Plant Phenomics最新文献

{"title":"DEKR-SPrior: An Efficient Bottom-Up Keypoint Detection Model for Accurate Pod Phenotyping in Soybean.","authors":"Jingjing He, Lin Weng, Xiaogang Xu, Ruochen Chen, Bo Peng, Nannan Li, Zhengchao Xie, Lijian Sun, Qiang Han, Pengfei He, Fangfang Wang, Hui Yu, Javaid Akhter Bhat, Xianzhong Feng","doi":"10.34133/plantphenomics.0198","DOIUrl":"https://doi.org/10.34133/plantphenomics.0198","url":null,"abstract":"<p><p>The pod and seed counts are important yield-related traits in soybean. High-precision soybean breeders face the major challenge of accurately phenotyping the number of pods and seeds in a high-throughput manner. Recent advances in artificial intelligence, especially deep learning (DL) models, have provided new avenues for high-throughput phenotyping of crop traits with increased precision. However, the available DL models are less effective for phenotyping pods that are densely packed and overlap in in situ soybean plants; thus, accurate phenotyping of the number of pods and seeds in soybean plant is an important challenge. To address this challenge, the present study proposed a bottom-up model, DEKR-SPrior (disentangled keypoint regression with structural prior), for in situ soybean pod phenotyping, which considers soybean pods and seeds analogous to human people and joints, respectively. In particular, we designed a novel structural prior (SPrior) module that utilizes cosine similarity to improve feature discrimination, which is important for differentiating closely located seeds from highly similar seeds. To further enhance the accuracy of pod location, we cropped full-sized images into smaller and high-resolution subimages for analysis. The results on our image datasets revealed that DEKR-SPrior outperformed multiple bottom-up models, viz., Lightweight-OpenPose, OpenPose, HigherHRNet, and DEKR, reducing the mean absolute error from 25.81 (in the original DEKR) to 21.11 (in the DEKR-SPrior) in pod phenotyping. This paper demonstrated the great potential of DEKR-SPrior for plant phenotyping, and we hope that DEKR-SPrior will help future plant phenotyping.</p>","PeriodicalId":20318,"journal":{"name":"Plant Phenomics","volume":"6 ","pages":"0198"},"PeriodicalIF":7.6,"publicationDate":"2024-06-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11209727/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141470375","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Segment Anything for Comprehensive Analysis of Grapevine Cluster Architecture and Berry Properties.","authors":"Efrain Torres-Lomas, Jimena Lado-Bega, Guillermo Garcia-Zamora, Luis Diaz-Garcia","doi":"10.34133/plantphenomics.0202","DOIUrl":"https://doi.org/10.34133/plantphenomics.0202","url":null,"abstract":"<p><p>Grape cluster architecture and compactness are complex traits influencing disease susceptibility, fruit quality, and yield. Evaluation methods for these traits include visual scoring, manual methodologies, and computer vision, with the latter being the most scalable approach. Most of the existing computer vision approaches for processing cluster images often rely on conventional segmentation or machine learning with extensive training and limited generalization. The Segment Anything Model (SAM), a novel foundation model trained on a massive image dataset, enables automated object segmentation without additional training. This study demonstrates out-of-the-box SAM's high accuracy in identifying individual berries in 2-dimensional (2D) cluster images. Using this model, we managed to segment approximately 3,500 cluster images, generating over 150,000 berry masks, each linked with spatial coordinates within their clusters. The correlation between human-identified berries and SAM predictions was very strong (Pearson's <i>r²</i> = 0.96). Although the visible berry count in images typically underestimates the actual cluster berry count due to visibility issues, we demonstrated that this discrepancy could be adjusted using a linear regression model (adjusted <i>R</i> ² = 0.87). We emphasized the critical importance of the angle at which the cluster is imaged, noting its substantial effect on berry counts and architecture. We proposed different approaches in which berry location information facilitated the calculation of complex features related to cluster architecture and compactness. Finally, we discussed SAM's potential integration into currently available pipelines for image generation and processing in vineyard conditions.