scholarly journals Using Visual Ozone Damage Scores and Spectroscopy to Quantify Soybean Responses to Background Ozone

2019 ◽  
Vol 12 (1) ◽  
pp. 93
Author(s):  
Nichole Gosselin ◽  
Vasit Sagan ◽  
Matthew Maimaitiyiming ◽  
Jack Fishman ◽  
Kelley Belina ◽  
...  
Keyword(s):  
Near Infrared ◽  
Pearson Correlation ◽  
Hyperspectral Data ◽  
Coefficient Of Determination ◽  
Biophysical Properties ◽  
Yield Data ◽  
Indicator Plants ◽  
Snap Beans ◽  
Visual Damage ◽  
Ozone Stress

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.

scholarly journals Predicting sensitivity of recently harvested tomatoes and tomato sepals to future fungal infections

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Sanja Brdar ◽  
Marko Panić ◽  
Esther Hogeveen-van Echtelt ◽  
Manon Mensink ◽  
Željana Grbović ◽  
...  
Keyword(s):  
Early Detection ◽  
Fungal Infection ◽  
Dynamic Pricing ◽  
Near Infrared ◽  
Fungal Infections ◽  
Pearson Correlation ◽  
Pathogenic Fungi ◽  
Hyperspectral Data ◽  
Final Decision ◽  
Model Interpretation

AbstractTomato is an important commercial product which is perishable by nature and highly susceptible to fungal incidence once it is harvested. Not all tomatoes are equally vulnerable to pathogenic fungi, and an early detection of the vulnerable ones can help in taking timely preventive actions, ranging from isolating tomato batches to adjusting storage conditions, but also in making right business decisions like dynamic pricing based on quality or better shelf life estimate. More importantly, early detection of vulnerable produce can help in taking timely actions to minimize potential post-harvest losses. This paper investigates Near-infrared (NIR) hyperspectral imaging (1000–1700 nm) and machine learning to build models to automatically predict the susceptibility of sepals of recently harvested tomatoes to future fungal infections. Hyperspectral images of newly harvested tomatoes (cultivar Brioso) from 5 different growers were acquired before the onset of any visible fungal infection. After imaging, the tomatoes were placed under controlled conditions suited for fungal germination and growth for a 4-day period, and then imaged using normal color cameras. All sepals in the color images were ranked for fungal severity using crowdsourcing, and the final severity of each sepal was fused using principal component analysis. A novel hyperspectral data processing pipeline is presented which was used to automatically segment the tomato sepals from spectral images with multiple tomatoes connected via a truss. The key modelling question addressed in this research is whether there is a correlation between the hyperspectral data captured at harvest and the fungal infection observed 4 days later. Using 10-fold and group k-fold cross-validation, XG-Boost and Random Forest based regression models were trained on the features derived from the hyperspectral data corresponding to each sepal in the training set and tested on hold out test set. The best model found a Pearson correlation of 0.837, showing that there is strong linear correlation between the NIR spectra and the future fungal severity of the sepal. The sepal specific predictions were aggregated to predict the susceptibility of individual tomatoes, and a correlation of 0.92 was found. Besides modelling, focus is also on model interpretation, particularly to understand which spectral features are most relevant to model prediction. Two approaches to model interpretation were explored, feature importance and SHAP (SHapley Additive exPlanations), resulting in similar conclusions that the NIR range between 1390–1420 nm contributes most to the model’s final decision.

scholarly journals Assessing within-Field Corn and Soybean Yield Variability from WorldView-3, Planet, Sentinel-2, and Landsat 8 Satellite Imagery

2021 ◽  
Vol 13 (5) ◽  
pp. 872 ◽  
Author(s):  
Sergii Skakun ◽  
Natacha I. Kalecinski ◽  
Meredith G. L. Brown ◽  
David M. Johnson ◽  
Eric F. Vermote ◽  
...  
Keyword(s):  
Spatial Resolution ◽  
Satellite Imagery ◽  
Near Infrared ◽  
Temporal Frequency ◽  
Coefficient Of Determination ◽  
Yield Variability ◽  
Landsat 8 ◽  
Yield Data ◽  
Resolution Data ◽  
Sentinel 2

