Artificial Intelligence in Agriculture 3 (2019) 1–10

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Artificial Intelligence in Agriculture

journal homepage: http://www.keaipublishing.com/en/journals/artificial-
intelligence-in-agriculture/

Recent advances in Raman technology with applications in agriculture,

food and biosystems: A review
Shizhuang Weng b,⁎,1, Wenxiu Zhu b,1, Xueyan Zhang b,1, Hecai Yuan b,1, Ling Zheng b,1, Jinling Zhao b,1,
Linsheng Huang b,1, Ping Han a,1
a
Agricultural Product Quality and Safety Risk Assessment Laboratory of Ministry of Agriculture (Beijing), Beijing Academy of Agricultural and Forestry Sciences, China
b
National Engineering Research Center for Agro-Ecological Big Data Analysis & Application, Anhui University, 111 Jiulong Road, Hefei, China

a r t i c l e i n f o a b s t r a c t

Article history: Raman technology, which covers Raman spectroscopy (RS) and its various derivative methods, has been widely
Received 18 October 2019 applied in detection of various substances in agriculture, food and biosystems. This article reviews the recent ad-
Received in revised form 7 November 2019 vances in two mainstream Raman technologies as RS and SERS, including technical evolution, application and
Accepted 7 November 2019
challenges, and spectral processing methods. Firstly, the origin, principle, defect, and development of RS were in-
Available online 11 November 2019
troduced. Then, the current situation, existing problems, and development trend of RS and SERS were discussed
Keywords:
in agriculture, food, and biosystems, such as adulteration recognition, plant diseases identification, farm
Raman technology chemicals detection, food additives determination, and toxins analysis. At last, the spectral analysis methods in-
Adulteration clude noise reduction, feature extraction or variable selection, and modeling were introduced in detail, which can
Plant diseases realize the automatic and intelligent analysis of spectra without relying on professionals.
Farm chemicals © 2019 The Authors. Production and hosting by Elsevier B.V. on behalf of KeAi Communications Co., Ltd. This is an
Toxins open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/).
Spectral processing methods

Contents

1. Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1
2. Technological evolution . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2
3. Application and challenges . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3
4. Spectral analytical methods . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5
5. Conclusions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8
Acknowledgements . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8
References . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8

1. Introduction inelastic collision of excitation laser and molecules of analyte, scattered

light of different wavelengths with excitation laser appears; this phe-
Raman technology covers Raman spectroscopy (RS) and its various nomenon was first discovered by Raman in 1928 (Raman, 1928). In gen-
derivative methods. RS is a kind of scattering spectroscopy with molec- eral, scattered lights of higher wavelengths are collected and known as
ular structure characterization ability (Colthup, 2012). Due to the RS. For RS, the light intensity at different wavelength is diverse,
reflecting the molecular vibration and rotation information. In other
⁎ Corresponding author at: Anhui University, Hefei 230601, Anhui, China.
words, each molecular structure has its specific spectrum, namely, the
E-mail address: weng_1989@126.com (S. Weng). fingerprint characteristic of RS, which is highly valuable for molecular
1
These authors equally contributed in present work. structure analysis (D'Ippolito et al., 2015). The measurement of RS is

