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Reddy P, Guthridge KM, Panozzo J, Ludlow EJ, Spangenberg GC, Rochfort SJ. Near-Infrared Hyperspectral Imaging Pipelines for Pasture Seed Quality Evaluation: An Overview. SENSORS 2022; 22:s22051981. [PMID: 35271127 PMCID: PMC8914962 DOI: 10.3390/s22051981] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Revised: 02/22/2022] [Accepted: 02/24/2022] [Indexed: 11/30/2022]
Abstract
Near-infrared (800–2500 nm; NIR) spectroscopy coupled to hyperspectral imaging (NIR-HSI) has greatly enhanced its capability and thus widened its application and use across various industries. This non-destructive technique that is sensitive to both physical and chemical attributes of virtually any material can be used for both qualitative and quantitative analyses. This review describes the advancement of NIR to NIR-HSI in agricultural applications with a focus on seed quality features for agronomically important seeds. NIR-HSI seed phenotyping, describing sample sizes used for building high-accuracy calibration and prediction models for full or selected wavelengths of the NIR region, is explored. The molecular interpretation of absorbance bands in the NIR region is difficult; hence, this review offers important NIR absorbance band assignments that have been reported in literature. Opportunities for NIR-HSI seed phenotyping in forage grass seed are described and a step-by-step data-acquisition and analysis pipeline for the determination of seed quality in perennial ryegrass seeds is also presented.
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Affiliation(s)
- Priyanka Reddy
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, VIC 3083, Australia; (P.R.); (K.M.G.); (E.J.L.); (G.C.S.)
| | - Kathryn M. Guthridge
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, VIC 3083, Australia; (P.R.); (K.M.G.); (E.J.L.); (G.C.S.)
| | - Joe Panozzo
- Agriculture Victoria Research, 110 Natimuk Road, Horsham, VIC 3400, Australia;
- Centre for Agriculture Innovation, University of Melbourne, Parkville, VIC 3010, Australia
| | - Emma J. Ludlow
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, VIC 3083, Australia; (P.R.); (K.M.G.); (E.J.L.); (G.C.S.)
| | - German C. Spangenberg
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, VIC 3083, Australia; (P.R.); (K.M.G.); (E.J.L.); (G.C.S.)
- School of Applied Systems Biology, La Trobe University, Bundoora, VIC 3083, Australia
| | - Simone J. Rochfort
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, VIC 3083, Australia; (P.R.); (K.M.G.); (E.J.L.); (G.C.S.)
- School of Applied Systems Biology, La Trobe University, Bundoora, VIC 3083, Australia
- Correspondence:
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Lassalle G. Monitoring natural and anthropogenic plant stressors by hyperspectral remote sensing: Recommendations and guidelines based on a meta-review. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 788:147758. [PMID: 34020093 DOI: 10.1016/j.scitotenv.2021.147758] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Revised: 05/05/2021] [Accepted: 05/10/2021] [Indexed: 06/12/2023]
Abstract
This review outlines the advances achieved in monitoring natural and anthropogenic plant stressors by hyperspectral remote sensing over the last 50 years. A broad diversity of methods based on field and imaging spectroscopy were developed in that field for precision farming and environmental monitoring purposes. From the 466 articles reviewed, we identified the main factors to consider to achieve accurate monitoring of plant stress, namely: The plant species and the stressor to monitor, the goal (detection or quantification), and scale (field or broad-scale) of monitoring, and the need for controlled experiments. Based on these factors, we then provide recommendations and guidelines for the development of reliable methods to monitor 11 major biotic and abiotic plant stressors. For each stressor, the effects on plant health and reflectance are described and the most suited spectral regions, scale, spatial resolution, and processing approaches to achieve accurate monitoring are presented. As a perspective, we discuss two major components that should be implemented in future methods to improve stress monitoring: The discrimination of plant stressors with similar effects on plants and the transferability of the methods across scales.
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Affiliation(s)
- Guillaume Lassalle
- University of Campinas, UNICAMP, PO Box 6152, 13083-855 Campinas, SP, Brazil.