Crop yield monitoring is an important component in agricultural assessment. Multi-spectral remote sensing instruments onboard space-borne platforms such as Advanced Very High Resolution Radiometer (AVHRR), Moderate Resolution Imaging Spectroradiometer (MODIS), and Visible Infrared Imaging Radiometer Suite (VIIRS) have shown to be useful for efficiently generating timely and synoptic information on the yield status of crops across regional levels. However, the coarse spatial resolution data inherent to these sensors provides little utility at the management level. Recent satellite imagery collection advances toward finer spatial resolution (down to 1 m) alongside increased observational cadence (near daily) implies information on crops obtainable at field and within-field scales to support farming needs is now possible. To test this premise, we focus on assessing the efficiency of multiple satellite sensors, namely WorldView-3, Planet/Dove-Classic, Sentinel-2, and Landsat 8 (through Harmonized Landsat Sentinel-2 (HLS)), and investigate their spatial, spectral (surface reflectance (SR) and vegetation indices (VIs)), and temporal characteristics to estimate corn and soybean yields at sub-field scales within study sites in the US state of Iowa. Precision yield data as referenced to combine harvesters’ GPS systems were used for validation. We show that imagery spatial resolution of 3 m is critical to explaining 100% of the within-field yield variability for corn and soybean. Our simulation results show that moving to coarser resolution data of 10 m, 20 m, and 30 m reduced the explained variability to 86%, 72%, and 59%, respectively. We show that the most important spectral bands explaining yield variability were green (0.560 μm), red-edge (0.726 μm), and near-infrared (NIR − 0.865 μm). Furthermore, the high temporal frequency of Planet and a combination of Sentinel-2/Landsat 8 (HLS) data allowed for optimal date selection for yield map generation. Overall, we observed mixed performance of satellite-derived models with the coefficient of determination (R2) varying from 0.21 to 0.88 (averaging 0.56) for the 30 m HLS and from 0.09 to 0.77 (averaging 0.30) for 3 m Planet. R2 was lower for fields with higher yields, suggesting saturation of the satellite-collected reflectance features in those cases. Therefore, other biophysical variables, such as soil moisture and evapotranspiration, at similar fine spatial resolutions are likely needed alongside the optical imagery to fully explain the yields.

scholarly journals Contrasting Influences of Seasonal and Intra-Seasonal Hydroclimatic Variabilities on the Irrigated Rice Paddies of Northern Peninsular Malaysia for Weather Index Insurance Design

2021 ◽  
Vol 13 (9) ◽  
pp. 5207
Author(s):  
Zed Zulkafli ◽  
Farrah Melissa Muharam ◽  
Nurfarhana Raffar ◽  
Amirparsa Jajarmizadeh ◽  
Mukhtar Jibril Abdi ◽  
...  
Keyword(s):  
Pearson Correlation ◽  
Extreme Rainfall ◽  
Peninsular Malaysia ◽  
Coefficient Of Determination ◽  
Index Insurance ◽  
Weather Index ◽  
Basis Risk ◽  
Insurance Contracts ◽  
Weather Index Insurance ◽  
Streamflow Statistics

Good index selection is key to minimising basis risk in weather index insurance design. However, interannual, seasonal, and intra-seasonal hydroclimatic variabilities pose challenges in identifying robust proxies for crop losses. In this study, we systematically investigated 574 hydroclimatic indices for their relationships with yield in Malaysia’s irrigated double planting system, using the Muda rice granary as a case study. The responses of seasonal rice yields to seasonal and monthly averages and to extreme rainfall, temperature, and streamflow statistics from 16 years’ observations were examined by using correlation analysis and linear regression. We found that the minimum temperature during the crop flowering to the maturity phase governed yield in the drier off-season (season 1, March to July, Pearson correlation, r = +0.87; coefficient of determination, R2 = 74%). In contrast, the average streamflow during the crop maturity phase regulated yield in the main planting season (season 2, September to January, r = +0.82, R2 = 67%). During the respective periods, these indices were at their lowest in the seasons. Based on these findings, we recommend temperature- and water-supply-based indices as the foundations for developing insurance contracts for the rice system in northern Peninsular Malaysia.

