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Kantor C, Eisenback JD, Kantor M. Biosecurity risks to human food supply associated with plant-parasitic nematodes. FRONTIERS IN PLANT SCIENCE 2024; 15:1404335. [PMID: 38745921 PMCID: PMC11091314 DOI: 10.3389/fpls.2024.1404335] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/20/2024] [Accepted: 04/11/2024] [Indexed: 05/16/2024]
Abstract
Biosecurity in agriculture is essential for preventing the introduction and spread of plant-parasitic nematodes (PPNs) which threaten global food security by reducing crop yields and facilitating disease spread. These risks are exacerbated by increased global trade and climate change, which may alter PPN distribution and activity, increasing their impact on agricultural systems. Addressing these challenges is vital to maintaining the integrity of the food supply chain. This review highlights significant advancements in managing PPN-related biosecurity risks within the food supply chain, particularly considering climate change's evolving influence. It discusses the PPN modes of transmission, factors increasing the risk of infestation, the impact of PPNs on food safety and security, and traditional and emerging approaches for detecting and managing these pests. Literature suggests that implementing advanced biosecurity measures could decrease PPN infestation rates by up to 70%, substantially reducing crop yield losses and bolstering food security. Notably, the adoption of modern detection and management techniques, (molecular diagnostics and integrated pest management) and emerging geospatial surveillance and analysis systems (spectral imaging, change-detection analysis) has shown greater effectiveness than traditional methods. These innovations offer promising avenues for enhancing crop health and securing the food supply chain against environmental shifts. The integration of these strategies is crucial, demonstrating the potential to transform biosecurity practices and sustain agricultural productivity in the face of changing climatic conditions. This analysis emphasizes the importance of adopting advanced measures to protect crop health and ensure food supply chain resilience, providing valuable insights for stakeholders across the agricultural sector.
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Affiliation(s)
- Camelia Kantor
- Huck Institutes of the Life Sciences, Pennsylvania State University, State College, PA, United States
| | - Jonathan D. Eisenback
- School of Plant and Environmental Science, Virginia Tech, State College, Blacksburg, VA, United States
| | - Mihail Kantor
- Plant Pathology and Environmental Microbiology Department, Pennsylvania State University, University Park, State College, PA, United States
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2
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Pun TB, Neupane A, Koech R. A Deep Learning-Based Decision Support Tool for Plant-Parasitic Nematode Management. J Imaging 2023; 9:240. [PMID: 37998089 PMCID: PMC10671933 DOI: 10.3390/jimaging9110240] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Revised: 10/13/2023] [Accepted: 11/03/2023] [Indexed: 11/25/2023] Open
Abstract
Plant-parasitic nematodes (PPN), especially sedentary endoparasitic nematodes like root-knot nematodes (RKN), pose a significant threat to major crops and vegetables. They are responsible for causing substantial yield losses, leading to economic consequences, and impacting the global food supply. The identification of PPNs and the assessment of their population is a tedious and time-consuming task. This study developed a state-of-the-art deep learning model-based decision support tool to detect and estimate the nematode population. The decision support tool is integrated with the fast inferencing YOLOv5 model and used pretrained nematode weight to detect plant-parasitic nematodes (juveniles) and eggs. The performance of the YOLOv5-640 model at detecting RKN eggs was as follows: precision = 0.992; recall = 0.959; F1-score = 0.975; and mAP = 0.979. YOLOv5-640 was able to detect RKN eggs with an inference time of 3.9 milliseconds, which is faster compared to other detection methods. The deep learning framework was integrated into a user-friendly web application system to build a fast and reliable prototype nematode decision support tool (NemDST). The NemDST facilitates farmers/growers to input image data, assess the nematode population, track the population growths, and recommend immediate actions necessary to control nematode infestation. This tool has the potential for rapid assessment of the nematode population to minimise crop yield losses and enhance financial outcomes.
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Affiliation(s)
- Top Bahadur Pun
- School of Engineering and Technology, Central Queensland University, Rockhampton, QLD 4701, Australia;
| | - Arjun Neupane
- School of Engineering and Technology, Central Queensland University, Rockhampton, QLD 4701, Australia;
| | - Richard Koech
- School of Health, Medical and Applied Sciences, Central Queensland University, Bundaberg, QLD 4760, Australia;
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3
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AlDahoul N, Karim HA, Momo MA, Escobar FIF, Magallanes VA, Tan MJT. Parasitic egg recognition using convolution and attention network. Sci Rep 2023; 13:14475. [PMID: 37660120 PMCID: PMC10475085 DOI: 10.1038/s41598-023-41711-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Accepted: 08/30/2023] [Indexed: 09/04/2023] Open
Abstract
Intestinal parasitic infections (IPIs) caused by protozoan and helminth parasites are among the most common infections in humans in low-and-middle-income countries. IPIs affect not only the health status of a country, but also the economic sector. Over the last decade, pattern recognition and image processing techniques have been developed to automatically identify parasitic eggs in microscopic images. Existing identification techniques are still suffering from diagnosis errors and low sensitivity. Therefore, more accurate and faster solution is still required to recognize parasitic eggs and classify them into several categories. A novel Chula-ParasiteEgg dataset including 11,000 microscopic images proposed in ICIP2022 was utilized to train various methods such as convolutional neural network (CNN) based models and convolution and attention (CoAtNet) based models. The experiments conducted show high recognition performance of the proposed CoAtNet that was tuned with microscopic images of parasitic eggs. The CoAtNet produced an average accuracy of 93%, and an average F1 score of 93%. The finding opens door to integrate the proposed solution in automated parasitological diagnosis.
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Affiliation(s)
- Nouar AlDahoul
- Computer Science, New York University, Abu Dhabi, United Arab Emirates.
- Faculty of Engineering, Multimedia University, Cyberjaya, Malaysia.
| | | | - Mhd Adel Momo
- Fleet Management Systems and Technologies, Istanbul, Turkey
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4
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Devi MG, Rustia DJA, Braat L, Swinkels K, Espinosa FF, van Marrewijk BM, Hemming J, Caarls L. Eggsplorer: a rapid plant-insect resistance determination tool using an automated whitefly egg quantification algorithm. PLANT METHODS 2023; 19:49. [PMID: 37210517 DOI: 10.1186/s13007-023-01027-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Accepted: 05/09/2023] [Indexed: 05/22/2023]
Abstract
BACKGROUND A well-known method for evaluating plant resistance to insects is by measuring insect reproduction or oviposition. Whiteflies are vectors of economically important viral diseases and are, therefore, widely studied. In a common experiment, whiteflies are placed on plants using clip-on-cages, where they can lay hundreds of eggs on susceptible plants in a few days. When quantifying whitefly eggs, most researchers perform manual eye measurements using a stereomicroscope. Compared to other insect eggs, whitefly eggs are many and very tiny, usually 0.2 mm in length and 0.08 mm in width; therefore, this process takes a lot of time and effort with and without prior expert knowledge. Plant insect resistance experiments require multiple replicates from different plant accessions; therefore, an automated and rapid method for quantifying insect eggs can save time and human resources. RESULTS In this work, a novel automated tool for fast quantification of whitefly eggs is presented to accelerate the determination of plant insect resistance and susceptibility. Leaf images with whitefly eggs were collected from a commercial microscope and a custom-built imaging system. A deep learning-based object detection model was trained using the collected images. The model was incorporated into an automated whitefly egg quantification algorithm, deployed in a web-based application called Eggsplorer. Upon evaluation on a testing dataset, the algorithm was able to achieve a counting accuracy as high as 0.94, r2 of 0.99, and a counting error of ± 3 eggs relative to the actual number of eggs counted by eye. The automatically collected counting results were used to determine the resistance and susceptibility of several plant accessions and were found to yield significantly comparable results as when using the manually collected counts for analysis. CONCLUSION This is the first work that presents a comprehensive step-by-step method for fast determination of plant insect resistance and susceptibility with the assistance of an automated quantification tool.
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Affiliation(s)
- Micha Gracianna Devi
- Plant Breeding, Wageningen University & Research, Po Box 384, 6700 AJ, Wageningen, The Netherlands.
| | - Dan Jeric Arcega Rustia
- Greenhouse Horticulture and Flower Bulbs, Wageningen Plant Research, Wageningen University & Research, 6708 PB, Wageningen, The Netherlands
| | - Lize Braat
- Plant Breeding, Wageningen University & Research, Po Box 384, 6700 AJ, Wageningen, The Netherlands
| | - Kas Swinkels
- Plant Breeding, Wageningen University & Research, Po Box 384, 6700 AJ, Wageningen, The Netherlands
| | | | - Bart M van Marrewijk
- Greenhouse Horticulture and Flower Bulbs, Wageningen Plant Research, Wageningen University & Research, 6708 PB, Wageningen, The Netherlands
| | - Jochen Hemming
- Greenhouse Horticulture and Flower Bulbs, Wageningen Plant Research, Wageningen University & Research, 6708 PB, Wageningen, The Netherlands
| | - Lotte Caarls
- Plant Breeding, Wageningen University & Research, Po Box 384, 6700 AJ, Wageningen, The Netherlands
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5
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Agarwal S, Curran ZC, Yu G, Mishra S, Baniya A, Bogale M, Hughes K, Salichs O, Zare A, Jiang Z, DiGennaro P. Plant Parasitic Nematode Identification in Complex Samples with Deep Learning. J Nematol 2023; 55:20230045. [PMID: 37849469 PMCID: PMC10578830 DOI: 10.2478/jofnem-2023-0045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Indexed: 10/19/2023] Open
Abstract
Plant parasitic nematodes are significant contributors to yield loss worldwide, causing devastating losses to every crop species, in every climate. Mitigating these losses requires swift and informed management strategies, centered on identification and quantification of field populations. Current plant parasitic nematode identification methods rely heavily on manual analyses of microscope images by a highly trained nematologist. This mode is not only expensive and time consuming, but often excludes the possibility of widely sharing and disseminating results to inform regional trends and potential emergent issues. This work presents a new public dataset containing annotated images of plant parasitic nematodes from heterologous soil extractions. This dataset serves to propagate new automated methodologies or speedier plant parasitic nematode identification using multiple deep learning object detection models and offers a path towards widely shared tools, results, and meta-analyses.
