Computers and Electronics in Agriculture 210 (2023) 107920

Contents lists available at ScienceDirect

Computers and Electronics in Agriculture

journal homepage: www.elsevier.com/locate/compag

Review

A review on the combination of deep learning techniques with proximal

hyperspectral images in agriculture
Jayme Garcia Arnal Barbedo
Embrapa Digital Agriculture, Campinas, SP, Brazil

ARTICLE INFO ABSTRACT

Keywords: Hyperspectral images can capture the spectral characteristics of surfaces and objects, providing a 2-D spacial
Electromagnetic spectrum component to the spectral profiles found in a given scene. There are several techniques that can be used to
Machine learning extract information from hyperspectral images, with deep learning becoming the preferred choice in the last
Convolutional neural network
decade due to its ability to implicitly extract features from images. The combination of hyperspectral images
with deep learning has been extensively explored in the context of remote sensing (data collected by drones
and satellites), which has generated an extensive literature that has been thoroughly analyzed in a series of
reviews and surveys. The application of deep learning to proximal hyperspectral images is more recent, but
there are already many articles dedicated to this objective, especially in the areas of agriculture and food
science. Although significant progress has been made in just a few years, there are still many aspects that are
not well understood and many problems that have not yet been overcome. This review aims at characterizing
the current state of the art of deep learning applied to hyperspectral images captured at close range, focusing
on the main challenges and research gaps that still need to be properly addressed. Some possible solutions
and potential directions for future research are suggested, as an effort to bring the techniques developed in
the academy closer to meeting the requirements found in practice. Only applications related to vegetable
production and products were considered in this review, because applications related to animal farming and
products of animal origin have their own particularities and the literature on the subject is not as extensive.

1. Introduction Hyperspectral imaging systems extend the capabilities of spectrom-

The automation of processes in agriculture is a long-sought goal.
Currently, the decision-making process in farms is heavily reliant on
human observations and inputs. While human experience and intuition
are very valuable when decisions have to be made, the data and
information that support those decisions should be as objective as
possible. This is particularly true in the case of visual inspections,
because as remarkable as the human sight is, it is also prone to optical
and psychological phenomena that can skew perception and, as a result,
produce unreliable observations (Bock et al., 2010; Barbedo, 2018;
Pandey et al., 2021). This has motivated the search for image-based
techniques for automation of agriculture processes (Xiao et al., 2022).
As imaging technologies evolved and techniques for image processing
and analysis became more successful, the number of studies dedicated
to the subject grew sharply (Bock et al., 2020). While most studies
employ conventional RGB (red–green–blue) images, more sophisticated
sensors are being increasingly used, among which hyperspectral imag-
ing systems have been particularly successful (Nguyen et al., 2021).
Fig. 1 illustrates the difference between RGB and hyperspectral images
in terms of their typical electromagnetic spectrum.
eters by capturing the spectral profiles of whole areas instead of single
points. This makes it possible to analyze surfaces or objects of interest
as a whole, thus providing a more complete characterization about the
absorption and reflection bands associated to those objects and condi-
tions to which they are subjected at that particular moment. Remote
sensing applications employing hyperspectral images (HSI) captured
by satellites and drones have been particularly successful, spawning
a large number of methods that can effectively extract the wealth of
information contained in those images (Lu et al., 2020). This is in large
part due to the availability of datasets such as Indian Pines, Salinas and
University of Pavia datasets (Makantasis et al., 2015), which have been
widely used in remote sensing (Paoletti et al., 2019).
Proximal hyperspectral images, which are captured in close prox-
imity to the objects of interest, are particularly useful for applications
related to agriculture and food science (Lu et al., 2020). As in the
case of remote sensing, research activity on this subject has been
steadily growing, but at a slower pace (Wendel et al., 2018). The most
likely reason for this is the lack of datasets available for research,
which means that any new research will require the collection of data

E-mail address: jayme.barbedo@embrapa.br.

https://doi.org/10.1016/j.compag.2023.107920
Received 19 December 2022; Received in revised form 14 April 2023; Accepted 7 May 2023
Available online 16 May 2023
0168-1699/© 2023 Elsevier B.V. All rights reserved.
J.G.A. Barbedo
Fig. 1. Electromagnetic spectrum range of RGB and hyperspectral images (Bock et al., 2020). RGB images encode the visible range into 3 color channels, while hyperspectral
images can have several hundred wavebands.
suitable for its specific objectives. It is worth pointing out that the
range of applications for hyperspectral images in agriculture is rather
extensive, so even if there were some datasets available, they would
likely only cover a small part of the data needs. The main challenge
with collecting new hyperspectral images is probably the relatively high
cost of the equipment. However, as the technology evolves and prices
fall, hyperspectral imaging systems tend to become more accessible.
This is a major reason for the growing number of articles observed in
the last few years (Brugger et al., 2021).
Another reason for the proliferation of new methods exploring hy-
perspectral images is the evolution of techniques to extract information
from the raw data. While some success has been achieved by methods
employing empirical approaches (Barbedo et al., 2015, 2017) and con-
ventional machine learning (Ang and Seng, 2021), deep learning mod-
els have quickly become prevalent (Wang et al., 2021). The inception of
deep learning techniques in the early 2010 decade has had a profound
effect on the way digital images are analyzed (Barbedo, 2022a). This
type of technique can recognize patterns and capture spatial relation-
ships without the need for handcrafted features. Deep learning has been
remarkably successful in classification, object recognition and semantic
segmentation tasks using the information contained in RGB images. In
the case of hyperspectral images, usually there are hundreds of spectral
bands, instead of the three color channels found in RGB images (Bock
et al., 2020). Exploring the wealth of information contained in such
a detailed spectral characterization is not as straightforward, usually
requiring either new types of network architectures (Yang, 2022) or
the inclusion of processing steps that are not found in the case of RGB
images.
Despite the growing number of studies investigating the use of
hyperspectral images to deal with problems relevant to agriculture,
there are still many challenges without a suitable solution and research
gaps to be addressed (Rangarajan et al., 2022). This is particularly
true in the case of deep learning, because this type of technique,
although powerful, has many subtleties and particularities that, if not
properly addressed, may lead to sub-optimal models and unreliable
results. In this context, the objectives of this review are threefold: (1)
characterize the current state of the art, with emphasis on the main
challenges reported in the literature; (2) identify major research gaps
and methodological flaws that can potentially prevent the proposed
methods to be applied under real conditions; (3) propose some solutions
and directions for future research. It is important to emphasize that
the objective is not to provide technical details about every work
mentioned in the article, but to identify general trends and common
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Computers and Electronics in Agriculture 210 (2023) 107920
issues that are relevant to this field of research as a whole. Further
information about aspects of hyperspectral imaging in agriculture that
are only briefly addressed in this article can be found in other reviews
(Table 1).
2. Definitions and acronyms
Some terms deemed of particular importance in the context of this
work are defined in this section. Most of the definitions are adapted
from Bock et al. (2022) and Barbedo (2022b). A list of acronyms used
in this article with the respective meanings is given in Table 2.
Artificial intelligence: a computational data-driven approach capa-
ble of performing tasks that normally require human intelligence to
independently detect, track, or classify fish.
Convolutional neural network: the most common class of deep neural
networks used in deep learning; this type of architecture is often a
regularized version of multilayer perceptrons, thus being more robust
to overfitting.
Cross-validation: a technique often used to assess the generalization
capability of a model. In k-fold cross-validation, a given dataset is
divided into k subsets, from which one is retained for testing and the
remainder k-1 subsets are used for training. The process is repeated k
times (folds), always using a different subset for testing.
Deep learning : a special case of machine learning that utilizes ar-
tificial neural networks with many layers of processing to implicitly
extract features from the data and recognize patterns of interest. Deep
learning is appropriate for large datasets with complex features and
where there are unknown relationships within the data.
Feature: measurement of a specific property of a data sample. It can
be a color, texture, shape, reflectance intensity, index values, or spatial
information.
Hyperspectral imaging : the process of using a spectral imaging sensor
to collect and process reflectance information from the electromagnetic
spectrum to obtain a spectral signature of each pixel in the image of
the object of interest. Hyperspectral imaging typically assesses several
hundred narrow wavebands extending beyond the visible spectrum.
Image augmentation: process of applying different image processing
techniques to alter existing images in order to create more data for
training the model.
Imaging : use of sensors capable of capturing images in a certain
range of the electromagnetic spectrum. Imaging sensors include RGB
(red–green–blue), multispectral, hyperspectral and thermal images.
Machine learning : application of artificial intelligence (AI) algo-
rithms that underpin the ability to learn characteristics of fish via
J.G.A. Barbedo Computers and Electronics in Agriculture 210 (2023) 107920

Table 1
Review and survey articles dealing with hyperspectral imaging in agriculture.
Reference
Ang and Seng (2021)
Golhani et al. (2018)
Khan et al. (2022)
Lowe et al. (2017)
Lu et al. (2020)
Mishra et al. (2020)
Sarić et al. (2022)
Sethy et al. (2022)
Su (2020)
Thomas et al. (2018)
Wan et al. (2022)
Wang et al. (2021)
Wang et al. (2022)
Wieme et al. (2022)
Theme
Machine learning applied to HSI in agriculture
Neural networks and HSI for plant disease recognition
Machine and deep learning with HSI for agriculture applications
Detection and classification of plant stresses using HSI
Applications of HSI in agriculture
HSI for plant phenotyping
Applications of HSI in plant phenotyping
HSI applications for precision agriculture
Machine Learning and digital images for crop/weed discrimination
HSI for plant disease detection
Hyperspectral Sensing of Plant Diseases
Deep learning with HSI for agriculture applications
Deep learning in multiscale agricultural sensing
HSI and artificial intelligence for quality assessment of fruit