https://doi.org/10.1016/j.aiia.2019.11.001
2589-7217/© 2019 The Authors. Production and hosting by Elsevier B.V. on behalf of KeAi Communications Co., Ltd. This is an open access article under the CC BY-NC-ND license
(http://creativecommons.org/licenses/by-nc-nd/4.0/).
2 S. Weng et al. / Artificial Intelligence in Agriculture 3 (2019) 1–10
not restricted by morphology and states of the analyte. Thus, sample
pretreatment is relatively simple. At same time, the extremely weak
RS response of water prevents the interference of moisture in the anal-
ysis results, avoiding the common problem in other analytical technol-
ogies. Considering these advantages, RS has been applied for the
analysis of various adulteration and plant diseases (Crow et al., 2005;
Mandrile et al., 2019).
However, the RS intensity is about 10−6 fold that of excitation laser.
This low sensitivity severely limits its practical application. Various en-
hanced methods, such as resonance Raman spectroscopy (RRS), coher-
ent anti-Stokes Raman spectroscopy (CARS), stimulated Raman
spectroscopy (SRS), surface-enhanced Raman spectroscopy (SERS),
and tip-enhanced Raman spectroscopy (TERS) have been developed to
improve the intensity of RS. Among these technologies, SERS is the
most widely used and effective. SERS was first discovered by
Fleischmann, who observed that the Raman signal of pyridine molecule
adsorbed on the rough silver surface is largely stronger than that of pyr-
idine in solution (Fleischmann et al., 1974). Compared with that of nor-
mal RS, the enhancement factor of SERS is increased by about 106–1015,
improving the low sensitivity of normal RS. The enhancement effect is
mainly derived from the local electric field on the metal surface and
the chemical interaction between the compound and the reinforcement
substrate. Furthermore, the advantages of RS are perfectly inherited by
SERS. SERS is a highly competitive method for the rapid detection of
trace amounts of substances, such as herbicide (Tsen et al., 2019), insec-
ticide (S. Li et al., 2012; Y. Li et al., 2012; He et al., 2014), disinfectant
(Fan et al., 2015), bactericide (Zhang et al., 2014), and additives (Zhai
et al., 2011; He et al., 2010) in various food or agricultural products
(Xu et al., 2017).
In this review, recent advances of Raman technology were intro-
duced from the three aspects of technological evolution, application
and challenges, and spectral analysis methods. We hope this work can
provide technical references for follow-up research.
2. Technological evolution
RS is a technique specialized in measuring the frequency shift of in-
elastic scattered light from the sample (Rostron et al., 2016). When the
photons from incident light strike a molecule, scattering photons of dif-
ferent frequency appear. The effect of scattering photons with low fre-
quency is called as Stokes Raman scattering, and the effect of the
appearance of high-frequency photons is known as anti-Stokes Raman
scattering (Asher, 1993). RS is the spectroscopy obtained based on the
effect of Raman scattering.
The origins of RS can be traced to the first half of the 20th century,
and the scattering of monochromatic radiation with the frequency
change was theoretically built by Smekal (1923). In 1928, Raman
(1928), discovered the phenomenon of inelastic scattering of light,
termed as the Raman effect. Then, Raman and Krishnan (1928) first ex-
perimentally observed the phenomenon in the same year. RS is ob-
tained based on the Raman effect of molecules and excitation light.
The frequency variation caused by the inelastic scattering of light
Table 1
Classification and comparison of Raman techniques.
Classification Advantages
RRS High sensitivity
CARS High sensitivity, excellent spatial and spectral
resolution
SRS Improve signal to noise ratio and signal intensity
FT-RS Low fluorescence interference
Confocal micrograph Raman High spatial resolution, low detection limit
spectroscopy
TERS High sensitivity, good reproducibility.
SERS High sensitivity, low detection limit
perfectly matches the difference in vibrational energy levels, which en-
ables each type of molecule to produce different Raman spectra. Thus,
the main advantage of RS is the ability to have molecular fingerprint
characteristics for each different analyte. Meanwhile, given the weak
Raman scattering effect of water molecules, RS is immune to water in-
terference during detection. These properties allow RS to greatly im-
prove the molecular selection of specific substances in natural water-
containing solutions (Patel et al., 2019).
However, RS had limited application for many decades because of
the low efficiency of normal Raman scattering (Kudelski, 2008). With
the continuous development of optical instruments, lasers, and nano-
technology, various techniques have emerged to enhance the sensitiv-
