soybean29
Optimization of ribosome profiling in plants including structural analysis of rRNA fragments29
Detection of TuMV by a toehold switch sensor coupled with NASBA amplification in Pseudostellaria heterophylla29
Novel in silico screening system for plant defense activators using deep learning-based prediction of reactive oxygen species accumulation29
Improved wood species identification based on multi-view imagery of the three anatomical planes29
Non-destructive detection of early wheat germination via deep learning-optimized terahertz imaging29
Innovation of strip fertilization planting for rice straw crushing with back-throwing and interrow-laying29
Synchrotron tomography applications in agriculture and food sciences research: a review28
Truncated CMV2bN43 enhances virus-induced gene silencing in pepper by retaining systemic but not local silencing suppression28
Local mapping of root orientation traits by X-ray micro-CT and 3d image analysis: A study case on carrot seedlings grown in simulated vs real weightlessness28
High-throughput estimation of allele frequencies using combined pooled-population sequencing and haplotype-based data processing27
An improved bacterial mRNA enrichment strategy in dual RNA sequencing to unveil the dynamics of plant-bacterial interactions27
Installation and imaging of thousands of minirhizotrons to phenotype root systems of field-grown plants27
Assembly and operation of an imaging system for long-term monitoring of bioluminescent and fluorescent reporters in plants26
Development and application of a virus-induced gene silencing protocol for the study of gene function in narrow-leafed lupin26
Improvement of germination rate and hybridization to facilitate breeding of an industrial oil crop, Euphorbia lagascae Spreng25
A statistical method for high-throughput emergence rate calculation for soybean breeding plots based on field phenotypic characteristics25
An advanced method for the release, enrichment and purification of high-quality Arabidopsis thaliana rosette leaf trichomes enables profound insights into the trichome proteome25
A comparative study on point cloud down-sampling strategies for deep learning-based crop organ segmentation24
Evaluation of deep learning for predicting rice traits using structural and single-nucleotide genomic variants24
Inter-row navigation line detection for cotton with broken rows24
ScAnalyzer: an image processing tool to monitor plant disease symptoms and pathogen spread in Arabidopsis thaliana leaves24
SYMPATHIQUE: image-based tracking of symptoms and monitoring of pathogenesis to decompose quantitative disease resistance in the field23
A new and effective method to induce infection of Phyllachora maydis into corn for tar spot studies in controlled environments23
Automatic rape flower cluster counting method based on low-cost labelling and UAV-RGB images23
GrainNet: efficient detection and counting of wheat grains based on an improved YOLOv7 modeling23
Using near-infrared spectroscopy to predict nitrogen and phosphorus concentrations of herbarium specimens under different storage conditions23
A high-throughput phenotyping method for sugarcane rind penetrometer resistance and breaking force characterization by near-infrared spectroscopy23
RGB image-based method for phenotyping rust disease progress in pea leaves using R22
Machine learning provides specific detection of salt and drought stresses in cucumber based on miRNA characteristics22
Automated, image-based disease measurement for phenotyping resistance to soybean frogeye leaf spot22
A method of two-dimensional correlation spectroscopy combined with residual neural network for comparison and differentiation of medicinal plants raw materials superior to traditional machine learning22
A rapid and non-destructive method for spatial–temporal quantification of colonization by Pseudomonas syringae pv. tomato DC3000 in Arabidopsis and tomato22
DWTFormer: a frequency-spatial features fusion model for tomato leaf disease identification22
BerryPortraits: Phenotyping Of Ripening Traits in cranberry (Vaccinium macrocarpon Ait.) with YOLOv821
Mapping of cotton bolls and branches with high-granularity through point cloud segmentation21
Optimization of preparation conditions for Salsola laricifolia protoplasts using response surface methodology and artificial neural network modeling21
Sorting biotic and abiotic stresses on wild rocket by leaf-image hyperspectral data mining with an artificial intelligence model21
Detection and characterization of spike architecture based on deep learning and X-ray computed tomography in barley21
Statistical analysis of organelle movement using state-space models21
Ribozyme-mediated CRISPR/Cas9 gene editing in pyrethrum (Tanacetum cinerariifolium) hairy roots using a RNA polymerase II-dependent promoter21
Evaluation of an intelligent artificial climate chamber for high-throughput crop phenotyping in wheat21
In vitro micropropagation protocols for two endangered Dianthus species - via in vitro culture for conservation and recultivation purposes20
