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Haw YH, Lai KW, Chuah JH, Bejo SK, Husin NA, Hum YC, Yee PL, Tee CATH, Ye X, Wu X. Classification of basal stem rot using deep learning: a review of digital data collection and palm disease classification methods. PeerJ Comput Sci 2023; 9:e1325. [PMID: 37346512 PMCID: PMC10280561 DOI: 10.7717/peerj-cs.1325] [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: 11/09/2022] [Accepted: 03/13/2023] [Indexed: 06/23/2023]
Abstract
Oil palm is a key agricultural resource in Malaysia. However, palm disease, most prominently basal stem rot caused at least RM 255 million of annual economic loss. Basal stem rot is caused by a fungus known as Ganoderma boninense. An infected tree shows few symptoms during early stage of infection, while potentially suffers an 80% lifetime yield loss and the tree may be dead within 2 years. Early detection of basal stem rot is crucial since disease control efforts can be done. Laboratory BSR detection methods are effective, but the methods have accuracy, biosafety, and cost concerns. This review article consists of scientific articles related to the oil palm tree disease, basal stem rot, Ganoderma Boninense, remote sensors and deep learning that are listed in the Web of Science since year 2012. About 110 scientific articles were found that is related to the index terms mentioned and 60 research articles were found to be related to the objective of this research thus included in this review article. From the review, it was found that the potential use of deep learning methods were rarely explored. Some research showed unsatisfactory results due to limitations on dataset. However, based on studies related to other plant diseases, deep learning in combination with data augmentation techniques showed great potentials, showing remarkable detection accuracy. Therefore, the feasibility of analyzing oil palm remote sensor data using deep learning models together with data augmentation techniques should be studied. On a commercial scale, deep learning used together with remote sensors and unmanned aerial vehicle technologies showed great potential in the detection of basal stem rot disease.
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Affiliation(s)
- Yu Hong Haw
- Department of Biomedical Engineering, Universiti Malaya, Kuala Lumpur, Malaysia
| | - Khin Wee Lai
- Department of Biomedical Engineering, Universiti Malaya, Kuala Lumpur, Malaysia
| | - Joon Huang Chuah
- Department of Electrical Engineering, Universiti Malaya, Kuala Lumpur, Malaysia
| | - Siti Khairunniza Bejo
- Department of Biological and Agricultural Engineering, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
| | - Nur Azuan Husin
- Department of Biological and Agricultural Engineering, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
| | - Yan Chai Hum
- Department of Mechatronics and Biomedical Engineering, Universiti Tunku Abdul Rahman, Bandar Sungai Long, Cheras, Kajang, Selangor, Malaysia
| | - Por Lip Yee
- Department of Computer System and Technology, Universiti Malaya, Kuala Lumpur, Malaysia
| | | | - Xin Ye
- YLZ Eaccessy Information Technology Co., Ltd, Xiamen, China
| | - Xiang Wu
- School of Medical Information and Engineering, Xuzhou Medical University, Xuzhou, China
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Caceres-Hernandez D, Gutierrez R, Kung K, Rodriguez J, Lao O, Contreras K, Jo KH, Sanchez-Galan JE. Recent Advances in Automatic Feature Detection and Classification of Fruits including with a special emphasis on Watermelon (Citrillus lanatus): a Review. Neurocomputing 2023. [DOI: 10.1016/j.neucom.2023.01.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
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Baharim MSA, Adnan NA, Mohd FA, Othman AN, Abdul Rahim H, Azis MHA, Seman IA, Izzuddin MA, Shahabuddin NA, Nordiana AA. A review of ganoderma Basal Stem Rot (BSR) disease detection and mapping using geospatial and advanced techniques. GEOCARTO INTERNATIONAL 2022; 37:8100-8126. [DOI: 10.1080/10106049.2021.1993350] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Revised: 09/01/2021] [Accepted: 10/08/2021] [Indexed: 09/01/2023]
Affiliation(s)
- Mohd Sharul Aikal Baharim
- Centre of Studies Surveying Science and Geomatics, Faculty of Architecture, Planning & Surveying, Universiti Teknologi MARA, Shah Alam, Malaysia
| | - Nor Aizam Adnan
- Centre of Studies Surveying Science and Geomatics, Faculty of Architecture, Planning & Surveying, Universiti Teknologi MARA, Shah Alam, Malaysia
| | - Fazly Amri Mohd
- Centre of Studies Surveying Science and Geomatics, Faculty of Architecture, Planning & Surveying, Universiti Teknologi MARA Perlis, Arau, Malaysia
| | - Ainon Nisa Othman
- Centre of Studies Surveying Science and Geomatics, Faculty of Architecture, Planning & Surveying, Universiti Teknologi MARA, Shah Alam, Malaysia
| | - Haris Abdul Rahim
- Centre of Studies Surveying Science and Geomatics, Faculty of Architecture, Planning & Surveying, Universiti Teknologi MARA, Shah Alam, Malaysia
| | - Mohamad Haris Abd Azis
- Centre of Studies Surveying Science and Geomatics, Faculty of Architecture, Planning & Surveying, Universiti Teknologi MARA, Shah Alam, Malaysia
| | - Idris Abu Seman
- Malaysian Palm Oil Board (MPOB), Persiaran Institusi, Kajang, Selangor, Malaysia
| | | | | | - Abd Aziz Nordiana
- Malaysian Palm Oil Board (MPOB), Persiaran Institusi, Kajang, Selangor, Malaysia
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On-field optical imaging data for the pre-identification and estimation of leaf deformities. Sci Data 2022; 9:698. [DOI: 10.1038/s41597-022-01795-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Accepted: 10/20/2022] [Indexed: 11/15/2022] Open
Abstract