ity, resolution, and stability of RS. At present, advanced Raman
technologies include RRS, CARS, SRS, FT-RS, confocal micrograph
Raman spectroscopy, TERS, and SERS (Table 1). RRS is an instrument
that measures the frequency shift of photons when the photon energy
from the incident light is approximately similar to the energy needed
for electronic transition (Das and Agrawal, 2011). The resonance excita-
tion can increase the oscillation charge displacement of electrons, which
will directly enhance the efficiency of Raman scattering. Compared with
that of normal Raman scattering, the enhancement factor of resonance
Raman scattering can reach as 108, but the shortcoming of this technol-
ogy is its vulnerability to interference from a fluorescence background
(Asher, 1993). CARS is a nonlinear Raman technique used to enhance
the Raman signal (Zumbusch et al., 1999). It uses coherent laser
beams to generate a signal with a frequency higher than the excitation
frequency, which is considered as anti-Stokes frequency technique.
SRS is another nonlinear process with strong directivity and high scat-
tering intensity (Basiev et al., 1999). The increase in the radiation inten-
sity of this technique is attributed to the two-photon process and
simulated Raman scattering (Woodbury and Ng, 1962; White, 1987).
FT-RS uses a neodymium doped yttrium aluminum garnet (Nd: YAG)
laser with a wavelength of 1064 nm as the light source, which elimi-
nates the fluorescence interference problem and reduces the laser dam-
age to samples. Therefore, FT-RS can be used to determine the Raman
spectra of compounds containing fluorescence and photoinstability
(Keller et al., 1993). Confocal micrograph Raman spectroscopy collects
Raman signals by laser scanning confocal microscopy, which has a
high spatial resolution and can analyze samples with an order of magni-
tude in micrometers and obtain Raman and microscopic images of sam-
ples (Dieing et al., 2011). However, the disadvantage of this technique is
that the single detection range is small, and the confocal area easily pro-
duces heat radiation. TERS (Fig. 1.a) is a technology that combines with
scanning probe microscopy to improve spatial resolution to the nano-
meter level (Deckert, 2009). The metal tip or a metal nanoparticle is
brought into close proximity of nanometer distance with the sample.
The excited laser beam will then illuminate the tip apex, creating an en-
hanced and confined electric field zone. This localized field will result in
enhanced Raman scattered light from the sample located under the tip
(Bailo and Deckert, 2008). The most important feature of TERS is the
possibility of quantitative analysis due to the identical electromagnetic
field enhancement at all points (Stockle et al., 2000). In addition, TERS
Disadvantages Reference
Fluorescence interference Das and Agrawal,
2011
Non-zero background nature Zumbusch et al.,
1999
Low sensitivity Basiev et al., 1999
Low sensitivity Keller et al., 1993
Single detection range is small, easily produces heat Dieing et al., 2011
radiation
Low stability Stockle et al., 2000
Low stability, difficult quantitative analysis Kudelski, 2008
 S. Weng et al. / Artificial Intelligence in Agriculture 3 (2019) 1–10
Fig. 1. Tip-enhanced Raman spectroscopy concept (a) (Sharma et al., 2012) and surface-enhanced Raman scattering system (b) (Rostron et al., 2016).
improves the reproducibility issue of RS techniques (Gibson et al., 2006)
and can work in an environment with water and humidity (Yeo et al.,
2009).
SERS (Fig. 1.b) can be a historic breakthrough in the study of Raman
spectroscopy, abolishing the inherent low detection sensitivity of
Raman technologies (Sharma et al., 2012). Compared with the weak sig-
nal obtained by RS, the strength of the Raman signal generated by SERS
is much higher (Kudelski, 2008). The surface enhanced Raman effect
was first discovered by Fleischmann et al. in 1974, which catalyzed re-
search on enhanced Raman technology. The enhancement mechanism
of SERS can be classified into physical enhancement and chemical en-
hancement (Ban et al., 2017). In the former, signal enhancement occurs
from localized surface plasmon resonance of noble metals and transi-
tion metal surfaces to generate electromagnetic fields (Jayram et al.,
2016; Fu et al., 2015). In the latter, signal enhancement is derived
from metal–electron-mediated resonance Raman effect via a charge
transfer intermediate state, which occurs at so-called “active sites”
(Otto et al., 1992). Although SERS has high sensitivity and low detection
limit, it suffers from low stability and difficult quantitative analysis.
Many new technologies, such as dynamic SERS (Qian et al., 2013;
Yang et al., 2015), self-assembly technology (Yu et al., 2019; Liang