Table 2
Acronyms used in this review.
Acronym Meaning Acronym Meaning
AI Artificial Intelligence RBF Radial Basis Function
CAE Convolutional Autoencoder RCNN Recursive CNN
CNN Convolutional Neural Networks RF Random Forest
DBN Deep Belief Network SACNN Symmetric All CNN
DNN Deep Neural Network SAE Stacked Autoencoder
GAN Generative Adversarial Net SAN Self-Attention Networks
LSSVM Least Squares SVM SCNN Shallow CNN
LSTM Long Short Term Memory SSAE Stacked Sparse Autoencoder
NN Neural Network SSD Single Shot Detector
PCA Principal Component Analysis SVM Support Vector Machine
PCNN Point-Centered CNN TCN Temporal Convolutional Network
PLS Partial Least Squares WT Wavelet Transform

extraction of features from a large dataset. Machine learning models are
often based on knowledge obtained from annotated training data. Once
the model is developed, it can be used to predict the desired output on
test data or unknown images.
Mathematical morphology: this type of technique, usually applied to
binary images, can simplify image data, eliminating irrelevant struc-
tures while retaining the basic shapes of the objects. All morphological
operations are based on two basic operators, dilation and erosion.
Model: a representation of what a machine learning program has
learned from the data.
Overfitting : when a model closely predicts the training data but fails
to fit testing data.
Proximal sensing : optical information obtained at relatively close
distances.
Reflectance: the proportion of the incident light in the electromag-
netic spectrum reflected by an object per wave band.
Remote sensing : optical information of an object obtained in the
field or landscape, in a noninvasive manner, without contact with the
sampling units using a sensor.
Segmentation: the process of partitioning a digital image containing
the objects of interest (fish) into multiple segments of similarity or
classes (based on sets of pixels with common characteristics of hue,
saturation, and intensity) either automatically or manually. In the latter
case, the human-powered task is also called image annotation in the
context of training AI algorithms. When performed at the pixel level,
the process is referred to as semantic segmentation.
Semi-supervised learning : a combination of supervised and unsuper-
vised learning in which a small portion of the data is used for a first
supervised training, and the remainder of the process is carried out with
unlabeled data.
Supervised learning : a machine learning model, based on a known la-
beled training dataset that is able to predict a class label (classification)
or numeric value (regression) for new unknown data.
Unsupervised learning : machine learning that finds patterns in unla-
beled data.
3. Literature review
The search for articles was carried out in November 2022 on Scopus
and Google Scholar, as both encompass virtually all relevant bibli-
ographic databases. Two sets of terms were used. The first, more
specific, employed the terms ‘‘hyperspectral’’, ‘‘deep learning’’ and
‘‘agriculture’’. In order to check for articles that were missed in the first
search, a second more general set of terms (‘‘hyperspectral’’, ‘‘image’’
and ‘‘deep learning’’) was also employed. Lastly, the reference lists of a
few selected review articles were also peered. Only articles published in
peer-reviewed journals were retained. A single highly relevant confer-
ence article was included. Studies dealing with industrialized food and
with products of animal origin were removed as those possess specific
characteristics that would broaden too much the scope of this review.
The selected articles were divided into nine groups according to
their main application. Since there is no standardized classification, this
division is rather arbitrary, and some groups are related. For example,
the detection of Fusarium Head Blight (FHB) in kernels falls into the
stress detection/quantification group, but the presence of this disease
is also associated with the presence of toxins and with degraded product
quality. The group division adopted in this work had as main objective
to provide a quick way to visualize the current research trends and
should not be taken as definitive. Although there are many different
applications for hyperspectral images and deep learning in agriculture,
four are clearly the most explored: stress detection and quantification
(30 articles), product quality (28), distinction between product varieties
(21), and detection/quantification of impurities and contaminants (18).
This section is organized into two subsections. The first subsection
addresses characteristics and challenges that are intrinsic to each type
of application. The second subsection is dedicated to aspects that are
intrinsic to the use of hyperspectral images and deep learning, being
common to all applications.
3.1. Characteristics and challenges intrinsic to each type of application
This section contains several tables revealing some technical details
about the articles considered in this article. In order to keep the tables

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J.G.A. Barbedo Computers and Electronics in Agriculture 210 (2023) 107920

Table 3
Articles dealing with stress detection and quantification.
Reference DL model Application Accuracy Band (nm)
Brugger et al. (2021) SAN (1D) Disease detection in barley leaves (B) 0.89–0.911 262–500
Chu et al. (2022) SCNN-ATT (1D) Identification of herbicide stress (M) 0.80–0.961 400–1000
Cui et al. (2022a) CNN (1D,3D) Early detection of apple valsa canker (B) 0.981,2 400–1000
Fazari et al. (2021) CNN (3D) Detection of anthracnose in olives (B) 0.92–0.951,2 450–1050
Feng et al. (2020) CNN (3D) Salt-stress phenotyping (Q) 0.59–0.943,4 380–1030
Gao et al. (2021) CNN (3D) Heat stress detection (B) 0.94–0.971,2 600–1700
Gui et al. (2021) CNN-SVM (1D) Severity estimation of soybean mosaic disease (M) 0.941 383.7–1032.7
Jin et al. (2018) DCRNN (1D) Fusarium Head Blight detection in wheat∗ (B) 0.751,2 400–1000
Liang et al. (2021) DNN (1D) Detection and classification of rice leaf folder (B) 0.981 380–1030
Nagasubramanian et al. (2019) CNN (3D) Plant disease identification (B) 0.87–0.961,2 400–1000
Nguyen et al. (2021) CNN (2D,3D) Disease detection in grapevines∗ (B) 0.71–0.971 400–1000
Pandey et al. (2021) Faster RCNN, DeepLabv3+ (1D) Detection of fusiform rust disease in pine (B) 0.62–0.831 400–1000
Park et al. (2018) CNN + FCN (3D) Disease severity in apple leaves (M) 0.851 356–1018
Polder et al. (2019) FCN (3D) Virus Y detection in potatoes∗ (B) 0.78–0.885,6 400–1000
Qi et al. (2021) CNN (2D,3D) Detection of potato late blight∗ (M) 0.791 N/A
Rangarajan et al. (2022) CNN (1D) Detection of FHB in wheat kernels (B) 1.001,2 400–750
Rehman et al. (2020) 1D CNN (1D) Relative water content of maize plants (Q) 0.877 370–1030
Wang et al. (2019) GAN (1D) Early detection of tomato spotted wilt virus (B) 0.961 400–1000
Weng et al. (2021) Residual attention CNN (3D) Detection of FHB in wheat kernels (B) 0.981 374–1030
Xiao et al. (2022) CNN (3D) Pest identification (B) 0.991 400–1000
Yang et al. (2019) CNN (1D) Estimation of plant cold damage levels (Q) 0.824 450–885
Yang (2022) CNN (3D) Disorder recognition in plant leaves (M) 0.952 400–1000
Yipeng et al. (2022) Self-search deep net (3D) Detection of FHB in wheat kernels (M) 0.981 374-1030
Zhang et al. (2020b) Deep forests (1D) Identification of frost-damaged rice seeds (B) 0.995,6 866.4-1701.0
Zhang et al. (2020e) CNN (1D) Identification of blight resistant rice seeds (M) 0.912 975.0–1645.8
Zhang et al. (2020a) CNN (3D) Detection of FHB in wheat kernels (Q) 0.977 400–1000
Zhang et al. (2021b) CNN (1D) Detection of freezing damage in corn seeds (M) 0.97-1.001 400-1000
Zhang et al. (2022b) CNN (1D) Identification of blight resistant rice seeds (B,M) 0.89–0.921 413–1016
Zhao et al. (2021) Inception-v3, VGG-16 (1D) Detection of cotton waterlogging stress (M) 0.971 450–950
Zhu et al. (2022a) CNN (3D) Nitrogen stress quantification in rice (M) 0.991 400–1000

In the ‘‘Application’’ column, the asterisks indicate that the images were collected in the field (all others were collected in controlled environments), while the
letters B, M and Q indicate binary classification, multi-class classification and quantification problems, respectively. In the ‘‘Accuracy’’ column, the specific metrics
adopted are given by the following superscript numbers: ‘‘1’’ is the percentage of correctly classified samples; ‘‘2’’ is the F1-score; ‘‘3’’ is the Intersection over
union (IoU); ‘‘4’’ is the Correlation coefficient (r); ‘‘5’’ is the Precision; ‘‘6’’ is the Recall; ‘‘7’’ is the Coefficient of determination (r2 ).

concise, some information is presented in an abbreviated manner, as
detailed in the captions. All values in the ‘‘Accuracy’’ column were
obtained on the test sets, and not on the validation or training sets.
3.1.1. Stress detection and quantification
Stress detection and quantification are very important to support
decisions and farm management. Thus, it is no surprise that this is
among the most common applications for hyperspectral images in agri-
culture. Both biotic (e.g. diseases and pests) and abiotic (e.g. drought
and herbicides) stresses are commonly tackled (Table 3). Hyperspectral
images are particularly useful for assessing specific changes in plant
reflectance patterns, which can be associated with physiological pro-
cesses (Brugger et al., 2021). More importantly, hyperspectral images
have the potential to enable stress detection before they produce visible
symptoms (Chu et al., 2022; Fazari et al., 2021; Liang et al., 2021;
Nguyen et al., 2021). Technologies offering accurate early stress de-
tection can arguably be the most impactful in agriculture, as they can
avoid losses, reduce the use of chemicals and increase yield (Liang
et al., 2021). Hyperspectral images can also be a suitable replacement
for expensive and time consuming laboratorial analysis (Gui et al.,
2021; Wang et al., 2019; Zhang et al., 2021a; Zhu et al., 2022a), being
particularly useful for timely detection of diseases and contaminants
in seeds (Wang et al., 2021). High-throughput phenotyping for quick
assessment of stress resistance across several samples is another com-
mon application for hyperspectral images (Pandey et al., 2021; Rehman
et al., 2020; Yang, 2022; Zhang et al., 2022b).
The detection of stress-related damage in products (especially
grains) after harvest is usually done under controlled conditions us-
ing fixed equipment with dedicated illumination. Early detection of
stresses, particularly diseases, is more useful in the field, but most
research on the subject is still carried out under laboratory conditions,
with only a few exceptions (Nguyen et al., 2021; Polder et al., 2019;
Qi et al., 2021). This is probably due to the difficulties caused by
uncontrolled conditions (especially varying illumination and angle of
insolation), and also because fixed setups have a longer history of
success (Sethy et al., 2022). However, the technology of portable
hyperspectral cameras is evolving fast, so it is reasonable to expect
more research employing this type of equipment in the near future.
Most research on stress detection focus on discriminating between
healthy samples and those affected with the stress of interest. Under
a controlled experimental setup, it is possible to guarantee that the
samples will never be affected by other factors, but under real condi-
tions different stresses (diseases, pests, drought, nutrition problem, etc.)
may be present, sometimes simultaneously. Discriminating between
different stresses based on their spectral profiles is difficult, not only
because it is challenging to design and carry out experiments dedicated
to this objective, but also because most stresses tend to manifest more
strongly in the water absorption bands (especially 1450 nm) (Barbedo
et al., 2017). As a result, unless there is some ancillary data to help nar-
row down the possible answers (e.g. meteorological data and weather
reports), it is unlikely that hyperspectral images can be used to discrim-
inate between stresses. It is worth pointing out, however, that even a
simple warning indicating that something is wrong can by itself be very
useful, but the goal of specifying the problem will likely continue to be
pursued in the future.
The automatic detection of stresses is highly dependent on their
severity. When severity is high, even crude methods are able to detect
the problem. On the other hand, when the stress onset is recent,
signs and symptoms (visible or not) tend to be slight and difficult to
detect. Since stress detection should ideally occur as early as possible,
determining the sensitivity of the models (and equipment) and the
earliest moment in which the stress can be detected is essential to assess
the potential impact of the technology being developed. Although most
studies investigate and report results on the matter (Brugger et al.,
2021; Chu et al., 2022; Fazari et al., 2021; Gui et al., 2021; Liang et al.,
2021; Nguyen et al., 2021; Pandey et al., 2021; Wang et al., 2019),