</p>","PeriodicalId":20318,"journal":{"name":"Plant Phenomics","volume":"6 ","pages":"0202"},"PeriodicalIF":7.6,"publicationDate":"2024-06-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11208874/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141470376","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Simulation of Automatically Annotated Visible and Multi-/Hyperspectral Images Using the Helios 3D Plant and Radiative Transfer Modeling Framework.","authors":"Tong Lei, Jan Graefe, Ismael K Mayanja, Mason Earles, Brian N Bailey","doi":"10.34133/plantphenomics.0189","DOIUrl":"10.34133/plantphenomics.0189","url":null,"abstract":"<p><p>Deep learning and multimodal remote and proximal sensing are widely used for analyzing plant and crop traits, but many of these deep learning models are supervised and necessitate reference datasets with image annotations. Acquiring these datasets often demands experiments that are both labor-intensive and time-consuming. Furthermore, extracting traits from remote sensing data beyond simple geometric features remains a challenge. To address these challenges, we proposed a radiative transfer modeling framework based on the Helios 3-dimensional (3D) plant modeling software designed for plant remote and proximal sensing image simulation. The framework has the capability to simulate RGB, multi-/hyperspectral, thermal, and depth cameras, and produce associated plant images with fully resolved reference labels such as plant physical traits, leaf chemical concentrations, and leaf physiological traits. Helios offers a simulated environment that enables generation of 3D geometric models of plants and soil with random variation, and specification or simulation of their properties and function. This approach differs from traditional computer graphics rendering by explicitly modeling radiation transfer physics, which provides a critical link to underlying plant biophysical processes. Results indicate that the framework is capable of generating high-quality, labeled synthetic plant images under given lighting scenarios, which can lessen or remove the need for manually collected and annotated data. Two example applications are presented that demonstrate the feasibility of using the model to enable unsupervised learning by training deep learning models exclusively with simulated images and performing prediction tasks using real images.</p>","PeriodicalId":20318,"journal":{"name":"Plant Phenomics","volume":"6 ","pages":"0189"},"PeriodicalIF":6.5,"publicationDate":"2024-05-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11136674/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141180561","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Out-of-Distribution Detection Algorithms for Robust Insect Classification.","authors":"Mojdeh Saadati, Aditya Balu, Shivani Chiranjeevi, Talukder Zaki Jubery, Asheesh K Singh, Soumik Sarkar, Arti Singh, Baskar Ganapathysubramanian","doi":"10.34133/plantphenomics.0170","DOIUrl":"https://doi.org/10.34133/plantphenomics.0170","url":null,"abstract":"<p><p>Plants encounter a variety of beneficial and harmful insects during their growth cycle. Accurate identification (i.e., detecting insects' presence) and classification (i.e., determining the type or class) of these insect species is critical for implementing prompt and suitable mitigation strategies. Such timely actions carry substantial economic and environmental implications. Deep learning-based approaches have produced models with good insect classification accuracy. Researchers aim to implement identification and classification models in agriculture, facing challenges when input images markedly deviate from the training distribution (e.g., images like vehicles, humans, or a blurred image or insect class that is not yet trained on). Out-of-distribution (OOD) detection algorithms provide an exciting avenue to overcome these challenges as they ensure that a model abstains from making incorrect classification predictions on images that belong to non-insect and/or untrained insect classes. As far as we know, no prior in-depth exploration has been conducted on the role of the OOD detection algorithms in addressing agricultural issues. Here, we generate and evaluate the performance of state-of-the-art OOD algorithms on insect detection classifiers. These algorithms represent a diversity of methods for addressing an OOD problem. Specifically, we focus on extrusive algorithms, i.e., algorithms that wrap around a well-trained classifier without the need for additional co-training. We compared three OOD detection algorithms: (a) maximum softmax probability, which uses the softmax value as a confidence score; (b) Mahalanobis distance (MAH)-based algorithm, which uses a generative classification approach; and (c) energy-based algorithm, which maps the input data to a scalar value, called energy. We performed an extensive series of evaluations of these OOD algorithms across three performance axes: (a) Base model accuracy: How does the accuracy of the classifier impact OOD performance? (b) How does the level of dissimilarity to the domain impact OOD performance? (c) Data imbalance: How sensitive is OOD performance to the imbalance in per-class sample size? Evaluating OOD algorithms across these performance axes provides practical guidelines to ensure the robust performance of well-trained models in the wild, which is a key consideration for agricultural applications. Based on this analysis, we proposed the most effective OOD algorithm as wrapper for the insect classifier with highest accuracy. We presented the results of its OOD detection performance in the paper. Our results indicate that OOD detection algorithms can significantly enhance user trust in insect pest classification by abstaining classification under uncertain conditions.