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Affiliation(s)
- Sahil Agarwal
- Department of Electrical & Computer Engineering, University of Florida, Gainesville, Florida, 32611
| | - Zachary C. Curran
- Department of Computer & Information Science and Engineering, University of Florida, Gainesville, Florida32611
| | - Guohao Yu
- Department of Electrical & Computer Engineering, University of Florida, Gainesville, Florida, 32611
| | - Shova Mishra
- Department of Entomology and Nematology, University of Florida, Gainesville, Florida32611
| | - Anil Baniya
- Department of Entomology and Nematology, University of Florida, Gainesville, Florida32611
| | - Mesfin Bogale
- Department of Entomology and Nematology, University of Florida, Gainesville, Florida32611
| | - Kody Hughes
- Department of Entomology and Nematology, University of Florida, Gainesville, Florida32611
| | - Oscar Salichs
- Department of Entomology and Nematology, University of Florida, Gainesville, Florida32611
| | - Alina Zare
- Department of Electrical & Computer Engineering, University of Florida, Gainesville, Florida, 32611
| | - Zhe Jiang
- Department of Computer & Information Science and Engineering, University of Florida, Gainesville, Florida32611
| | - Peter DiGennaro
- Department of Entomology and Nematology, University of Florida, Gainesville, Florida32611
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6
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Sulyok M, Luibrand J, Strohäker J, Karacsonyi P, Frauenfeld L, Makky A, Mattern S, Zhao J, Nadalin S, Fend F, Schürch CM. Implementing deep learning models for the classification of Echinococcus multilocularis infection in human liver tissue. Parasit Vectors 2023; 16:29. [PMID: 36694210 PMCID: PMC9875509 DOI: 10.1186/s13071-022-05640-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Accepted: 12/26/2022] [Indexed: 01/26/2023] Open
Abstract
BACKGROUND The histological diagnosis of alveolar echinococcosis can be challenging. Decision support models based on deep learning (DL) are increasingly used to aid pathologists, but data on the histology of tissue-invasive parasitic infections are missing. The aim of this study was to implement DL methods to classify Echinococcus multilocularis liver lesions and normal liver tissue and assess which regions and structures play the most important role in classification decisions. METHODS We extracted 15,756 echinococcus tiles from 28 patients using 59 whole slide images (WSI); 11,602 tiles of normal liver parenchyma from 18 patients using 33 WSI served as a control group. Different pretrained model architectures were used with a 60-20-20% random splitting. We visualized the predictions using probability-thresholded heat maps of WSI. The area-under-the-curve (AUC) value and other performance metrics were calculated. The GradCAM method was used to calculate and visualize important spatial features. RESULTS The models achieved a high validation and test set accuracy. The calculated AUC values were 1.0 in all models. Pericystic fibrosis and necrotic areas, as well as germinative and laminated layers of the metacestodes played an important role in decision tasks according to the superimposed GradCAM heatmaps. CONCLUSION Deep learning models achieved a high predictive performance in classifying E. multilocularis liver lesions. A possible next step could be to validate the model using other datasets and test it against other pathologic entities as well, such as, for example, Echinococcus granulosus infection.
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Affiliation(s)
- Mihaly Sulyok
- grid.411544.10000 0001 0196 8249Department of Pathology and Neuropathology, University Hospital and Comprehensive Cancer Center Tübingen, Tübingen, Germany
| | - Julia Luibrand
- grid.411544.10000 0001 0196 8249Department of Pathology and Neuropathology, University Hospital and Comprehensive Cancer Center Tübingen, Tübingen, Germany
| | - Jens Strohäker
- grid.411544.10000 0001 0196 8249Department of Surgery, University Hospital and Comprehensive Cancer Center Tübingen, Tübingen, Germany
| | - Peter Karacsonyi
- grid.411544.10000 0001 0196 8249Department of Pathology and Neuropathology, University Hospital and Comprehensive Cancer Center Tübingen, Tübingen, Germany
| | - Leonie Frauenfeld
- grid.411544.10000 0001 0196 8249Department of Pathology and Neuropathology, University Hospital and Comprehensive Cancer Center Tübingen, Tübingen, Germany
| | - Ahmad Makky
- grid.411544.10000 0001 0196 8249Department of Pathology and Neuropathology, University Hospital and Comprehensive Cancer Center Tübingen, Tübingen, Germany
| | - Sven Mattern
- grid.411544.10000 0001 0196 8249Department of Pathology and Neuropathology, University Hospital and Comprehensive Cancer Center Tübingen, Tübingen, Germany
| | - Jing Zhao
- grid.411544.10000 0001 0196 8249Department of Pathology and Neuropathology, University Hospital and Comprehensive Cancer Center Tübingen, Tübingen, Germany
| | - Silvio Nadalin
- grid.411544.10000 0001 0196 8249Department of Surgery, University Hospital and Comprehensive Cancer Center Tübingen, Tübingen, Germany
| | - Falko Fend
- grid.411544.10000 0001 0196 8249Department of Pathology and Neuropathology, University Hospital and Comprehensive Cancer Center Tübingen, Tübingen, Germany
| | - Christian M. Schürch
- grid.411544.10000 0001 0196 8249Department of Pathology and Neuropathology, University Hospital and Comprehensive Cancer Center Tübingen, Tübingen, Germany
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Shao H, Zhang P, Peng D, Huang W, Kong LA, Li C, Liu E, Peng H. Current advances in the identification of plant nematode diseases: From lab assays to in-field diagnostics. FRONTIERS IN PLANT SCIENCE 2023; 14:1106784. [PMID: 36760630 PMCID: PMC9902721 DOI: 10.3389/fpls.2023.1106784] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Accepted: 01/10/2023] [Indexed: 06/18/2023]
Abstract
Plant parasitic nematodes (PPNs) cause an important class of diseases that occur in almost all types of crops, seriously affecting yield and quality and causing great economic losses. Accurate and rapid diagnosis of nematodes is the basis for their control. PPNs often have interspecific overlays and large intraspecific variations in morphology, therefore identification is difficult based on morphological characters alone. Instead, molecular approaches have been developed to complement morphology-based approaches and/or avoid these issues with various degrees of achievement. A large number of PPNs species have been successfully detected by biochemical and molecular techniques. Newly developed isothermal amplification technologies and remote sensing methods have been recently introduced to diagnose PPNs directly in the field. These methods have been useful because they are fast, accurate, and cost-effective, but the use of integrative diagnosis, which combines remote sensing and molecular methods, is more appropriate in the field. In this paper, we review the latest research advances and the status of diagnostic approaches and techniques for PPNs, with the goal of improving PPNs identification and detection.
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Affiliation(s)
- Hudie Shao
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
- College of Agriculture, Yangtze University, Jingzhou, Hubei, China
| | - Pan Zhang
- College of Agriculture, Yangtze University, Jingzhou, Hubei, China
| | - Deliang Peng
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Wenkun Huang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Ling-an Kong
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Chuanren Li
- College of Agriculture, Yangtze University, Jingzhou, Hubei, China
| | - Enliang Liu
- Grain Crops Institute, XinJiang Academy of Agricultural Sciences, Urumqi, China
| | - Huan Peng
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
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8
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Zhang G, Xu T, Tian Y. Hyperspectral imaging-based classification of rice leaf blast severity over multiple growth stages. PLANT METHODS 2022; 18:123. [PMID: 36403061 PMCID: PMC9675130 DOI: 10.1186/s13007-022-00955-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Accepted: 11/10/2022] [Indexed: 06/16/2023]
Abstract
BACKGROUND Rice blast, which is prevalent worldwide, represents a serious threat to harvested crop yield and quality. Hyperspectral imaging, an emerging technology used in plant disease research, is a stable, repeatable method for disease grading. Current methods for assessing disease severity have mostly focused on individual growth stages rather than multiple ones. In this study, the spectral reflectance ratio (SRR) of whole leaves were calculated, the sensitive wave bands were selected using the successive projections algorithm (SPA) and the support vector machine (SVM) models were constructed to assess rice leaf blast severity over multiple growth stages. RESULTS The average accuracy, micro F1 values, and macro F1 values of the full-spectrum-based SVM model were respectively 94.75%, 0.869, and 0.883 in 2019; 92.92%, 0.823, and 0.808 in 2021; and 88.09%, 0.702, and 0.757 under the 2019-2021 combined model. The SRR-SVM model could be used to evaluate rice leaf blast disease during multiple growth stages and had good generalizability. CONCLUSIONS The proposed SRR data analysis method is able to eliminate differences among individuals to some extent, thus allowing for its application to assess rice leaf blast severity over multiple growth stages. Our approach, which can supplement single-stage disease-degree classification, provides a possible direction for future research on the assessment of plant disease severity during multiple growth stages.