scholarly journals A Raman algorithm to estimate human age from protein structural variations in autopsy skin samples: a protein biological clock

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Daisuke Miyamori ◽  
Takeshi Uemura ◽  
Wenliang Zhu ◽  
Kei Fujikawa ◽  
Takaaki Nakaya ◽  
...  
Keyword(s):  
Protein Folding ◽  
Age Estimation ◽  
Mean Squared Error ◽  
Pearson Correlation ◽  
Biological Clock ◽  
Estimation Method ◽  
Forensic Identification ◽  
Random Coil ◽  
Coefficient Of Determination ◽  
Skin Samples

AbstractThe recent increase of the number of unidentified cadavers has become a serious problem throughout the world. As a simple and objective method for age estimation, we attempted to utilize Raman spectrometry for forensic identification. Raman spectroscopy is an optical-based vibrational spectroscopic technique that provides detailed information regarding a sample’s molecular composition and structures. Building upon our previous proof-of-concept study, we measured the Raman spectra of abdominal skin samples from 132 autopsy cases and the protein-folding intensity ratio, RPF, defined as the ratio between the Raman signals from a random coil an α-helix. There was a strong negative correlation between age and RPF with a Pearson correlation coefficient of r = 0.878. Four models, based on linear (RPF), squared (RPF2), sex, and RPF by sex interaction terms, were examined. The results of cross validation suggested that the second model including linear and squared terms was the best model with the lowest root mean squared error (11.3 years of age) and the highest coefficient of determination (0.743). Our results indicate that the there was a high correlation between the age and RPF and the Raman biological clock of protein folding can be used as a simple and objective forensic age estimation method for unidentified cadavers.

scholarly journals Histamine Control in Raw and Processed Tuna: A Rapid Tool Based on NIR Spectroscopy

Foods ◽  
2021 ◽  
Vol 10 (4) ◽  
pp. 885
Author(s):  
Sergio Ghidini ◽  
Luca Maria Chiesa ◽  
Sara Panseri ◽  
Maria Olga Varrà ◽  
Adriana Ianieri ◽  
...  
Keyword(s):  
Root Mean Square ◽  
Near Infrared ◽  
Nir Spectroscopy ◽  
Partial Least Square ◽  
Least Square ◽  
Partial Least Square Regression ◽  
Coefficient Of Determination ◽  
Mean Square ◽  
Tuna Fish ◽  
Mean Square Errors

The present study was designed to investigate whether near infrared (NIR) spectroscopy with minimal sample processing could be a suitable technique to rapidly measure histamine levels in raw and processed tuna fish. Calibration models based on orthogonal partial least square regression (OPLSR) were built to predict histamine in the range 10–1000 mg kg−1 using the 1000–2500 nm NIR spectra of artificially-contaminated fish. The two models were then validated using a new set of naturally contaminated samples in which histamine content was determined by conventional high-performance liquid chromatography (HPLC) analysis. As for calibration results, coefficient of determination (r2) > 0.98, root mean square of estimation (RMSEE) ≤ 5 mg kg−1 and root mean square of cross-validation (RMSECV) ≤ 6 mg kg−1 were achieved. Both models were optimal also in the validation stage, showing r2 values > 0.97, root mean square errors of prediction (RMSEP) ≤ 10 mg kg−1 and relative range error (RER) ≥ 25, with better results showed by the model for processed fish. The promising results achieved suggest NIR spectroscopy as an implemental analytical solution in fish industries and markets to effectively determine histamine amounts.

scholarly journals Atmospheric Compensation of PRISMA Data by Means of a Learning Based Approach

