Human vs. Machine, the Eyes Have It. Assessment of Stemphylium Leaf Blight on Onion Using Aerial Photographs from an NIR Camera

Aerial surveillance could be a useful tool for early detection and quantification of plant diseases, however, there are often confounding effects of other types of plant stress. Stemphylium leaf blight (SLB), caused by the fungus Stemphylium vesicarium, is a damaging foliar disease of onion. Studies were conducted to determine if near-infrared photographic images could be used to accurately assess SLB severity in onion research trials in the Holland Marsh in Ontario, Canada. The site was selected for its uniform soil and level topography. Aerial photographs were taken in 2015 and 2016 using an Xnite-Canon SX230NDVI with a near-infrared filter, mounted on a modified Cine Star—8 MK Heavy Lift RTF octocopter UAV. Images were taken at 15–20 m above the ground, providing an average of 0.5 cm/pixel and a field of view of 15 × 20 m. Photography and ground assessments of disease were carried out on the same day. NDVI (normalized difference vegetation index), green NDVI, chlorophyll index and plant senescence reflective index (PSRI) were calculated from the images. There were differences in SLB incidence and severity in the field plots and differences in the vegetative indices among the treatments, but there were no correlations between disease assessments and any of the indices.

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Using remote sensing for identification of late-season grass weed patches in wheat

Weed Science ◽

10.1614/ws-05-54.2.346 ◽

2006 ◽

Vol 54 (02) ◽

pp. 346-353 ◽

Cited By ~ 41

Author(s):

Francisca López-Granados ◽

Montse Jurado-Expósito ◽

Jose M. Peña-Barragán ◽

Luis García-Torres

Keyword(s):

Vegetation Index ◽

Near Infrared ◽

Normalized Difference Vegetation Index ◽

Vegetation Indices ◽

Field Research ◽

Aerial Images ◽

Wild Oat ◽

Late Season ◽

High Resolution Satellite Imagery ◽

Grass Weed

Field research was conducted to determine the potential of hyperspectral and multispectral imagery for late-season discrimination and mapping of grass weed infestations in wheat. Differences in reflectance between weed-free wheat and wild oat, canarygrass, and ryegrass were statistically significant in most 25-nm-wide wavebands in the 400- and 900-nm spectrum, mainly due to their differential maturation. Visible (blue, B; green, G; red, R) and near infrared (NIR) wavebands and five vegetation indices: Normalized Difference Vegetation Index (NDVI), Ratio Vegetation Index (RVI), R/B, NIR-R and (R − G)/(R + G), showed potential for discriminating grass weeds and wheat. The efficiency of these wavebands and indices were studied by using color and color-infrared aerial images taken over three naturally infested fields. In StaCruz, areas infested with wild oat and canarygrass patches were discriminated using the indices R, NIR, and NDVI with overall accuracies (OA) of 0.85 to 0.90. In Florida–West, areas infested with wild oat, canarygrass, and ryegrass were discriminated with OA from 0.85 to 0.89. In Florida–East, for the discrimination of the areas infested with wild oat patches, visible wavebands and several vegetation indices provided OA of 0.87 to 0.96. Estimated grass weed area ranged from 56 to 71%, 43 to 47%, and 69 to 80% of the field in the three locations, respectively, with per-class accuracies from 0.87 to 0.94. NDVI was the most efficient vegetation index, with a highly accurate performance in all locations. Our results suggest that mapping grass weed patches in wheat is feasible with high-resolution satellite imagery or aerial photography acquired 2 to 3 wk before crop senescence.

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Using Near-Infrared-Enabled Digital Repeat Photography to Track Structural and Physiological Phenology in Mediterranean Tree–Grass Ecosystems

Remote Sensing ◽

10.3390/rs10081293 ◽

2018 ◽

Vol 10 (8) ◽

pp. 1293 ◽

Cited By ~ 26

Author(s):

Yunpeng Luo ◽

Tarek S. El-Madany ◽

Gianluca Filippa ◽

Xuanlong Ma ◽

Bernhard Ahrens ◽

...