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Affiliation(s)
| | - Tongyu Xu
- Shenyang Agricultural University, Shenyang, China
| | - Youwen Tian
- Shenyang Agricultural University, Shenyang, China
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9
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Zhang G, Xu T, Tian Y, Feng S, Zhao D, Guo Z. Classification of rice leaf blast severity using hyperspectral imaging. Sci Rep 2022; 12:19757. [PMID: 36396749 PMCID: PMC9672119 DOI: 10.1038/s41598-022-22074-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Accepted: 10/10/2022] [Indexed: 11/18/2022] Open
Abstract
Rice leaf blast is prevalent worldwide and a serious threat to rice yield and quality. Hyperspectral imaging is an emerging technology used in plant disease research. In this study, we calculated the standard deviation (STD) of the spectral reflectance of whole rice leaves and constructed support vector machine (SVM) and probabilistic neural network (PNN) models to classify the degree of rice leaf blast at different growth stages. Average accuracies at jointing, booting and heading stages under the full-spectrum-based SVM model were 88.89%, 85.26%, and 87.32%, respectively, versus 80%, 83.16%, and 83.41% under the PNN model. Average accuracies at jointing, booting and heading stages under the STD-based SVM model were 97.78%, 92.63%, and 92.20%, respectively, versus 88.89%, 91.58%, and 92.20% under the PNN model. The STD of the spectral reflectance of the whole leaf differed not only within samples with different disease grades, but also among those at the same disease level. Compared with raw spectral reflectance data, STDs performed better in assessing rice leaf blast severity.
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Affiliation(s)
- Guosheng Zhang
- grid.412557.00000 0000 9886 8131Shenyang Agricultural University, Shenyang, China
| | - Tongyu Xu
- grid.412557.00000 0000 9886 8131Shenyang Agricultural University, Shenyang, China
| | - Youwen Tian
- grid.412557.00000 0000 9886 8131Shenyang Agricultural University, Shenyang, China
| | - Shuai Feng
- grid.412557.00000 0000 9886 8131Shenyang Agricultural University, Shenyang, China
| | - Dongxue Zhao
- grid.412557.00000 0000 9886 8131Shenyang Agricultural University, Shenyang, China
| | - Zhonghui Guo
- grid.412557.00000 0000 9886 8131Shenyang Agricultural University, Shenyang, China
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10
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Rairdin A, Fotouhi F, Zhang J, Mueller DS, Ganapathysubramanian B, Singh AK, Dutta S, Sarkar S, Singh A. Deep learning-based phenotyping for genome wide association studies of sudden death syndrome in soybean. FRONTIERS IN PLANT SCIENCE 2022; 13:966244. [PMID: 36340398 PMCID: PMC9634489 DOI: 10.3389/fpls.2022.966244] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Accepted: 09/26/2022] [Indexed: 06/07/2023]
Abstract
Using a reliable and accurate method to phenotype disease incidence and severity is essential to unravel the complex genetic architecture of disease resistance in plants, and to develop disease resistant cultivars. Genome-wide association studies (GWAS) involve phenotyping large numbers of accessions, and have been used for a myriad of traits. In field studies, genetic accessions are phenotyped across multiple environments and replications, which takes a significant amount of labor and resources. Deep Learning (DL) techniques can be effective for analyzing image-based tasks; thus DL methods are becoming more routine for phenotyping traits to save time and effort. This research aims to conduct GWAS on sudden death syndrome (SDS) of soybean [Glycine max L. (Merr.)] using disease severity from both visual field ratings and DL-based (using images) severity ratings collected from 473 accessions. Images were processed through a DL framework that identified soybean leaflets with SDS symptoms, and then quantified the disease severity on those leaflets into a few classes with mean Average Precision of 0.34 on unseen test data. Both visual field ratings and image-based ratings identified significant single nucleotide polymorphism (SNP) markers associated with disease resistance. These significant SNP markers are either in the proximity of previously reported candidate genes for SDS or near potentially novel candidate genes. Four previously reported SDS QTL were identified that contained a significant SNPs, from this study, from both a visual field rating and an image-based rating. The results of this study provide an exciting avenue of using DL to capture complex phenotypic traits from images to get comparable or more insightful results compared to subjective visual field phenotyping of traits for disease symptoms.
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Affiliation(s)
- Ashlyn Rairdin
- Department of Agronomy, Iowa State University, Ames, IA, United States
| | - Fateme Fotouhi
- Department of Mechanical Engineering, Iowa State University, Ames, IA, United States
- Department of Computer Science, Iowa State University, Ames, IA, United States
| | - Jiaoping Zhang
- Department of Agronomy, Iowa State University, Ames, IA, United States
| | - Daren S. Mueller
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, IA, United States
| | | | - Asheesh K. Singh
- Department of Agronomy, Iowa State University, Ames, IA, United States
| | - Somak Dutta
- Department of Statistics, Iowa State University, Ames, IA, United States
| | - Soumik Sarkar
- Department of Mechanical Engineering, Iowa State University, Ames, IA, United States
- Department of Computer Science, Iowa State University, Ames, IA, United States
| | - Arti Singh
- Department of Agronomy, Iowa State University, Ames, IA, United States
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11
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Chen L, Daub M, Luigs HG, Jansen M, Strauch M, Merhof D. High-throughput phenotyping of nematode cysts. FRONTIERS IN PLANT SCIENCE 2022; 13:965254. [PMID: 36186075 PMCID: PMC9515587 DOI: 10.3389/fpls.2022.965254] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Accepted: 08/08/2022] [Indexed: 06/16/2023]
Abstract
The beet cyst nematode Heterodera schachtii is a plant pest responsible for crop loss on a global scale. Here, we introduce a high-throughput system based on computer vision that allows quantifying beet cyst nematode infestation and measuring phenotypic traits of cysts. After recording microscopic images of soil sample extracts in a standardized setting, an instance segmentation algorithm serves to detect nematode cysts in these images. In an evaluation using both ground truth samples with known cyst numbers and manually annotated images, the computer vision approach produced accurate nematode cyst counts, as well as accurate cyst segmentations. Based on such segmentations, cyst features could be computed that served to reveal phenotypical differences between nematode populations in different soils and in populations observed before and after the sugar beet planting period. The computer vision approach enables not only fast and precise cyst counting, but also phenotyping of cyst features under different conditions, providing the basis for high-throughput applications in agriculture and plant breeding research. Source code and annotated image data sets are freely available for scientific use.
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Affiliation(s)
- Long Chen
- Institute of Imaging and Computer Vision (LfB), RWTH Aachen University, Aachen, Germany
| | - Matthias Daub
- Federal Research Center for Cultivated Plants, Julius Kühn Institute (JKI), Elsdorf, Germany
| | | | | | - Martin Strauch
- Institute of Imaging and Computer Vision (LfB), RWTH Aachen University, Aachen, Germany
| | - Dorit Merhof
- Institute of Imaging and Computer Vision (LfB), RWTH Aachen University, Aachen, Germany
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12
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Arjoune Y, Sugunaraj N, Peri S, Nair SV, Skurdal A, Ranganathan P, Johnson B. Soybean cyst nematode detection and management: a review. PLANT METHODS 2022; 18:110. [PMID: 36071455 PMCID: PMC9450454 DOI: 10.1186/s13007-022-00933-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Accepted: 08/04/2022] [Indexed: 06/15/2023]
Abstract
Soybeans play a key role in global food security. U.S. soybean yields, which comprise [Formula: see text] of the total soybeans planted in the world, continue to experience unprecedented grain loss due to the soybean cyst nematode (SCN) plant pathogen. SCN remains one of the primary disruptive pests despite the existence of advanced management techniques such as crop rotation and SCN-resistant varieties. SCN detection is a key step in managing this disease; however, early detection is challenging because soybeans do not show any above ground symptoms unless they are significantly damaged. Direct soil sampling remains the most common method for SCN detection, however, this method has several problems. For example, the threshold damage methods-adopted by most of the laboratories to make recommendations-is not reliable as it does not consider soil pH, N, P, and K values and relies solely on the egg count instead of assessment of the root infection. To overcome the challenges of manual soil sampling methods, deep learning and hyperspectral imaging are important current topics in precision agriculture for plant disease detection and have been proposed as cost-effective and efficient detection methods that can work at scale. We have reviewed more than 150 research papers focusing on soybean cyst nematodes with an emphasis on deep learning techniques for detection and management. First: we describe soybean vegetation and reproduction stages, SCN life cycles, and factors influencing this disease. Second: we highlight the impact of SCN on soybean yield loss and the challenges associated with its detection. Third: we describe direct sampling methods in which the soil samples are procured and analyzed to evaluate SCN egg counts. Fourth: we highlight the advantages and limitations of these direct methods, then review computer vision- and remote sensing-based detection methods: data collection using ground, aerial, and satellite approaches followed by a review of machine learning methods for image analysis-based soybean cyst nematode detection. We highlight the evaluation approaches and the advantages of overall detection workflow in high-performance and big data environments. Lastly, we discuss various management approaches, such as crop rotation, fertilization, SCN resistant varieties such as PI 88788, and SCN's increasing resistance to these strategies. We review machine learning approaches for soybean crop yield forecasting as well as the influence of pesticides, herbicides, and fertilizers on SCN infestation reduction. We provide recommendations for soybean research using deep learning and hyperspectral imaging to accommodate the lack of the ground truth data and training and testing methodologies, such as data augmentation and transfer learning, to achieve a high level of detection accuracy while keeping costs as low as possible.
