Precision Agriculture and Hyperspectral

Sensors: Monitoring Against Drought,

Disease, and Nutrient Stress
https://surfaceoptics.com/applications/p
recision-agriculture-hyperspectral-sensors/

Crop monitoring for nutrients, water-stress, disease, insect attack and overall plant
health is a vital aspect of successful agricultural operations. Traditionally this has been
carried out by visual examination of crops on the ground or sometimes from the air. However
these methods are limited by the ability of the human eye to discriminate between healthy
foliage and foliage suffering various kinds of stress. Often a specific condition must be well-
advanced before visual symptoms become noticeable even to experienced observers.

Modern precision agriculture relies on site-specific management tactics to maximize

yield and resources while reducing environmental impacts such as over-fertilization and the
broad applications of pesticides. Pin-pointing areas requiring attention – be it water, weed or
pathogen treatment, or nutrient adjustments – allows for spot application rather than whole-
field treatment. The collection of key data at a sufficient level of accuracy depends on the
availability of equipment that can be operated at a cost-effective level.

Some of the benefits of hyperspectral and multispectral

imaging are that these technologies are: low cost (when compared

with traditional scouting methods), give consistent results, simple

 to use, allow for rapid assessments, non-destructive, highly

accurate, and have a broad range of applications.

The development of aerial and ground-based hyperspectral and multispectral

imaging equipment has been a major breakthrough in the expansion and practical application
of precision agriculture techniques. This technology has made possible the assessment of
crop stresses, characterization of soils and vegetative cover and yield estimation, in addition
to its predictive capabilities. Some of the benefits of hyperspectral and multispectral imaging
are that these technologies are: low cost (when compared with traditional scouting methods),
give consistent results, simple to use, allow for rapid assessments, non-destructive, highly
accurate, and have a broad range of applications.[1]

BASICS OF HYPERSPECTRAL IMAGING

Spectral reflectance, measured by hyperspectral imaging equipment, is the amount
of reflected light from a surface. Hyperspectral imaging is the process by which images are
taken and numerical values (spectral radiance) assigned to each pixel, utilizing a range of
wavelengths across the electromagnetic spectrum, including visible and infrared regions.

Through the use of specialized software and statistical analysis, these pixels are
sorted and characterized to distinguish between groups of pixels or in the case of precision
agriculture, plant characteristics and environmental conditions. Earlier remote sensing
technology, in particular multispectral imaging, collects data at a few widely-spaced
wavelengths.The data from each wave-length band is assembled into a three-dimensional
hyperspectral ‘data cube’ for processing and analysis. Each layer of the cube represents data
at a specific wavelength.
 Spectral imaging data captured by the SOC710-VP highlights areas of Merlot leaves suffering from
fungal infection. Viewed using Surface Optics hyperspectral processing and analysis software.

DETECTION OF STRESS-RELATED SPECTRAL

VARIATIONS
The ability of hyperspectral imaging to provide valuable data on the condition and
health of crops is predicated on the interaction and relationship between electromagnetic
radiation (EMR) and foliage. EMR may be absorbed, transmitted or reflected and although
the internal and external physical structure of vegetation affects this, the primary influences
on EMR are the various photosynthetic pigments.[2]
In the red and blue parts of the visible spectrum, reflectance is primarily a result of
absorption by the photosynthetic pigments. Water content is the primary influence on
reflectance in the mid-infrared (MIR) while reflectance in the near-infrared area (NIR) is
influenced by the shape and condition of air spaces in the spongy mesophyll.[3] Senescence,
nutrient stress, pathogen and insect infestation have all been shown to significantly reduce
reflectance in the mid-infrared spectral region.[6] It has been well recorded that a vegetation
index of NIR and red wavelengths can monitor a range of plant-health issues including fungal
pathogens, excess salt and nutrient deficiencies.

By measuring changes at waveband 531nm, which is affected

by the production of zeaxanthin and comparing it with waveband

570 nm, which is not affected, a standard Photochemical

 Reflectance Index (PRI) has been developed which serves as a

measure of photosynthetic light use efficiency. This index can be

readily generated from hyperspectral imaging data.

