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Methodologies Used in Hyperspectral Remote Sensing in Agriculture
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Methodologies Used in Hyperspectral Remote Sensing in Agriculture

A special issue of Sensors (ISSN 1424-8220). This special issue belongs to the section "Remote Sensors".

Deadline for manuscript submissions: closed (20 October 2024) | Viewed by 13222

Special Issue Editor

Dr. Jiyul Chang

E-Mail Website
Guest Editor
Department of Agronomy, Horticulture & Plant Science, South Dakota State University, Brookings, SD 57007, USA
Interests: site-specific fertilizer management; using remote sensing data (satellite and drone images) for crop managements; using variouse spatial data (yield monitoring data, elevation data, soil data, RS data, soil test data) to describe spatial variability of production fields
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

The new term in agriculture is ‘Digital Agriculture’. Data from traditional sampling in production fields are being saved in digital formats. Real-time field data collected by sensors is being saved in computer devices. Scouting data during the growing season is being uploaded to cloud servers directly from fields. Planting and harvesting data are being transferred to home computers and are uploaded onto cloud servers immediately. Digital platforms for agriculture gather data from producers, analyze accumulated data, display results, and give recommendations of better managements next year. Many producers and agronomists are using digital agriculture platforms not just for precision agriculture practices but for all kinds of field management. So, ‘Digital Agriculture’ has become a broader term than ‘Precision Agriculture’.

Common multispectral sensors that contain RGB, red-edge, and NIR wavelengths can detect crop plant healthiness using NDVI, NDRE, or other indicis. However, these indicis cannot differentiate between certain type of stresses. Specific wavelengths in hyperspectral sensors at specific times might be more sensitive in plants under a specific type of stress than other stresses and in soil under a specific property than others. Findings by hyperspectral sensors can be applied to make sensors that can detect specific targets.

Huge data analysis from hyperspectral sensors requires robust statistical and computational methods instead of simple linear regression analysis.

So, in the Special Issue ‘Methodologies Used in Hyperspectral Remote Sensing in Agriculture’, we welcome recent experimental research or cases studies such as statistical and computational (Artificially Intelligent) methods for hyperspectral data analysis to detect specific targets which includes:

  • different types of crop stress detection;
  • weed type differentiation;
  • crop type differentiation;
  • insect/pest infestation identification;
  • soil property and fertility sensing;
  • using different sensors including ground, UAV, airborne, and satellite platforms.

Dr. Jiyul Chang
Guest Editor

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Keywords

  • hyperspectral sensor
  • artificial intelligence
  • machine learning
  • plant healthiness
  • plant stresses
  • fertilizer stress
  • water stress
  • pest infestation
  • insect infestation
  • soil property
  • crop type
  • weed type

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Published Papers (8 papers)