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Affiliation(s)
- Youness Arjoune
- School of Electrical Engineering and Computer Science (SEECS), University of North Dakota, Grand Forks, USA
| | - Niroop Sugunaraj
- School of Electrical Engineering and Computer Science (SEECS), University of North Dakota, Grand Forks, USA
| | - Sai Peri
- School of Electrical Engineering and Computer Science (SEECS), University of North Dakota, Grand Forks, USA
| | - Sreejith V. Nair
- Department of Aviation, University of North Dakota, Grand Forks, USA
| | - Anton Skurdal
- School of Electrical Engineering and Computer Science (SEECS), University of North Dakota, Grand Forks, USA
| | - Prakash Ranganathan
- School of Electrical Engineering and Computer Science (SEECS), University of North Dakota, Grand Forks, USA
| | - Burton Johnson
- Plant Sciences, North Dakota State University, Fargo, USA
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13
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Filgueiras CC, Kim Y, Wickings KG, El Borai F, Duncan LW, Willett DS. The Smart Soil Organism Detector: An instrument and machine learning pipeline for soil species identification. Biosens Bioelectron 2022; 221:114417. [PMID: 35690558 DOI: 10.1016/j.bios.2022.114417] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Revised: 05/10/2022] [Accepted: 05/19/2022] [Indexed: 11/30/2022]
Abstract
Understanding the diversity of soil organisms is complicated by both scale and substrate. Every footprint we leave in the soil covers hundreds to millions of organisms yet we cannot see them without extremely laborious extraction and microsopy endeavors. Studying them is also challenging. Keeping them alive so that we can understand their lifecycles and ecological roles ranges from difficult to impossible. Functional and taxonomic identification of soil organisms, while possible, is also challenging. Here we present the Smart Soil Organism Detector, an instrument and machine learning pipeline that combines high-resolution imaging, multi-spectral sensing, large-bore flow cytometry, and machine learning to extract, isolate, count, identify, and separate soil organisms in a high-throughput, high-resolution, non-destructive, and reproducible manner. This system is not only capable of separating alive nematodes, dead nematodes, and nematode cuticles from soil with 100% out-of-sample accuracy, but also capable of identifying nematode strains (sub-species) with 95.5% out-of-sample accuracy and 99.4% specificity. Soil micro-arthropods were identified to class with 96.1% out-of-sample accuracy. Broadly applicable across soil taxa, the Smart SOD system is a tool for understanding global soil biodiversity.
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Affiliation(s)
- Camila C Filgueiras
- Department of Biology, University of North Carolina Asheville, One University Heights, Asheville, 28804, NC, USA.
| | - Yongwoon Kim
- Union Biometrica, 84 October Hill Rd, Holliston, 01746, MA, USA
| | - Kyle G Wickings
- Department of Entolomogy, Cornell University, Cornell AgriTech, 15 Castle Creek Drive, Geneva, 14456, NY, USA
| | - Faheim El Borai
- Department of Entolomogy and Nematology, University of Florida, Gulf Coast Research and Education Center, 14625 CR 672, Wimauma, 33598, FL, USA
| | - Larry W Duncan
- Department of Entolomogy and Nematology, University of Florida, Citrus Research and Education Center, 700 Experiment Station Rd, Lake Alfred, 33850, FL, USA
| | - Denis S Willett
- North Carolina Institute for Climate Studies, North Carolina State University, 151 Patton Avenue, Asheville, 28801, NC, USA.
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14
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Xu Z, York LM, Seethepalli A, Bucciarelli B, Cheng H, Samac DA. Objective Phenotyping of Root System Architecture Using Image Augmentation and Machine Learning in Alfalfa (Medicago sativa L.). PLANT PHENOMICS (WASHINGTON, D.C.) 2022; 2022:9879610. [PMID: 35479182 PMCID: PMC9012978 DOI: 10.34133/2022/9879610] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Accepted: 03/03/2022] [Indexed: 12/28/2022]
Abstract
Active breeding programs specifically for root system architecture (RSA) phenotypes remain rare; however, breeding for branch and taproot types in the perennial crop alfalfa is ongoing. Phenotyping in this and other crops for active RSA breeding has mostly used visual scoring of specific traits or subjective classification into different root types. While image-based methods have been developed, translation to applied breeding is limited. This research is aimed at developing and comparing image-based RSA phenotyping methods using machine and deep learning algorithms for objective classification of 617 root images from mature alfalfa plants collected from the field to support the ongoing breeding efforts. Our results show that unsupervised machine learning tends to incorrectly classify roots into a normal distribution with most lines predicted as the intermediate root type. Encouragingly, random forest and TensorFlow-based neural networks can classify the root types into branch-type, taproot-type, and an intermediate taproot-branch type with 86% accuracy. With image augmentation, the prediction accuracy was improved to 97%. Coupling the predicted root type with its prediction probability will give breeders a confidence level for better decisions to advance the best and exclude the worst lines from their breeding program. This machine and deep learning approach enables accurate classification of the RSA phenotypes for genomic breeding of climate-resilient alfalfa.
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Affiliation(s)
- Zhanyou Xu
- USDA-ARS, Plant Science Research Unit, 1991 Upper Buford Circle, St. Paul, MN 55108, USA
| | - Larry M. York
- Biosciences Division and Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37830, USA
| | | | - Bruna Bucciarelli
- Department of Agronomy and Plant Genetics, University of Minnesota, 1991 Upper Buford Circle, St. Paul, MN 55108, USA
| | - Hao Cheng
- Department of Animal Science, University of California, 2251 Meyer Hall, One Shields Ave., Davis, CA 95616, USA
| | - Deborah A. Samac
- USDA-ARS, Plant Science Research Unit, 1991 Upper Buford Circle, St. Paul, MN 55108, USA
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15
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Papaiakovou M, Littlewood DTJ, Doyle SR, Gasser RB, Cantacessi C. Worms and bugs of the gut: the search for diagnostic signatures using barcoding, and metagenomics-metabolomics. Parasit Vectors 2022; 15:118. [PMID: 35365192 PMCID: PMC8973539 DOI: 10.1186/s13071-022-05225-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Accepted: 02/25/2022] [Indexed: 02/07/2023] Open
Abstract
Gastrointestinal (GI) helminth infections cause significant morbidity in both humans and animals worldwide. Specific and sensitive diagnosis is central to the surveillance of such infections and to determine the effectiveness of treatment strategies used to control them. In this article, we: (i) assess the strengths and limitations of existing methods applied to the diagnosis of GI helminth infections of humans and livestock; (ii) examine high-throughput sequencing approaches, such as targeted molecular barcoding and shotgun sequencing, as tools to define the taxonomic composition of helminth infections; and (iii) discuss the current understanding of the interactions between helminths and microbiota in the host gut. Stool-based diagnostics are likely to serve as an important tool well into the future; improved diagnostics of helminths and their environment in the gut may assist the identification of biomarkers with the potential to define the health/disease status of individuals and populations, and to identify existing or emerging anthelmintic resistance.