EBS-YOLO: edge-optimized bidirectional spatial feature augmentation for in-field detection of wheat Fusarium head blight epidemics20
Rapid Ragi: A speed breeding protocol for finger millet20
WheatLFANet: in-field detection and counting of wheat heads with high-real-time global regression network20
Refining bulk segregant analyses: ontology-mediated discovery of flowering time genes in Brassica oleracea20
Scoring the number of B chromosomes in Zea mays L. using droplet digital PCR assay20
Estimation of plant height and yield based on UAV imagery in faba bean (Vicia faba L.)20
Quantitative phenotyping of crop roots with spectral electrical impedance tomography: a rhizotron study with optimized measurement design20
An electrophoretic mobility shift assay using the protein isolated from host plants19
A compact deep learning approach integrating depthwise convolutions and spatial attention for plant disease classification19
A custom library construction method for super-resolution ribosome profiling in Arabidopsis18
Assessing data analysis techniques in a high-throughput meiosis-like induction detection system18
Intelligent identification on cotton verticillium wilt based on spectral and image feature fusion18
Spectral estimation of the aboveground biomass of cotton under water–nitrogen coupling conditions18
Mitochondrial DNA editing in potato through mitoTALEN and mitoTALECD: molecular characterization and stability of editing events18
Transmembrane potential, an indicator in situ reporting cellular senescence and stress response in plant tissues18
A hybrid CNN–SVM classifier for weed recognition in winter rape field18
SeedSeg: image-based transgenic seed counting for segregation analysis of T-DNA loci17
Insights into lncRNA-mediated regulatory networks in Hevea brasiliensis under anthracnose stress17
Optimizing cannabis cultivation: an efficient in vitro system for flowering induction17
A vector-free gene interference system using delaminated Mg–Al-lactate layered double hydroxide nanosheets as molecular carriers to intact plant cells17
A high-throughput approach for quantifying turgor loss point in grapevine17
Acceleration of wheat breeding: enhancing efficiency and practical application of the speed breeding system17
Automating high-throughput screening for anthracnose resistance in common bean using allele specific PCR17
ADAM-DETR: an intelligent rice disease detection method based on adaptive multi-scale feature fusion17
Spatial and Texture Analysis of Root System distribution with Earth mover’s Distance (STARSEED)17
Correction: Whole mount multiplexed visualization of DNA, mRNA, and protein in plant-parasitic nematodes17
Pre-trained protein language model sheds new light on the prediction of Arabidopsis protein–protein interactions16
Eggsplorer: a rapid plant–insect resistance determination tool using an automated whitefly egg quantification algorithm16
Efficient mutagenesis and genotyping of maize inbreds using biolistics, multiplex CRISPR/Cas9 editing, and Indel-Selective PCR16
CRISPR-Cas13a as a next-generation tool for rapid and precise plant RNA virus diagnostics16
Monitoring of plant water uptake by measuring root dielectric properties on a fine timescale: diurnal changes and response to leaf excision16
A method to determine antifungal activity in seed exudates by nephelometry16
Mapping and quantifying unique branching structures in lentil (Lens culinaris Medik.)16
A novel method for measuring heat injury in leaves provides insights into the sequence of processes of heat injury development16
An efficient chromatin immunoprecipitation (ChIP) protocol for studying histone modifications in peach reproductive tissues16
A deep learning approach for deriving wheat phenology from near-surface RGB image series using spatiotemporal fusion16
Low-cost and reliable substrate-based phenotyping platform for screening salt tolerance of cutting propagation-dependent grass, paspalum vaginatum16
BioCurve Analyzer: a web-based shiny app for analyzing biological response curves16
Tracking deuterium uptake in hydroponically grown maize roots using correlative helium ion microscopy and Raman micro-spectroscopy16
AraDQ: an automated digital phenotyping software for quantifying disease symptoms of flood-inoculated Arabidopsis seedlings16
Publisher Correction: New improvements in grapevine genome editing: high efficiency biallelic homozygous knock-out from regenerated plantlets by using an optimized zCas9i15
CMSAF-Net: integrative network design with enhanced decoder for precision segmentation of pear leaf diseases15
Apnet: Lightweight network for apricot tree disease and pest detection in real-world complex backgrounds15
Sensor-based phenotyping of above-ground plant-pathogen interactions15
Advancing radiation-induced mutant screening through high-throughput technology: a preliminary evaluation of mutant screening in Arabidopsis thaliana15