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J.G.A. Barbedo Computers and Electronics in Agriculture 210 (2023) 107920

Table 4
Articles dealing with product quality.
Reference DL model Application Accuracy Band (nm)
Chen et al. (2021a) RBF-PLS (1D) Determination of pomelo fruit quality (Q) 0.90–0.924 1000–2500
Chen et al. (2022a) CNN (2D,3D) Defect detection of green coffee beans (M) 0.981 660–980
Chen et al. (2022b) CNN (1D) Sugar content in apples (Q) N/A 400–1700
Feng et al. (2019) CNN (1D) Bruises on detection on winter jujube (B) 0.90–1.001 380–1030
Gomes et al. (2021) CNN (1D) Prediction of sugar and pH levels in grapes (Q) 0.66–0.957 N/A
Han et al. (2021) CNN (3D) Quality estimation of nuts (M) 0.90–0.961 388.9–1005.3
He et al. (2021b) CNN (1D) Estimation of micro-components in flowers (Q) 0.60–0.937 874–1734
Jie et al. (2020) CNN (1D) Determination of granulation in citrus (B) 0.851 400–1000
Li et al. (2022) CNN (1D) Prediction of soluble solid content in jujubes (Q) 0.867 1000–2500
Liu et al. (2022b) Autoencoder (1D) Anomaly detection in strawberries (M) 0.76–0.912,8 885–1733
Mesa and Chiang (2021) CNN (3D) Banana quality grading (B,M) 0.981 1000–2500
Ni et al. (2020) SAE (1D) Mulch film sorting on cotton (M) 0.951 1000–2500
Pang et al. (2022) YOLOv3 (3D) Bruise detection on apples (B) 1.002 930–2548
Raghavendra et al. (2022) CNN (3D) Banana quality grading (M) 0.991 1000–2500
Su et al. (2021) CNN (1D,3D) Quality evaluation of strawberries (M,Q) 0.55–0.841,7 380–1030
Wang et al. (2018) CNN (3D) Detection of internal damage in blueberries (B) 0.882 328.8–1113.5
Xiang et al. (2022) CNN (1D) Estimation of soluble solids content and firmness of tomatoes (Q) 0.977 400–1000
Xu et al. (2022) SAE-PLS, LSSVM (1D) Prediction of firmness and pH in grapes (Q) 0.90–0.927 400.7–1001.6
Yan et al. (2021) DNN (3D) Phenolic-level prediction of barley malt (M) 0.991 950–1760
Yang et al. (2020b) SAE-RF (1D) Estimation of soluble solid content in peach (Q) 0.927 908.1–1735.6
Zhang et al. (2020d) CNN (1D) Chemical composition of black goji berries (Q) 0.84–0.902 874–1734
Zhang et al. (2020c) Deep forests (1D) Identification of sprouted wheat kernels (B) 0.87–0.901 866.4–1701.0
Zhang et al. (2022a) Attention-Based CNN (1D) Prediction of oil content in maize kernels (Q) 0.927 866.4–1701.0
Zhang et al. (2022d) Convolutional GAN (1D) Prediction of oil content in maize kernels (Q) 0.73–0.907 866.4–1701.0
Zhang et al. (2022e) CNN, LSTM (1D) Moisture detection in corn seeds (Q) 0.91–0.984 968–2575
Zhao et al. (2020) CNN (3D) Hyperspectral images built from RGB images (Q) 0.51–0.927 397–1003
Zheng et al. (2022) SACNN (3D) Detection of adulteration in wheat flour (M) 0.92–0.981 380–1030
Zhu et al. (2023) CNN (2D,3D,mixed) Identification of sprouted wheat kernels (B) 0.96–0.981 866.4–1701

In the ‘‘Application’’ column, the letters B, M and Q indicate binary classification, multi-class classification and quantification problems, respectively. In the ‘‘Accuracy’’
column, the specific metrics adopted are given by the following superscript numbers: ‘‘1’’ is the percentage of correctly classified samples; ‘‘2’’ is the F1-score; ‘‘4’’ is the
Correlation coefficient (r); ‘‘7’’ is the Coefficient of determination (r2 ); ‘‘8’’ is the Area under the curve (AUC).

some fail to do so in a comprehensive manner. It is worth pointing out
that, depending on the problem being addressed and the objectives of
the study, a sensitivity analysis may not be applicable, so its absence is
not always indicative of a methodological flaw.
3.1.2. Product quality
Determining agricultural product quality is important not only to
guarantee that the expectations of potential consumers will be met, but
it is also essential for selecting the most appropriate batches for further
processing (for example, selecting the best grapes for wine production)
(Table 3). Damaged products also tend to become more susceptible
to pathogen infections and other types of contamination (Wang et al.,
2018). The identification of damage and product sorting is usually done
manually and visually, in a process that tends to be time consuming
and error prone (Liu et al., 2022b; Zhang et al., 2020c; Zhu et al.,
2023). In many cases, factors that lead to low quality do not produce
visible effects, a fact that is usually addressed by means of expensive
and time consuming laboratory analyses (Han et al., 2021; He et al.,
2021b; Li et al., 2022; Zheng et al., 2022), for which, under certain
conditions, hyperspectral images may be a cost- and time-effective
alternative (Chen et al., 2022a).
One of the main applications for models capable of determining the
quality of products is real-time product sorting. In this case, latency,
which is the time the whole system takes to complete the action,
needs to be very low. Deep learning is usually seen as a computing
intensive technique, and while this is certainly true for the training
process, trained models can be lightweight and run even in devices
with limited computational resources (Barbedo, 2022b). Other delaying
factors should also be taken into account, particularly the time needed
for the hardware to respond and perform the proper action. Even with
these difficulties, there is evidence that real-time equipment are indeed
viable (Chen et al., 2022a).
Quality indicators can be highly dependent on the variety and even
vintage of the agricultural product (Su et al., 2021). This can make it
difficult to develop models that adapt well to samples with character-
istics that deviate only mildly from those found in the samples used
for training the model (Gomes et al., 2021). This problem is difficult
to address, because including samples from varieties with different
characteristics may actually cause the model to converge to a sub-
optimal point instead of improving its generalization capabilities (Raviv
et al., 2022). Although some strategies and techniques can partially
compensate for those difficulties (Gomes et al., 2021), in most cases
it may be more productive to create dedicated models that fit better
the specific characteristics of individual varieties (Zhang et al., 2022a).
Another important factor to consider when detecting damage and
defects is that their sources and visual characteristics can vary consid-
erably. The variability associated to the problem may be such that it
becomes unfeasible to generate training datasets covering the whole
range of possibilities. One way to deal with this problem is to employ
semi-supervised methods capable of correctly interpret different types
of damage without specific training (Liu et al., 2022b). Although some
success has been achieved in this study, more research is needed to
better understand how semi-supervised and unsupervised learning can
be applied to hyperspectral images (Section 3.2).
The positioning of fruits and seeds can have a strong impact on the
detectability and measurement of the factors that are relevant to the
product’s quality (Li et al., 2022; Zhang et al., 2022a). However, in a
practical setup, it can be difficult to guarantee that all samples will be
ideally positioned, especially if real-time operation is required (Zhang
et al., 2020c). This motivated some studies to either capture multiple
images of the same objects arranged in different positions (Zhang et al.,
2020c, 2022c), or capture images with the sample container positioned
at multiple different angles, with all data cubes being concatenated
afterwards (Yan et al., 2021). Regardless of the feasibility of enforcing
sample positions and capturing multiple angles, it is important to inves-
tigate the impact of this factor and how this can affect the reliability
of the model.
3.1.3. Distinction of product varieties
Different varieties of a given product can have different properties
that are more or less suitable to different uses (Qiu et al., 2018; Wu
et al., 2018; Zhang et al., 2020f). Thus, mixing up varieties may lead

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Table 5
Articles dealing with distinction of product varieties.
Reference DL model Application Accuracy Band (nm)
Cui et al. (2022b) MobileNetV2 + SVM (3D) Tea type classification (M) 0.99 908–1735
Fu et al. (2022a) SSAE (1D) Identification of maize seed varieties (M) 0.96 871.6–1766.3
Jin et al. (2022b) CNN (1D) Identification of rice seed varieties (M) 0.86 900–1700
Kabir et al. (2022) VGGNet (CNN) (1D) Discrimination of tea varieties (M) 0.89 874–1734
Li et al. (2021b) 1D CNN (1D) Identification of soybean varieties (M) 0.95 866.4–1701.0
Nie et al. (2019) CNN (1D) Classification of hybrid rice seeds (M) 0.95 975–1648
Onmankhong et al. (2022) CNN (1D) Classification of rice varieties (M) 0.95 1002–1998
Qiu et al. (2018) CNN (1D) Variety identification of rice seeds (M) 0.87 380–1734
Weng et al. (2020) PCA network (3D) Determination of rice variety (M) 0.98 400–1000
Wu et al. (2018) CNN (1D) Discrimination of Chrysanthemum varieties (M) 1.00 874–1734
Wu et al. (2019) CNN (1D) Variety identification of oat seeds (M) 0.99 874–1734
Wu et al. (2021) CNN (1D) Variety classification of crop seeds (M) 0.99 874–1734
Yu et al. (2021) SSAE, CNN (1D) Hybrid okra seed identification (M) 0.94–0.98 948.2–1649.2
Zhang et al. (2020f) CNN, RCNN, LSTM (1D) Variety identification of coated maize kernels (M) 0.90 874–1734
Zhang et al. (2021a) CNN (1D) Corn seed variety classification (M) 0.93 450–979
Zhang et al. (2022c) CAE (1D) Identification of maize seed varieties (M) 1.00 382.2–1026.7
Zhao et al. (2022) 1D CNN (1D) Classification wheat seed varieties (M) 0.96 400–1000
Zhou et al. (2021) CNN (1D) Identification of maize seed varieties (M) 0.93–0.98 326.7–1098.1
Zhu et al. (2019a) CNN (1D) Identification of cotton seed varieties (M) 0.88–0.94 942–1646
Zhu et al. (2019b) CNN (1D) Identification of soybean seed varieties (M) 0.90 874–1734
Zhu et al. (2020) Several CNN Models (1D) Identification of soybean seed varieties (M) 0.91–0.97 400–1000

