Plant Methods

Article	Citations
TreeJ: an ImageJ plugin for interactive cell lineage reconstruction from static images	107
Orchid2024: A cultivar-level dataset and methodology for fine-grained classification of Chinese Cymbidium Orchids	81
Coconut tree modeling based on abiotic factors and modified cosserat rod theory	80
A simple and high-throughput single pollen genotyping pipeline to study meiosis in apple (Malus x domestica)	79
Investigating phloem transport dynamics in Arabidopsis through compartmental modelling of positron emission tomography data	71
Targeted gene deletion with SpCas9 and multiple guide RNAs in Arabidopsis thaliana: four are better than two	58
Spectral image classification of asymptomatic peanut leaf diseases based on deep learning algorithms	57
A lightweight hybrid transformer approach for hyperspectral imaging-based drought tolerance evaluation in tea plants	55
A deep learning approach to track Arabidopsis seedlings’ circumnutation from time-lapse videos	54
The semi-automated development of plant cell wall finite element models	47
Crop phenotype prediction using SNP context and whole-genome feature embedding based on DNABERT-2	44
Classification of multi-year and multi-variety pumpkin seeds using hyperspectral imaging technology and three-dimensional convolutional neural network	42
Non-destructive real-time monitoring of underground root development with distributed fiber optic sensing	41
An automated method for stem diameter measurement based on laser module and deep learning	41
The influence of water content on the longitudinal modulus of elasticity of maize stalk pith and rind tissues	40
The isolation strategy and chemical analysis of oil cells from Asari Radix et Rhizoma	40
A novel method for extraction of high purity and high production Phytophthora sojae oospores	40
Development of a multi-targeted real-time PCR assay for the detection of the grapevine pathogen Xylophilus ampelinus	39
Estimation of cotton canopy parameters based on unmanned aerial vehicle (UAV) oblique photography	39
Combination of long-term 13CO2 labeling and isotopolog profiling allows turnover analysis of photosynthetic pigments in Arabidopsis leaves	37
Non-destructive detection of early wheat germination via deep learning-optimized terahertz imaging	36
Improved wood species identification based on multi-view imagery of the three anatomical planes	36
Improved estimation of forage nitrogen in alpine grassland by integrating Sentinel-2 and SIF data	35
Truncated CMV2bN43 enhances virus-induced gene silencing in pepper by retaining systemic but not local silencing suppression	35
A simple and efficient method to quantify the cell parameters of the seed coat, embryo and silique wall in rapeseed	35

An improved bacterial mRNA enrichment strategy in dual RNA sequencing to unveil the dynamics of plant-bacterial interactions	34
pSIG plasmids, MoClo-compatible vectors for efficient production of chimeric double-stranded RNAs in Escherichia coli HT115 (DE3) strain	33
Novel in silico screening system for plant defense activators using deep learning-based prediction of reactive oxygen species accumulation	33
OpenEar: an ultra-affordable, high-throughput, and accurate maize ear phenotyping system	33
Optimization of ribosome profiling in plants including structural analysis of rRNA fragments	33
Synchrotron tomography applications in agriculture and food sciences research: a review	32
Detection of TuMV by a toehold switch sensor coupled with NASBA amplification in Pseudostellaria heterophylla	31
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 weightlessness	31
The evaluation of different combinations of enzyme set, aligner and caller in GBS sequencing of soybean	31
A high-throughput phenotyping method for sugarcane rind penetrometer resistance and breaking force characterization by near-infrared spectroscopy	30
Using near-infrared spectroscopy to predict nitrogen and phosphorus concentrations of herbarium specimens under different storage conditions	30
A statistical method for high-throughput emergence rate calculation for soybean breeding plots based on field phenotypic characteristics	30
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 learning	30
Improvement of germination rate and hybridization to facilitate breeding of an industrial oil crop, Euphorbia lagascae Spreng	30
SYMPATHIQUE: image-based tracking of symptoms and monitoring of pathogenesis to decompose quantitative disease resistance in the field	30
Automatic rape flower cluster counting method based on low-cost labelling and UAV-RGB images	30