De novo assembly provides new insights into the evolution of Elaeagnus angustifolia L.15
Determining water status of walnut orchards using the crop water stress index and canopy temperature measurements15
A novel selection model based on multivariate methods and arbitrary genetic parameters: a case study on tomato families15
A CNN model for early detection of pepper Phytophthora blight using multispectral imaging, integrating spectral and textural information15
RP-DETR: end-to-end rice pests detection using a transformer15
Establishment of a low-temperature immersion method for extracting high-activity and high-purity mitochondria from Syntrichia caninervis Mitt.15
Phenotyping seedlings for selection of root system architecture in alfalfa (Medicago sativa L.)14
Simple and efficient isolation of plant genomic DNA using magnetic ionic liquids14
Characterizing the effects of different chemicals on stem bending of cut snapdragon flower14
Combining novel feature selection strategy and hyperspectral vegetation indices to predict crop yield14
One pattern analysis (OPA) for the quantitative determination of protein interactions in plant cells14
YOLO-PEST: a novel rice pest detection approach based on YOLOv5s14
Accelerating eucalypt clone selection pipeline via cloned progeny trials and molecular data14
Improved genomic prediction using machine learning with Variational Bayesian sparsity14
A non-destructive approach for measuring rice panicle-level photosynthetic responses using 3D-image reconstruction14
Utilizing X-ray radiography for non-destructive assessment of paddy rice grain quality traits14
Segmentation and counting of wheat spike grains based on deep learning and textural feature14
Correction: Rapid and cost-effective molecular karyotyping in wheat, barley, and their crossprogeny by chromosome-specific multiplex PCR13
Clarification of the infection pattern of Xanthomonas citri subsp. citri on citrus fruit by artificial inoculation13
Dual discriminator GAN-based synthetic crop disease image generation for precise crop disease identification13
SSR_VibraProfiler: a Python package for accurate classification of varieties using SSRs with intra-variety specificity and inter-variety polymorphism13
Non-wounding contact-based Inoculation of fruits with fungal pathogens in postharvest13
Establishment of an efficient tissue culture system for Paeonia ostii by combining vernalization and etiolation pretreatment with optimized culture conditions13
Identifying and mapping individual medicinal plant Lamiophlomis rotata at high elevations by using unmanned aerial vehicles and deep learning13
Efficient induction of tetraploids via adventitious bud regeneration and subsequent phenotypic variation in Acacia melanoxylon13
A rapid and efficient in vivo inoculation method for introducing tree stem canker pathogens onto leaves: suitable for large-scale assessment of resistance in poplar breeding progeny13
A cell P system with membrane division and dissolution rules for soybean leaf disease recognition13
Assessing and avoiding C isotopic contamination artefacts in mesocosm-scale 13CO2/12CO2 labelling systems: from biomass components to purified carbohydrates and dark respiration13
A novel approach integrating multispectral imaging and machine learning to identify seed maturity and vigor in smooth bromegrass13
Optimized deep learning framework for pomegranate disease detection using nature-inspired algorithms12
Yield estimation of high-density cotton fields using low-altitude UAV imaging and deep learning12
Accelerating leaf area measurement using a volumetric approach12
Low-cost and automated phenotyping system “Phenomenon” for multi-sensor in situ monitoring in plant in vitro culture12
Characterization of leaf surface phenotypes based on light interaction12
YOLOV8-CMS: a high-accuracy deep learning model for automated citrus leaf disease classification and grading12
PhenoTrack3D: an automatic high-throughput phenotyping pipeline to track maize organs over time12
ShinyCore: An R/Shiny program for establishing core collection based on single nucleotide polymorphism data12
Swin-Unet++: a study on phenotypic parameter analysis of cabbage seedling roots11
Meta-learning prediction of physical and chemical properties of magnetized water and fertilizer based on LSTM11
RhizoMAP: a comprehensive, nondestructive, and sensitive platform for metabolic imaging of the rhizosphere11
Development of a semi-open chamber system for the gas exchange measurement of whole-canopy under steady and unsteady states in cucumber seedlings11
Opening the black box: explainable deep-learning classification of wood microscopic image of endangered tree species11
Photolysis of caged cytokinin in single cells of Arabidopsis thaliana11
Development of a highly efficient virus-free regeneration system of Salvia miltiorrhiza from Sichuan using apical meristem as explants11
Deep learning for detecting herbicide weed control spectrum in turfgrass11
In-vivo Raman microspectroscopy reveals differential nitrate concentration in different developmental zones in Arabidopsis roots11