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Early Detection of Plant Viral Disease Using Hyperspectral Imaging and Deep Learning. SENSORS 2021; 21:s21030742. [PMID: 33499335 PMCID: PMC7866105 DOI: 10.3390/s21030742] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Revised: 01/14/2021] [Accepted: 01/19/2021] [Indexed: 11/21/2022]
Abstract
Early detection of grapevine viral diseases is critical for early interventions in order to prevent the disease from spreading to the entire vineyard. Hyperspectral remote sensing can potentially detect and quantify viral diseases in a nondestructive manner. This study utilized hyperspectral imagery at the plant level to identify and classify grapevines inoculated with the newly discovered DNA virus grapevine vein-clearing virus (GVCV) at the early asymptomatic stages. An experiment was set up at a test site at South Farm Research Center, Columbia, MO, USA (38.92 N, −92.28 W), with two grapevine groups, namely healthy and GVCV-infected, while other conditions were controlled. Images of each vine were captured by a SPECIM IQ 400–1000 nm hyperspectral sensor (Oulu, Finland). Hyperspectral images were calibrated and preprocessed to retain only grapevine pixels. A statistical approach was employed to discriminate two reflectance spectra patterns between healthy and GVCV vines. Disease-centric vegetation indices (VIs) were established and explored in terms of their importance to the classification power. Pixel-wise (spectral features) classification was performed in parallel with image-wise (joint spatial–spectral features) classification within a framework involving deep learning architectures and traditional machine learning. The results showed that: (1) the discriminative wavelength regions included the 900–940 nm range in the near-infrared (NIR) region in vines 30 days after sowing (DAS) and the entire visual (VIS) region of 400–700 nm in vines 90 DAS; (2) the normalized pheophytization index (NPQI), fluorescence ratio index 1 (FRI1), plant senescence reflectance index (PSRI), anthocyanin index (AntGitelson), and water stress and canopy temperature (WSCT) measures were the most discriminative indices; (3) the support vector machine (SVM) was effective in VI-wise classification with smaller feature spaces, while the RF classifier performed better in pixel-wise and image-wise classification with larger feature spaces; and (4) the automated 3D convolutional neural network (3D-CNN) feature extractor provided promising results over the 2D convolutional neural network (2D-CNN) in learning features from hyperspectral data cubes with a limited number of samples.
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Using Visual Ozone Damage Scores and Spectroscopy to Quantify Soybean Responses to Background Ozone. REMOTE SENSING 2019. [DOI: 10.3390/rs12010093] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Remotely-sensed identification of ozone stress in crops can allow for selection of ozone resistant genotypes, improving yields. This is critical as population, food demand, and background tropospheric ozone are projected to increase over the next several decades. Visual scores of common ozone damage have been used to identify ozone-stress in bio-indicator plants. This paper evaluates the use of a visual scoring metric of ozone damage applied to soybeans. The scoring of the leaves is then combined with hyperspectral data to identify spectral indices specific to ozone damage. Two genotypes of soybean, Dwight and Pana, that have shown different sensitivities to ozone, were grown and visually scored for ozone-specific damage on multiple dates throughout the growing season. Leaf reflectance, foliar biophysical properties, and yield data were collected. Additionally, ozone bio-indicator plants, snap beans, and common milkweed, were investigated with visual scores and hyperspectral leaf data for comparison. The normalized difference spectral index (NDSI) was used to identify the significant bands in the visible (VIS), near infrared (NIR), and shortwave infrared (SWIR) that best correlated with visual damage score when used in the index. Results were then compared to multiple well-established indices. Indices were also evaluated for correlation with seed and pod weight. The ozone damage scoring metric for soybeans evaluated in August had a coefficient of determination of 0.60 with end-of-season pod weight and a Pearson correlation coefficient greater than 0.6 for photosynthetic rate, stomatal conductance, and transpiration. NDSI [R558, R563] correlated best with visual scores of ozone damage in soybeans when evaluating data from all observation dates. These wavelengths were similar to those identified as most sensitive to visual damage in August when used in NDSI (560 nm, 563 nm). NDSI [R560, R563] in August had the highest coefficient of determination for individual pod weight (R2 = 0.64) and seed weight (R2 = 0.54) when compared against 21 well-established indices used for identification of pigment or photosynthetic stress in plants. When evaluating use of spectral bands in NDSI, longer wavelengths in SWIR were identified as more sensitive to ozone visual damage. Trends in the bands and biophysical properties of the soybeans combined with evaluation of ozone data indicate likely timing of significant ozone damage as after late-July for this season. This work has implications for better spectral detection of ozone stress in crops and could help with efforts to identify ozone tolerant varieties to increase future yield.