One of the most powerful techniques for the measurement of overall photosynthetic
efficiency and thus of plant productivity, is the fluorescence of chlorophyll a in photosystem
II. The indexes produced give a good measure, however they are limited in their use by the
need for the active excitation of photosynthesis by, for example, a saturating light
pulse.[4] This severely restricts the possibility of using this measure for remote sensing, so
research has been directed to finding new, genuinely remote indices suitable for
hyperspectral imaging equipment.
Besides the photosynthetic pigments, reflectance is also influenced by the presence
of zeaxanthin. This pigment is produced by plants to safely remove excess photons when
light intensity exceeds the ability of photosystem II to absorb photons without becoming over-
energized. Zeaxanthin accumulation can therefore be used as a quantitative indicator of non-
photochemical energy dissipation and therefore of light-use efficiency.[4]
By measuring changes at waveband 531nm, which is affected by the production of
zeaxanthin and comparing it with waveband 570 nm, which is not affected, a standard
Photochemical Reflectance Index (PRI) has been developed which serves as a measure of
photosynthetic light use efficiency. This index can be readily generated from hyperspectral
imaging data.[5]
Of particular importance is a comparison with traditional spectrometric equipment to
ensure the ability of hyperspectral imaging to deliver equivalent data to traditional equipment.
A study by Rascher et al. (2007) utilizing the SOC-700 instrument showed that portable
hyperspectral imaging equipment could be used to “quantify dynamic, biochemical changes
in photosynthetic efficiency” by measuring PRI.[5]
In this study it was demonstrated that PRI could provide measurements of both the
biochemical adaptions to high light intensity and the gradual de-activation of photosynthesis
during drying, making PRI monitoring by remote sensing a valuable methodology for drought
investigations. The Rascher study relied on detached leaves, but the same methodology and
instrumentation has been shown in the controlled conditions of Biosphere 2 to give effective
data on whole vegetation-canopies.[4]
 Above is an example of the picture processing and Photochemical Reflectance Index
of four tropical leaves during the drying process as seen in the Rascher et al. (2007) study.
(A) True-color-composite picture of the imaged leaves; (B) Normalized Difference Vegetation
Index (NDVI), calculated for all pixels; (C) NDVI threshold image, (D) PRI, calculated for all
pixels.(E through H): A time series of PRI during the drying process. The mask from (C) was
used to show the leaf PRI values only.

DROUGHT STRESS
Drought is a significant factor in predicting crop yields and the final success of a crop.
Early detection of water related stresses in field crops can allow producers to identify specific
areas for irrigation, saving water, energy, and time. Early detection might also allow
producers to deliver water to crops before drought stress results in yield losses.

Colombo et al. (2008) tested various indices of drought stress and found that leaf
reflectance in the infrared and visible spectrum was related to changes in leaf equivalent
water thickness (EWT). Using hyperspectral imaging they tested various models for
estimating EWT at the canopy level in Italian poplar plantations and found suitable models
giving error levels of only 2.6%. They concluded that hyperspectral regression indices
derived from hyperspectral imaging were strong tools for estimating water content at both
leaf and landscape level.[7]
 The SOC-700 hyperspectral imager was able to track the

development of water stress four days before the effects of the stress

were observed with the naked eye

Higher levels of stress do ultimately manifest themselves in changes in

photosynthetic pigments. These changes lead to the familiar symptom of chlorosis when the
reflectance of red wavelengths increases to equal that of green, producing the typical yellow
colour. These changes are detected much earlier by hyperspectral imaging well before any
change is visible to the human eye.[2]
As discussed above, Rascher et al. used the Photochemical Reflectance Index and
a portable hyperspectral imager to assess drought stress in leaves of tropical trees and they
could clearly observe the effect of dehydration over time on the individual tree leaves.[5]
That this stress-detection methodology could be applied to grain was demonstrated
in trials of corn subjected to different water and nutrient regimes in field plots. Though the
traits of leaf and canopy water stress were subtle, hyperspectral imaging technology could
distinguish between treatments in both the controlled and field experiments.[8] Even with
senescing leaves of barley due to flowering, the SOC-700 hyperspectral imager was able to
track the development of water stress four days before the effects of the stress were
observed with the naked eye. Under the field conditions, with variability of light and plot
differences, the imaging technology could correctly characterize three out of the four
treatment groups.This demonstrated the suitability of hyperspectral imaging for early
detection of drought-stress and nutrient-stress in practical agricultural conditions.
 Spatio-temporal dynamics of drought stress in barley, visualized with false color images. Images
for drought-stressed plants stop at day 10 as plants were only observed until drought stress was visible to
the naked eye. The green color indicated a high probability that the signature corresponds to a pixel
belonging to the healthy archetypes, whereas a dark red color indicated a high probability of being
associated with the stressed archetype.