In the ‘‘Application’’ column, the letters B, M and Q indicate binary classification, multi-class classification and quantification problems, respectively. All values in
the ‘‘Accuracy’’ column represent the percentage of correctly classified samples.

to quality and economic loss (Onmankhong et al., 2022). In addi-
tion, it is necessary to devise effective screening methods in order to
avoid fraud (Jin et al., 2022b; Zhang et al., 2022c). Currently, variety
discrimination is largely done by physical and chemical laboratory
analysis, which are usually expensive, time consuming (Cui et al.,
2022b; Fu et al., 2022a; Onmankhong et al., 2022; Wu et al., 2018; Zhu
et al., 2019b) and have many other shortcomings that cannot be easily
addressed (Li et al., 2021b; Wu et al., 2019). Since in most cases the
visible differences between varieties are too minute for visual inspec-
tion or for RGB images to be applicable (Li et al., 2021b; Onmankhong
et al., 2022), hyperspectral images appear as a potential alternative.
Most of the research on the combination of hyperspectral images with
deep learning is dedicated to grains, especially rice, soybean and maize
(Table 4).
Classifying seeds and crops by variety is among the most chal-
lenging problems, because differences that enable discrimination often
are minute, even at the chemical level (Cui et al., 2022b; Fu et al.,
2022a; Jin et al., 2022b). The problem becomes even more challeng-
ing when the number of possible varieties is high (Yu et al., 2021).
Combining hyperspectral images with deep learning has led to some
success, with accuracies near 100% being quite common (Table 5).
However, experiments are normally carried out under ideal conditions,
so achieving a similar degree of success under real world conditions is
not straightforward (Kabir et al., 2022).
The characteristics of the problems and the approaches adopted
in the studies shown in Table 5 are for the most part similar. This
makes variety identification a prime candidate for the application of
transfer learning. Instead of training models from scratch, transfer
learning makes it possible to reuse models trained on different data
by exploring the idea that basic information extracted by the network
is common to many classification problems. This technique has been
widely applied in computer vision, but have rarely been applied in
the context of spectral analysis. Wu et al. (2021) trained the original
model on a large dataset containing pea varieties, and used this as the
basis to train models for rice, oat, wheat, and cotton. The technique
showed promise, especially with small and limited datasets, but more
investigation is needed to realize the full potential of transfer learning
applied to hyperspectral images. Transfer learning was also employed
by Zhu et al. (2020) for classification of soybean varieties.
3.1.4. Detection and quantification of impurities and contaminants
Impurities and contaminants can not only reduce the quality of final
products, but can also represent a significant health hazard (Feng et al.,
2022; Han and Gao, 2019; Seo et al., 2021; Sun et al., 2019, 2021; Yang
et al., 2022; Ye et al., 2022; Zhou et al., 2022; Zhu et al., 2022b). Visual
screening is sometimes possible, but in many cases this requires trained
personnel, and the subjectivity of the detection may cause the process
to become unreliable (Agarwal et al., 2020). Thus, proper screening
for harmful objects and substances often requires laboratorial analysis,
which can be time consuming and expensive (Mansuri et al., 2022; Sun
et al., 2019; Yang et al., 2022; Zhou et al., 2020a). In this context,
hyperspectral images arise as a potential high throughput alternative
for detecting insects (Agarwal et al., 2020), heavy metals (Sun et al.,
2019, 2021; Xin et al., 2020; Zhou et al., 2020a,b, 2022), toxins (Han
and Gao, 2019; Zhu et al., 2022b), pesticides (He et al., 2021a; Jiang
et al., 2019; Ye et al., 2022), mold (Liu et al., 2020; Mansuri et al.,
2022; Yang et al., 2022; Yuan et al., 2022), among others (Table 6).
Most countries have legal limits for the amount of each type of
impurity and contaminant, and reliably determining if a given batch
comply with those limits is usually the most important objective of a
system employing hyperspectral images and deep learning (Agarwal
et al., 2020). Legal limits can be quite low, so one of the biggest
challenges in the detection of foreign objects and substances using
hyperspectral images is to determine if the method and equipment
being adopted are sensitive enough for that purpose (Ye et al., 2022).
The datasets used in the experiments should contain samples covering
a wide range of contamination levels in order to make it possible
to reliably determine the detection threshold. Most studies fulfill this
requirement, but there are a few cases in the literature that employ
datasets that are too limited for meaningful conclusions.
In the specific case of insect detection (whole body and fragments),
an additional challenge is to associate the foreign bodies to the re-
spective species. This is important because some species are more
harmful than other, either as a health hazard or as a biosecurity pest
threat (Agarwal et al., 2020). Although there are not many studies ded-
icated to this issue, results seem to indicate that current hyperspectral
imaging devices are not sensitive enough to allow for reliable species
identification, unless the objects of interest are carefully selected and
positioned (Agarwal et al., 2020).
The detection and recognition of toxins in kernels also have some
specific challenges. In controlled experiments, it is possible to guaran-
tee that the samples will only be affected by the contaminant of interest.
In the real world, however, other substances are likely to be present.
Those substances can have spectral profiles that are relatively similar
to those associated to the toxins, skewing the detection process (Han

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Table 6
Articles dealing with detection/quantification of impurities and contaminants.
Reference DL model Application Accuracy Band (nm)
Agarwal et al. (2020) CNN, Capsule Network (1D) Detection of insect fragments (M) 0.90–0.961 800–1000
Feng et al. (2022) CNN-LSTM (2D) Detection of foreign bodies in hickory nuts (M) 0.991 400–1000
Han and Gao (2019) CNN (1D) Aflatoxin detection in peanuts (B) 0.90–0.951 292–865
He et al. (2021a) 1D CNN (1D) Recognition of pesticide residues on leaves (M) 0.981 920–1700
Jiang et al. (2019) CNN (3D) Detection of pesticide residues in apple (B) 0.951 865.1–1711.7
Liu et al. (2020) CNN (1D) Detection of moldy peanut kernels (M) 0.94–0.991 400–1000
Mansuri et al. (2022) CNN (1D) Detection of mold in maize kernels (B) 0.971 398–1003
Seo et al. (2021) U-Net + CNN (1D) Detection of vegetable residues (M) 0.941 400–1000
Sun et al. (2019) DBN (1D) Cadmium content estimation in lettuce leaves (Q) 0.927 431–961
Sun et al. (2021) DBN (3D) Lead content estimation in lettuce leaves (M) 0.971 478–978
Xin et al. (2020) SAE (1D) Prediction of cadmium residue in lettuce (Q) 0.957 380–1030
Yang et al. (2022) SAE, CNN, SVM (1D) Detection of moldy maize kernels (M) 0.991 400-1000
Ye et al. (2022) CNN, ResNet (1D) Detection of pesticide residue grapes (M) 0.93–0.971 376–1044
Yuan et al. (2022) PCNN (3D) Detection of moldy peanuts (B) 0.981 960–2568
Zhou et al. (2020a) WT-SAE (1D) Prediction of lead content in lettuce (Q) 0.967 380–1030
Zhou et al. (2020b) SAE (1D) Detection of heavy metals in lettuce (Q) 0.947 400.7–1001.6
Zhou et al. (2022) WT-SAE (1D) Detection of lead in lettuce (Q) 0.95–0.987 480.5–1001.6
Zhu et al. (2022b) 1D-modified TCN (1D) Detection of aflatoxin B1 in peanuts (B) 0.991,2 415–799

In the ‘‘Application’’ column, the letters B, M and Q indicate binary classification, multi-class classification and quantification problems, respectively. In the ‘‘Accuracy’’
column, the specific metrics adopted are given by the following superscript numbers: ‘‘1’’ is the percentage of correctly classified samples; ‘‘2’’ is the F1-score; ‘‘7’’ is the
Coefficient of determination (r2 ).

Table 7
Articles dealing with determination of viability/vigor.
Reference DL model Application Accuracy Band (nm)
Jin et al. (2022a) CNN (1D) Viability and vigor of rice seeds (B) 0.851 900–1700
Ma et al. (2020) CNN (1D) Viability prediction of Japanese mustard spinach seeds (B) 0.901 1002–2300
Pang et al. (2020) CNN (1D,2D) Vitality Estimation of corn seeds (B) 0.90–0.991 370.2–1042.3
Pang et al. (2021) CNN, LSTM (1D,2D) Viability estimation of Sophora japonica (M) 0.991 370–1042
Wu et al. (2022) CNN (1D) Determination of rice seed vigor (M) 0.981,2 874–1734
Yang et al. (2020a) CNN (1D,3D) Determination of rice seed vigor (B) 0.991 873–1734

In the ‘‘Application’’ column, the letters B, M and Q indicate binary classification, multi-class classification and quantification problems, respectively. In the ‘‘Accuracy’’
column, the specific metrics adopted are given by the following superscript numbers: ‘‘1’’ is the percentage of correctly classified samples; ‘‘2’’ is the F1-score.