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Abstract
Mapping maize water stress status and monitoring its spatial variability at a farm scale are a prerequisite for precision irrigation. High-resolution multispectral images acquired from an unmanned aerial vehicle (UAV) were used to evaluate the applicability of the data in mapping water stress status of maize under different levels of deficit irrigation at the late vegetative, reproductive and maturation growth stages. Canopy temperature, field air temperature and relative humidity obtained by a handheld infrared thermometer and a portable air temperature/relative humidity meter were used to establish a crop water stress index (CWSI) empirical model under the weather conditions in Ordos, Inner Mongolia, China. Nine vegetation indices (VIs) related to crop water stress were derived from the UAV multispectral imagery and used to establish CWSI inversion models. The results showed that non-water-stressed baseline had significant difference in the reproductive and maturation stages with an increase of 2.1 °C, however, the non-transpiring baseline did not change significantly with an increase of 0.1 °C. The ratio of transformed chlorophyll absorption in reflectance index (TCARI) and renormalized difference vegetation index (RDVI), and the TCARI and soil-adjusted vegetation index (SAVI) had the best correlations with CWSI. R2 values were 0.47 and 0.50 for TCARI/RDVI and TCARI/SAVI at the reproductive and maturation stages, respectively; and 0.81 and 0.80 for TCARI/RDVI and TCARI/SAVI at the late reproductive and maturation stages, respectively. Compared to CWSI calculated by on-site measurements, CWSI values retrieved by VI-CWSI regression models established in this study had more abilities to assess the field variability of crop and soil. This study demonstrates the potentiality of using high-resolution UAV multispectral imagery to map maize water stress.
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UAV-Based High Resolution Thermal Imaging for Vegetation Monitoring, and Plant Phenotyping Using ICI 8640 P, FLIR Vue Pro R 640, and thermoMap Cameras. REMOTE SENSING 2019. [DOI: 10.3390/rs11030330] [Citation(s) in RCA: 126] [Impact Index Per Article: 25.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The growing popularity of Unmanned Aerial Vehicles (UAVs) in recent years, along with decreased cost and greater accessibility of both UAVs and thermal imaging sensors, has led to the widespread use of this technology, especially for precision agriculture and plant phenotyping. There are several thermal camera systems in the market that are available at a low cost. However, their efficacy and accuracy in various applications has not been tested. In this study, three commercially available UAV thermal cameras, including ICI 8640 P-series (Infrared Cameras Inc., USA), FLIR Vue Pro R 640 (FLIR Systems, USA), and thermoMap (senseFly, Switzerland) have been tested and evaluated for their potential for forest monitoring, vegetation stress detection, and plant phenotyping. Mounted on multi-rotor or fixed wing systems, these cameras were simultaneously flown over different experimental sites located in St. Louis, Missouri (forest environment), Columbia, Missouri (plant stress detection and phenotyping), and Maricopa, Arizona (high throughput phenotyping). Thermal imagery was calibrated using procedures that utilize a blackbody, handheld thermal spot imager, ground thermal targets, emissivityand atmospheric correction. A suite of statistical analyses, including analysis of variance (ANOVA), correlation analysis between camera temperature and plant biophysical and biochemical traits, and heritability were utilized in order to examine the sensitivity and utility of the cameras against selected plant phenotypic traits and in the detection of plant water stress. In addition, in reference to quantitative assessment of image quality from different thermal cameras, a non-reference image quality evaluator, which primarily measures image focus that is based on the spatial relationship of pixels in different scales, was developed. Our results show that (1) UAV-based thermal imaging is a viable tool in precision agriculture and (2) the three examined cameras are comparable in terms of their efficacy for plant phenotyping. Overall, accuracy, when compared against field measured ground temperature and estimating power of plant biophysical and biochemical traits, the ICI 8640 P-series performed better than the other two cameras, followed by FLIR Vue Pro R 640 and thermoMap cameras. Our results demonstrated that all three UAV thermal cameras provide useful temperature data for precision agriculture and plant phenotying, with ICI 8640 P-series presenting the best results among the three systems. Cost wise, FLIR Vue Pro R 640 is more affordable than the other two cameras, providing a less expensive option for a wide range of applications.
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