DNA-free high-quality RNA extraction from 39 difficult-to-extract plant species (representing seasonal tissues and tissue types) of 32 families, and its validation for downstream molecular application11
Gray mold and anthracnose disease detection on strawberry leaves using hyperspectral imaging11
NRTPredictor: identifying rice root cell state in single-cell RNA-seq via ensemble learning10
Open-source analytical pipeline for robust data analysis, visualizations and sharing in crop breeding10
Segmentation of structural parts of rosebush plants with 3D point-based deep learning methods10
Disentangling soybean GxE effects in an integrated genomic prediction and machine learning-GWAS workflow10
Developing non-invasive 3D quantificational imaging for intelligent coconut analysis system with X-ray10
Improved phenotyping procedure for evaluating resistance in rice against gall midge (Orseolia oryzae, Wood-Mason)10
Rapid real-time quantitative colorimetric LAMP methodology for field detection of Verticillium dahliae in crude olive-plant samples10
The mechanisms and prediction of non-structural carbohydrates accretion and depletion after mechanical wounding in slash pine (Pinus elliottii) using near-infrared reflectance spectroscopy10
IMPLANT: a new technique for transgene copy number estimation in plants using a single end-point PCR reaction10
An automated phenotyping method for Chinese Cymbidium seedlings based on 3D point cloud10
A protoplast-based transient gene expression assay for the identification of heat and oxidative stress-regulatory genes in perennial ryegrass10
Overexpressing Arabidopsis thaliana ACBP6 in transgenic rapid-cycling Brassica napus confers cold tolerance10
An efficient multiplex approach to CRISPR/Cas9 gene editing in citrus10
Soybean seed pest damage detection method based on spatial frequency domain imaging combined with RL-SVM10
MAPtools: command-line tools for mapping-by-sequencing and QTL-Seq analysis and visualization10
Quality assurance of hyperspectral imaging systems for neural network supported plant phenotyping10
An integrated isotopic labeling and freeze sampling apparatus (ILSA) to support sampling leaf metabolomics at a centi-second scale10
A CNN-LSTM-att hybrid model for classification and evaluation of growth status under drought and heat stress in chinese fir (Cunninghamia lanceolata)10
Trans2express – de novo transcriptome assembly pipeline optimized for gene expression analysis10
Establishment of an NPK nutrient monitor system in yield-graded cotton petioles under drip irrigation10
Monitoring of drought stress and transpiration rate using proximal thermal and hyperspectral imaging in an indoor automated plant phenotyping platform10
Exploring the impact of light intensity under speed breeding conditions on the development and growth of lentil and chickpea10
Enhancing cotton whitefly (Bemisia tabaci) detection and counting with a cost-effective deep learning approach on the Raspberry Pi9
A modified aeroponic system for growing small-seeded legumes and other plants to study root systems9
Novel cultivation techniques for water lily (Nymphaea micrantha Guill. & Perr) production based on in vitro technology9
Genomic prediction for root and yield traits of barley under a water availability gradient: a case study comparing different spatial adjustments9
A prediction model of rubber content in the dried root of Taraxacum kok-saghyz Rodin based on near-infrared spectroscopy9
Identification of an emerging cucumber virus in Taiwan using Oxford nanopore sequencing technology9
Effect of a suitable treatment period on the genetic transformation efficiency of the plant leaf disc method9
Colour-analyzer: a new dual colour model-based imaging tool to quantify plant disease9
A Cotyledon-based Virus-Induced Gene Silencing (Cotyledon-VIGS) approach to study specialized metabolism in medicinal plants9
OneRosette to predict them all: single plant prompting on a visual foundation model to segment symptomatic Arabidopsis thaliana time series9
A simple new method to determine leaf specific heat capacity9
Optimization of immune receptor-related hypersensitive cell death response assay using agrobacterium-mediated transient expression in tobacco plants9
Correction: BerryPortraits: phenotyping of ripening traits in cranberry (Vaccinium macrocarpon Ait.) With YOLOv89
DeLTa-Seq: direct-lysate targeted RNA-Seq from crude tissue lysate9
A protocol for Chenopodium quinoa pollen germination9
Vapor pressure deficit control and mechanical vibration techniques to induce self-pollination in strawberry flowers9
Two-fold red excess (TREx): a simple and novel digital color index that enables non-invasive real-time monitoring of green-leaved as well as anthocyanin-rich crops9
Production of HSVd- and PPV-free apricot cultivars by in vitro thermotherapy followed by meristem culture9
Research on anthracnose grade of Camellia oleifera based on the combined LIBS and THz technology9