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Affiliation(s)
- Marina Papaiakovou
- Department of Veterinary Medicine, University of Cambridge, Cambridge, CB3 0ES UK
- Department of Life Sciences, Natural History Museum, Cromwell Road, London, SW7 5BD UK
| | | | | | - Robin B. Gasser
- Melbourne Veterinary School, The University of Melbourne, Parkville, VIC 3010 Australia
| | - Cinzia Cantacessi
- Department of Veterinary Medicine, University of Cambridge, Cambridge, CB3 0ES UK
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16
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De Cesaro Júnior T, Rieder R, Di Domênico JR, Lau D. InsectCV: A system for insect detection in the lab from trap images. ECOL INFORM 2022. [DOI: 10.1016/j.ecoinf.2021.101516] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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17
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Nissan N, Mimee B, Cober ER, Golshani A, Smith M, Samanfar B. A Broad Review of Soybean Research on the Ongoing Race to Overcome Soybean Cyst Nematode. BIOLOGY 2022; 11:211. [PMID: 35205078 PMCID: PMC8869295 DOI: 10.3390/biology11020211] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Revised: 01/24/2022] [Accepted: 01/26/2022] [Indexed: 12/12/2022]
Abstract
Plant pathogens greatly impact food security of the ever-growing human population. Breeding resistant crops is one of the most sustainable strategies to overcome the negative effects of these biotic stressors. In order to efficiently breed for resistant plants, the specific plant-pathogen interactions should be understood. Soybean is a short-day legume that is a staple in human food and animal feed due to its high nutritional content. Soybean cyst nematode (SCN) is a major soybean stressor infecting soybean worldwide including in China, Brazil, Argentina, USA and Canada. There are many Quantitative Trait Loci (QTLs) conferring resistance to SCN that have been identified; however, only two are widely used: rhg1 and Rhg4. Overuse of cultivars containing these QTLs/genes can lead to SCN resistance breakdown, necessitating the use of additional strategies. In this manuscript, a literature review is conducted on research related to soybean resistance to SCN. The main goal is to provide a current understanding of the mechanisms of SCN resistance and list the areas of research that could be further explored.
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Affiliation(s)
- Nour Nissan
- Agriculture and Agri-Food Canada, Ottawa Research and Development Centre, Ottawa, ON K1Y 4X2, Canada; (N.N.); (E.R.C.)
- Ottawa Institute of Systems Biology and Department of Biology, Carleton University, Ottawa, ON K1S 5B6, Canada; (A.G.); (M.S.)
| | - Benjamin Mimee
- Agriculture and Agri-Food Canada, Saint-Jean-sur-Richelieu Research and Development Centre, Saint-Jean-sur-Richelieu, QC J3B 7B5, Canada;
| | - Elroy R. Cober
- Agriculture and Agri-Food Canada, Ottawa Research and Development Centre, Ottawa, ON K1Y 4X2, Canada; (N.N.); (E.R.C.)
| | - Ashkan Golshani
- Ottawa Institute of Systems Biology and Department of Biology, Carleton University, Ottawa, ON K1S 5B6, Canada; (A.G.); (M.S.)
| | - Myron Smith
- Ottawa Institute of Systems Biology and Department of Biology, Carleton University, Ottawa, ON K1S 5B6, Canada; (A.G.); (M.S.)
| | - Bahram Samanfar
- Agriculture and Agri-Food Canada, Ottawa Research and Development Centre, Ottawa, ON K1Y 4X2, Canada; (N.N.); (E.R.C.)
- Ottawa Institute of Systems Biology and Department of Biology, Carleton University, Ottawa, ON K1S 5B6, Canada; (A.G.); (M.S.)
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18
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Rice Leaf Blast Classification Method Based on Fused Features and One-Dimensional Deep Convolutional Neural Network. REMOTE SENSING 2021. [DOI: 10.3390/rs13163207] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Rice leaf blast, which is seriously affecting the yield and quality of rice around the world, is a fungal disease that easily develops under high temperature and humidity conditions. Therefore, the use of accurate and non-destructive diagnostic methods is important for rice production management. Hyperspectral imaging technology is a type of crop disease identification method with great potential. However, a large amount of redundant information mixed in hyperspectral data makes it more difficult to establish an efficient disease classification model. At the same time, the difficulty and small scale of agricultural hyperspectral imaging data acquisition has resulted in unrepresentative features being acquired. Therefore, the focus of this study was to determine the best classification features and classification models for the five disease classes of leaf blast in order to improve the accuracy of grading the disease. First, the hyperspectral imaging data were pre-processed in order to extract rice leaf samples of five disease classes, and the number of samples was increased by data augmentation methods. Secondly, spectral feature wavelengths, vegetation indices and texture features were obtained based on the amplified sample data. Thirdly, seven one-dimensional deep convolutional neural networks (DCNN) models were constructed based on spectral feature wavelengths, vegetation indices, texture features and their fusion features. Finally, the model in this paper was compared and analyzed with the Inception V3, ZF-Net, TextCNN and bidirectional gated recurrent unit (BiGRU); support vector machine (SVM); and extreme learning machine (ELM) models in order to determine the best classification features and classification models for different disease classes of leaf blast. The results showed that the classification model constructed using fused features was significantly better than the model constructed with a single feature in terms of accuracy in grading the degree of leaf blast disease. The best performance was achieved with the combination of the successive projections algorithm (SPA) selected feature wavelengths and texture features (TFs). The modeling results also show that the DCNN model provides better classification capability for disease classification than the Inception V3, ZF-Net, TextCNN, BiGRU, SVM and ELM classification models. The SPA + TFs-DCNN achieved the best classification accuracy with an overall accuracy (OA) and Kappa of 98.58% and 98.22%, respectively. In terms of the classification of the specific different disease classes, the F1-scores for diseases of classes 0, 1 and 2 were all 100%, while the F1-scores for diseases of classes 4 and 5 were 96.48% and 96.68%, respectively. This study provides a new method for the identification and classification of rice leaf blast and a research basis for assessing the extent of the disease in the field.
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19
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Fudickar S, Nustede EJ, Dreyer E, Bornhorst J. Mask R-CNN Based C. Elegans Detection with a DIY Microscope. BIOSENSORS 2021; 11:257. [PMID: 34436059 PMCID: PMC8391161 DOI: 10.3390/bios11080257] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Revised: 07/26/2021] [Accepted: 07/27/2021] [Indexed: 11/24/2022]
Abstract
Caenorhabditis elegans (C. elegans) is an important model organism for studying molecular genetics, developmental biology, neuroscience, and cell biology. Advantages of the model organism include its rapid development and aging, easy cultivation, and genetic tractability. C. elegans has been proven to be a well-suited model to study toxicity with identified toxic compounds closely matching those observed in mammals. For phenotypic screening, especially the worm number and the locomotion are of central importance. Traditional methods such as human counting or analyzing high-resolution microscope images are time-consuming and rather low throughput. The article explores the feasibility of low-cost, low-resolution do-it-yourself microscopes for image acquisition and automated evaluation by deep learning methods to reduce cost and allow high-throughput screening strategies. An image acquisition system is proposed within these constraints and used to create a large data-set of whole Petri dishes containing C. elegans. By utilizing the object detection framework Mask R-CNN, the nematodes are located, classified, and their contours predicted. The system has a precision of 0.96 and a recall of 0.956, resulting in an F1-Score of 0.958. Considering only correctly located C. elegans with an AP@0.5 IoU, the system achieved an average precision of 0.902 and a corresponding F1 Score of 0.906.
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Affiliation(s)
- Sebastian Fudickar
- Assistance Systems and Medical Device Technology, Faculty of Medicine and Health Sciences, CvO University of Oldenburg, Ammerländer Heerstraße 140, 26129 Oldenburg, Germany; (E.J.N.); (E.D.)
| | - Eike Jannik Nustede
- Assistance Systems and Medical Device Technology, Faculty of Medicine and Health Sciences, CvO University of Oldenburg, Ammerländer Heerstraße 140, 26129 Oldenburg, Germany; (E.J.N.); (E.D.)
| | - Eike Dreyer
- Assistance Systems and Medical Device Technology, Faculty of Medicine and Health Sciences, CvO University of Oldenburg, Ammerländer Heerstraße 140, 26129 Oldenburg, Germany; (E.J.N.); (E.D.)
| | - Julia Bornhorst
- Faculty Mathematik und Naturwissenschaften, Bergische Universität Wuppertal, Lebensmittelchemie, Gaußstr. 20, 42119 Wuppertal, Germany;
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20
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Riera LG, Carroll ME, Zhang Z, Shook JM, Ghosal S, Gao T, Singh A, Bhattacharya S, Ganapathysubramanian B, Singh AK, Sarkar S. Deep Multiview Image Fusion for Soybean Yield Estimation in Breeding Applications. PLANT PHENOMICS (WASHINGTON, D.C.) 2021; 2021:9846470. [PMID: 34250507 PMCID: PMC8240512 DOI: 10.34133/2021/9846470] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Accepted: 05/19/2021] [Indexed: 05/17/2023]
Abstract
Reliable seed yield estimation is an indispensable step in plant breeding programs geared towards cultivar development in major row crops. The objective of this study is to develop a machine learning (ML) approach adept at soybean (Glycine max L. (Merr.)) pod counting to enable genotype seed yield rank prediction from in-field video data collected by a ground robot. To meet this goal, we developed a multiview image-based yield estimation framework utilizing deep learning architectures. Plant images captured from different angles were fused to estimate the yield and subsequently to rank soybean genotypes for application in breeding decisions. We used data from controlled imaging environment in field, as well as from plant breeding test plots in field to demonstrate the efficacy of our framework via comparing performance with manual pod counting and yield estimation. Our results demonstrate the promise of ML models in making breeding decisions with significant reduction of time and human effort and opening new breeding method avenues to develop cultivars.