GrainNet: efficient detection and counting of wheat grains based on an improved YOLOv7 modeling	29
Research on the classification model of rubber leaf powdery mildew disease severity based on hyperspectral multi-dimensional feature fusion	29
A new and effective method to induce infection of Phyllachora maydis into corn for tar spot studies in controlled environments	29
RGB image-based method for phenotyping rust disease progress in pea leaves using R	28
Inter-row navigation line detection for cotton with broken rows	28
DWTFormer: a frequency-spatial features fusion model for tomato leaf disease identification	28
ScAnalyzer: an image processing tool to monitor plant disease symptoms and pathogen spread in Arabidopsis thaliana leaves	27
Evaluation of deep learning for predicting rice traits using structural and single-nucleotide genomic variants	27
Automated, image-based disease measurement for phenotyping resistance to soybean frogeye leaf spot	27
Spectral estimation of the aboveground biomass of cotton under water–nitrogen coupling conditions	26
PestDetectSim: an integrated approach for crop pest diagnosis using object detection and similarity-based image retrieval	26
Assembly and operation of an imaging system for long-term monitoring of bioluminescent and fluorescent reporters in plants	26
Machine learning provides specific detection of salt and drought stresses in cucumber based on miRNA characteristics	26
A comparative study on point cloud down-sampling strategies for deep learning-based crop organ segmentation	26
Evaluation of an intelligent artificial climate chamber for high-throughput crop phenotyping in wheat	25
In vitro micropropagation protocols for two endangered Dianthus species - via in vitro culture for conservation and recultivation purposes	25
Quantitative phenotyping of crop roots with spectral electrical impedance tomography: a rhizotron study with optimized measurement design	25
An electrophoretic mobility shift assay using the protein isolated from host plants	24
WheatLFANet: in-field detection and counting of wheat heads with high-real-time global regression network	24
Scoring the number of B chromosomes in Zea mays L. using droplet digital PCR assay	24
EBS-YOLO: edge-optimized bidirectional spatial feature augmentation for in-field detection of wheat Fusarium head blight epidemics	24
Optimization of preparation conditions for Salsola laricifolia protoplasts using response surface methodology and artificial neural network modeling	24
A compact deep learning approach integrating depthwise convolutions and spatial attention for plant disease classification	24
Rapid Ragi: A speed breeding protocol for finger millet	23
Refining bulk segregant analyses: ontology-mediated discovery of flowering time genes in Brassica oleracea	23
Statistical analysis of organelle movement using state-space models	23
Mapping of cotton bolls and branches with high-granularity through point cloud segmentation	22
Assessing data analysis techniques in a high-throughput meiosis-like induction detection system	22
Detection and characterization of spike architecture based on deep learning and X-ray computed tomography in barley	22
Profiling DNA-protein interactions in Meloidogyne incognita using dCas9-based affinity purification	22
BerryPortraits: Phenotyping Of Ripening Traits in cranberry (Vaccinium macrocarpon Ait.) with YOLOv8	22
A high-throughput approach for quantifying turgor loss point in grapevine	22
Pre-trained protein language model sheds new light on the prediction of Arabidopsis protein–protein interactions	21
A vector-free gene interference system using delaminated Mg–Al-lactate layered double hydroxide nanosheets as molecular carriers to intact plant cells	21

Correction: Whole mount multiplexed visualization of DNA, mRNA, and protein in plant-parasitic nematodes	21
A method to determine antifungal activity in seed exudates by nephelometry	21
SeedSeg: image-based transgenic seed counting for segregation analysis of T-DNA loci	21
Insights into lncRNA-mediated regulatory networks in Hevea brasiliensis under anthracnose stress	21
Mitochondrial DNA editing in potato through mitoTALEN and mitoTALECD: molecular characterization and stability of editing events	20
Automating high-throughput screening for anthracnose resistance in common bean using allele specific PCR	20
Go Big or go home: a new gene ontology subset that improves plant gene function prediction	20
Optimizing cannabis cultivation: an efficient in vitro system for flowering induction	20