et al., 2017), internal standard technology (Jie et al., 2018; Kammer
et al., 2014), and functionalized substrates (Gukowsky et al., 2018;
Yaseen et al., 2018a, 2018b), have been developed to solve the problem.
Considering the board application, the current situation and develop-
ment of RS and SERS were discussed.
3. Application and challenges
RS is generally used to detect elements with a high content of sub-
stances (Schulz and Baranska, 2007), such as in food adulteration.
Uysal et al. (2013) developed a method to determine butter adultera-
tion by using RS combined with chemometric methods. Different butter
and margarine samples were mixed at various concentrations ranging
from 0% to 100% (w/w), and concentrations of mixed butter and marga-
rine samples were analyzed on the basis of unique spectral bands
(380–760 cm−1). The modeling results showed that the measured coef-
ficients were all higher than 0.968. S. Li et al. (2012) and Y. Li et al.
(2012) used RS to detect adulteration of high-fructose corn syrup and
maltose syrup in honey. A classification model is established with the
aid of partial least squares–linear discriminant analysis to classify the
authenticity of honey with a total accuracy of 84.4%. Boyacı et al.
(2014) developed a novel RS-based method to distinguish beef from
horse meat and analyzed pure fat in 49 samples of beef and horse
meat. Horse meat with different concentrations of beef was successfully
identified by using the established model system. RS is also used for the
early detection of plant diseases (Baranska et al., 2013). Pérez et al.
(2016) applied RS for the early detection of Citrus Huanglongbing
3
(HLB) (Fig. 3.a, b, c, d, e). The statistical analysis results show that this
method provides a high degree of reliability with a precision of 89.2%
in discriminating between orange plants HLB-positive and healthy
plants. Farber et al. (2019) used RS as an early detection tool for rose ro-
sette disease (RRD). The work demonstrates that RS can detect RRD in
intact leaf tissue, and chemometric analysis can distinguish between
spectra collected from symptomatic and asymptomatic tissue, as well
as between healthy and asymptomatic tissue. Mandrile et al. (2019)
adopted RS combined with chemometric analysis to monitor the infec-
tion of tomato, by two different viral pathogens, Tomato yellow leaf curl
Sardinia virus (TYLCSV) and Tomato spotted wilt virus (TSWV). PCA
then was used for analysis, reaching an accuracy of N70% for TYLCSV
and N85% for TSWV. And RS have also been used to detect Abutilon mo-
saic virus (Yeturu et al., 2016) (Fig. 3.f, g, h), identify resistant trees
(Conrad and Bonello, 2016), and Plant Pathogens (Farber and
Kurouski, 2018).
SERS has a wide range of applications because of its higher detection
sensitivity and is generally used to detect trace analytes. In recent years,
the widespread use and abuse of farm chemicals have caused numerous
residues to form in crops and foods, affecting the health and life safety of
human beings. At present, SERS technology is widely used to detect var-
ious pesticide residues in crops and foods. Zhang et al. (2014) used SERS
to quantitatively detect thiram and methamidophos on the surface of
apples (Fig. 4.a). The lowest detectable concentration on apple surfaces
was 4.6 × 10−7 for thiram and 4.4 × 10−4 for methamidophos. Au@Ag
NPs coupled with SERS was used for the analysis of flusilazole, which
is widely applied in pears (Fig. 2.c); the minimum detectable concentra-
tion of flusilazole in pears was 0.1 μg/g (Zhao et al., 2018). Huang et al.
(2016) quantitatively detected difenoconazole pesticides in pak choi
by SERS coupled with chemometrics, and the correlation coefficient of
the prediction model (Rp) was 0.9458. By combining SERS with a
quick pre-treatment method, Huang et al. (2015) detected chlorpyri-
phos (CP) pesticide residues in rice with the lowest detection concen-
tration of CP pesticide in rice, with the lowest detection concentration
of b0.506 mg/L. Tang et al. (2012) developed an ultrasensitive method
based on SERS, which uses silver colloid as a substrate and pyridine as
an internal standard to determine the content of tricyclazole pesticides
in rice with the lowest detection limit of 0.002 mg/L. Weng et al. (2018a,
2018b) detected ediphenphos residue in rice by using SERS and ob-
tained the lowest detection limit of 0.1 mg/L. In addition,
thiophanate–methyl in red pepper (Li et al., 2017), omethoate in
peach (Yaseen et al., 2018a, 2018b), paraquat on fruits skins (Fang
et al., 2015) (Fig. 4.c), and deltamethrin in strawberry (Dong et al.,
2018) (Fig. 2.a, b) have also been detected with SERS.
Food additives are a common issue threatening food safety and qual-
ity. Cheung et al. (2010) analyzed Sudan-1 in chili powder by using SERS