Overexpression of Vitis GRF4-GIF1 improves regeneration efficiency in diploid Fragaria vesca Hawaii 49
A cotton organ segmentation method with phenotypic measurements from a point cloud using a transformer8
Correction: The rapid-tome, a 3D-printed microtome, and an updated hand-sectioning method for high-quality plant sectioning8
A system for the study of roots 3D kinematics in hydroponic culture: a study on the oscillatory features of root tip8
Starch phosphorylation—A needle in a haystack8
Carbon dioxide expanded liquid: an effective solvent for the extraction of quercetin from South African medicinal plants8
Enhanced Bayesian model for multienvironmental selection of winter hybrids maize: assessing grain yield using ‘ProbBreed’8
A plant protein farnesylation system in prokaryotic cells reveals Arabidopsis AtJ3 produced and farnesylated in E. coli maintains its function of protecting proteins from heat inactivation8
Lightweight highland barley detection based on improved YOLOv58
An ensemble deep learning models approach using image analysis for cotton crop classification in AI-enabled smart agriculture8
Towards portable MRI in the plant sciences8
Maui: modular analytics of UAS imagery for specialty crop research8
Wheat grain width: a clue for re-exploring visual indicators of grain weight8
A successive time-to-event model of phyllochron dynamics for hypothesis testing: application to the analysis of genetic and environmental effects in maize8
A novel application of laser speckle imaging technique for prediction of hypoxic stress of apples8
Validating a multi-locus metabarcoding approach for characterizing mixed-pollen samples8
Completing the picture of field-grown cereal crops: a new method for detailed leaf surface models in wheat8
2023: a soil odyssey–HeAted soiL-Monoliths (HAL-Ms) to examine the effect of heat emission from HVDC underground cables on plant growth8
Establishment of virus-induced gene silencing (VIGS) system in Luffa acutangula using Phytoene desaturase (PDS) and tendril synthesis related gene (TEN)8
Resource-optimized cnns for real-time rice disease detection with ARM cortex-M microprocessors8
Rapid quantification of whole seed fatty acid amount, composition, and shape phenotypes from diverse oilseed species with large differences in seed size8
Improved estimation of aboveground biomass of regional coniferous forests integrating UAV-LiDAR strip data, Sentinel-1 and Sentinel-2 imageries7
Estimation of chlorophyll content in rice canopy leaves using 3D radiative transfer modeling and unmanned aerial hyperspectral images7
LDSL framework: a lightweight dual-stream learning framework for wheat disease detection7
A survey of few-shot learning in smart agriculture: developments, applications, and challenges7
Tunisian Artemisia campestris L.: a potential therapeutic agent against myeloma - phytochemical and pharmacological insights7
Plant trait measurement in 3D for growth monitoring7
Early detection of verticillium wilt in eggplant leaves by fusing five image channels: a deep learning approach7
Genetic transformation of the oilseed crop camelina using immature zygotic embryos7
Soybean leaf estimation based on RGB images and machine learning methods7
A simple and low-cost method for fluoride analysis of plant materials using alkali extraction and ion-selective electrode7
Correction: Revisiting superiority and stability metrics of cultivar performances using genomic data: derivations of new estimators7
High-throughput phenotyping allows the selection of soybean genotypes for earliness and high grain yield7
Development of an accurate low cost NDVI imaging system for assessing plant health7
Development of a controlled-environment assay to induce iron deficiency chlorosis in soybean by adjusting calcium carbonates, pH, and nodulation7
Hyperspectral imaging-based classification of rice leaf blast severity over multiple growth stages7
VA-TIRFM-based SM kymograph analysis for dwell time and colocalization of plasma membrane protein in plant cells7
Optimizing PGRs for in vitro shoot proliferation of pomegranate with bayesian-tuned ensemble stacking regression and NSGA-II: a comparative evaluation of machine learning models7
HairNet2: deep learning to quantify cotton leaf hairiness, a complex genetic and environmental trait7
Ripening dynamics revisited: an automated method to track the development of asynchronous berries on time-lapse images7
Optical coherence tomography for early detection of crop infection7
X-ray fluorescence spectroscopy (XRF) for metallome analysis of herbarium specimens7
Prediction of fruit characteristics of grafted plants of Camellia oleifera by deep neural networks7
High-throughput interspecies profiling of acidic plant hormones using miniaturised sample processing7
High-throughput phenotyping for non-destructive estimation of soybean fresh biomass using a machine learning model and temporal UAV data7
A Bayesian framework to model variance of grain yield response to plant density6
0.42166805267334