and Gao, 2019; Zhu et al., 2022b). This is a considerable barrier for
the practical application of the methods found in the literature. Another
challenge that can be difficult to address is the fact that toxin screening
is usually carried out on kernel batches, and not on individual seeds.
A given batch can exceed legal limits due to several kernels being
moderately contaminated, but also due to a single kernel having high
contamination levels (Han and Gao, 2019). Thus, it is not enough to
determine how many kernels are contaminated, it is also necessary to
quantify the toxin levels. Given the current sensitivity of hyperspectral
equipment, this is not easy to achieve (Barbedo et al., 2017).
3.1.5. Determination of viability and vigor
Determining viability and vigor of seeds prior to sowing is very
important to maximize germination and yield. Poor storage conditions,
high temperature, high humidity, or physical damage during mechan-
ical processing after harvest will cause the seeds to lose vitality (Jin
et al., 2022a; Pang et al., 2020). Most traditional methods for determin-
ing seed viability and vigor are destructive and time consuming (Ma
et al., 2020; Pang et al., 2020; Wu et al., 2022; Yang et al., 2020a),
and visual distinction is nearly impossible (Pang et al., 2021). The use
of hyperspectral images for this task has been showing some promise,
especially when combined with deep learning (Table 7).
A problem that is common to almost all the research employing hy-
perspectral images in agriculture is that experimental conditions often
depart significantly from those expected to be found in practice. In the
case of viability and vigor, many studies employ artificial accelerated
seed aging, as this strategy is faster and more controllable than natural
aging (Jin et al., 2022a). Although the conclusions reached using this
setup can still be relevant, the development of technologies suitable
for operation under real conditions depends on more realistic data (Ma
et al., 2020; Pang et al., 2021).
Another challenge that is not always properly addressed is the fact
the seeds (especially the small ones) tend to be very heterogeneous in
terms of their chemical properties, and significant variations can be
found even within the same seed samples (Ma et al., 2020). In many
cases, the spectrum is averaged over the entire batch and differences
between the samples are lost (Jin et al., 2022a; Pang et al., 2020; Wu
et al., 2022). Properly evaluating and exploring those variations is not
trivial though, and more research is needed for the development of
models capable of providing more sensitive estimations for vigor and
viability (Ma et al., 2020).
Different vigor and viability conditions generate spectral profiles
that can differ between crop varieties. Thus, in most cases it may be
necessary to generate specific models for each variety, and considering
that the number of varieties is usually high, the effort required both
in terms of data collection and model training can be too high. This is
an important obstacle for the development of commercial technologies.
One way to mitigate the effects of this spectral diversity is to employ
transfer learning to enable successful models to be retrained for other
varieties using a fraction of the data that would be needed in case of
training from scratch (Yang et al., 2020a).
3.1.6. Determination of geographic origin
Products that have a geographic indication associated usually have
significant added value based on their quality and reputation (Hao
et al., 2022; Wang et al., 2023). Also, the same plant species cultivated
in different regions can have different properties that can affect quality
and prices (Dong et al., 2022; Li et al., 2021a). Manual and visual
sorting is sometimes possible (Xiao et al., 2020), but their reliability
can be severely affected by the subjectivity of the process (Gao et al.,
2019). Thus, reliable confirmation of geographical usually involves
expensive and time consuming laboratorial analysis (Hao et al., 2022;
Li et al., 2021a), for which hyperspectral images have been shown to
be a suitable replacement (Table 8).
One important factor to be considered when using samples from dif-
ferent geographical areas is the fact that, unless portable hyperspectral

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Table 8
Articles dealing with determination of geographic origin.
Reference DL model Application Accuracy Band (nm)
Dong et al. (2022) CNN (2D) Geographic origin of wolfberries (M) 0.96–1.001 900–1700
Gao et al. (2019) CNN (1D) Geographic origin of fruits (M) 0.901 874–1734
Hao et al. (2022) CNN (2D) Geographic origin of wolfberries (M) 0.971,2 400–1000
Li et al. (2021a) CNN (1D) Geographic origin of nuts (M) 0.971 383.4–990.4
Wang et al. (2023) CNN + LSTM (1D) Geographic origin of Coix seeds (M,Q) 0.85–0.931,7 350–2550
Xiao et al. (2020) CNN (1D) Geographic origin of Radix Astragali (B) 0.981 380–1734

In the ‘‘Application’’ column, the letters B, M and Q indicate binary classification, multi-class classification and quantification problems, respectively. In the
‘‘Accuracy’’ column, the specific metrics adopted are given by the following superscript numbers: ‘‘1’’ is the percentage of correctly classified samples; ‘‘2’’
is the F1-score; ‘‘7’’ is the Coefficient of determination (r2 ).

Table 9
Articles dealing with determination of maturity.
Reference DL model Application Accuracy Band (nm)
Gao et al. (2020) CNN (3D) Estimation of strawberry ripeness∗ (B) 0.981 370–1015
Garillos-Manliguez and Chiang (2021) Several CNN models (3D) Papaya maturity estimation (M) 0.902 400–900
Su et al. (2021) CNN (1D,3D) Maturity evaluation of strawberries (M,Q) 0.55-0.841,7 380–1030
Wendel et al. (2018) CNN (1D) Maturity estimation of mangoes∗ (Q) 0.977 411.3–867.0

In the ‘‘Application’’ column, the asterisks indicate that the images were collected in the field (all others were collected in controlled environments), while the letters
B, M and Q indicate binary classification, multi-class classification and quantification problems, respectively. In the ‘‘Accuracy’’ column, the specific metrics adopted
are given by the following superscript numbers: ‘‘1’’ is the percentage of correctly classified samples; ‘‘2’’ is the F1-score; ‘‘7’’ is the Coefficient of determination (r2 ).

imaging devices are employed for in-site image acquisition, samples
need to be harvested, prepared and transported to the site where
imaging will take place. Inevitably, the samples collected in different
areas will be subjected to different storage and transportation durations
and conditions, which can potentially cause spectral changes (Karoui
and Blecker, 2011). Since samples collected in the same areas will likely
be subjected to the same conditions, the spectral correlation among
them can artificially increase. In turn, this will artificially increase the
separability between classes, artificially making the model’s task easier.
If post-harvest alterations are not properly considered, it may become
difficult to determine if the differences explored by the deep learning
model for the classification are indeed due to regional traits, or if the
classification is biased due to spectral alterations occurring during the
time between harvest and imaging. None of the studies mentioned in
Table 8 addressed this issue, but Wang et al. (2023) mentioned plans of
taking into accounting different storage conditions in future research.
3.1.7. Determination of maturity
The ripeness of fruits is arguably the most important factor that
drives the optimal moment for harvest and for trade. Hyperspectral
images have the potential to detect the minute spectral differences
of fruits at different maturity stages without the subjectivity involved
in visual inspections and the complexity of conventional laboratorial
analyses (Gao et al., 2020; Garillos-Manliguez and Chiang, 2021).
Hyperspectral images have been employed for maturity and ripeness
estimation at least since the early 2010 decade (Gao et al., 2020), but
only recently deep learning techniques were introduced to the problem
(Table 9).
Hyperspectral images can be applied to maturity determination
because the spectral characteristics of the fruits usually reflect the
different levels of ripeness. However, depending on the fruit being
considered, those spectral changes can be mild, making it difficult to
achieve a useful maturity classification. On the other hand, maturity
changes are often reflected on the visual characteristics of the fruit as
well, a fact that has been explored frequently in the literature (Li et al.,
2018). For this reason, some studies have adopted multimodal deep
learning architectures to fuse the information provided by hyperspec-
tral and RGB images, thus effectively exploring the complementarity
that may exist between them (Garillos-Manliguez and Chiang, 2021).
Fruit maturity estimation is important not only to determine the
optimal moment for harvest and the best storage and trade strategy,
but can also be explored by robotic platforms for automated selective
picking (Halstead et al., 2018). However, conditions in the field can
be difficult, particularly due to the wide range of possible illumination
conditions (Wendel et al., 2018). An additional difficulty that affects
all kinds of images is the possibility of occlusions due to nearby fruits,
leaves and other objects (Gao et al., 2020). Solving this problem may
require employing multiple sensors or other alternative strategies that
have yet to be investigated, at least in the context of hyperspectral
images.
Most of the methods found in the literature address the maturity
problem at the individual fruit level. As mentioned above, this can be
very useful for selective picking by robots, but such technology is not
yet mature enough for use in a wide scale (Wendel et al., 2018). Thus,
in real orchard and farms, for operational and cost reasons harvesting
may need to be done all at once, or at least over relatively large blocks.
Since maturity is usually not uniform across the entire area, optimizing
harvest timing or the selection of harvesting areas within orchards
is not a trivial task. According to Wendel et al. (2018), a suitable
solution for this problem could increase yield by reducing harvested
fruit at suboptimal maturity and minimizing mature fruit that drop
from trees prior to harvest. These authors have proposed a robotic
platform capable of mapping maturity at higher granularity levels, with
promising results.
3.1.8. Nutrition status
Optimal yield is highly dependent on a carefully balanced nutri-
tion, as both deficiency and excess of any given nutrient can cause
production to be sub-optimal. Timely monitoring of nutrition param-
eters throughout extensive fields is difficult, especially considering
that problems may take some time to manifest visually. Hyperspectral
images can potentially detect chemical alterations before symptoms
are visible, which has motivated their use for nutrition monitoring
using Unmanned Aerial Vehicles (UAVs). However, the relatively low
spatial resolution still limits the applicability of this approach (Chen
et al., 2021b). Portable hyperspectral imaging devices can be used to
capture images at close proximity to the plants, and can be installed
in machinery and robots to carry out the imaging autonomously (Chen
et al., 2021b). The number of studies adopting this approach is still
small, especially in combination with deep learning, and only Nitrogen
has been consistently studied (Table 10).
The exact same challenges discussed for stress detection applica-
tions are present in the case of nutrition status. First, although the
estimation of the nutrition status is more useful in the field (Chen
et al., 2021b; Yang et al., 2021), most research is carried out with hy-
perspectral images collected under laboratory conditions. Second, the
spectral alterations caused by nutrition issues can easily be emulated
by other factors, especially other stresses. This type of situation can

