IPM Strategies and Their Dilemmas Including an Introduction to www. eurowheat.org

Information about disease management in winter wheat （Triticum aestiva） in eight European countries was collated and analysed by scientists and extension workers within the European Network for the Durable Exploitation of Crop Protection Strategies （ENDURE）. This included information about specific disease thresholds, decision support systems, host varieties, disease prevalence and pathogen virulence. Major differences in disease prevalence and economic importance were observed. Septoria tritici blotch （Mycosphaerella graminicola） was recognized as the most yield reducing disease in countries with intensive wheat production, but also rust diseases （Puccinia striiformis and Puccinia triticina）, powdery mildew （Blumeria graminis） and Fusarium head blight （Fusarium spp.） were seen as serious disease problems. Examples of current integrated pest management （IPM） strategies in different countries have been reported. Disease management and fungicide use patterns showed major differences, with an average input equivalent to 2.3 full dose rates （TFI） in the UK and a TFI of 0.6 in Denmark. These differences are most likely due to a combination of different cropping systems, climatic differences, disease prevalence, and socio-economic factors. The web based information platform www.eurowheat.org was used for dissemination of information and results including information on control thresholds, cultural practices which can influence disease attack, fungicide efficacy, fungicide resistance, and pathogen virulence, which are all elements supporting 1PM for disease control in wheat. The platform is open to all users. The target groups of EuroWheat information are researchers, advisors, breeders, and similar partners dealing with disease management in wheat.

From Prototype to Inference:A Pipeline to Apply Deep Learning in Sorghum Panicle Detection

Head(panicle)density is a major component in understanding crop yield,especially in crops that produce variable numbers of tillers such as sorghum and wheat.Use of panicle density both in plant breeding and in the agronomy scouting of commercial crops typically relies on manual counts observation,which is an inefficient and tedious process.Because of the easy availability of red–green–blue images,machine learning approaches have been applied to replacing manual counting.However,much of this research focuses on detection per se in limited testing conditions and does not provide a general protocol to utilize deep-learning-based counting.In this paper,we provide a comprehensive pipeline from data collection to model deployment in deep-learning-assisted panicle yield estimation for sorghum.This pipeline provides a basis from data collection and model training,to model validation and model deployment in commercial fields.Accurate model training is the foundation of the pipeline.However,in natural environments,the deployment dataset is frequently different from the training data(domain shift)causing the model to fail,so a robust model is essential to build a reliable solution.Although we demonstrate our pipeline in a sorghum field,the pipeline can be generalized to other grain species.Our pipeline provides a high-resolution head density map that can be utilized for diagnosis of agronomic variability within a field,in a pipeline built without commercial software.

Self-Supervised Plant Phenotyping by Combining Domain Adaptation with 3D Plant Model Simulations: Application to Wheat Leaf Counting at Seedling Stage

The number of leaves at a given time is important to characterize plant growth and development.In this work,we developed a high-throughput method to count the number of leaves by detecting leaf tips in RGB images.The digital plant phenotyping platform was used to simulate a large and diverse dataset of RGB images and corresponding leaf tip labels of wheat plants at seedling stages(150,000 images with over 2 million labels).The realism of the images was then improved using domain adaptation methods before training deep learning models.The results demonstrate the efficiency of the proposed method evaluated on a diverse test dataset,collecting measurements from 5 countries obtained under different environments,growth stages,and lighting conditions with different cameras(450 images with over 2,162 labels).Among the 6 combinations of deep learning models and domain adaptation techniques,the Faster-RCNN model with cycle-consistent generative adversarial network adaptation technique provided the best performance(R^(2)=0.94,root mean square error=8.7).Complementary studies show that it is essential to simulate images with sufficient realism(background,leaf texture,and lighting conditions)before applying domain adaptation techniques.Furthermore,the spatial resolution should be better than 0.6 mm per pixel to identify leaf tips.The method is claimed to be self-supervised since no manual labeling is required for model training.The self-supervised phenotyping approach developed here offers great potential for addressing a wide range of plant phenotyping problems.The trained networks are available at https://github.com/YinglunLi/Wheat-leaf-tip-detection.