</p>","PeriodicalId":20318,"journal":{"name":"Plant Phenomics","volume":"6 ","pages":"0170"},"PeriodicalIF":6.5,"publicationDate":"2024-04-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11065417/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140854492","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"PAT (Periderm Assessment Toolkit): A Quantitative and Large-Scale Screening Method for Periderm Measurements.","authors":"Gonzalo Villarino, Signe Dahlberg-Wright, Ling Zhang, Marianne Schaedel, Lin Wang, Karyssa Miller, Jack Bartlett, Albert Martin Dang Vu, Wolfgang Busch","doi":"10.34133/plantphenomics.0156","DOIUrl":"10.34133/plantphenomics.0156","url":null,"abstract":"<p><p>The periderm is a vital protective tissue found in the roots, stems, and woody elements of diverse plant species. It plays an important function in these plants by assuming the role of the epidermis as the outermost layer. Despite its critical role for protecting plants from environmental stresses and pathogens, research on root periderm development has been limited due to its late formation during root development, its presence only in mature root regions, and its impermeability. One of the most straightforward measurements for comparing periderm formation between different genotypes and treatments is periderm (phellem) length. We have developed PAT (Periderm Assessment Toolkit), a high-throughput user-friendly pipeline that integrates an efficient staining protocol, automated imaging, and a deep-learning-based image analysis approach to accurately detect and measure periderm length in the roots of <i>Arabidopsis thaliana</i>. The reliability and reproducibility of our method was evaluated using a diverse set of 20 Arabidopsis natural accessions. Our automated measurements exhibited a strong correlation with human-expert-generated measurements, achieving a 94% efficiency in periderm length quantification. This robust PAT pipeline streamlines large-scale periderm measurements, thereby being able to facilitate comprehensive genetic studies and screens. Although PAT proves highly effective with automated digital microscopes in Arabidopsis roots, its application may pose challenges with nonautomated microscopy. Although the workflow and principles could be adapted for other plant species, additional optimization would be necessary. While we show that periderm length can be used to distinguish a mutant impaired in periderm development from wild type, we also find it is a plastic trait. Therefore, care must be taken to include sufficient repeats and controls, to minimize variation, and to ensure comparability of periderm length measurements between different genotypes and growth conditions.</p>","PeriodicalId":20318,"journal":{"name":"Plant Phenomics","volume":"6 ","pages":"0156"},"PeriodicalIF":6.5,"publicationDate":"2024-03-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10981931/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140336642","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Maturity classification of rapeseed using hyperspectral image combined with machine learning","authors":"Hui Feng, Yongqi Chen, Jingyan Song, Bingjie Lu, Caixia Shu, Jiajun Qiao, Yitao Liao, Wanneng Yang","doi":"10.34133/plantphenomics.0139","DOIUrl":"https://doi.org/10.34133/plantphenomics.0139","url":null,"abstract":"","PeriodicalId":20318,"journal":{"name":"Plant Phenomics","volume":"23 2","pages":""},"PeriodicalIF":6.5,"publicationDate":"2024-01-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139388486","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The Dissection of Nitrogen Response Traits Using Drone Phenotyping and Dynamic Phenotypic Analysis to Explore N Responsiveness and Associated Genetic Loci in Wheat.","authors":"Guohui Ding, Liyan Shen, Jie Dai, Robert Jackson, Shuchen Liu, Mujahid Ali, Li Sun, Mingxing Wen, Jin Xiao, Greg Deakin, Dong Jiang, Xiu-E Wang, Ji Zhou","doi":"10.34133/plantphenomics.0128","DOIUrl":"10.34133/plantphenomics.0128","url":null,"abstract":"<p><p>Inefficient nitrogen (N) utilization in agricultural production has led to many negative impacts such as excessive use of N fertilizers, redundant plant growth, greenhouse gases, long-lasting toxicity in ecosystem, and even effect on human health, indicating the importance to optimize N applications in cropping systems. Here, we present a multiseasonal study that focused on measuring phenotypic changes in wheat plants when they were responding to different N treatments under