Additionally, Rossini et al. (2013) showed that hyperspectral imaging could be used
to detect drought stress at the farm level with corn. They conducted a comparison of three
irrigation conditions with airborne remote sensing equipment and found that they were able
to accurately map irrigation deficits even before water stress affected the canopy structure.[9]
Field crops are not the only application of hyperspectral imaging, this technology can
be used to assess water stress and scheduling of irrigation in turf grasses. Jiang and Carrow
(2005) examined the correlation of spectral reflectance and drought stress on turf grass (turf
quality and leaf firing). They screened 12 grasses and found that the reflectance models
varied by cultivar, suggesting that species differences should be taken into account when
using indexes. They also conclude that hyperspectral imaging might be useful in screening
grasses for drought tolerance.[10]

PLANT PATHOGENS
Fungal pathogens cause serious losses to yields and quality of agricultural crops
globally. In the United States alone, plant pathogens are reported to cause economic losses
of 33 billion annually.[11] Early detection of plant disease in the field can allow producers to
rapidly treat affected areas and to more accurately predict yield losses. Conventional
methods of detection rely on scouting and visual examination and often result in detection
after the optimum time for control has passed.
In addition to preventing individual producer losses, early detection will allow for the
prevention of spread to neighboring fields or crops. Using diagnostic symptoms of pathogens
such as changes in leaf pigments, leaf structure and moisture content, hyperspectral and
multispectral imaging can aid in mapping fields for plant disease management.

For example, the fungal pathogen, Puccinia recondite, causes wheat rust
characterized by small brown pustules on the leaf surface. In a greenhouse study, wheat
plants were inoculated and then hyperspectral and multispectral imaging technologies were
compared for their accuracy in distinguishing treated plants from non-treated plants. Franke
et al. (2005) reported that both hyperspectral and multispectral imaging proved efficient at
detecting leaf rust as few as five days post inoculation.
 In a 2005 study, the SOC-700 was able to detect wheat leaf rust days before it was visible with the
naked eye. Early detection allows for increased efficiency in applying site-specific fungicide application.

Compared to multispectral imaging, the higher spectral sensitivity of hyperspectral

imaging produced superior detection at an earlier stage of development of the pathogen,
when only slight visual symptoms were apparent. In addition, hyperspectral imaging was
much less sensitive to external factors such as illumination conditions than multispectral
imaging was. This prevented the poor classification accuracy found in the multispectral
imaging data sets.[12]

A comparison of relative reflectance between healthy and leaf rust infected wheat spectral
signatures from 400-1000 nm showed a decreased reflectance for the infected wheat in the blue and green
region of the visible spectrum and a strong decreased near-infrared reflectance plateau.

Venturia inaequalis is the pathogen responsible for apple scab in apple trees.
Infection first appears as yellow or chlorotic spots on leaves progressing to darker spots and
yellowing of the leaves. Economic losses are caused primarily by damage to the fruit
surfaces. Using hyperspectral imaging and statistical procedures for classification, Delalieux
et al (2007) concluded that stress from apple scab was able to be detected before symptoms
were visible to the human eye.[13]
Under controlled conditions, Mahlein et al (2012) reported that hyperspectral imaging
was suitable for, not only the detection, but also the identification and quantification of fungal
diseases of sugar beets at the leaf level. This study examined three pathogens of sugar
beets, Cercospora leaf spot (Cercospora beticola (Sacc.)), powdery mildew (Erysiphe betae
(Vanha) Weltzien), and sugar beet rust (Uromyces betae (Persoon) Lev.). Hyperspectral
imaging technology was able to distinguish between these three pathogens with as little as
10% diseased leaf area for powdery mildew and leaf spot.[14]
The use of hyperspectral imaging can be applied successfully on a larger scale.
Orange rust of sugarcane (caused by Puccinia kuehnii) is a fungal disease that produces
lesions which rupture allowing water to escape from the plant. From images taken at the field
level, Apan et al. (2004) successfully discriminated patches of orange rust of sugarcane from
non-affected areas by detecting changes in leaf pigments.[15]Similarly, Zhang et al. (2003)
demonstrated the effectiveness of hyperspectral imaging for disease detection at the field
level. Late blight of tomato, caused by Phytophthora infestans, is a major threat to tomato
production in California. Using bands in the range of 0.7–0.9mm, these authors demonstrated
that late blight could be successfully detected in tomatoes at the field level.[16]