8
J.G.A. Barbedo
Table 10
Articles dealing with determination of nutrition status.
Reference DL model
Chen et al. (2021b) SSD CNN (3D)
Fu et al. (2022b) Modified SSAE (1D)
Sabzi et al. (2021) 1D CNN (1D)
Yang et al. (2021) CNN (3D)
Yu et al. (2018) SAE-FNN (1D)
In the ‘‘Application’’ column, the asterisks indicate that the images were collected in the field (all others were collected in controlled environments), while the
letters B, M and Q indicate binary classification, multi-class classification and quantification problems, respectively. In the ‘‘Accuracy’’ column, the specific metrics
adopted are given by the following superscript numbers: ‘‘4’’ is the correlation coefficient (r); ‘‘7’’ is the coefficient of determination (r2 ).
Table 11
Articles dealing with other applications.
Reference DL model
Abbas et al. (2021) 5-layer network (1D)
Diao et al. (2022) Lightweight-3D-CNN (3D)
Liu et al. (2021) GAN (1D)
Liu et al. (2022a) Complex-valued NN (1D)
Mishra et al. (2021) U-Net (2D)
Steinbrener et al. (2019) CNN (3D)
In the ‘‘Application’’ column, the asterisks indicate that the images were collected in the field (all others were collected in controlled environments), while the
letters B, M and Q indicate binary classification, multi-class classification and quantification problems, respectively. In the ‘‘Accuracy’’ column, the specific metrics
adopted are given by the following superscript numbers: ‘‘1’’ is the percentage of correctly classified samples; ‘‘3’’ is the Intersection over union (IoU).
be avoided in controlled experiments, but is mostly unavoidable under
real conditions. As a result, accurate estimates for the nutrition status
may only be possible with the use of ancillary data (Barbedo, 2019).
Third, investigating the sensitivity of the hyperspectral-based system is
important to determine how severe nutrition problems should become
before the system is able to detect them. Because the application of
proximal hyperspectral images and deep learning for assessment of
nutrition status is still in its infancy, these challenges (particularly the
latter two) have only been superficially addressed in the literature.
3.1.9. Other applications
There are a few other applications for which the combination of hy-
perspectral images and deep learning have been explored. The studies
in Table 11 can be roughly divided into two main groups, segmentation
of objects of interest and discrimination between different plant species.
One of the main objectives of the segmentation studies in Table 11 is
to enable harvest automation. As mentioned before, despite the remark-
able advancements achieved in agricultural robotics, more research is
needed to meet current practical demands. Liu et al. (2021) focused on
the objective of reducing costs by adapting a filter to an RGB sensor
in order to simulate the technical characteristics of a hyperspectral
device. Liu et al. (2022a) and Mishra et al. (2021) aimed at improving
the robustness to illumination variations by employing complex-valued
neural networks.
In the case of plant species recognition, one of the main challenges
is the seasonality of the spectral profiles, which may have strong varia-
tions over the year. As a result, the separability of the different classes
also vary, making it difficult to develop a single deep learning model
that is always valid, unless sophisticated multitemporal strategies are
employed (Abbas et al., 2021). Different growth stages also introduce
variability to the problem, increasing the challenge involved in the
task (Diao et al., 2022).
3.2. General aspects related to hyperspectral images and deep learning
3.2.1. Data reduction
Hyperspectral images provide a wealth of information encoded in
the spatial distribution of spectral characteristics of a given surface
or object. The downside is that large amounts of data need to be
stored and processed (Fazari et al., 2021), as the number of bands
can sometimes surpass 1000 (Table 12 ). In many cases, this can
overwhelm the available computational resources (Onmankhong et al.,
2022). Often, the bands that contain the information that is actually
Computers and Electronics in Agriculture 210 (2023) 107920
Application Accuracy Band (nm)
Nitrogen prediction in maize∗ (Q) 0.737 450–900
Determination of Zn content in rape leaves (Q) 0.967 431–962
Estimation of nitrogen content in cucumber (Q) 0.96–0.984 400–1000
Estimation of leaf nitrogen content in wheat∗ (Q) 0.867 360–1025
Prediction of nitrogen in oilseed rape (Q) 0.907 380–1030
Application Accuracy Band (nm)
Tree species classification∗ (M) 0.85–0.961 400–1000
Discrimination between corn and weeds∗ (B) 0.981 400–1000
Green pepper segmentation∗ (B) 0.911 400–1000
Green pepper segmentation∗ (B) 0.931 400–1000
Semantic segmentation of plants (B) 0.963 407–997
Fruit and vegetable classification (M) 0.921 470–630
relevant to the problem at hand are few (Brugger et al., 2021), so
most of the data can be discarded without loss of accuracy (He et al.,
2021b), and this redundancy removal can even increase the robustness
of the model (Zhang et al., 2020c; Onmankhong et al., 2022; Hao
et al., 2022). Narrowing down the bands of interest is among the most
common objectives found in the literature (Barbedo et al., 2017; Chu
et al., 2022; Liang et al., 2021; Park et al., 2018; Wang et al., 2019;
Zhang et al., 2020b; Chen et al., 2022a; Xu et al., 2022; Wu et al.,
2019; Zhang et al., 2020f; Yuan et al., 2022; Sabzi et al., 2021), being
important not only to reduce the computational burden, but it is also an
important step toward the development of portable and cost effective
equipment for potential practical use (Weng et al., 2021; Yipeng et al.,
2022; Zhang et al., 2020a; Gao et al., 2020). One way to do so is by
observing the typical spectral curves produced by the different classes,
and then identifying the wavelengths that provide the best distinction
among the classes. For example, if the classes of interest tend to present
significant differences in water content, the wavelength of 1450 nm
will certainly be of interest. The advantage of this approach is that
cheaper equipment dedicated only to the wavelengths of interest can
be developed. In addition, if exactly three wavelengths are selected,
standard deep learning architectures broadly used to process the three
channels of RGB images can now be directly applied, making the
training process more straightforward.
Another way to decrease the amount of data to be processed by the
models is by applying some kind of data reduction technique, among
which Principal Component Analysis (PCA) is by far the most widely
used (Rangarajan et al., 2022; Zhang et al., 2022e; Zhao et al., 2021;
Chen et al., 2022b; Han et al., 2021; Pang et al., 2022; Yan et al., 2021;
Kabir et al., 2022; Weng et al., 2020; Yu et al., 2021; Zhu et al., 2019a;
Pandey et al., 2021; Pang et al., 2020). This technique transforms
the original spectral bands into a few decorrelated components which
concentrate most of the relevant information contained in the image.
Although this is a proven approach (Mishra et al., 2021; Yan et al.,
2021), the entire spectrum is still needed for extraction of the principal
components, so the goal of enabling compact and cost effective equip-
ment may not be met. Also, data reduction techniques may alter the
original spectral patterns into a non-optimal representation of the data,
thus reducing the effectiveness of the models (Rehman et al., 2020).
On the other hand, if individual wavelengths do not provide enough
distinctiveness between classes, data reduction approaches tend to yield
superior results.
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Table 12
Number of bands and spectral range adopted in the studies.
Reference Bands Range (nm) Reference Bands Range (nm)
Abbas et al. (2021) 204 400–1000 Sabzi et al. (2021) 327 400–1000
Agarwal et al. (2020) 80 800–1000 Seo et al. (2021) 128 400–1000
Chen et al. (2021a) 177 1000–2500 Steinbrener et al. (2019) 16 470–630
Chen et al. (2022a) 25 660–980 Su et al. (2021) 400 380–1030
Chen et al. (2022b) 1367 400–1700 Sun et al. (2019) 618 431–961
Chu et al. (2022) 350 400–1000 Sun et al. (2021) 240 478–978
Cui et al. (2022b) 616 908–1735 Wang et al. (2018) 1002 329–1113
Cui et al. (2022a) 512 400–1000 Wang et al. (2019) 83 400–1000
Diao et al. (2022) 305 400–1000 Wang et al. (2023) 396 350–2550
Dong et al. (2022) 256 900–1700 Wendel et al. (2018) 244 411–867
Fazari et al. (2021) 61 450–1050 Weng et al. (2020) 260 400–1000
Feng et al. (2019) 256 380–1030 Weng et al. (2021) 260 374–1030
Feng et al. (2020) 512 380–1030 Wu et al. (2018) 256 874–1734
Feng et al. (2022) 400 400–1000 Wu et al. (2019) 256 874–1734
Fu et al. (2022b) 618 431–962 Wu et al. (2021) 256 874–1734
Gao et al. (2019) 256 874–1734 Wu et al. (2022) 200 874–1734
Gao et al. (2020) 256 370–1015 Xiang et al. (2022) 462 400–1000
Gao et al. (2021) 268 600–1700 Xiao et al. (2020) 600 380–1734
Garillos-Manliguez and Chiang (2021) 150 400–900 Xiao et al. (2022) 224 400–1000
Gui et al. (2021) 256 384–1033 Xin et al. (2020) 953 380–1030
Han and Gao (2019) 1200 292–865 Xu et al. (2022) 478 400–1001
Han et al. (2021) 462 389–1005 Yan et al. (2021) 220 950–1760
Hao et al. (2022) 125 400–1000 Yang et al. (2019) 240 450–885
He et al. (2021a) 79 920–1700 Yang et al. (2020b) 508 908–1736
Jiang et al. (2019) 256 865–1712 Yang et al. (2020a) 256 874–1734
Jie et al. (2020) 120 400–1000 Yang et al. (2021) 520 360–1025
Jin et al. (2018) 339 400–1000 Yang (2022) 300 400–1000
Jin et al. (2022b) 100 900–1700 Yang et al. (2022) 824 400–1000
Jin et al. (2022a) 100 900–1700 Ye et al. (2022) 310 376–1044
Kabir et al. (2022) 256 874–1734 Yipeng et al. (2022) 260 374–1030
Li et al. (2021b) 224 866–1701 Yu et al. (2018) 512 380–1030
Li et al. (2021a) 176 383–990 Yu et al. (2021) 256 948–1649
Li et al. (2022) 233 1000–2500 Yuan et al. (2022) 288 960–2568
Liang et al. (2021) 616 380–1030 Zhang et al. (2020b) 256 866–1701
Liu et al. (2020) 128 400–1000 Zhang et al. (2020f) 200 874–1734
Liu et al. (2021) 121 400–1000 Zhang et al. (2020d) 256 874–1734
Liu et al. (2022b) 256 885–1733 Zhang et al. (2020a) 696 400–1000
Liu et al. (2022a) 121 400–1000 Zhang et al. (2020c) 254 866–1701
Ma et al. (2020) 207 1002–2300 Zhang et al. (2021b) 420 400–1000
Mansuri et al. (2022) 97 398–1003 Zhang et al. (2021a) 420 450–979
Mesa and Chiang (2021) 288 1000–2500 Zhang et al. (2022c) 678 382–1027
Mishra et al. (2021) 186 407–997 Zhang et al. (2022a) 254 866–1701
Nagasubramanian et al. (2019) 240 400–1000 Zhang et al. (2022b) 473 413–1016
Nguyen et al. (2021) 204 400–1000 Zhang et al. (2022d) 254 866–1701
Ni et al. (2020) 288 1000–2500 Zhang et al. (2022e) 288 968–2575
Nie et al. (2019) 172 975–1648 Zhao et al. (2020) 204 397–1003
Onmankhong et al. (2022) 256 1002–1998 Zhao et al. (2021) 126 450–950
Pandey et al. (2021) 462 400–1000 Zhao et al. (2022) 94 400–1000
Pang et al. (2020) 128 370–1042 Zheng et al. (2022) 1650 380–1030
Pang et al. (2021) 115 370–1042 Zhou et al. (2020a) 953 380–1030
Pang et al. (2022) 256 930–2548 Zhou et al. (2020b) 478 400–1002
Park et al. (2018) 519 356–1018 Zhou et al. (2021) 1000 327–1098
Polder et al. (2019) 224 400–1000 Zhou et al. (2022) 411 481–1002
Qi et al. (2021) 204 N/A Zhu et al. (2019b) 256 874–1734
Qiu et al. (2018) 512 380–1734 Zhu et al. (2020) 128 400–1000
Raghavendra et al. (2022) 288 1000–2500 Zhu et al. (2022a) 237 400–1000
Rangarajan et al. (2022) 1208 400–750 Zhu et al. (2022b) 400 415–799
Rehman et al. (2020) 540 370–1030 Zhu et al. (2023) 254 866–1701