A custom library construction method for super-resolution ribosome profiling in Arabidopsis	20
Intelligent identification on cotton verticillium wilt based on spectral and image feature fusion	20
Spatial and Texture Analysis of Root System distribution with Earth mover’s Distance (STARSEED)	20
ADAM-DETR: an intelligent rice disease detection method based on adaptive multi-scale feature fusion	20
Transmembrane potential, an indicator in situ reporting cellular senescence and stress response in plant tissues	20
BioCurve Analyzer: a web-based shiny app for analyzing biological response curves	19
AraDQ: an automated digital phenotyping software for quantifying disease symptoms of flood-inoculated Arabidopsis seedlings	19
Efficient mutagenesis and genotyping of maize inbreds using biolistics, multiplex CRISPR/Cas9 editing, and Indel-Selective PCR	19
Acceleration of wheat breeding: enhancing efficiency and practical application of the speed breeding system	19
Tracking deuterium uptake in hydroponically grown maize roots using correlative helium ion microscopy and Raman micro-spectroscopy	19
Attention-PestNet: hierarchical scaled dot-product attention for insect pest detection	18
Mapping and quantifying unique branching structures in lentil (Lens culinaris Medik.)	18
A deep learning approach for deriving wheat phenology from near-surface RGB image series using spatiotemporal fusion	18
FE-SEM visualization of cortical microtubules in plant cells using freeze-fracture techniques	18
A novel method for measuring heat injury in leaves provides insights into the sequence of processes of heat injury development	18
Monitoring of plant water uptake by measuring root dielectric properties on a fine timescale: diurnal changes and response to leaf excision	18
Eggsplorer: a rapid plant–insect resistance determination tool using an automated whitefly egg quantification algorithm	18
YOLO-RBSD: an efficient and accurate rice blast spore detector based on improved YOLOv8	18
CRISPR-Cas13a as a next-generation tool for rapid and precise plant RNA virus diagnostics	18
MicroDeblurNet: high-fidelity restoration of spatially variant defocus in microscopic images for cucumber downy mildew	17
Publisher Correction: New improvements in grapevine genome editing: high efficiency biallelic homozygous knock-out from regenerated plantlets by using an optimized zCas9i	17
Low-cost and reliable substrate-based phenotyping platform for screening salt tolerance of cutting propagation-dependent grass, paspalum vaginatum	17
Apnet: Lightweight network for apricot tree disease and pest detection in real-world complex backgrounds	17
A novel selection model based on multivariate methods and arbitrary genetic parameters: a case study on tomato families	17
CMSAF-Net: integrative network design with enhanced decoder for precision segmentation of pear leaf diseases	16
A wireless leaf movement sensor system for early detection of abiotic stresses in Zea mays L.	16
A non-destructive approach for measuring rice panicle-level photosynthetic responses using 3D-image reconstruction	16
Determining water status of walnut orchards using the crop water stress index and canopy temperature measurements	16
Advancing radiation-induced mutant screening through high-throughput technology: a preliminary evaluation of mutant screening in Arabidopsis thaliana	16
Utilizing X-ray radiography for non-destructive assessment of paddy rice grain quality traits	16
Accelerating eucalypt clone selection pipeline via cloned progeny trials and molecular data	16
Improved genomic prediction using machine learning with Variational Bayesian sparsity	16
One pattern analysis (OPA) for the quantitative determination of protein interactions in plant cells	16
Introduction of the Ribo-BiFC method to plants using a split mVenus approach	16
RP-DETR: end-to-end rice pests detection using a transformer	15
A CNN model for early detection of pepper Phytophthora blight using multispectral imaging, integrating spectral and textural information	15
Identifying and mapping individual medicinal plant Lamiophlomis rotata at high elevations by using unmanned aerial vehicles and deep learning	15
Segmentation and counting of wheat spike grains based on deep learning and textural feature	15
Combining novel feature selection strategy and hyperspectral vegetation indices to predict crop yield	15
Establishment of a low-temperature immersion method for extracting high-activity and high-purity mitochondria from Syntrichia caninervis Mitt.	15
De novo assembly provides new insights into the evolution of Elaeagnus angustifolia L.	15