Analyzing Changes in Maize Leaves Orientation due to GxExM Using an Automatic Method from RGB Images

The sowing pattern has an important impact on light interception efficiency in maize by determining the spatial distribution of leaves within the canopy.Leaves orientation is an important architectural trait determining maize canopies light interception.Previous studies have indicated how maize genotypes may adapt leaves orientation to avoid mutual shading with neighboring plants as a plastic response to intraspecific competition.The goal of the present study is 2-fold:firstly,to propose and validate an automatic algorithm(Automatic Leaf Azimuth Estimation from Midrib detection[ALAEM])based on leaves midrib detection in vertical red green blue(RGB)images to describe leaves orientation at the canopy level;and secondly,to describe genotypic and environmental differences in leaves orientation in a panel of 5 maize hybrids sowing at 2 densities(6 and 12 plants.m^(−2))and 2 row spacing(0.4 and 0.8 m)over 2 different sites in southern France.The ALAEM algorithm was validated against in situ annotations of leaves orientation,showing a satisfactory agreement(root mean square[RMSE]error=0.1,R^(2)=0.35)in the proportion of leaves oriented perpendicular to rows direction across sowing patterns,genotypes,and sites.The results from ALAEM permitted to identify significant differences in leaves orientation associated to leaves intraspecific competition.In both experiments,a progressive increase in the proportion of leaves oriented perpendicular to the row is observed when the rectangularity of the sowing pattern increases from 1(6 plants.m^(−2),0.4 m row spacing)towards 8(12 plants.m^(−2),0.8 m row spacing).Significant differences among the 5 cultivars were found,with 2 hybrids exhibiting,systematically,a more plastic behavior with a significantly higher proportion of leaves oriented perpendicularly to avoid overlapping with neighbor plants at high rectangularity.Differences in leaves orientation were also found between experiments in a squared sowing pattern(6 plants.m^(−2),0.4 m row spacing),indicating a possible contribution of illumination conditions inducing a preferential orientation toward east-west direction when intraspecific competition is low.

Global Wheat Head Detection Challenges:Winning Models and Application for Head Counting

Data competitions have become a popular approach to crowdsource new data analysis methods for general and specialized data science problems.Data competitions have a rich history in plant phenotyping,and new outdoor field datasets have the potential to embrace solutions across research and commercial applications.We developed the Global Wheat Challenge as a generalization competition in 2020 and 2021 to find more robust solutions for wheat head detection using field images from different regions.We analyze the winning challenge solutions in terms of their robustness when applied to new datasets.We found that the design of the competition had an influence on the selection of winning solutions and provide recommendations for future competitions to encourage the selection of more robust solutions.

Estimates of Maize Plant Density from UAV RGB Images Using Faster-RCNN Detection Model:Impact of the Spatial Resolution

Early-stage plant density is an essential trait that determines the fate of a genotype under given environmental conditions and management practices.The use of RGB images taken from UAVs may replace the traditional visual counting in fields with improved throughput,accuracy,and access to plant localization.However,high-resolution images are required to detect the small plants present at the early stages.This study explores the impact of image ground sampling distance(GSD)on the performances of maize plant detection at three-to-five leaves stage using Faster-RCNN object detection algorithm.Data collected at high resolution(GSD≈0:3 cm)over six contrasted sites were used for model training.Two additional sites with images acquired both at high and low(GSD≈0:6 cm)resolutions were used to evaluate the model performances.Results show that Faster-RCNN achieved very good plant detection and counting(rRMSE=0:08)performances when native high-resolution images are used both for training and validation.Similarly,good performances were observed(rRMSE=0:11)when the model is trained over synthetic low-resolution images obtained by downsampling the native training high-resolution images and applied to the synthetic low-resolution validation images.Conversely,poor performances are obtained when the model is trained on a given spatial resolution and applied to another spatial resolution.Training on a mix of high-and low-resolution images allows to get very good performances on the native high-resolution(rRMSE=0:06)and synthetic low-resolution(rRMSE=0:10)images.However,very low performances are still observed over the native low-resolution images(rRMSE=0:48),mainly due to the poor quality of the native low-resolution images.Finally,an advanced super resolution method based on GAN(generative adversarial network)that introduces additional textural information derived from the native high-resolution images was applied to the native low-resolution validation images.Results show some significant improvement(rRMSE=0:22)compared to bicubic upsampling approach,while still far below the performances achieved over the native high-resolution images.