3.2.2. Extraction of useful information
Hyperspectral images have two spatial dimensions and one spec-
tral dimension, making it challenging to find the best way to ex-
tract relevant information. One of four general approaches is usually
adopted (Nguyen et al., 2021). The first one extracts the 1D spectral
information separately for each pixel in the image (Brugger et al., 2021;
Gomes et al., 2021; Kabir et al., 2022; Mansuri et al., 2022; Sabzi
et al., 2021; Fu et al., 2022b), frequently employing a 1D CNN. This is
roughly equivalent to employing a conventional spectrograph to every
point in the surface of interest. Since each pixel is treated as a sep-
arate sample with its own associated spectrum, this approach has the
advantage of enabling large training sets with many individual spectra,
even if few images are available (Zhu et al., 2019b). On the other hand,
spatial relationships are ignored, making this a poor option when image
textures and the spatial distributions of the spectral bands are relevant.
However, some authors argue that keeping the spatial relationships
is not always the best course of action, because irregularities in the
topography of the objects may cause variations in the spectrum that
are not actually related to the problem being addressed (Zhang et al.,
2020e). This fact inspired many studies to average the spectrum over
the entire area (Gui et al., 2021; Rehman et al., 2020; Seo et al., 2021;
Sun et al., 2021; Weng et al., 2020), thus integrating the information
and diluting possible spurious variations. In other words, instead of
treating each pixel separately, they are averaged into a single spectrum
associated to the whole image (or object of interest). The set of spectra
using this approach will be much smaller, but outlier pixels producing
spurious spectra will have their impact significantly diminished. This