2021 ◽  
Vol 13 (15) ◽  
pp. 2967
Author(s):  
Nicola Acito ◽  
Marco Diani ◽  
Gregorio Procissi ◽  
Giovanni Corsini
Keyword(s):  
Spectral Range ◽  
Near Infrared ◽  
Random Noise ◽  
Synthetic Data ◽  
Regression Function ◽  
Short Wave ◽  
Hyperspectral Data ◽  
Electromagnetic Spectrum ◽  
Great Opportunity ◽  
Atmospheric Compensation

Atmospheric compensation (AC) allows the retrieval of the reflectance from the measured at-sensor radiance and is a fundamental and critical task for the quantitative exploitation of hyperspectral data. Recently, a learning-based (LB) approach, named LBAC, has been proposed for the AC of airborne hyperspectral data in the visible and near-infrared (VNIR) spectral range. LBAC makes use of a parametric regression function whose parameters are learned by a strategy based on synthetic data that accounts for (1) a physics-based model for the radiative transfer, (2) the variability of the surface reflectance spectra, and (3) the effects of random noise and spectral miscalibration errors. In this work we extend LBAC with respect to two different aspects: (1) the platform for data acquisition and (2) the spectral range covered by the sensor. Particularly, we propose the extension of LBAC to spaceborne hyperspectral sensors operating in the VNIR and short-wave infrared (SWIR) portion of the electromagnetic spectrum. We specifically refer to the sensor of the PRISMA (PRecursore IperSpettrale della Missione Applicativa) mission, and the recent Earth Observation mission of the Italian Space Agency that offers a great opportunity to improve the knowledge on the scientific and commercial applications of spaceborne hyperspectral data. In addition, we introduce a curve fitting-based procedure for the estimation of column water vapor content of the atmosphere that directly exploits the reflectance data provided by LBAC. Results obtained on four different PRISMA hyperspectral images are presented and discussed.

scholarly journals Rapid Quantification of Microalgae Growth with Hyperspectral Camera and Vegetation Indices

Plants ◽  
2021 ◽  
Vol 10 (2) ◽  
pp. 341
Author(s):  
Pauliina Salmi ◽  
Matti A. Eskelinen ◽  
Matti T. Leppänen ◽  
Ilkka Pölönen
Keyword(s):  
Chlorophyll Fluorescence ◽  
Chlorophyll A ◽  
Near Infrared ◽  
Vegetation Indices ◽  
Hyperspectral Data ◽  
Strong Correlations ◽  
Algae Biomass ◽  
Chlorophyll A Concentration ◽  
Cost Efficient ◽  
Hyperspectral Camera

Spectral cameras are traditionally used in remote sensing of microalgae, but increasingly also in laboratory-scale applications, to study and monitor algae biomass in cultures. Practical and cost-efficient protocols for collecting and analyzing hyperspectral data are currently needed. The purpose of this study was to test a commercial, easy-to-use hyperspectral camera to monitor the growth of different algae strains in liquid samples. Indices calculated from wavebands from transmission imaging were compared against algae abundance and wet biomass obtained from an electronic cell counter, chlorophyll a concentration, and chlorophyll fluorescence. A ratio of selected wavebands containing near-infrared and red turned out to be a powerful index because it was simple to calculate and interpret, yet it yielded strong correlations to abundances strain-specifically (0.85 < r < 0.96, p < 0.001). When all the indices formulated as A/B, A/(A + B) or (A − B)/(A + B), where A and B were wavebands of the spectral camera, were scrutinized, good correlations were found amongst them for biomass of each strain (0.66 < r < 0.98, p < 0.001). Comparison of near-infrared/red index to chlorophyll a concentration demonstrated that small-celled strains had higher chlorophyll absorbance compared to strains with larger cells. The comparison of spectral imaging to chlorophyll fluorescence was done for one strain of green algae and yielded strong correlations (near-infrared/red, r = 0.97, p < 0.001). Consequently, we described a simple imaging setup and information extraction based on vegetation indices that could be used to monitor algae cultures.

scholarly journals Are Saliva Tests Important in the Prediction of Carious Disease?