ECOLOGICAL MONITORING
Following on from the verification of the Photochemical Reflectance Index (PRI) for
whole canopies discussed above, studies have addressed the deficiencies of current
ecological monitoring systems to measure global carbon utilization.[4] Although current
models can accurately obtain data on overall light intensity in the appropriate range (400-700
nm) as well as the fraction of light being absorbed, they cannot obtain accurate data on light-
use efficiency. Without this third data-set, models of global carbon contain substantial
uncertainties which restrict their usefulness. The development of PRI, in combination with
hyperspectral imaging, provides a new methodology to obtain more accurate data on light-
use efficiency of whole-canopies on a global scale.
This methodology offers promise for monitoring large areas of agricultural land for
photosynthetic efficiency, which translates into land output and yield data of great value for
food production estimations.

NUTRIENT STRESS
Nutrient stress in plants causes various symptoms that may be measured by the use
of hyperspectral or multispectral imaging. Both deficiencies in nutrients and heavy metal
contamination of soils can be assessed with this technology. Schuerger et al (2002)
measured zinc deficiency and toxicity in Bahia grass by using a hyperspectral imager to
determine plant chlorophyll levels correlated with stress symptoms.[17]They state that the use
of this technology could map a contaminated site for a much lower cost than traditional direct
sampling methods. Similarly, mercury levels in mustard plants was assessed by Dunagan et
al (2006) and spectral reflectance values were significantly correlated with levels of the
contaminant.[18]
In addition to investigating contamination, another application of hyperspectral
imaging is to determine areas in a crop field that are nutrient poor so that fertilizer inputs
could be minimized and directly targeted to nutrient poor areas. Nitrogen and phosphorus
are the major yield limiting nutrients in midwestern U.S. field crops (non-leguminous).
Osborne et al. (2002) describes how hyperspectral imaging can be used to estimate nitrogen
and phosphorous concentrations, biomass and yield under these nutrient stresses. One
important finding of this study was that timing of the images was critical to making accurate
estimations of yield.[19]

ANALYSIS OF SOIL PROPERTIES

The analysis and mapping of soil characteristics is also possible with hyperspectral
and multispectral imaging. Maps of soil properties can improve precision agriculture
technologies and enhance capabilities. Researchers in Israel were able to determine soil
properties, even for soils under vegetation, with the use of hyperspectral sensors. Ben-Dor
et al (2000) mapped soil organic matter, moisture, and soil salinity in a field scale
experiment.[20] Rossel and Bratney (2008) accurately predicted soil organic carbon in a case
study in Australia[21], and soil salinity was mapped in several locations in Europe by Farifteh
et al. (2007)[22], both using hyperspectral imaging techniques.

CONCLUSIONS
The possibilities for these types of studies related to precision agriculture are virtually
endless as indexes for each species, nutrient or soil property continue to be developed and
improved. Studies have been conducted to estimate yield in corn by taking images during
the midgrain filling stage and developing yield maps.[23] And, Okamoto and Lee (2009)
demonstrated that immature fruits in orchards of oranges could be detected on individual
trees.[24] Assessment of chilling, heat or insect injuries in the field would be another use of this
technology in yield estimation. Currently, many other applications of hyperspectral and
multispectral imaging are being tested in: post-harvest quality control, grading, and sorting
of agricultural products, insect and contaminant detection, and numerous other uses in food
safety. Hyperspectral imaging delivered by lower-cost, portable devices that still deliver high-
quality accurate data has become a vital tool for researchers and farmers. The ability of these
devices to enhance and enable day-to-day monitoring promises to create a new paradigm of
agricultural efficiency.
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