Keyword(s):

Vegetation Index ◽

Near Infrared ◽

Normalized Difference Vegetation Index ◽

Growing Season ◽

Plant Phenology ◽

Mediterranean Ecosystem ◽

Near Infrared Reflectance ◽

Seasonally Dry ◽

Growing Season Length ◽

Dry Down

Tree–grass ecosystems are widely distributed. However, their phenology has not yet been fully characterized. The technique of repeated digital photographs for plant phenology monitoring (hereafter referred as PhenoCam) provide opportunities for long-term monitoring of plant phenology, and extracting phenological transition dates (PTDs, e.g., start of the growing season). Here, we aim to evaluate the utility of near-infrared-enabled PhenoCam for monitoring the phenology of structure (i.e., greenness) and physiology (i.e., gross primary productivity—GPP) at four tree–grass Mediterranean sites. We computed four vegetation indexes (VIs) from PhenoCams: (1) green chromatic coordinates (GCC), (2) normalized difference vegetation index (CamNDVI), (3) near-infrared reflectance of vegetation index (CamNIRv), and (4) ratio vegetation index (CamRVI). GPP is derived from eddy covariance flux tower measurement. Then, we extracted PTDs and their uncertainty from different VIs and GPP. The consistency between structural (VIs) and physiological (GPP) phenology was then evaluated. CamNIRv is best at representing the PTDs of GPP during the Green-up period, while CamNDVI is best during the Dry-down period. Moreover, CamNIRv outperforms the other VIs in tracking growing season length of GPP. In summary, the results show it is promising to track structural and physiology phenology of seasonally dry Mediterranean ecosystem using near-infrared-enabled PhenoCam. We suggest using multiple VIs to better represent the variation of GPP.

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Monitoring Winter Stress Vulnerability of High-Latitude Understory Vegetation Using Intraspecific Trait Variability and Remote Sensing Approaches

Sensors ◽

10.3390/s20072102 ◽

2020 ◽

Vol 20 (7) ◽

pp. 2102

Author(s):

Elmar Ritz ◽

Jarle W. Bjerke ◽

Hans Tømmervik

Keyword(s):

Remote Sensing ◽

Vegetation Index ◽

Normalized Difference Vegetation Index ◽

Plant Traits ◽

Soil Depth ◽

Plant Stress ◽

Understory Vegetation ◽

Stress Vulnerability ◽

Multi Method Approach ◽

Common Plant

In this study, we focused on three species that have proven to be vulnerable to winter stress: Empetrum nigrum, Vaccinium vitis-idaea and Hylocomium splendens. Our objective was to determine plant traits suitable for monitoring plant stress as well as trait shifts during spring. To this end, we used a combination of active and passive handheld normalized difference vegetation index (NDVI) sensors, RGB indices derived from ordinary cameras, an optical chlorophyll and flavonol sensor (Dualex), and common plant traits that are sensitive to winter stress, i.e. height, specific leaf area (SLA). Our results indicate that NDVI is a good predictor for plant stress, as it correlates well with height (r = 0.70, p < 0.001) and chlorophyll content (r = 0.63, p < 0.001). NDVI is also related to soil depth (r = 0.45, p < 0.001) as well as to plant stress levels based on observations in the field (r = −0.60, p < 0.001). Flavonol content and SLA remained relatively stable during spring. Our results confirm a multi-method approach using NDVI data from the Sentinel-2 satellite and active near-remote sensing devices to determine the contribution of understory vegetation to the total ecosystem greenness. We identified low soil depth to be the major stressor for understory vegetation in the studied plots. The RGB indices were good proxies to detect plant stress (e.g. Channel G%: r = −0.77, p < 0.001) and showed high correlation with NDVI (r = 0.75, p < 0.001). Ordinary cameras and modified cameras with the infrared filter removed were found to perform equally well.

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Temporal covariance structure of multi-spectral phenotypes and their predictive ability for end-of-season traits in maize

Theoretical and Applied Genetics ◽

10.1007/s00122-020-03637-6 ◽

2020 ◽

Vol 133 (10) ◽

pp. 2853-2868

Author(s):

Mahlet T. Anche ◽

Nicholas S. Kaczmar ◽

Nicolas Morales ◽

James W. Clohessy ◽

Daniel C. Ilut ◽

...

Keyword(s):