2021 ◽  
Vol 11 (13) ◽  
pp. 5932
Author(s):  
Daniela Luminita Ichim ◽  
Liliana Sachelarie ◽  
Alexandra Burlui
Keyword(s):  
Health Promotion ◽  
Pearson Correlation ◽  
Coefficient Of Determination ◽  
Data Series ◽  
Study Group ◽  
Complex Phenomenon ◽  
Oral Health Promotion ◽  
Group 4 ◽  
Carious Lesions ◽  
Pearson Correlation Test

(1) Background: The appearance and progression of carious lesions represent a complex phenomenon of interactions of microbial factors (the action of bacteria on the tooth), of the factors related to the host, to the diet, and to the time factor. Which hasan influence on the rate of microbismof the oral cavity on the installation of carious disease? (2) Methods: In order to correctly assess the cariogenic risk of an individual, it is recommended to perform twoor more tests based on different principles (microbiological, clinical, epidemiological). The representative data series for the investigation were analyzed statistically and by applying the Pearson correlation test considering the coefficient of determination R for all pairs of data series. (3) Results: Salivary tests played animportant role in establishing control sessions, in carrying out prophylactic caries therapy, and establishing prognosis. The existence of a statistical associationwas confirmed between the prevalence of dental caries and the results of salivary tests for the study group. (4) Conclusions: The results of the saliva tests can be used in oral health promotion.

scholarly journals Early Detection of Plant Viral Disease Using Hyperspectral Imaging and Deep Learning

Sensors ◽  
2021 ◽  
Vol 21 (3) ◽  
pp. 742
Author(s):  
Canh Nguyen ◽  
Vasit Sagan ◽  
Matthew Maimaitiyiming ◽  
Maitiniyazi Maimaitijiang ◽  
Sourav Bhadra ◽  
...  
Keyword(s):  
Neural Network ◽  
Deep Learning ◽  
Early Detection ◽  
Convolutional Neural Network ◽  
Near Infrared ◽  
Hyperspectral Data ◽  
Viral Diseases ◽  
Support Vector ◽  
Spectral Features ◽  
Feature Spaces

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.

Prediction of Fatty Acid Content in Beef Neck Lean by near Infrared Reflectance Analysis

1998 ◽  
Vol 6 (1) ◽  
pp. 229-234 ◽  
Author(s):  
William R. Windham ◽  
W.H. Morrison
Keyword(s):  
Fatty Acids ◽  
Fatty Acid ◽  
Near Infrared ◽  
Fatty Acid Content ◽  
Reference Method ◽  
Nir Spectroscopy ◽  
Coefficient Of Determination ◽  
Longissimus Dorsi ◽  
Near Infrared Reflectance ◽  
Total Fatty Acids

Near infrared (NIR) spectroscopy in the prediction of individual and total fatty acids of bovine M. Longissimus dorsi neck muscles has been studied. Beef neck lean was collected from meat processing establishments using advanced meat recovery systems and hand-deboning. Samples ( n = 302) were analysed to determine fatty acid (FA) composition and scanned from 400 to 2498 nm. Total saturated and unsaturated FA values ranged from 43.2 to 62.0% and 38.3 to 56.2%, respectively. Results of partial least squares (PLS) modeling shown reasonably accurate models were attained for total saturate content [standard error of performance ( SEP = 1.10%); coefficient of determination on the validation set ( r2 = 0.77)], palmitic ( SEP = 0.94%; r2 = 0.69), unsaturate ( SEP = 1.13%; r2 = 0.77), and oleic ( SEP = 0.97; r2 = 0.78). Prediction of other individual saturated and unsaturated FAs was less accurate with an r2 range of 0.10 to 0.53. However, the sum of individual predicted saturated and unsaturated FA was acceptable compared with the reference method ( SEP = 1.10 and 1.12%, respectively). This study shows that NIR can be used to predict accurately total fatty acids in M. Longissimus dorsi muscle.

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