AbstractVisually nonidentifiable pathological symptoms at an early stage are a major limitation in agricultural plantations. Thickness reduction in palisade parenchyma (PP) and spongy parenchyma (SP) layers is one of the most common symptoms that occur at the early stage of leaf diseases, particularly in apple and persimmon. To visualize variations in PP and SP thickness, we used optical coherence tomography (OCT)-based imaging and analyzed the acquired datasets to determine the threshold parameters for pre-identifying and estimating persimmon and apple leaf abnormalities using an intensity-based depth profiling algorithm. The algorithm identified morphological differences between healthy, apparently-healthy, and infected leaves by applying a threshold in depth profiling to classify them. The qualitative and quantitative results revealed changes and abnormalities in leaf morphology in addition to disease incubation in both apple and persimmon leaves. These can be used to examine how initial symptoms are influenced by disease growth. Thus, these datasets confirm the significance of OCT in identifying disease symptoms nondestructively and providing a benchmark dataset to the agriculture community for future reference.
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Krivitsky V, Granot E, Avidor Y, Borberg E, Voegele RT, Patolsky F. Rapid Collection and Aptamer-Based Sensitive Electrochemical Detection of Soybean Rust Fungi Airborne Urediniospores. ACS Sens 2021; 6:1187-1198. [PMID: 33507747 PMCID: PMC8023804 DOI: 10.1021/acssensors.0c02452] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Accepted: 01/20/2021] [Indexed: 02/07/2023]
Abstract
Plants are the central source of food for humans around the world. Unfortunately, plants can be negatively affected by diverse kinds of diseases that are responsible for major economic losses worldwide. Thus, monitoring plant health and early detection of pathogens are essential to reduce disease spread and facilitate effective management practices. Various detection approaches are currently practiced. These methods mainly include visual inspection and laboratory tests. Nonetheless, these methods are labor-intensive, time-consuming, expensive, and inefficient in the early stages of infection. Thus, it is extremely important to detect diseases at the early stages of the epidemic. Here, we would like to present a fast, sensitive, and reliable electrochemical sensing platform for the detection of airborne soybean rust spores. The suspected airborne soybean rust spores are first collected and trapped inside a carbon 3D electrode matrix by high-capacity air-sampling means. Then, a specific biotinylated aptamer, suitable to target specific sites of soybean rust spores is applied. This aptamer agent binds to the surface of the collected spores on the electrode. Finally, spore-bound aptamer units are incubated with a streptavidin-alkaline phosphatase agent leading to the enzymatic formation of p-nitrophenol, which is characterized by its unique electrochemical properties. Our method allows for the rapid (ca. 2 min), selective, and sensitive collection and detection of soybean rust spores (down to the limit of 100-200 collected spores per cm2 of electrode area). This method could be further optimized for its sensitivity and applied to the future multiplex early detection of various airborne plant diseases.
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Affiliation(s)
- Vadim Krivitsky
- School
of Chemistry, Faculty of Exact Sciences, Tel Aviv University, Tel Aviv 69978, Israel
| | - Eran Granot
- School
of Chemistry, Faculty of Exact Sciences, Tel Aviv University, Tel Aviv 69978, Israel
| | | | - Ella Borberg
- School
of Chemistry, Faculty of Exact Sciences, Tel Aviv University, Tel Aviv 69978, Israel
| | - Ralf T. Voegele
- Institute
of Phytomedicine, University of Hohenheim, Stuttgart 70599, Germany
| | - Fernando Patolsky
- School
of Chemistry, Faculty of Exact Sciences, Tel Aviv University, Tel Aviv 69978, Israel
- Department
of Materials Science and Engineering, the Iby and Aladar Fleischman
Faculty of Engineering, Tel Aviv University, Tel Aviv 69978, Israel
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Early Detection of Ganoderma boninense in Oil Palm Seedlings Using Support Vector Machines. REMOTE SENSING 2020. [DOI: 10.3390/rs12233920] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Ganodermaboninense (G. boninense) is a fungus that causes one of the most destructive diseases in oil palm plantations in Southeast Asia called basal stem rot (BSR), resulting in annual losses of up to USD 500 million. The G. boninense infects both mature trees and seedlings. The current practice of detection still depends on manual inspection by a human expert every two weeks. This study aimed to detect early G. boninense infections using visible-near infrared (VIS-NIR) hyperspectral images where there are no BSR symptoms present. Twenty-eight samples of oil palm seedlings at five months old were used whereby 15 of them were inoculated with the G. boninense pathogen. Five months later, spectral reflectance oil palm leaflets taken from fronds 1 (F1) and 2 (F2) were obtained from the VIS-NIR hyperspectral images. The significant bands were identified based on the high separation between uninoculated (U) and inoculated (I) seedlings. The results indicate that the differences were evidently seen in the NIR spectrum. The bands were later used as input parameters for the development of Support Vector Machine (SVM) classification models, and these bands were optimized according to the classification accuracy achieved by the classifiers. It was observed that the U and I seedlings were excellently classified with 100% accuracy using 35 bands and 18 bands of F1. However, the combination of F1 and F2 (F12) gave better accuracy than F2 and almost similar to F1 for specific classifiers. This finding will provide an advantage when using aerial images where there is no need to separate F1 and F2 during the data pre-processing stage.