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Research

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21 pages, 6484 KiB  
Article
A Small-Sample Classification Strategy for Extracting Fractional Cover of Native Grass Species and Noxious Weeds in the Alpine Grasslands
by Zetian Ai and Ru An
Sensors 2024, 24(20), 6571; https://doi.org/10.3390/s24206571 - 12 Oct 2024
Viewed by 507
Abstract
The fractional cover of native grass species (NGS) and noxious weeds (NW) provides a more comprehensive understanding of grassland health in the alpine grasslands. However, coverage extraction of NGS and NW from satellite hyperspectral imagery can be challenging due to the small spectral [...] Read more.
The fractional cover of native grass species (NGS) and noxious weeds (NW) provides a more comprehensive understanding of grassland health in the alpine grasslands. However, coverage extraction of NGS and NW from satellite hyperspectral imagery can be challenging due to the small spectral and spatial feature difference, insufficient training samples, and the lack of effective fractional cover extraction methods. In this research, firstly, a feature optimization method is proposed to optimize the difference feature between NGS and NW. Secondly, a spectral–spatial constrained re-clustering training sample extension method (SSCTSE) is proposed to increase the number of training samples. Thirdly, a composite three-kernel SVM method (CTK-SVM) is developed to produce fractional cover maps of NGS and NW. The experimental results show that (1) the feature optimization method is effective in preserving the spectral and spatial difference features while eliminating invalid features; (2) the SSCTSE algorithm is capable of significantly increasing the number of training samples; (3) the fractional cover maps of NGS and NW are produced with the CTK-SVM method with overall accuracies of approximately 65%, and the RMSEs of NGS and NW are approximately 16% and 11%, respectively. The results provide a foundation for the fractional cover extraction of different grass species in alpine grasslands based on satellite hyperspectral imagery. Full article
(This article belongs to the Special Issue Methodologies Used in Hyperspectral Remote Sensing in Agriculture)
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24 pages, 36155 KiB  
Article
Heavy Metal Concentration Estimation for Different Farmland Soils Based on Projection Pursuit and LightGBM with Hyperspectral Images
by Nan Lin, Xiaofan Shao, Huizhi Wu, Ranzhe Jiang and Menghong Wu
Sensors 2024, 24(10), 3251; https://doi.org/10.3390/s24103251 - 20 May 2024
Viewed by 953
Abstract
Heavy metal pollution in farmland soil threatens soil environmental quality. It is an important task to quickly grasp the status of heavy metal pollution in farmland soil in a region. Hyperspectral remote sensing technology has been widely used in soil heavy metal concentration [...] Read more.
Heavy metal pollution in farmland soil threatens soil environmental quality. It is an important task to quickly grasp the status of heavy metal pollution in farmland soil in a region. Hyperspectral remote sensing technology has been widely used in soil heavy metal concentration monitoring. How to improve the accuracy and reliability of its estimation model is a hot topic. This study analyzed 440 soil samples from Sihe Town and the surrounding agricultural areas in Yushu City, Jilin Province. Considering the differences between different types of soils, a local regression model of heavy metal concentrations (As and Cu) was established based on projection pursuit (PP) and light gradient boosting machine (LightGBM) algorithms. Based on the estimations, a spatial distribution map of soil heavy metals in the region was drawn. The findings of this study showed that considering the differences between different soils to construct a local regression estimation model of soil heavy metal concentration improved the estimation accuracy. Specifically, the relative percent difference (RPD) of As and Cu element estimations in black soil increased the most, by 0.30 and 0.26, respectively. The regional spatial distribution map of heavy metal concentration derived from local regression showed high spatial variability. The number of characteristic bands screened by the PP method accounted for 10–13% of the total spectral bands, effectively reducing the model complexity. Compared with the traditional machine model, the LightGBM model showed better estimation ability, and the highest determination coefficients (R2) of different soil validation sets reached 0.73 (As) and 0.75 (Cu), respectively. In this study, the constructed PP–LightGBM estimation model takes into account the differences in soil types, which effectively improves the accuracy and reliability of hyperspectral image estimation of soil heavy metal concentration and provides a reference for drawing large-scale spatial distributions of heavy metals from hyperspectral images and mastering soil environmental quality. Full article
(This article belongs to the Special Issue Methodologies Used in Hyperspectral Remote Sensing in Agriculture)
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17 pages, 6238 KiB  
Article
Investigation of Using Hyperspectral Vegetation Indices to Assess Brassica Downy Mildew
by Bo Liu, Marco Antonio Fernandez, Taryn Michelle Liu and Shunping Ding
Sensors 2024, 24(6), 1916; https://doi.org/10.3390/s24061916 - 16 Mar 2024
Viewed by 1106
Abstract
Downy mildew caused by Hyaloperonospora brassicae is a severe disease in Brassica oleracea that significantly reduces crop yield and marketability. This study aims to evaluate different vegetation indices to assess different downy mildew infection levels in the Brassica variety Mildis using hyperspectral data. [...] Read more.
Downy mildew caused by Hyaloperonospora brassicae is a severe disease in Brassica oleracea that significantly reduces crop yield and marketability. This study aims to evaluate different vegetation indices to assess different downy mildew infection levels in the Brassica variety Mildis using hyperspectral data. Artificial inoculation using H. brassicae sporangia suspension was conducted to induce different levels of downy mildew disease. Spectral measurements, spanning 350 nm to 1050 nm, were conducted on the leaves using an environmentally controlled setup, and the reflectance data were acquired and processed. The Successive Projections Algorithm (SPA) and signal sensitivity calculation were used to extract the most informative wavelengths that could be used to develop downy mildew indices (DMI). A total of 37 existing vegetation indices and three proposed DMIs were evaluated to indicate downy mildew (DM) infection levels. The results showed that the classification using a support vector machine achieved accuracies of 71.3%, 80.7%, and 85.3% for distinguishing healthy leaves from DM1 (early infection), DM2 (progressed infection), and DM3 (severe infection) leaves using the proposed downy mildew index. The proposed new downy mildew index potentially enables the development of an automated DM monitoring system and resistance profiling in Brassica breeding lines. Full article
(This article belongs to the Special Issue Methodologies Used in Hyperspectral Remote Sensing in Agriculture)
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18 pages, 8095 KiB  
Article
A Novel Correction Methodology to Improve the Performance of a Low-Cost Hyperspectral Portable Snapshot Camera
by Andrea Genangeli, Giovanni Avola, Marco Bindi, Claudio Cantini, Francesco Cellini, Ezio Riggi and Beniamino Gioli
Sensors 2023, 23(24), 9685; https://doi.org/10.3390/s23249685 - 7 Dec 2023
Viewed by 1595
Abstract
The development of spectral sensors (SSs) capable of retrieving spectral information have opened new opportunities to improve several environmental and agricultural practices, e.g., crop breeding, plant phenotyping, land use monitoring, and crop classification. The SSs are classified as multispectral and hyperspectral (HS) based [...] Read more.