Grain Yield ◽

Vegetation Index ◽

Near Infrared ◽

Normalized Difference Vegetation Index ◽

Crop Improvement ◽

Genetic Correlations ◽

Random Regression ◽

Multiple Time ◽

Heritable Variation ◽

Using Data

Abstract Key message Heritable variation in phenotypes extracted from multi-spectral images (MSIs) and strong genetic correlations with end-of-season traits indicates the value of MSIs for crop improvement and modeling of plant growth curve. Abstract Vegetation indices (VIs) derived from multi-spectral imaging (MSI) platforms can be used to study properties of crop canopy, providing non-destructive phenotypes that could be used to better understand growth curves throughout the growing season. To investigate the amount of variation present in several VIs and their relationship with important end-of-season traits, genetic and residual (co)variances for VIs, grain yield and moisture were estimated using data collected from maize hybrid trials. The VIs considered were Normalized Difference Vegetation Index (NDVI), Green NDVI, Red Edge NDVI, Soil-Adjusted Vegetation Index, Enhanced Vegetation Index and simple Ratio of Near Infrared to Red (Red) reflectance. Genetic correlations of VIs with grain yield and moisture were used to fit multi-trait models for prediction of end-of-season traits and evaluated using within site/year cross-validation. To explore alternatives to fitting multiple phenotypes from MSI, random regression models with linear splines were fit using data collected in 2016 and 2017. Heritability estimates ranging from (0.10 to 0.82) were observed, indicating that there exists considerable amount of genetic variation in these VIs. Furthermore, strong genetic and residual correlations of the VIs, NDVI and NDRE, with grain yield and moisture were found. Considerable increases in prediction accuracy were observed from the multi-trait model when using NDVI and NDRE as a secondary trait. Finally, random regression with a linear spline function shows potential to be used as an alternative to mixed models to fit VIs from multiple time points.

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Ecosystem Drought Response Timescales from Thermal Emission versus Shortwave Remote Sensing

Advances in Meteorology ◽

10.1155/2017/8434020 ◽

2017 ◽

Vol 2017 ◽

pp. 1-10 ◽

Cited By ~ 9

Author(s):

Erika Andujar ◽

Nir Y. Krakauer ◽

Chuixiang Yi ◽

Felix Kogan

Keyword(s):

Remote Sensing ◽

Large Scale ◽

Vegetation Index ◽

Normalized Difference Vegetation Index ◽

Thermal Emission ◽

Plant Stress ◽

Meteorological Drought ◽

Condition Index ◽

Vegetation Health ◽

Vegetation Health Index

Remote sensing is used for monitoring the impacts of meteorological drought on ecosystems, but few large-scale comparisons of the response timescale to drought of different vegetation remote sensing products are available. We correlated vegetation health products derived from polar-orbiting radiometer observations with a meteorological drought indicator available at different aggregation timescales, the Standardized Precipitation Evapotranspiration Index (SPEI), to evaluate responses averaged globally and over latitude and biome. The remote sensing products are Vegetation Condition Index (VCI), which uses normalized difference vegetation index (NDVI) to identify plant stress, Temperature Condition Index (TCI), based on thermal emission as a measure of surface temperature, and Vegetation Health Index (VHI), the average of VCI and TCI. Globally, TCI correlated best with 2-month timescale SPEI, VCI correlated best with longer timescale droughts (peak mean correlation at 13 months), and VHI correlated best at an intermediate timescale of 4 months. Our results suggest that thermal emission (TCI) may better detect incipient drought than vegetation color (VCI). VHI had the highest correlations with SPEI at aggregation times greater than 3 months and hence may be the most suitable product for monitoring the effects of long droughts.

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Spectral signature of brown rust and orange rust in sugarcane

Revista Facultad de Ingeniería Universidad de Antioquia ◽

10.17533/udea.redin.20191042 ◽

2020 ◽

pp. 9-20

Author(s):

Eniel Rodríguez-Machado ◽

Osmany Aday-Díaz ◽

Luis Hernández-Santana ◽

Jorge Luís Soca-Muñoz ◽

Rubén Orozco-Morales

Keyword(s):

Precision Agriculture ◽

Spectral Reflectance ◽

Vegetation Index ◽

Near Infrared ◽

Normalized Difference Vegetation Index ◽

Brown Rust ◽

Spectral Signature ◽

Spatial And Temporal Variability ◽

Mean Values ◽

Index Value

Precision agriculture, making use of the spatial and temporal variability of cultivable land, allows farmers to refine fertilization, control field irrigation, estimate planting productivity, and detect pests and disease in crops. To that end, this paper identifies the spectral reflectance signature of brown rust (Puccinia melanocephala) and orange rust (Puccinia kuehnii), which contaminate sugar cane leaves (Saccharum spp.). By means of spectrometry, the mean values and standard deviations of the spectral reflectance signature are obtained for five levels of contamination of the leaves in each type of rust, observing the greatest differences between healthy and diseased leaves in the red (R) and near infrared (NIR) bands. With the results obtained, a multispectral camera was used to obtain images of the leaves and calculate the Normalized Difference Vegetation Index (NDVI). The results identified the presence of both plagues by differentiating healthy from contaminated leaves through the index value with an average difference of 11.9% for brown rust and 9.9% for orange rust.