SegVeg: Segmenting RGB Images into Green and Senescent Vegetation by Combining Deep and Shallow Methods

Pixel segmentation of high-resolution RGB images into chlorophyll-active or nonactive vegetation classes is a first step often required before estimating key traits of interest.We have developed the SegVeg approach for semantic segmentation of RGB images into three classes(background,green,and senescent vegetation).This is achieved in two steps:A U-net model is first trained on a very large dataset to separate whole vegetation from background.The green and senescent vegetation pixels are then separated using SVM,a shallow machine learning technique,trained over a selection of pixels extracted from images.The performances of the SegVeg approach is then compared to a 3-class U-net model trained using weak supervision over RGB images segmented with SegVeg as groundtruth masks.Results show that the SegVeg approach allows to segment accurately the three classes.However,some confusion is observed mainly between the background and senescent vegetation,particularly over the dark and bright regions of the images.The U-net model achieves similar performances,with slight degradation over the green vegetation:the SVM pixel-based approach provides more precise delineation of the green and senescent patches as compared to the convolutional nature of U-net.The use of the components of several color spaces allows to better classify the vegetation pixels into green and senescent.Finally,the models are used to predict the fraction of three classes over whole images or regularly spaced grid-pixels.Results show that green fraction is very well estimated(R^(2)=0.94)by the SegVeg model,while the senescent and background fractions show slightly degraded performances(R^(2)=0.70 and 0.73,respectively)with a mean 95%confidence error interval of 2.7%and 2.1%for the senescent vegetation and background,versus 1%for green vegetation.We have made SegVeg publicly available as a ready-to-use script and model,along with the entire annotated grid-pixels dataset.We thus hope to render segmentation accessible to a broad audience by requiring neither manual annotation nor knowledge or,at least,offering a pretrained model for more specific use.

A Double Swath Configuration for Improving Throughput and Accuracy of Trait Estimate from UAV Images

Multispectral observations from unmanned aerial vehicles(UAVs)are currently used for precision agriculture and crop phenotyping applications to monitor a series of traits allowing the characterization of the vegetation status.However,the limited autonomy of UAVs makes the completion of flights difficult when sampling large areas.Increasing the throughput of data acquisition while not degrading the ground sample distance(GSD)is,therefore,a critical issue to be solved.We propose here a new image acquisition configuration based on the combination of two focal length(f)optics:an optics with f=4:2 mm is added to the standard f=8 mm(SS:single swath)of the multispectral camera(DS:double swath,double of the standard one).Two flights were completed consecutively in 2018 over a maize field using the AIRPHEN multispectral camera at 52 m altitude.The DS flight plan was designed to get 80%overlap with the 4.2 mm optics,while the SS one was designed to get 80%overlap with the 8 mm optics.As a result,the time required to cover the same area is halved for the DS as compared to the SS.The georeferencing accuracy was improved for the DS configuration,particularly for the Z dimension due to the larger view angles available with the small focal length optics.Application to plant height estimates demonstrates that the DS configuration provides similar results as the SS one.However,for both the DS and SS configurations,degrading the quality level used to generate the 3D point cloud significantly decreases the plant height estimates.

Global Wheat Head Detection(GWHD)Dataset:A Large and Diverse Dataset of High-Resolution RGB-Labelled Images to Develop and Benchmark Wheat Head Detection Methods

The detection of wheat heads in plant images is an important task for estimating pertinent wheat traits including head population density and head characteristics such as health,size,maturity stage,and the presence of awns.Several studies have developed methods for wheat head detection from high-resolution RGB imagery based on machine learning algorithms.However,these methods have generally been calibrated and validated on limited datasets.High variability in observational conditions,genotypic differences,development stages,and head orientation makes wheat head detection a challenge for computer vision.Further,possible blurring due to motion or wind and overlap between heads for dense populations make this task even more complex.Through a joint international collaborative effort,we have built a large,diverse,and well-labelled dataset of wheat images,called the Global Wheat Head Detection(GWHD)dataset.It contains 4700 high-resolution RGB images and 190000 labelled wheat heads collected from several countries around the world at different growth stages with a wide range of genotypes.Guidelines for image acquisition,associating minimum metadata to respect FAIR principles,and consistent head labelling methods are proposed when developing new head detection datasets.The GWHD dataset is publicly available at http://www.global-wheat.com/and aimed at developing and benchmarking methods for wheat head detection.

Global Wheat Head Detection 2021:An Improved Dataset for Benchmarking Wheat Head Detection Methods

The Global Wheat Head Detection(GWHD)dataset was created in 2020 and has assembled 193,634 labelled wheat heads from 4700 RGB images acquired from various acquisition platforms and 7 countries/institutions.With an associated competition hosted in Kaggle,GWHD_2020 has successfully attracted attention from both the computer vision and agricultural science communities.From this first experience,a few avenues for improvements have been identified regarding data size,head diversity,and label reliability.To address these issues,the 2020 dataset has been reexamined,relabeled,and complemented by adding 1722 images from 5 additional countries,allowing for 81,553 additional wheat heads.We now release in 2021 a new version of the Global Wheat Head Detection dataset,which is bigger,more diverse,and less noisy than the GWHD_2020 version.