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Affiliation(s)
- Luis G. Riera
- Department of Mechanical Engineering, Iowa State University, Ames, Iowa, USA
| | | | - Zhisheng Zhang
- Department of Mechanical Engineering, Iowa State University, Ames, Iowa, USA
| | | | - Sambuddha Ghosal
- Department of Mechanical Engineering, Iowa State University, Ames, Iowa, USA
| | - Tianshuang Gao
- Department of Computer Science, Iowa State University, Ames, Iowa, USA
| | - Arti Singh
- Department of Agronomy, Iowa State University, Ames, Iowa, USA
| | | | | | | | - Soumik Sarkar
- Department of Mechanical Engineering, Iowa State University, Ames, Iowa, USA
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21
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Guo W, Carroll ME, Singh A, Swetnam TL, Merchant N, Sarkar S, Singh AK, Ganapathysubramanian B. UAS-Based Plant Phenotyping for Research and Breeding Applications. PLANT PHENOMICS (WASHINGTON, D.C.) 2021; 2021:9840192. [PMID: 34195621 PMCID: PMC8214361 DOI: 10.34133/2021/9840192] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2021] [Accepted: 04/29/2021] [Indexed: 05/19/2023]
Abstract
Unmanned aircraft system (UAS) is a particularly powerful tool for plant phenotyping, due to reasonable cost of procurement and deployment, ease and flexibility for control and operation, ability to reconfigure sensor payloads to diversify sensing, and the ability to seamlessly fit into a larger connected phenotyping network. These advantages have expanded the use of UAS-based plant phenotyping approach in research and breeding applications. This paper reviews the state of the art in the deployment, collection, curation, storage, and analysis of data from UAS-based phenotyping platforms. We discuss pressing technical challenges, identify future trends in UAS-based phenotyping that the plant research community should be aware of, and pinpoint key plant science and agronomic questions that can be resolved with the next generation of UAS-based imaging modalities and associated data analysis pipelines. This review provides a broad account of the state of the art in UAS-based phenotyping to reduce the barrier to entry to plant science practitioners interested in deploying this imaging modality for phenotyping in plant breeding and research areas.
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Affiliation(s)
- Wei Guo
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Japan
| | | | - Arti Singh
- Department of Agronomy, Iowa State University, Ames, Iowa, USA
| | | | - Nirav Merchant
- Data Science Institute, University of Arizona, Tucson, USA
| | - Soumik Sarkar
- Department of Mechanical Engineering, Iowa State University, Ames, Iowa, USA
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22
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Singh A, Jones S, Ganapathysubramanian B, Sarkar S, Mueller D, Sandhu K, Nagasubramanian K. Challenges and Opportunities in Machine-Augmented Plant Stress Phenotyping. TRENDS IN PLANT SCIENCE 2021; 26:53-69. [PMID: 32830044 DOI: 10.1016/j.tplants.2020.07.010] [Citation(s) in RCA: 49] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Revised: 07/15/2020] [Accepted: 07/23/2020] [Indexed: 05/06/2023]
Abstract
Plant stress phenotyping is essential to select stress-resistant varieties and develop better stress-management strategies. Standardization of visual assessments and deployment of imaging techniques have improved the accuracy and reliability of stress assessment in comparison with unaided visual measurement. The growing capabilities of machine learning (ML) methods in conjunction with image-based phenotyping can extract new insights from curated, annotated, and high-dimensional datasets across varied crops and stresses. We propose an overarching strategy for utilizing ML techniques that methodically enables the application of plant stress phenotyping at multiple scales across different types of stresses, program goals, and environments.
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Affiliation(s)
- Arti Singh
- Department of Agronomy, Iowa State University, Ames, IA, USA.
| | - Sarah Jones
- Department of Agronomy, Iowa State University, Ames, IA, USA
| | | | - Soumik Sarkar
- Department of Mechanical Engineering, Iowa State University, Ames, IA, USA
| | - Daren Mueller
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, IA, USA
| | - Kulbir Sandhu
- Department of Agronomy, Iowa State University, Ames, IA, USA
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23
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Jubery TZ, Carley CN, Singh A, Sarkar S, Ganapathysubramanian B, Singh AK. Using Machine Learning to Develop a Fully Automated Soybean Nodule Acquisition Pipeline (SNAP). PLANT PHENOMICS (WASHINGTON, D.C.) 2021; 2021:9834746. [PMID: 34396150 PMCID: PMC8343430 DOI: 10.34133/2021/9834746] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Accepted: 06/21/2021] [Indexed: 05/19/2023]
Abstract
Nodules form on plant roots through the symbiotic relationship between soybean (Glycine max L. Merr.) roots and bacteria (Bradyrhizobium japonicum) and are an important structure where atmospheric nitrogen (N2) is fixed into bioavailable ammonia (NH3) for plant growth and development. Nodule quantification on soybean roots is a laborious and tedious task; therefore, assessment is frequently done on a numerical scale that allows for rapid phenotyping, but is less informative and suffers from subjectivity. We report the Soybean Nodule Acquisition Pipeline (SNAP) for nodule quantification that combines RetinaNet and UNet deep learning architectures for object (i.e., nodule) detection and segmentation. SNAP was built using data from 691 unique roots from diverse soybean genotypes, vegetative growth stages, and field locations and has a good model fit (R 2 = 0.99). SNAP reduces the human labor and inconsistencies of counting nodules, while acquiring quantifiable traits related to nodule growth, location, and distribution on roots. The ability of SNAP to phenotype nodules on soybean roots at a higher throughput enables researchers to assess the genetic and environmental factors, and their interactions on nodulation from an early development stage. The application of SNAP in research and breeding pipelines may lead to more nitrogen use efficiency for soybean and other legume species cultivars, as well as enhanced insight into the plant-Bradyrhizobium relationship.
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Affiliation(s)
| | | | - Arti Singh
- Department of Agronomy, Iowa State University, Ames, IA, USA
| | - Soumik Sarkar
- Department of Mechanical Engineering, Iowa State University, Ames, IA, USA
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24
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Nematode Identification Techniques and Recent Advances. PLANTS 2020; 9:plants9101260. [PMID: 32987762 PMCID: PMC7598616 DOI: 10.3390/plants9101260] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Revised: 09/21/2020] [Accepted: 09/22/2020] [Indexed: 01/02/2023]
Abstract
Nematodes are among the most diverse but least studied organisms. The classic morphology-based identification has proved insufficient to the study of nematode identification and diversity, mainly for lack of sufficient morphological variations among closely related taxa. Different molecular methods have been used to supplement morphology-based methods and/or circumvent these problems with various degrees of success. These methods range from fingerprint to sequence analyses of DNA- and/or protein-based information. Image analyses techniques have also contributed towards this success. In this review, we highlight what each of these methods entail and provide examples where more recent advances of these techniques have been employed in nematode identification. Wherever possible, emphasis has been given to nematodes of agricultural significance. We show that these alternative methods have aided nematode identification and raised our understanding of nematode diversity and phylogeny. We discuss the pros and cons of these methods and conclude that no one method by itself provides all the answers; the choice of method depends on the question at hand, the nature of the samples, and the availability of resources.
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25
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Lino-Silva LS, Xinaxtle DL. Artificial intelligence technology applications in the pathologic diagnosis of the gastrointestinal tract. Future Oncol 2020; 16:2845-2851. [PMID: 32892631 DOI: 10.2217/fon-2020-0678] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Artificial intelligence (AI) is a complex technology with a steady flow of new applications, including in the pathology laboratory. Applications of AI in pathology are scarce but increasing; they are based on complex software-based machine learning with deep learning trained by pathologists. Their uses are based on tissue identification on histologic slides for classification into categories of normal, nonneoplastic and neoplastic conditions. Most AI applications are based on digital pathology. This commentary describes the role of AI in the pathological diagnosis of the gastrointestinal tract and provides insights into problems and future applications by answering four fundamental questions.
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Affiliation(s)
| | - Diana L Xinaxtle
- Anatomic Pathology, Instituto Nacional de Cancerología, Mexico City, 14080, Mexico
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Wu W, Zhang Z, Zheng L, Han C, Wang X, Xu J, Wang X. Research Progress on the Early Monitoring of Pine Wilt Disease Using Hyperspectral Techniques. SENSORS 2020; 20:s20133729. [PMID: 32635285 PMCID: PMC7374340 DOI: 10.3390/s20133729] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Revised: 06/24/2020] [Accepted: 06/27/2020] [Indexed: 11/30/2022]
Abstract
Pine wilt disease (PWD) caused by pine wood nematode (PWN, Bursaphelenchus xylophilus) originated in North America and has since spread to Asia and Europe. PWN is currently a quarantine object in 52 countries. In recent years, pine wilt disease has caused considerable economic losses to the pine forest production industry in China, as it is difficult to control. Thus, one of the key strategies for controlling pine wilt disease is to identify epidemic points as early as possible. The use of hyperspectral cameras mounted on drones is expected to enable PWD monitoring over large areas of forest, and hyperspectral images can reflect different stages of PWD. The trend of applying hyperspectral techniques to the monitoring of pine wilt disease is analyzed, and the corresponding strategies to address the existing technical problems are proposed, such as data collection of early warning stages, needs of using unmanned aerial vehicles (UAVs), and establishment of models after preprocessing.