The development of spectral sensors (SSs) capable of retrieving spectral information have opened new opportunities to improve several environmental and agricultural practices, e.g., crop breeding, plant phenotyping, land use monitoring, and crop classification. The SSs are classified as multispectral and hyperspectral (HS) based on the number of the spectral bands resolved and sampled during data acquisition. Large-scale applications of the HS remain limited due to the cost of this type of technology and the technical difficulties in hyperspectral data processing. Low-cost portable hyperspectral cameras (PHCs) have been progressively developed; however, critical aspects associated with data acquisition and processing, such as the presence of spectral discontinuities, signal jumps, and a high level of background noise, were reported. The aim of this work was to analyze and improve the hyperspectral output of a PHC Senop HSC-2 device by developing a general use methodology. Several signal gaps were identified as falls and jumps across the spectral signatures near 513, 650, and 930 nm, while the dark current signal magnitude and variability associated with instrumental noise showed an increasing trend over time. A data correction pipeline was successfully developed and tested, leading to 99% and 74% reductions in radiance signal jumps identified at 650 and 830 nm, respectively, while the impact of noise on the acquired signal was assessed to be in the range of 10% to 15%. The developed methodology can be effectively applied to other low-cost hyperspectral cameras. Full article
(This article belongs to the Special Issue Methodologies Used in Hyperspectral Remote Sensing in Agriculture)
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18 pages, 6654 KiB  
Article
Comparing Nadir and Oblique Thermal Imagery in UAV-Based 3D Crop Water Stress Index Applications for Precision Viticulture with LiDAR Validation
by Thomas Buunk, Sergio Vélez, Mar Ariza-Sentís and João Valente
Sensors 2023, 23(20), 8625; https://doi.org/10.3390/s23208625 - 21 Oct 2023
Cited by 7 | Viewed by 1936
Abstract
Unmanned Aerial Vehicle (UAV) thermal imagery is rapidly becoming an essential tool in precision agriculture. Its ability to enable widespread crop status assessment is increasingly critical, given escalating water demands and limited resources, which drive the need for optimizing water use and crop [...] Read more.
Unmanned Aerial Vehicle (UAV) thermal imagery is rapidly becoming an essential tool in precision agriculture. Its ability to enable widespread crop status assessment is increasingly critical, given escalating water demands and limited resources, which drive the need for optimizing water use and crop yield through well-planned irrigation and vegetation management. Despite advancements in crop assessment methodologies, including the use of vegetation indices, 2D mapping, and 3D point cloud technologies, some aspects remain less understood. For instance, mission plans often capture nadir and oblique images simultaneously, which can be time- and resource-intensive, without a clear understanding of each image type’s impact. This issue is particularly critical for crops with specific growth patterns, such as woody crops, which grow vertically. This research aims to investigate the role of nadir and oblique images in the generation of CWSI (Crop Water Stress Index) maps and CWSI point clouds, that is 2D and 3D products, in woody crops for precision agriculture. To this end, products were generated using Agisoft Metashape, ArcGIS Pro, and CloudCompare to explore the effects of various flight configurations on the final outcome, seeking to identify the most efficient workflow for each remote sensing product. A linear regression analysis reveals that, for generating 2D products (orthomosaics), combining flight angles is redundant, while 3D products (point clouds) are generated equally from nadir and oblique images. Volume calculations show that combining nadir and oblique flights yields the most accurate results for CWSI point clouds compared to LiDAR in terms of geometric representation (R2 = 0.72), followed by the nadir flight (R2 = 0.68), and, finally, the oblique flight (R2 = 0.54). Thus, point clouds offer a fuller perspective of the canopy. To our knowledge, this is the first time that CWSI point clouds have been used for precision viticulture, and this knowledge can aid farm managers, technicians, or UAV pilots in optimizing the capture of UAV image datasets in line with their specific goals. Full article
(This article belongs to the Special Issue Methodologies Used in Hyperspectral Remote Sensing in Agriculture)
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9 pages, 2360 KiB  
Communication
Remote Sensing Provides a Rapid Epidemiological Context for the Control of African Swine Fever in Germany
by Hannes Bergmann, Eva-Maria Czaja, Annett Frick, Ulf Klaaß, Ronny Marquart, Annett Rudovsky, Diana Holland, Patrick Wysocki, Daike Lehnau, Ronald Schröder, Lisa Rogoll, Carola Sauter-Louis and Timo Homeier-Bachmann
Sensors 2023, 23(19), 8202; https://doi.org/10.3390/s23198202 - 30 Sep 2023
Cited by 1 | Viewed by 1146
Abstract
Transboundary disease control, as for African swine fever (ASF), requires rapid understanding of the locally relevant potential risk factors. Here, we show how satellite remote sensing can be applied to the field of animal disease control by providing an epidemiological context for the [...] Read more.
Transboundary disease control, as for African swine fever (ASF), requires rapid understanding of the locally relevant potential risk factors. Here, we show how satellite remote sensing can be applied to the field of animal disease control by providing an epidemiological context for the implementation of measures against the occurrence of ASF in Germany. We find that remotely sensed observations are of the greatest value at a lower jurisdictional level, particularly in support of wild boar carcass search efforts. Full article
(This article belongs to the Special Issue Methodologies Used in Hyperspectral Remote Sensing in Agriculture)
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17 pages, 3557 KiB  
Article
Detecting Grapevine Virus Infections in Red and White Winegrape Canopies Using Proximal Hyperspectral Sensing
by Yeniu Mickey Wang, Bertram Ostendorf and Vinay Pagay
Sensors 2023, 23(5), 2851; https://doi.org/10.3390/s23052851 - 6 Mar 2023
Cited by 7 | Viewed by 2840
Abstract
Grapevine virus-associated disease such as grapevine leafroll disease (GLD) affects grapevine health worldwide. Current diagnostic methods are either highly costly (laboratory-based diagnostics) or can be unreliable (visual assessments). Hyperspectral sensing technology is capable of measuring leaf reflectance spectra that can be used for [...] Read more.
Grapevine virus-associated disease such as grapevine leafroll disease (GLD) affects grapevine health worldwide. Current diagnostic methods are either highly costly (laboratory-based diagnostics) or can be unreliable (visual assessments). Hyperspectral sensing technology is capable of measuring leaf reflectance spectra that can be used for the non-destructive and rapid detection of plant diseases. The present study used proximal hyperspectral sensing to detect virus infection in Pinot Noir (red-berried winegrape cultivar) and Chardonnay (white-berried winegrape cultivar) grapevines. Spectral data were collected throughout the grape growing season at six timepoints per cultivar. Partial least squares-discriminant analysis (PLS-DA) was used to build a predictive model of the presence or absence of GLD. The temporal change of canopy spectral reflectance showed that the harvest timepoint had the best prediction result. Prediction accuracies of 96% and 76% were achieved for Pinot Noir and Chardonnay, respectively. Our results provide valuable information on the optimal time for GLD detection. This hyperspectral method can also be deployed on mobile platforms including ground-based vehicles and unmanned aerial vehicles (UAV) for large-scale disease surveillance in vineyards. Full article
(This article belongs to the Special Issue Methodologies Used in Hyperspectral Remote Sensing in Agriculture)
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Review