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Evaluation of a Low-cost Camera for Agricultural Applications

Journal of Experimental Agriculture International ◽

10.9734/jeai/2019/v32i530117 ◽

2019 ◽

pp. 1-9 ◽

Cited By ~ 1

Author(s):

Abdon Francisco Aureliano Netto ◽

Rodrigo Nogueira Martins ◽

Guilherme Silverio Aquino De Souza ◽

Fernando Ferreira Lima Dos Santos ◽

Jorge Tadeu Fim Rosas

Keyword(s):

Vegetation Index ◽

Near Infrared ◽

Normalized Difference Vegetation Index ◽

Low Cost ◽

Vegetation Indices ◽

Paspalum Notatum ◽

Crop Canopy ◽

N Application ◽

Satisfactory Accuracy ◽

Agricultural Applications

This study aimed to modify a webcam by replacing its near-infrared (NIR) blocking filter to a low-cost red, green and blue (RGB) filter for obtaining NIR images and to evaluate its performance in two agricultural applications. First, the sensitivity of the webcam to differentiate normalized difference vegetation index (NDVI) levels through five nitrogen (N) doses applied to the Batatais grass (Paspalum notatum Flugge) was verified. Second, images from maize crops were processed using different vegetation indices, and thresholding methods with the aim of determining the best method for segmenting crop canopy from the soil. Results showed that the webcam sensor was capable of detecting the effect of N doses through different NDVI values at 7 and 21 days after N application. In the second application, the use of thresholding methods, such as Otsu, Manual, and Bayes when previously processed by vegetation indices showed satisfactory accuracy (up to 73.3%) in separating the crop canopy from the soil.

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Recurrence Quantification Techniques of vegetation time-series indices in semiarid grasslands

10.5194/egusphere-egu2020-9937 ◽

2020 ◽

Author(s):

Andres Almeida-Ñauñay ◽

Rosa M. Benito ◽

Miguel Quemada ◽

Juan Carlos Losada ◽

Ana Maria Tarquis

Keyword(s):

Time Series ◽

Recurrent Events ◽

Vegetation Index ◽

Near Infrared ◽

Normalized Difference Vegetation Index ◽

Dynamic Properties ◽

Distinct Pattern ◽

Climatic Variables ◽

Recurrence Quantification ◽

Semi Arid

Grassland ecosystems are extremely complex and set up intricate structures, whose characteristics and dynamic properties are greatly influenced by climate and meteorological patterns. Climate change and global warming are factors that could impact negatively in the quality and productivity of these ecosystems.Remote sensing techniques have been demonstrated as a powerful tool for monitoring extensive areas. In this study, two semi-arid grassland plots were selected in the centre of Spain. This region is characterized by low precipitation and moderate productivity per unit. Through scientific research, spectral vegetation indices (VIs) have been developed to characterize vegetation cover. The most common VI is the Normalized Difference Vegetation Index (NDVI). However, in vegetation scarcity conditions, bare soil reflectance is increased, and the feasibility of NDVI is reduced. This study aims to perform a method to compare soil and agro-climatic variables effect on vegetation time-series indices.The construction of the time series was based on multispectral images of MODIS TERRA (MOD09A1.006) product acquired from 2002 till 2018. Three pixels with a temporal resolution of 8 days and a spatial resolution of 500 x 500 m were chosen in each area. To estimate and analyse VIs series, Red (620-670 nm) and Near Infrared (841-876 nm) channels were extracted and filtered by the quality of pixel. All spectral bands showed statistically significant differences confirming that both areas presented different soil properties. Moreover, average annual precipitation was different in each area of study.NDVI calculation is only based on NIR and RED bands. To improve the estimation of vegetation in semi-arid areas, several indices have been developed to minimize the soil effect. Each one of them incorporates soil influence in a different way, i.e., Soil Adjusted Vegetation Index (SAVI) adds a constant soil adjustment factor (L), whereas, MSAVI, incorporate an L variable and dependant on soil characteristics.Recurrence plots (RP) and recurrence quantification analysis (RQA) were computed to characterize the influence of agro-climatic variables in vegetation index dynamics. Characterization was based on various RQA measures, such as Determinism (DET), average diagonal length (LT) or entropy (ENT).Our results showed different RPs depending on the area, VI utilized and precipitation. MSAVI patterns were further distinct, meanwhile, NDVI showed a noisy pattern. LT values in MSAVI were higher than in SAVI implying that MSAVI recurrent events are much longer than SAVI. Simultaneously, LT and DET values in ZSO, with a higher rain, were above ZEA values in MSAVI.This indicates that incorporating more detailed information of soil and precipitation reinforce vegetation index estimation and allow to obtain a more distinct pattern of the time series. Therefore, in arid-semiarid grasslands, they should be considered.ACKNOWLEDGEMENTSThe authors acknowledge support from Project No. PGC2018-093854-B-I00 of the Spanish Ministerio de Ciencia Innovaci&#243;n y Universidades of Spain and the funding from the Comunidad de Madrid (Spain) and Structural Funds 2014-2020 512 (ERDF and ESF), through project AGRISOST-CM S2018/BAA-4330, are highly appreciated.