with good sensitivity, such that Sudan-1 can be quantified in a complex
food matrix reliably over the range of 10−3–10−4 mol/L. A rapid SERS-
4 S. Weng et al. / Artificial Intelligence in Agriculture 3 (2019) 1–10
Fig. 2. SEM image of: AuNRs (a); AgNRs (b) (Dong et al., 2018); Au@ Ag nanoparticles (c) (Zhao et al., 2018); AuNPs before (d) and after (e) interaction with melamine (Giovannozzi et al.,
2014); Ag colloid (f) (Lin et al., 2015).
based method to detect melamine in liquid milk was presented by
Giovannozzi et al. (2014) with melamine-aggregated AuNPs (Fig. 2.d,
e), allowing melamine detection at a detection limit of 0.17 mg/L.
SERS was also used to detect Rhodamine B (RB), which is often added
illegally to chili powder. Lin et al. (2015) prepared a paper-based SERS
substrate for RB detection (Fig. 2.f), exhibiting simple sample treatment
and a detection limit that can reach 10−6 g/g for RB in chili powder. The
recovery of this detection method ranged from 96.4% to 108.9%. C. Li
et al. (2016) and X. Li et al. (2016) studied three easy-to-prepare
AuNPs substrates, and two commercial substrates were examined as
SERS substrates for methylene blue (MB) analysis. The lowest detection
limits of 5 ng/mL and 10 ng/g were observed for MB standard solutions
and MB in fish muscles, respectively.
Toxins are often detected through SERS. Yuan et al. (2017) used SERS
to rapidly determine mycotoxin deoxynivalenol in corn, kidney beans,
and oats, showing the lowest detection of 10−6, 10−6, and 10−4 M, re-
spectively. SERS was also applied to detect aflatoxin in maize. Lee
et al. (2014) mixed Ag nanosphere with sample extract for SERS mea-
surement with an accuracy of N93%. Zengin et al. (2015) developed a
novel SERS aptasensor for ricin B toxin recognition by using Ag nanopar-
ticles with a detection limit of 0.32 pM. Many toxins, such as
microcystin-LR (He et al., 2019) and saxitoxin (Cheng et al., 2019),
have also been detected by SERS.
With the discovery of SERS detection in single molecules, SERS has
gradually become a powerful technique for studying biological macro-
molecules, allowing the detection and characterization of various bio-
logical molecules in crops. Chen et al. (2012) successfully applied SERS
to detect Bacillus thuringiensis gene-transformed rice expressing insecti-
cidal proteins with a detection limit of 0.1 pg/mL (Fig. 4.b). Lee et al.
(2013) directly used SERS to detect crude protein and oil content in soy-
beans. Partial least squares analysis was then used to establish the opti-
mal prediction model of soybean crude protein and oil content. The
accuracy of crude protein and oil content was 0.916 and 0.872, respec-
tively. Furthermore, a novel method was proposed to characterize the
structure of buckwheat globulin through a combination of circular di-
chroism and Raman spectroscopy. Choi and Ma (2007) studied the con-
formation of globulin from buckwheat under the influence of various
buffer environments and heat treatment and discovered that buck-
wheat globulin contained a low level of α-helical and a large quantity
of β-sheets and disordered structures.
From the above application (Table 2), RS is mainly used for the iden-
tification and classification of substance adulteration. SERS has demon-
strated its potential in the quantitative analysis of substances due to its
rapid, sensitive, fingerprint, and informative analysis. However, RS is
limited in application because of its low sensitivity, and SERS also has
some challenges in practical detection, which requires extensive re-
search. SERS cannot isolate target compounds present in a complex
sample. Thus, the Raman signal of the target analyte is masked by sig-
nals from other components present in the sample during the detection.
This condition poses a challenge for SERS to detect trace target analytes
in complex matrices. Pang et al. (2014) successfully detected four or-
ganophosphate pesticides (phorate, profenofos, omethoate,
isocarbophos) in apple juice by using an Ag dendritic substrate conju-
gated with a thiol-modified ssDNA aptamer and a blocker molecule.
The apple juice compounds could not adsorb onto the substrate surface
and thus did not contribute to the SERS signal.
In addition, SERS has poor performance in terms of stability and sen-
sitivity, which is not only dependent on the interaction between the
adsorbed molecules and the substrate but also related to the substrate
itself. During decades of SERS development, researchers have been com-
mitted to optimizing the substrate structure and configuration to realize
trace-level detection. Currently, SERS substrates are highly diverse.
Montgomery et al. (2009) proposed and modeled potentially robust
SERS substrates composed of periodic arrays of chains of gold
 S. Weng et al. / Artificial Intelligence in Agriculture 3 (2019) 1–10 5