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Affiliation(s)
- Weibin Wu
- College of Engineering, South China Agricultural University, Guangzhou 510642, China; (W.W.); (Z.Z.); (C.H.); (X.W.); (J.X.)
- Division of Citrus Machinery, China Agriculture Research System, Guangzhou 510642, China
| | - Zhenbang Zhang
- College of Engineering, South China Agricultural University, Guangzhou 510642, China; (W.W.); (Z.Z.); (C.H.); (X.W.); (J.X.)
- Division of Citrus Machinery, China Agriculture Research System, Guangzhou 510642, China
| | - Lijun Zheng
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, College of Agriculture, South China Agricultural University, Guangzhou 510642, China;
| | - Chongyang Han
- College of Engineering, South China Agricultural University, Guangzhou 510642, China; (W.W.); (Z.Z.); (C.H.); (X.W.); (J.X.)
- Division of Citrus Machinery, China Agriculture Research System, Guangzhou 510642, China
| | - Xiaoming Wang
- College of Engineering, South China Agricultural University, Guangzhou 510642, China; (W.W.); (Z.Z.); (C.H.); (X.W.); (J.X.)
- Division of Citrus Machinery, China Agriculture Research System, Guangzhou 510642, China
| | - Jian Xu
- College of Engineering, South China Agricultural University, Guangzhou 510642, China; (W.W.); (Z.Z.); (C.H.); (X.W.); (J.X.)
- Division of Citrus Machinery, China Agriculture Research System, Guangzhou 510642, China
| | - Xinrong Wang
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, College of Agriculture, South China Agricultural University, Guangzhou 510642, China;
- Correspondence:
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Mirnezami SV, Young T, Assefa T, Prichard S, Nagasubramanian K, Sandhu K, Sarkar S, Sundararajan S, O’Neal ME, Ganapathysubramanian B, Singh A. Automated trichome counting in soybean using advanced image-processing techniques. APPLICATIONS IN PLANT SCIENCES 2020; 8:e11375. [PMID: 32765974 PMCID: PMC7394713 DOI: 10.1002/aps3.11375] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Accepted: 03/25/2020] [Indexed: 05/20/2023]
Abstract
PREMISE Trichomes are hair-like appendages extending from the plant epidermis. They serve many important biotic roles, including interference with herbivore movement. Characterizing the number, density, and distribution of trichomes can provide valuable insights on plant response to insect infestation and define the extent of plant defense capability. Automated trichome counting would speed up this research but poses several challenges, primarily because of the variability in coloration and the high occlusion of the trichomes. METHODS AND RESULTS We developed a simplified method for image processing for automated and semi-automated trichome counting. We illustrate this process using 30 leaves from 10 genotypes of soybean (Glycine max) differing in trichome abundance. We explored various heuristic image-processing methods including thresholding and graph-based algorithms to facilitate trichome counting. Of the two automated and two semi-automated methods for trichome counting tested and with the help of regression analysis, the semi-automated manually annotated trichome intersection curve method performed best, with an accuracy of close to 90% compared with the manually counted data. CONCLUSIONS We address trichome counting challenges including occlusion by combining image processing with human intervention to propose a semi-automated method for trichome quantification. This provides new opportunities for the rapid and automated identification and quantification of trichomes, which has applications in a wide variety of disciplines.
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Affiliation(s)
- Seyed Vahid Mirnezami
- Department of Mechanical EngineeringIowa State UniversityAmesIowaUSA
- Colaberry Inc.200 Portland StreetBostonMassachusetts02114USA
| | - Therin Young
- Department of Mechanical EngineeringIowa State UniversityAmesIowaUSA
| | | | | | | | - Kulbir Sandhu
- Department of AgronomyIowa State UniversityAmesIowaUSA
| | - Soumik Sarkar
- Department of Mechanical EngineeringIowa State UniversityAmesIowaUSA
| | | | | | | | - Arti Singh
- Department of AgronomyIowa State UniversityAmesIowaUSA
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Falk KG, Jubery TZ, O'Rourke JA, Singh A, Sarkar S, Ganapathysubramanian B, Singh AK. Soybean Root System Architecture Trait Study through Genotypic, Phenotypic, and Shape-Based Clusters. PLANT PHENOMICS (WASHINGTON, D.C.) 2020; 2020:1925495. [PMID: 33313543 PMCID: PMC7706349 DOI: 10.34133/2020/1925495] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2019] [Accepted: 04/16/2020] [Indexed: 05/24/2023]
Abstract
We report a root system architecture (RSA) traits examination of a larger scale soybean accession set to study trait genetic diversity. Suffering from the limitation of scale, scope, and susceptibility to measurement variation, RSA traits are tedious to phenotype. Combining 35,448 SNPs with an imaging phenotyping platform, 292 accessions (replications = 14) were studied for RSA traits to decipher the genetic diversity. Based on literature search for root shape and morphology parameters, we used an ideotype-based approach to develop informative root (iRoot) categories using root traits. The RSA traits displayed genetic variability for root shape, length, number, mass, and angle. Soybean accessions clustered into eight genotype- and phenotype-based clusters and displayed similarity. Genotype-based clusters correlated with geographical origins. SNP profiles indicated that much of US origin genotypes lack genetic diversity for RSA traits, while diverse accession could infuse useful genetic variation for these traits. Shape-based clusters were created by integrating convolution neural net and Fourier transformation methods, enabling trait cataloging for breeding and research applications. The combination of genetic and phenotypic analyses in conjunction with machine learning and mathematical models provides opportunities for targeted root trait breeding efforts to maximize the beneficial genetic diversity for future genetic gains.
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Affiliation(s)
- Kevin G. Falk
- Department of Agronomy, Iowa State University, Ames, Iowa, USA
| | | | - Jamie A. O'Rourke
- Department of Agronomy, Iowa State University, Ames, Iowa, USA
- USDA-Agricultural Research Service, Corn Insects and Crop Genetics Research Unit, Ames, Iowa, USA
| | - Arti Singh
- Department of Agronomy, Iowa State University, Ames, Iowa, USA
| | - Soumik Sarkar
- Department of Mechanical Engineering, Iowa State University, Ames, Iowa, USA
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Falk KG, Jubery TZ, Mirnezami SV, Parmley KA, Sarkar S, Singh A, Ganapathysubramanian B, Singh AK. Computer vision and machine learning enabled soybean root phenotyping pipeline. PLANT METHODS 2020; 16:5. [PMID: 31993072 PMCID: PMC6977263 DOI: 10.1186/s13007-019-0550-5] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2018] [Accepted: 12/27/2019] [Indexed: 05/20/2023]
Abstract
BACKGROUND Root system architecture (RSA) traits are of interest for breeding selection; however, measurement of these traits is difficult, resource intensive, and results in large variability. The advent of computer vision and machine learning (ML) enabled trait extraction and measurement has renewed interest in utilizing RSA traits for genetic enhancement to develop more robust and resilient crop cultivars. We developed a mobile, low-cost, and high-resolution root phenotyping system composed of an imaging platform with computer vision and ML based segmentation approach to establish a seamless end-to-end pipeline - from obtaining large quantities of root samples through image based trait processing and analysis. RESULTS This high throughput phenotyping system, which has the capacity to handle hundreds to thousands of plants, integrates time series image capture coupled with automated image processing that uses optical character recognition (OCR) to identify seedlings via barcode, followed by robust segmentation integrating convolutional auto-encoder (CAE) method prior to feature extraction. The pipeline includes an updated and customized version of the Automatic Root Imaging Analysis (ARIA) root phenotyping software. Using this system, we studied diverse soybean accessions from a wide geographical distribution and report genetic variability for RSA traits, including root shape, length, number, mass, and angle. CONCLUSIONS This system provides a high-throughput, cost effective, non-destructive methodology that delivers biologically relevant time-series data on root growth and development for phenomics, genomics, and plant breeding applications. This phenotyping platform is designed to quantify root traits and rank genotypes in a common environment thereby serving as a selection tool for use in plant breeding. Root phenotyping platforms and image based phenotyping are essential to mirror the current focus on shoot phenotyping in breeding efforts.