field conditions. Powered by drone-based aerial phenotyping and the AirMeasurer platform, we first quantified 6 N response-related traits as targets using plot-based morphological, spectral, and textural signals collected from 54 winter wheat varieties. Then, we developed dynamic phenotypic analysis using curve fitting to establish profile curves of the traits during the season, which enabled us to compute static phenotypes at key growth stages and dynamic phenotypes (i.e., phenotypic changes) during N response. After that, we combine 12 yield production and N-utilization indices manually measured to produce N efficiency comprehensive scores (NECS), based on which we classified the varieties into 4 N responsiveness (i.e., N-dependent yield increase) groups. The NECS ranking facilitated us to establish a tailored machine learning model for N responsiveness-related varietal classification just using N-response phenotypes with high accuracies. Finally, we employed the Wheat55K SNP Array to map single-nucleotide polymorphisms using N response-related static and dynamic phenotypes, helping us explore genetic components underlying N responsiveness in wheat. In summary, we believe that our work demonstrates valuable advances in N response-related plant research, which could have major implications for improving N sustainability in wheat breeding and production.</p>","PeriodicalId":20318,"journal":{"name":"Plant Phenomics","volume":"5 ","pages":"0128"},"PeriodicalIF":6.5,"publicationDate":"2023-12-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10750832/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139040396","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Bridging Time-series Image Phenotyping and Functional-Structural Plant Modeling to Predict Adventitious Root System Architecture.","authors":"Sriram Parasurama, Darshi Banan, Kyungdahm Yun, Sharon Doty, Soo-Hyung Kim","doi":"10.34133/plantphenomics.0127","DOIUrl":"https://doi.org/10.34133/plantphenomics.0127","url":null,"abstract":"<p><p>Root system architecture (RSA) is an important measure of how plants navigate and interact with the soil environment. However, current methods in studying RSA must make tradeoffs between precision of data and proximity to natural conditions, with root growth in germination papers providing accessibility and high data resolution. Functional-structural plant models (FSPMs) can overcome this tradeoff, though parameterization and evaluation of FSPMs are traditionally based in manual measurements and visual comparison. Here, we applied a germination paper system to study the adventitious RSA and root phenology of <i>Populus trichocarpa</i> stem cuttings using time-series image-based phenotyping augmented by FSPM. We found a significant correlation between timing of root initiation and thermal time at cutting collection (<i>P</i> value = 0.0061, <i>R</i>² = 0.875), but little correlation with RSA. We also present a use of RhizoVision [1] for automatically extracting FSPM parameters from time series images and evaluating FSPM simulations. A high accuracy of the parameterization was achieved in predicting 2D growth with a sensitivity rate of 83.5%. This accuracy was lost when predicting 3D growth with sensitivity rates of 38.5% to 48.7%, while overall accuracy varied with phenotyping methods. Despite this loss in accuracy, the new method is amenable to high throughput FSPM parameterization and bridges the gap between advances in time-series phenotyping and FSPMs.</p>","PeriodicalId":20318,"journal":{"name":"Plant Phenomics","volume":"5 ","pages":"0127"},"PeriodicalIF":6.5,"publicationDate":"2023-12-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10739341/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139032468","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"DomAda-FruitDet: Domain-adaptive anchor-free fruit detection model for auto labeling","authors":"Wenli Zhang, Chao Zheng, Chenhuizi Wang, Wei Guo","doi":"10.34133/plantphenomics.0135","DOIUrl":"https://doi.org/10.34133/plantphenomics.0135","url":null,"abstract":"","PeriodicalId":20318,"journal":{"name":"Plant Phenomics","volume":"117 12","pages":""},"PeriodicalIF":6.5,"publicationDate":"2023-12-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138953746","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Automatic Root Length Estimation from Images Acquired in Situ without Segmentation","authors":"Faina Khoroshevsky, Kaining Zhou, Sharon Chemweno, Yael Edan, Aharon Bar-Hillel, O. Hadar, Boris Rewald, Pavel Baykalov, J. Ephrath, N. Lazarovitch","doi":"10.34133/plantphenomics.0132","DOIUrl":"https://doi.org/10.34133/plantphenomics.0132","url":null,"abstract":"","PeriodicalId":20318,"journal":{"name":"Plant Phenomics","volume":" 23","pages":""},"PeriodicalIF":6.5,"publicationDate":"2023-12-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138994855","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}