YOLO-PEST: a novel rice pest detection approach based on YOLOv5s	15
Correction: Rapid and cost-effective molecular karyotyping in wheat, barley, and their crossprogeny by chromosome-specific multiplex PCR	14
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 progeny	14
RhizoMAP: a comprehensive, nondestructive, and sensitive platform for metabolic imaging of the rhizosphere	14
Establishment of an efficient tissue culture system for Paeonia ostii by combining vernalization and etiolation pretreatment with optimized culture conditions	14
PhenoTrack3D: an automatic high-throughput phenotyping pipeline to track maize organs over time	13
Deep learning for detecting herbicide weed control spectrum in turfgrass	13
YOLOV8-CMS: a high-accuracy deep learning model for automated citrus leaf disease classification and grading	13
Characterization of leaf surface phenotypes based on light interaction	13
ShinyCore: An R/Shiny program for establishing core collection based on single nucleotide polymorphism data	13
Accelerating leaf area measurement using a volumetric approach	13
SSR_VibraProfiler: a Python package for accurate classification of varieties using SSRs with intra-variety specificity and inter-variety polymorphism	13
Low-cost and automated phenotyping system “Phenomenon” for multi-sensor in situ monitoring in plant in vitro culture	13
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 application	13
Dual discriminator GAN-based synthetic crop disease image generation for precise crop disease identification	13
Gray mold and anthracnose disease detection on strawberry leaves using hyperspectral imaging	13
A conditional segmentation-guided network for pomegranate image completion under occlusion	13
Optimized deep learning framework for pomegranate disease detection using nature-inspired algorithms	13
Clarification of the infection pattern of Xanthomonas citri subsp. citri on citrus fruit by artificial inoculation	13
Efficient induction of tetraploids via adventitious bud regeneration and subsequent phenotypic variation in Acacia melanoxylon	12
Automatic root measurement: a lightweight method for measuring pea root length	12
Developing non-invasive 3D quantificational imaging for intelligent coconut analysis system with X-ray	12
Overexpressing Arabidopsis thaliana ACBP6 in transgenic rapid-cycling Brassica napus confers cold tolerance	12
Swin-Unet++: a study on phenotypic parameter analysis of cabbage seedling roots	12
Opening the black box: explainable deep-learning classification of wood microscopic image of endangered tree species	12
A cell P system with membrane division and dissolution rules for soybean leaf disease recognition	12
Development of a semi-open chamber system for the gas exchange measurement of whole-canopy under steady and unsteady states in cucumber seedlings	12
Photolysis of caged cytokinin in single cells of Arabidopsis thaliana	12
NRTPredictor: identifying rice root cell state in single-cell RNA-seq via ensemble learning	12
A systematic comparison of transformers and ConvNets for root segmentation across nine datasets	12
Establishment of an NPK nutrient monitor system in yield-graded cotton petioles under drip irrigation	12

Non-wounding contact-based Inoculation of fruits with fungal pathogens in postharvest	12
A novel approach integrating multispectral imaging and machine learning to identify seed maturity and vigor in smooth bromegrass	12
An automated phenotyping method for Chinese Cymbidium seedlings based on 3D point cloud	12
The mechanisms and prediction of non-structural carbohydrates accretion and depletion after mechanical wounding in slash pine (Pinus elliottii) using near-infrared reflectance spectroscopy	12
In-vivo Raman microspectroscopy reveals differential nitrate concentration in different developmental zones in Arabidopsis roots	12
Quality assurance of hyperspectral imaging systems for neural network supported plant phenotyping	12
Assessing and avoiding C isotopic contamination artefacts in mesocosm-scale 13CO2/12CO2 labelling systems: from biomass components to purified carbohydrates and dark respiration	12
MAPtools: command-line tools for mapping-by-sequencing and QTL-Seq analysis and visualization	11
Enhancing cotton whitefly (Bemisia tabaci) detection and counting with a cost-effective deep learning approach on the Raspberry Pi	11
Colour-analyzer: a new dual colour model-based imaging tool to quantify plant disease	11
Enhancing plant disease detection through multi-modal integration of visual and textual data	11