Jump to: Research

21 pages, 412 KiB  
Review
Can Metabolomic Approaches Become a Tool for Improving Early Plant Disease Detection and Diagnosis with Modern Remote Sensing Methods? A Review
by Anton Terentev and Viktor Dolzhenko
Sensors 2023, 23(12), 5366; https://doi.org/10.3390/s23125366 - 6 Jun 2023
Cited by 1 | Viewed by 2226
Abstract
The various areas of ultra-sensitive remote sensing research equipment development have provided new ways for assessing crop states. However, even the most promising areas of research, such as hyperspectral remote sensing or Raman spectrometry, have not yet led to stable results. In this [...] Read more.
The various areas of ultra-sensitive remote sensing research equipment development have provided new ways for assessing crop states. However, even the most promising areas of research, such as hyperspectral remote sensing or Raman spectrometry, have not yet led to stable results. In this review, the main methods for early plant disease detection are discussed. The best proven existing techniques for data acquisition are described. It is discussed how they can be applied to new areas of knowledge. The role of metabolomic approaches in the application of modern methods for early plant disease detection and diagnosis is reviewed. A further direction for experimental methodological development is indicated. The ways to increase the efficiency of modern early plant disease detection remote sensing methods through metabolomic data usage are shown. This article provides an overview of modern sensors and technologies for assessing the biochemical state of crops as well as the ways to apply them in synergy with existing data acquisition and analysis technologies for early plant disease detection. Full article
(This article belongs to the Special Issue Methodologies Used in Hyperspectral Remote Sensing in Agriculture)
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