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Assessing Hemlock Decline Using Visible and Near-Infrared Spectroscopy: Indices Comparison and Algorithm Development

Applied Spectroscopy ◽

10.1366/0003702054280595 ◽

2005 ◽

Vol 59 (6) ◽

pp. 836-843 ◽

Cited By ~ 24

Author(s):

Jennifer Pontius ◽

Richard Hallett ◽

Mary Martin

Keyword(s):

Linear Regression ◽

Vegetation Index ◽

Near Infrared ◽

Normalized Difference Vegetation Index ◽

Accuracy Assessment ◽

Stress Index ◽

Regression Equations ◽

Near Infrared Reflectance ◽

Full Spectrum ◽

Hemlock Decline

Near-infrared reflectance spectroscopy was evaluated for its effectiveness at predicting pre-visual decline in eastern hemlock trees. An ASD FieldSpec Pro FR field spectroradiometer measuring 2100 contiguous 1-nm-wide channels from 350 nm to 2500 nm was used to collect spectra from fresh hemlock foliage. Full spectrum partial least squares (PLS) regression equations and reduced stepwise linear regression equations were compared. The best decline predictive model was a 6-term linear regression equation ( R2 = 0.71, RMSE = 0.591) based on: Carter Miller Stress Index (R694/R760), Derivative Chlorophyll Index (FD705/FD723), Normalized Difference Vegetation Index ((R800 – R680)/(R800 + R680)), R950, R1922, and FD1388. Accuracy assessment showed that this equation predicted an 11-class decline rating with a 1-class tolerance accuracy of 96% and differentiated healthy trees from those in very early decline with 72% accuracy. These results indicate that narrow-band sensors could be developed to detect very early stages of hemlock decline, before visual symptoms are apparent. This capability would enable land managers to identify early hemlock woolly adelgid infestations and monitor forest health over large areas of the landscape.

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Removal of Contaminated Pixels from the Desert Target for AVHRR Vicarious Calibration

Journal of Atmospheric and Oceanic Technology ◽

10.1175/2009jtecha1171.1 ◽

2009 ◽

Vol 26 (7) ◽

pp. 1354-1366 ◽

Cited By ~ 13

Author(s):

Fangfang Yu ◽

Xiangqian Wu

Keyword(s):

Vegetation Index ◽

Near Infrared ◽

Normalized Difference Vegetation Index ◽

Dust Storms ◽

Screening Methods ◽

Vegetation Growth ◽

Vicarious Calibration ◽

Calibration Device ◽

Libyan Desert ◽

Cloud Screening

Abstract Desert-based vicarious calibration plays an important role in generating long-term reliable satellite radiances for the visible and near-infrared channels of the Advanced Very High Resolution Radiometer (AVHRR). Lacking an onboard calibration device, the AVHRR relies on reflected radiances from a target site, for example, a large desert, to calibrate its solar reflective channels. While the radiometric characteristics of the desert may be assumed to be stable, the reflected radiances from the target can occasionally be affected by the presence of clouds, sand storms, vegetation, and wet surfaces. These contaminated pixels must be properly identified and removed to ensure calibration performance. This paper describes an algorithm for removing the contaminated pixels from AVHRR measurements taken over the Libyan Desert based on the characteristics of consistent normalized difference vegetation index (NDVI) land-cover stratification. An NDVI histogram-determined threshold is first applied to screen pixels contaminated with vegetation in each individual AVHRR observation. The resulting analyses show that the vegetation growth inside the desert target has a negligibly small impact on the AVHRR operational calibration results. Two criteria based on the maximum NDVI compositing technique are then employed to remove pixels contaminated with clouds, severe sand storms, and wet sand surfaces. Compared to other cloud-screening methods, this algorithm is capable of not only identifying high-reflectance clouds, but also removing the low reflectance of wet surfaces and the nearly indifferent reflectance of severe dust storms. The use of clear pixels appears to improve AVHRR calibration accuracy in the first 3–4 yr after satellite launch.

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