Effect of a suitable treatment period on the genetic transformation efficiency of the plant leaf disc method	11
IMPLANT: a new technique for transgene copy number estimation in plants using a single end-point PCR reaction	11
Rapid real-time quantitative colorimetric LAMP methodology for field detection of Verticillium dahliae in crude olive-plant samples	11
A high-throughput fluorescence-based microplate reader assay to quantify total flavonol levels in plant tissues	11
Soybean seed pest damage detection method based on spatial frequency domain imaging combined with RL-SVM	11
Trans2express – de novo transcriptome assembly pipeline optimized for gene expression analysis	11
A modified aeroponic system for growing small-seeded legumes and other plants to study root systems	11
A protocol for Chenopodium quinoa pollen germination	11
Effect of hormone concentration on callus induction and plant regeneration induced from daylily (Hemerocallis fulva) anther	11
A Cotyledon-based Virus-Induced Gene Silencing (Cotyledon-VIGS) approach to study specialized metabolism in medicinal plants	11
Exploring the impact of light intensity under speed breeding conditions on the development and growth of lentil and chickpea	11
An efficient multiplex approach to CRISPR/Cas9 gene editing in citrus	11
DeLTa-Seq: direct-lysate targeted RNA-Seq from crude tissue lysate	11
A protoplast-based transient gene expression assay for the identification of heat and oxidative stress-regulatory genes in perennial ryegrass	11
Organ-level 3D phenotyping of saffron using a low-cost dual-camera workflow	11
Establishment of fluorescent protein-tagged lines for investigating dynamic localization of organelle and other cell structures in rice pollen tube	11
An integrated isotopic labeling and freeze sampling apparatus (ILSA) to support sampling leaf metabolomics at a centi-second scale	11
A CNN-LSTM-att hybrid model for classification and evaluation of growth status under drought and heat stress in chinese fir (Cunninghamia lanceolata)	11
Overexpression of Vitis GRF4-GIF1 improves regeneration efficiency in diploid Fragaria vesca Hawaii 4	10
Towards portable MRI in the plant sciences	10
Correction: BerryPortraits: phenotyping of ripening traits in cranberry (Vaccinium macrocarpon Ait.) With YOLOv8	10
Real-time identification and quantification of apple scab on fruit in preharvest and postharvest conditions using YOLO11: a deep learning approach	10
Production of HSVd- and PPV-free apricot cultivars by in vitro thermotherapy followed by meristem culture	10
A simple new method to determine leaf specific heat capacity	10
Validating a multi-locus metabarcoding approach for characterizing mixed-pollen samples	10
Lightweight highland barley detection based on improved YOLOv5	10
Identification of an emerging cucumber virus in Taiwan using Oxford nanopore sequencing technology	10
Completing the picture of field-grown cereal crops: a new method for detailed leaf surface models in wheat	10
Monitoring of drought stress and transpiration rate using proximal thermal and hyperspectral imaging in an indoor automated plant phenotyping platform	10
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 crops	10
SISE, free LabView-based software for ion flux measurements	10
A prediction model of rubber content in the dried root of Taraxacum kok-saghyz Rodin based on near-infrared spectroscopy	10
Novel cultivation techniques for water lily (Nymphaea micrantha Guill. & Perr) production based on in vitro technology	10
OneRosette to predict them all: single plant prompting on a visual foundation model to segment symptomatic Arabidopsis thaliana time series	10
Optimization of immune receptor-related hypersensitive cell death response assay using agrobacterium-mediated transient expression in tobacco plants	10
An ensemble deep learning models approach using image analysis for cotton crop classification in AI-enabled smart agriculture	10
Vapor pressure deficit control and mechanical vibration techniques to induce self-pollination in strawberry flowers	10
Disentangling soybean GxE effects in an integrated genomic prediction and machine learning-GWAS workflow	10
Genomic prediction for root and yield traits of barley under a water availability gradient: a case study comparing different spatial adjustments	10
Integrated experimental and computational workflows for single-cell transcriptomics in plants	10
A system for the study of roots 3D kinematics in hydroponic culture: a study on the oscillatory features of root tip	10
A cotton organ segmentation method with phenotypic measurements from a point cloud using a transformer	10