10
J.G.A. Barbedo
second approach also employs 1D models to explore the resulting in-
formation. In the third approach, spatial patterns are identified for the
bands of interest by processing the two spatial dimensions separately,
often by means of a 2D CNN (Feng et al., 2022; Hao et al., 2022;
Jin et al., 2018; Zhao et al., 2022; Pang et al., 2020). In this case,
the spectral relationship between different wavelengths is usually not
explored, which can cause valuable information to be lost. In the fourth
approach, spatial and spectral dimensions are processed in tandem,
either by applying the two previous approaches separately and then
combining the results appropriately, or by employing 3D CNNs capable
of processing the entire data cube at once (Diao et al., 2022; Su et al.,
2021). Both strategies have produced encouraging results, but there
is some evidence that 3D CNNs are more successful, especially if the
number of training samples is not high (Nguyen et al., 2021). In any
case, the third approach is the most likely to fully explore to wealth
of information contained in hyperspectral images (Rangarajan et al.,
2022), at the price of being more computationally intensive. Some
authors have also adopted a hybrid approach combining 2D and 3D
strategies (Chen et al., 2022a; Qi et al., 2021; Zhu et al., 2023).
3.2.3. Segmentation of the objects of interest
A crucial step that almost always needs to be carried out is the
segmentation of the region of interest (ROI), so the spectral analysis
is carried out solely on the relevant objects (Yan et al., 2021; Kabir
et al., 2022; Zhang et al., 2021a; Jiang et al., 2019; Seo et al., 2021;
Pang et al., 2021; Dong et al., 2022). This is usually done by identifying
one or more spectral bands in which objects of interest and background
are contrasting enough for proper segmentation (Pandey et al., 2021;
Yang et al., 2022). Under laboratory conditions, this task is relatively
straightforward, although errors are still possible (Barbedo et al., 2015;
Zhu et al., 2023). In the field, where conditions and background
objects are more unpredictable, achieving proper segmentation can be
harder (Liu et al., 2022a). Segmentation errors can be particularly dam-
aging if parts of the background are taken as objects of interest, because
their spectral profiles will likely be completely spurious, leading to the
wrong predictions. False negatives, in which an object or a portion of
the region of interest are discarded, can also have a deleterious effect,
especially if the lost region contains the cues needed for the correct
answer. Because segmentation can be a challenging task by itself, many
investigations have focused primarily on this problem (Liu et al., 2021,
2022a; Mishra et al., 2021).
3.2.4. Data diversity and generalization
Deep learning techniques are very effective in extracting infor-
mation from digital images, but their generalization capabilities are
relatively limited (Barbedo, 2022b). It is well established that deep
learning models need many images to be properly trained, but this
has more to do with the need for the data to properly represent the
variability associated to the problem at hand than with the number
of images itself. Data collection and annotation is usually expensive
and time demanding (Han and Gao, 2019), so most studies employ
limited datasets that cover only a small portion of potential real world
conditions (Cui et al., 2022a; Zhang et al., 2020a; Pang et al., 2022;
Yan et al., 2021; Zhu et al., 2020; He et al., 2021a; Zhou et al., 2022;
Jin et al., 2022a; Su et al., 2021). While it is acceptable to have this
type of experimental limitation, the results reported in the articles
should always be weighted against those limitations to avoid unrealistic
conclusions and claims. It is important to consider that data limitations
become more damaging as research matures, because the leap from
academic studies to practical technologies often requires models to be
developed and tested with more representative data (Rangarajan et al.,
2022; Sun et al., 2021). Given the difficulties in building truly repre-
sentative datasets, in many cases this objective may only be feasible
if data sharing becomes more widespread. Among all the studies cited
in this work, a single one made the dataset fully available (Gao et al.,
2021). This dataset contains hyperspectral images of rice seeds that are
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Computers and Electronics in Agriculture 210 (2023) 107920
either undamaged or submitted to heat stress. A number of articles
claim that the data is available upon request (Brugger et al., 2021;
Chen et al., 2021a, 2022b; Cui et al., 2022b,a; Garillos-Manliguez and
Chiang, 2021; Hao et al., 2022; Li et al., 2021a; Mesa and Chiang, 2021;
Nagasubramanian et al., 2019; Pandey et al., 2021; Polder et al., 2019;
Raghavendra et al., 2022; Rangarajan et al., 2022; Su et al., 2021; Wang
et al., 2019; Wu et al., 2021; Xiang et al., 2022; Yang, 2022; Ye et al.,
2022; Yu et al., 2021; Zhang et al., 2020e, 2022a,b; Zhu et al., 2022b),
but this does not guarantee access to the original material.
The main reason for the failure of models trained with limited
datasets is that they will closely fit the data distribution of the training
samples, which in turn causes a loss of generality and poor performance
with samples that differ from those used for training (Wu et al.,
2021). This phenomenon, commonly called overfitting, is among the
most challenging problems associated with machine learning and deep
learning techniques. As mentioned before, using more representative
training datasets is usually the best solution, but since this is often
difficult to achieve (Wu et al., 2021), the next best option is to apply
techniques that mitigate overfitting and improve generalization capa-
bilities. Regularization techniques such as dropout (Jin et al., 2018;
Wang et al., 2023) and batch normalization (Li et al., 2021b; Nie et al.,
2019; Wu et al., 2019) are particularly useful, showing promise in the
context of deep learning.
The generalization problem is even more challenging in the context
of hyperspectral images. There have been some evidence that classifiers
trained using a set of hyperspectral images with certain characteristics
will tend to fail even when they try to classify images captured with
the same equipment using only slightly different settings (Bruzzone
and Persello, 2009). This is a problem that has rarely been addressed,
perhaps because hyperspectral equipment are still expensive, making it
difficult to generate data with enough variability and even to properly
investigate the actual generalization capability of a given model. For
this reason, while the methodologies used in the studies cited in this
article can probably be applied to other hyperspectral image datasets,
the specific models are likely only valid for the exact conditions under
which the images originally used for training were captured.
There are some indirect ways to make the data more diverse, among
which image augmentation is probably the most employed (Barbedo,
2022a). Image augmentation is the process of applying different image
processing techniques to alter existing training images in order to create
more data with different characteristics for training the model. There
are some pitfalls that should be avoided when applying this type of
technique (see next two paragraphs), but if properly employed it can
improve the robustness of the model significantly (Shorten and Khosh-
goftaar, 2019; Zhu et al., 2023; Liu et al., 2020). A variation of image
augmentation, called test time augmentation, applies one or more of
the same image transformations applied during training to images to
be evaluated by the trained model. This allows for a better exploration
of the range of possible characteristics that the image being analyzed
could present, thus improving the robustness and performance of the
prediction (Fazari et al., 2021). In most cases, image augmentation
only deals with the spatial nature of the samples, usually ignoring
spectral aspects. To the best of the author’s knowledge, there are no
studies investigating possible problems caused by this, and augmenta-
tion techniques incorporating spectral aspects are absent even in the
case of remote sensing, an area of research that has several studies
dealing specifically with image augmentation applied to hyperspectral
images (Nalepa et al., 2020).
Image augmentation must be applied only to the training set after
the division of the original dataset (Barbedo, 2022a). Unfortunately,
many authors first apply image augmentation, and only afterwards the
division into training and test sets is carried out. As a result, both sets
will contain the exact same samples, with only some minute differences,
making it easier for the model to perform well on the test set. This pro-
duces heavily biased results that in no way represent the true accuracy
of the proposed model. Around 20% of the articles cited in this review
J.G.A. Barbedo
which apply image augmentation have this problem. It is important
that both authors and reviewers be aware of this fact, in order to
avoid publication of articles with a methodological error as serious
as this. It is worth pointing out that applying image augmentation
incorrectly aggravates training-test information leaks, a problem that
has caught the attention of many researchers of different areas (Nalepa
et al., 2019), but has been largely ignored in the case of proximal
hyperspectral images.
When spectral differences between classes are subtle, applying im-
age augmentation may actually cause the spectral characteristics of the
artificially generated images to completely depart from those found in
actual images. This is unlikely to occur with operations like translation,
rotation and shifting, but it is a real possibility with operations that
alter pixel values, like image noising and blurring. More importantly,
this phenomenon can occur when more sophisticated techniques like
GANs are applied (Wang et al., 2019; Zhang et al., 2022d). Avoiding
this type of problem is possible in most cases, but the effects of image
augmentation should always be a point of attention.
3.2.5. Class imbalance
In classification problems, it is common for some classes to have
a much larger number of samples than others (Fazari et al., 2021).
If not properly addressed during training, this may lead to severely
biased models that will tend to heavily favor the most numerous classes.
Although there are many strategies that can be employed to mitigate
this problem (Johnson and Khoshgoftaar, 2019), two are commonly
applied due to their simplicity: reducing larger classes by removing
part of the samples for training, or applying image augmentation to
the smaller classes. The former is normally used when the number of
training samples is high, which in the case of hyperspectral images only
happens when individual pixels are taken as samples (Jin et al., 2018).
The latter has been used in a few cases with limited number of training
samples (Rehman et al., 2020; Pandey et al., 2021; Polder et al., 2019),
with satisfactory results. Employing cost-sensitive learning techniques
during the training process is another approach that has yielded good
results (Nagasubramanian et al., 2019; Wang et al., 2019; Wu et al.,
2022; Li et al., 2021a).
3.2.6. Model training process
Almost all studies considered in this review adopted supervised
learning for model training. This approach relies on carefully annotated
images to teach the model to recognize the patters of interest. Data
annotation usually requires considerable effort, especially considering
that proper training of deep learning models frequently require a large
amount of samples. Data annotation can also be error prone, especially
at the pixel level (Zhu et al., 2022b). Some authors have been able
to successfully reduce the labor involved in the task by introducing an
imperfect but quick automatic pre-labeling process, followed by manual
correction of mislabeled samples (Pandey et al., 2021). Unsupervised
and semi-supervised learning approaches can drastically decrease the
amount of data that needs to be actually labeled (Gao et al., 2021;
Barbedo, 2022b) and reduce the impact of labeling errors (Zhu et al.,
2022b), but although these have been successfully applied with con-
ventional RGB images, it is not clear if existing techniques can be
successfully adapted to the characteristics of hyperspectral images, so
more research is needed to better understand their potential.
Data annotation can become even more challenging when the image
patterns to be identified are too subtle for human observers to dis-
cern (Polder et al., 2019). This is one major reason for the frequent
choice of assigning a single label to the whole image, instead of anno-
tating each pixel separately. The problem with this strategy is that the
objects and regions in the image may not have uniform characteristics,
so averaging it all into a single label may not represent well what
is happening in the image (Wang et al., 2019). Spatial relationships
that can be very valuable for classification purposes are also lost. In
addition, the number of labeled samples for training will be much
12
Computers and Electronics in Agriculture 210 (2023) 107920
Table 13
Articles adopting cross-validation.
Cross-validation Reference
5-fold Fu et al. (2022a), Han and Gao (2019), Han et al. (2021),
He et al. (2021b), Li et al. (2021b), Ma et al. (2020),
Nguyen et al. (2021), Onmankhong et al. (2022), Pang et al.
(2022), Wang et al. (2023), Wendel et al. (2018), Wu et al.
(2019), Zhang et al. (2020b), Zheng et al. (2022)
10-fold Dong et al. (2022), Feng et al. (2020, 2022), Hao et al.
(2022), Li et al. (2021a, 2022), Liang et al. (2021),
Nagasubramanian et al. (2019), Pandey et al. (2021),
Rehman et al. (2020), Zhang et al. (2020e,c), Zhao et al.
(2022)
smaller, increasing the chances of overfitting. Since labeling individual
pixels may be visually unfeasible, some authors have adopted the
strategy of assigning a label for each line in the image (Polder et al.,
2019). The procedure is similar to the image-based labeling, as the label
is assigned to entire regions and objects without considering possible
heterogeneities, but greatly increases the number of labeled samples by
considering each line separately.
In general, studies employing supervised learning divide their
datasets into training and test sets (and sometimes a validation set),
so the models can be tested against data that was not used in their
training. Such a division is almost always carried out randomly, which
means that there is always a chance that the data distributions in both
sets can be skewed and lead to unrealistic high or low accuracies.
Because of this fact, it is good practice to adopt cross-validation, in
which the division is carried out multiple times and results are averaged
afterwards. Cross-validations using 5 and 10 folds are the most common
(Table 13). Using this technique is particularly important in the case
of small datasets, but unfortunately most studies do not adopt this
practice.
3.2.7. External factors
Among the external factors that can cause difficulties, illumination
effects are likely the most challenging (Weng et al., 2021; Steinbrener
et al., 2019). Phenomena like shadows, specular reflections, angle of
incidence, among others, can greatly increase the variability associated
to the problem and introduce noise (Xiao et al., 2022), making it
difficult to guarantee that the model will be prepared to deal with
the whole range of conditions that can be found in practice. This
problem is more prominent when images are collected in the field
under uncontrolled conditions (Jin et al., 2018; Rangarajan et al., 2022;
Chen et al., 2021b; Wendel et al., 2018), but this can be challenging
even in a laboratory environment (Feng et al., 2020; Zhang et al.,
2020c; Ye et al., 2022; Ma et al., 2020). Although there are some
methods for mitigation of illumination variations (Wendel et al., 2018),
they are only partially effective and in many cases the only way to deal
with this problem without enforcing very strict image capture protocols
is to guarantee that the dataset used to train the model is representative
enough, which is by itself a considerable challenge.
Another factor that can decrease the robustness of deep learning
models is the presence of noise in certain bands. It is common practice
to discard the bands at the extremities of the captured spectral range,
as these tend to be very noisy and carry little information (Zhang et al.,
2020c; Zhu et al., 2023; Kabir et al., 2022; Li et al., 2021b; Pang et al.,
2021; Gao et al., 2019; Wendel et al., 2018). However, other bands can
become noisy due to capture conditions or the spectral characteristics
of the objects of interest (Polder et al., 2019). If this is a recurrent
problem, applying noise removal techniques may be recommended (Xu
et al., 2022; Yan et al., 2021; Zhou et al., 2021; He et al., 2021a; Sun
et al., 2019; Zhou et al., 2020a), as long as these do not also remove
relevant information (Xin et al., 2020). Outliers that for some reason
depart too much from the characteristics expected for the samples used
J.G.A. Barbedo
Fig. 2. Summary of all challenges discussed in this review.
for training should also be removed in order to avoid training models
with poor data (Xu et al., 2022).
The sensor itself is another source of noise that is mostly unavoid-
able. Sensor noise include thermal-driven (strip noise), quantization-
related, and shot (photon) noise (Zhu et al., 2022a). Strip noise, which
results from an increase in the temperature of the sensor, can sometimes
cause severe distortions that should be filtered out, a goal that may
require sophisticated techniques capable of preserving structural and
textural details (Zhu et al., 2022a).
3.2.8. Final remarks
Besides all the challenges discussed throughout this section, there
are some practical difficulties that further hinder a more widespread
use of hyperspectral images, especially in real world situations (Zhang
et al., 2022c). Compared with RGB sensors, hyperspectral equipment
are still rather expensive and, considering that most of those are non-
portable scanning devices, they are more difficult and time-consuming
to operate. Snapshot hyperspectral cameras, on the other hand, offer a
spatial resolution that is insufficient for many of the potential applica-
tions. Motivated by this situation, Zhao et al. (2020) investigated the
possibility of deriving hyperspectral-like images from plain RGB images
13
Computers and Electronics in Agriculture 210 (2023) 107920
using deep learning techniques, with promising results. Although this
type of approach cannot replace actual hyperspectral images in every
situation, it can greatly extend the practical applications of inexpensive
high-resolution RGB images. Even as the hyperspectral technology
evolves and costs decrease, having the ability to explore simpler im-
ages beyond their apparent limitations can be invaluable to enable
technologies that would otherwise be unfeasible.
Despite the prevalence of deep learning techniques for image anal-
ysis and classification observed in the last decade, there are situations
and conditions for which other approaches, including conventional
machine learning techniques and heuristic-inspired methods, can be
more appropriate (LeCun et al., 2015). Also, hybrid approaches com-
bining different types of models (deep or otherwise) can produce more
consistent results (Zhang et al., 2020f, 2022c). It is important to ana-
lyze different approaches using different criteria (accuracy, complexity,
robustness, etc.) in order to arrive at the best solution for a given
problem.
Finally, it is worth mentioning that reproducibility of published
studies has become an important problem, especially in the case of ma-
chine learning. The most straightforward way to address this problem
is to make implementations and codes publicly available. In the context
J.G.A. Barbedo
of this review, four articles made their codes fully available (Feng et al.,
2020; Gao et al., 2021; Liu et al., 2022b; Zhang et al., 2022b). This is
not a high number, but indicates that at least some research groups are
aware of this problem and are taking steps to minimize its effects.
Fig. 2 summarizes all application-specific and general challenges
raised in this review.
4. Concluding remarks
The combination of proximal hyperspectral images with deep learn-
ing techniques is relatively new, but the literature already contains
many examples of success. As encouraging as the results are, it is
important to have in mind that most studies are initial proofs of concept
carried out under ideal conditions that are unlikely to be found in a
potential practical application. Many of the challenges and issues raised
in this review still lack suitable solutions, so considerable research
effort is still needed in order for hyperspectral images to realize their
full potential and truly benefit the agricultural sector. Understanding
the real stage of maturity of the techniques and related technologies
is very important not only for scientists and researchers, but also
for entrepreneurs willing to explore the potential market, in order to
avoid botched products and services. The premature introduction of
technologies to the market can not only lead companies to fail, but may
also ruin the perception of potential customers regarding that particular
technology.
Deep learning techniques seem to adapt well to the characteristics
of hyperspectral images, and the studies mentioned in this review offer
several possible ways to explore the wealth of information provided by
this type of image. Among the many challenges mentioned in Section 3,
the need for more representative data and the development of models
more robust to the conditions found in practice seem to be the most
important. A third major challenge that was only briefly mentioned
for being out of the scope of this review is that hyperspectral imaging
equipment still lack the sensitivity required by some applications, such
as the discrimination between different stresses. However, this type of
technology is evolving fast, and new research exploring the possibilities
opened by new sensors will likely remain in high demand for the
foreseeable future.
Declaration of competing interest
The authors declare that they have no known competing finan-
cial interests or personal relationships that could have appeared to
influence the work reported in this paper.
Data availability
No data was used for the research described in the article.
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