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Affiliation(s)
- Kevin G. Falk
- Department of Agronomy, Iowa State University, Ames, USA
| | | | | | | | - Soumik Sarkar
- Department of Mechanical Engineering, Iowa State University, Ames, USA
| | - Arti Singh
- Department of Agronomy, Iowa State University, Ames, USA
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Falk KG, Jubery TZ, Mirnezami SV, Parmley KA, Sarkar S, Singh A, Ganapathysubramanian B, Singh AK. Computer vision and machine learning enabled soybean root phenotyping pipeline. PLANT METHODS 2020; 16:5. [PMID: 31993072 DOI: 10.1186/s,13007-019-0550-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 12/14/2018] [Accepted: 12/27/2019] [Indexed: 05/29/2023]
Abstract
BACKGROUND Root system architecture (RSA) traits are of interest for breeding selection; however, measurement of these traits is difficult, resource intensive, and results in large variability. The advent of computer vision and machine learning (ML) enabled trait extraction and measurement has renewed interest in utilizing RSA traits for genetic enhancement to develop more robust and resilient crop cultivars. We developed a mobile, low-cost, and high-resolution root phenotyping system composed of an imaging platform with computer vision and ML based segmentation approach to establish a seamless end-to-end pipeline - from obtaining large quantities of root samples through image based trait processing and analysis. RESULTS This high throughput phenotyping system, which has the capacity to handle hundreds to thousands of plants, integrates time series image capture coupled with automated image processing that uses optical character recognition (OCR) to identify seedlings via barcode, followed by robust segmentation integrating convolutional auto-encoder (CAE) method prior to feature extraction. The pipeline includes an updated and customized version of the Automatic Root Imaging Analysis (ARIA) root phenotyping software. Using this system, we studied diverse soybean accessions from a wide geographical distribution and report genetic variability for RSA traits, including root shape, length, number, mass, and angle. CONCLUSIONS This system provides a high-throughput, cost effective, non-destructive methodology that delivers biologically relevant time-series data on root growth and development for phenomics, genomics, and plant breeding applications. This phenotyping platform is designed to quantify root traits and rank genotypes in a common environment thereby serving as a selection tool for use in plant breeding. Root phenotyping platforms and image based phenotyping are essential to mirror the current focus on shoot phenotyping in breeding efforts.
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Affiliation(s)
- Kevin G Falk
- 1Department of Agronomy, Iowa State University, Ames, USA
| | - Talukder Z Jubery
- 2Department of Mechanical Engineering, Iowa State University, Ames, USA
| | - Seyed V Mirnezami
- 2Department of Mechanical Engineering, Iowa State University, Ames, USA
| | - Kyle A Parmley
- 1Department of Agronomy, Iowa State University, Ames, USA
| | - Soumik Sarkar
- 2Department of Mechanical Engineering, Iowa State University, Ames, USA
| | - Arti Singh
- 1Department of Agronomy, Iowa State University, Ames, USA
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Chen L, Strauch M, Daub M, Jansen M, Luigs HG, Merhof D. Instance Segmentation of Nematode Cysts in Microscopic Images of Soil Samples .. ANNUAL INTERNATIONAL CONFERENCE OF THE IEEE ENGINEERING IN MEDICINE AND BIOLOGY SOCIETY. IEEE ENGINEERING IN MEDICINE AND BIOLOGY SOCIETY. ANNUAL INTERNATIONAL CONFERENCE 2020; 2019:5932-5936. [PMID: 31947199 DOI: 10.1109/embc.2019.8856567] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Nematodes are plant parasites that cause damage to crops. In order to quantify nematode infestation based on soil samples, we propose an instance segmentation method that will serve as the basis of automatic quantitative analysis. We consider light microscopic images of cluttered object collections as they occur in realistic soil samples. We introduce an algorithm, LMBI (Local Maximum of Boundary Intensity) to propose instance segmentation candidates. In a second step, a SVM classifier separates the nematode cysts among the candidates from soil particles. On a data set of soil sample images, the LMBI detector achieves near-optimal recall with a limited number of candidate segmentations, and the combined detector/classifier achieves recall and precision of 0.7. The pipeline only requires simple dot annotations and ≈moderately sized training data, which enables quick annotating and training in laboratory applications.
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Kalwa U, Legner C, Wlezien E, Tylka G, Pandey S. New methods of removing debris and high-throughput counting of cyst nematode eggs extracted from field soil. PLoS One 2019; 14:e0223386. [PMID: 31613901 PMCID: PMC6793949 DOI: 10.1371/journal.pone.0223386] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2019] [Accepted: 09/19/2019] [Indexed: 02/05/2023] Open
Abstract
The soybean cyst nematode (SCN), Heterodera glycines, is the most damaging pathogen of soybeans in the United States. To assess the severity of nematode infestations in the field, SCN egg population densities are determined. Cysts (dead females) of the nematode must be extracted from soil samples and then ground to extract the eggs within. Sucrose centrifugation commonly is used to separate debris from suspensions of extracted nematode eggs. We present a method using OptiPrep as a density gradient medium with improved separation and recovery of extracted eggs compared to the sucrose centrifugation technique. Also, computerized methods were developed to automate the identification and counting of nematode eggs from the processed samples. In one approach, a high-resolution scanner was used to take static images of extracted eggs and debris on filter papers, and a deep learning network was trained to identify and count the eggs among the debris. In the second approach, a lensless imaging setup was developed using off-the-shelf components, and the processed egg samples were passed through a microfluidic flow chip made from double-sided adhesive tape. Holographic videos were recorded of the passing eggs and debris, and the videos were reconstructed and processed by custom software program to obtain egg counts. The performance of the software programs for egg counting was characterized with SCN-infested soil collected from two farms, and the results using these methods were compared with those obtained through manual counting.
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Affiliation(s)
- Upender Kalwa
- Department of Electrical and Computer Engineering, Iowa State University, Ames, Iowa, United States of America
| | - Christopher Legner
- Department of Electrical and Computer Engineering, Iowa State University, Ames, Iowa, United States of America
| | - Elizabeth Wlezien
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, Iowa, United States of America
| | - Gregory Tylka
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, Iowa, United States of America
| | - Santosh Pandey
- Department of Electrical and Computer Engineering, Iowa State University, Ames, Iowa, United States of America
- * E-mail:
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Nagasubramanian K, Jones S, Singh AK, Sarkar S, Singh A, Ganapathysubramanian B. Plant disease identification using explainable 3D deep learning on hyperspectral images. PLANT METHODS 2019; 15:98. [PMID: 31452674 PMCID: PMC6702735 DOI: 10.1186/s13007-019-0479-8] [Citation(s) in RCA: 81] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Accepted: 08/06/2019] [Indexed: 05/20/2023]
Abstract
BACKGROUND Hyperspectral imaging is emerging as a promising approach for plant disease identification. The large and possibly redundant information contained in hyperspectral data cubes makes deep learning based identification of plant diseases a natural fit. Here, we deploy a novel 3D deep convolutional neural network (DCNN) that directly assimilates the hyperspectral data. Furthermore, we interrogate the learnt model to produce physiologically meaningful explanations. We focus on an economically important disease, charcoal rot, which is a soil borne fungal disease that affects the yield of soybean crops worldwide. RESULTS Based on hyperspectral imaging of inoculated and mock-inoculated stem images, our 3D DCNN has a classification accuracy of 95.73% and an infected class F1 score of 0.87. Using the concept of a saliency map, we visualize the most sensitive pixel locations, and show that the spatial regions with visible disease symptoms are overwhelmingly chosen by the model for classification. We also find that the most sensitive wavelengths used by the model for classification are in the near infrared region (NIR), which is also the commonly used spectral range for determining the vegetative health of a plant. CONCLUSION The use of an explainable deep learning model not only provides high accuracy, but also provides physiological insight into model predictions, thus generating confidence in model predictions. These explained predictions lend themselves for eventual use in precision agriculture and research application using automated phenotyping platforms.
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Affiliation(s)
| | - Sarah Jones
- Department of Agronomy, Iowa State University, Ames, IA USA
| | - Asheesh K. Singh
- Department of Agronomy, Iowa State University, Ames, IA USA
- Plant Sciences Institute, Iowa State University, Ames, IA USA
| | - Soumik Sarkar
- Department of Mechanical Engineering, Iowa State University, Ames, IA USA
- Plant Sciences Institute, Iowa State University, Ames, IA USA
- Department of Computer Science, Iowa State University, Ames, IA USA
| | - Arti Singh
- Department of Agronomy, Iowa State University, Ames, IA USA
| | - Baskar Ganapathysubramanian
- Department of Electrical and Computer Engineering, Iowa State University, Ames, IA USA
- Department of Mechanical Engineering, Iowa State University, Ames, IA USA
- Plant Sciences Institute, Iowa State University, Ames, IA USA
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Singh AK, Ganapathysubramanian B, Sarkar S, Singh A. Deep Learning for Plant Stress Phenotyping: Trends and Future Perspectives. TRENDS IN PLANT SCIENCE 2018; 23:883-898. [PMID: 30104148 DOI: 10.1016/j.tplants.2018.07.004] [Citation(s) in RCA: 183] [Impact Index Per Article: 30.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2018] [Revised: 06/17/2018] [Accepted: 07/11/2018] [Indexed: 05/18/2023]
Abstract
Deep learning (DL), a subset of machine learning approaches, has emerged as a versatile tool to assimilate large amounts of heterogeneous data and provide reliable predictions of complex and uncertain phenomena. These tools are increasingly being used by the plant science community to make sense of the large datasets now regularly collected via high-throughput phenotyping and genotyping. We review recent work where DL principles have been utilized for digital image-based plant stress phenotyping. We provide a comparative assessment of DL tools against other existing techniques, with respect to decision accuracy, data size requirement, and applicability in various scenarios. Finally, we outline several avenues of research leveraging current and future DL tools in plant science.
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Affiliation(s)
| | | | - Soumik Sarkar
- Department of Mechanical Engineering, Iowa State University, Ames, IA, USA.
| | - Arti Singh
- Department of Agronomy, Iowa State University, Ames, IA, USA.
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