2023: a soil odyssey–HeAted soiL-Monoliths (HAL-Ms) to examine the effect of heat emission from HVDC underground cables on plant growth	9
An efficient clear-native PAGE–based workflow for cryo-electron microscopy sample preparation of large protein complexes	9
Carbon dioxide expanded liquid: an effective solvent for the extraction of quercetin from South African medicinal plants	9
Plant trait measurement in 3D for growth monitoring	9
Wheat grain width: a clue for re-exploring visual indicators of grain weight	9
Development of an accurate low cost NDVI imaging system for assessing plant health	9
X-ray fluorescence spectroscopy (XRF) for metallome analysis of herbarium specimens	9
Maui: modular analytics of UAS imagery for specialty crop research	9
tRNA-based polycistronic CRISPR/Cas9 system boosts efficiency of multi-gene deletion in the moss Physcomitrella	9
Cross-species optimization of nuclei isolation in ten plant species	9
Enhanced Bayesian model for multienvironmental selection of winter hybrids maize: assessing grain yield using ‘ProbBreed’	9
Deep learning–based identification of visually similar foliar diseases in field-grown barley	9
Correction: The rapid-tome, a 3D-printed microtome, and an updated hand-sectioning method for high-quality plant sectioning	9
Rapid quantification of whole seed fatty acid amount, composition, and shape phenotypes from diverse oilseed species with large differences in seed size	9
Prediction of fruit characteristics of grafted plants of Camellia oleifera by deep neural networks	9
A successive time-to-event model of phyllochron dynamics for hypothesis testing: application to the analysis of genetic and environmental effects in maize	9
Correction: Revisiting superiority and stability metrics of cultivar performances using genomic data: derivations of new estimators	8
Terrestrial laser scanning and low magnetic field digitization yield similar architectural coarse root traits for 32-year-old Pinus ponderosa trees	8
Early detection of verticillium wilt in eggplant leaves by fusing five image channels: a deep learning approach	8
Tensor methods in data analysis of chromatography/mass spectroscopy-based plant metabolomics	8
HairNet2: deep learning to quantify cotton leaf hairiness, a complex genetic and environmental trait	8
Genetic transformation of the oilseed crop camelina using immature zygotic embryos	8
Establishment of virus-induced gene silencing (VIGS) system in Luffa acutangula using Phytoene desaturase (PDS) and tendril synthesis related gene (TEN)	8
Multimodal learning on RGB-D image for precise litchi phenotyping and weight estimation	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 inactivation	8
The Tonoplast Topology Index—a new metric for describing vacuole organization	8
High-throughput phenotyping for non-destructive estimation of soybean fresh biomass using a machine learning model and temporal UAV data	8
Soybean leaf estimation based on RGB images and machine learning methods	8
Robust estimation of rice flag leaf inclination angle from SfM-MVS point clouds via ensemble skeleton extraction: validation in field and pot experiments	8
MoEGP: an efficient crop genomic prediction approach based on the mixture of experts network	8
Ripening dynamics revisited: an automated method to track the development of asynchronous berries on time-lapse images	8
Starch phosphorylation—A needle in a haystack	8
A novel application of laser speckle imaging technique for prediction of hypoxic stress of apples	8
High-throughput interspecies profiling of acidic plant hormones using miniaturised sample processing	8
Improved estimation of aboveground biomass of regional coniferous forests integrating UAV-LiDAR strip data, Sentinel-1 and Sentinel-2 imageries	8
Optical coherence tomography for early detection of crop infection	8
Estimation of chlorophyll content in rice canopy leaves using 3D radiative transfer modeling and unmanned aerial hyperspectral images	8
Hyperspectral imaging-based classification of rice leaf blast severity over multiple growth stages	8
A simple and low-cost method for fluoride analysis of plant materials using alkali extraction and ion-selective electrode	8
LDSL framework: a lightweight dual-stream learning framework for wheat disease detection	8
Tunisian Artemisia campestris L.: a potential therapeutic agent against myeloma - phytochemical and pharmacological insights	8
VA-TIRFM-based SM kymograph analysis for dwell time and colocalization of plasma membrane protein in plant cells	8