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Husin NA, Khairunniza-Bejo S, Abdullah AF, Kassim MSM, Ahmad D, Azmi ANN. Application of Ground-Based LiDAR for Analysing Oil Palm Canopy Properties on the Occurrence of Basal Stem Rot (BSR) Disease. Sci Rep 2020; 10:6464. [PMID: 32296108 PMCID: PMC7160211 DOI: 10.1038/s41598-020-62275-6] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Accepted: 03/06/2020] [Indexed: 11/25/2022] Open
Abstract
Ground-based LiDAR also known as Terrestrial Laser Scanning (TLS) technology is an active remote sensing imaging method said to be one of the latest advances and innovations for plant phenotyping. Basal Stem Rot (BSR) is the most destructive disease of oil palm in Malaysia that is caused by white-rot fungus Ganoderma boninense, the symptoms of which include flattening and hanging-down of the canopy, shorter leaves, wilting green fronds and smaller crown size. Therefore, until now there is no critical investigation on the characterisation of canopy architecture related to this disease using TLS method was carried out. This study proposed a novel technique of BSR classification at the oil palm canopy analysis using the point clouds data taken from the TLS. A total of 40 samples of oil palm trees at the age of nine-years-old were selected and 10 trees for each health level were randomly taken from the same plot. The trees were categorised into four health levels - T0, T1, T2 and T3, which represents the healthy, mildly infected, moderately infected and severely infected, respectively. The TLS scanner was mounted at a height of 1 m and each palm was scanned at four scan positions around the tree to get a full 3D image. Five parameters were analysed: S200 (canopy strata at 200 cm from the top), S850 (canopy strata at 850 cm from the top), crown pixel (number of pixels inside the crown), frond angle (degree of angle between fronds) and frond number. The results taken from statistical analysis revealed that frond number was the best single parameter to detect BSR disease as early as T1. In classification models, a linear model with a combination of parameters, ABD – A (frond number), B (frond angle) and D (S200), delivered the highest average accuracy for classification of healthy-unhealthy trees with an accuracy of 86.67 per cent. It also can classify the four severity levels of infection with an accuracy of 80 per cent. This model performed better when compared to the severity classification using frond number. The novelty of this research is therefore on the development of new approach to detect and classify BSR using point clouds data of TLS.
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Affiliation(s)
- Nur A Husin
- Department of Biological and Agricultural Engineering, Faculty of Engineering, Universiti Putra Malaysia, 43400 UPM, Serdang, Selangor, Malaysia
| | - Siti Khairunniza-Bejo
- Department of Biological and Agricultural Engineering, Faculty of Engineering, Universiti Putra Malaysia, 43400 UPM, Serdang, Selangor, Malaysia. .,Smart Farming Technology Research Centre, Universiti Putra Malaysia, 43400 UPM, Serdang, Selangor, Malaysia.
| | - Ahmad F Abdullah
- Department of Biological and Agricultural Engineering, Faculty of Engineering, Universiti Putra Malaysia, 43400 UPM, Serdang, Selangor, Malaysia.,Smart Farming Technology Research Centre, Universiti Putra Malaysia, 43400 UPM, Serdang, Selangor, Malaysia
| | - Muhamad S M Kassim
- Department of Biological and Agricultural Engineering, Faculty of Engineering, Universiti Putra Malaysia, 43400 UPM, Serdang, Selangor, Malaysia.,Smart Farming Technology Research Centre, Universiti Putra Malaysia, 43400 UPM, Serdang, Selangor, Malaysia
| | - Desa Ahmad
- Department of Biological and Agricultural Engineering, Faculty of Engineering, Universiti Putra Malaysia, 43400 UPM, Serdang, Selangor, Malaysia
| | - Aiman N N Azmi
- Department of Biological and Agricultural Engineering, Faculty of Engineering, Universiti Putra Malaysia, 43400 UPM, Serdang, Selangor, Malaysia
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