Fig. 3. Procedure to obtain spectral Raman signatures from HLB-positive and HLB-negative (healthy) citrus samples (a), (b), (c); principal component analysis and linear discriminant
analysis of Raman spectra obtained from samples of sweet orange positive for HLB and sweet orange plants negative to the disease by real-time PCR (d); Raman spectra from HLB-
positive Sweet Orange trees (red spectrum) and HLB-negative Sweet Orange trees (black spectrum) (e) (Pérez et al., 2016); Abutilon mosaic virus infecting Abutilon hybridum plant
showing bright yellow mosaic symptoms (left sick plant and right healthy plant) (f); agarose gel electrophoretic analysis of amplicons of PCR for detection of AbMV in Abutilon (g);
average Raman spectra of leaves from healthy plants (blue), early-stage infected plants (green), and full infected plants (red) without normalization (h) (Yeturu et al., 2016).

nanoparticles atop silver film structures and successfully obtained high
sensitivity. Musumeci et al. (2009) investigated the Raman scattering of
molecules adsorbed on the surface of TiO2 nanoparticles and obtained
strong enhancement of Raman scattering in hybrid composites that ex-
hibit charge transfer absorption with TiO2 nanoparticles. Some new
functionalized substrates have also been developed. Pan et al. (2015)
developed a sensitive substrate for SERS. It consists of a column material
that is obtained by modifying the surface of capillary monoliths with sil-
ver nanoparticles. This substrate has been applied to the determination
of 4-mercaptopyridine and Rhodamine 6G, showing detection limits as
low as 100 and 10 pM, respectively. Wang et al. (2017) rapidly detected
and differentiated bacteria in skimmed milk by using surface-enhanced
Raman scattering mapping on 4-mercaptophenylboronic acid-
functionalized silver dendrites (Fig. 4.d). The capture efficiency for Sal-
monella enterica subsp. enterica BAA1045 was 99.65%. The other tech-
nologies were also adopted in combination with functional
technologies to improve the stability and sensitivity of substrates. Fu-
ture research should focus on investigating new materials and metals
together as SERS active substrate and combining some advanced analy-
sis methods with SERS (Lv et al., 2015; Convertino et al., 2016).
If the problems can be overcome, the application prospects of RS and
SERS will be very broad in the future. Specifically, the measurement of
RS is not affected by the morphology and state of the analyte, and inter-
ference of water, which will play an important role in the detection of
various substances of high amount and plant diseases. Meanwhile,
SERS possesses the in-depth applications in detection of farm chemicals,
additives, toxins, and biological molecules due to its advantages of high
sensitivity and fingerprint structure information analysis.
4. Spectral analytical methods
Spectral analytical methods are generally used to process RS or SERS
spectra to determine the type and content of analytes, including noise
reduction, feature extraction and variable selection, and modeling
methods. Automatic and intelligent analysis is beneficial for the promo-
tion and popularization of RS or SERS technology.
Spectral measurement is always accompanied with interferences
from fluorescence background, detector and environment noise, and
laser fluctuation. These interferences cannot be completely eliminated
by the improvement of equipment and experimental operation. Thus,
proper noise reduction methods are necessary to eliminate or reduce
the negative effect of interferences. The common methods include de-
rivative (Archibald et al., 1998), Savitzky–Golay (SG) smoothing, asym-
metric least squares method (asLS), standard normal variate (SNV),
wavelet transform (WT), and multiplicative scatter correction (MSC)
(Hancewicz and Petty, 1995). Derivative methods can not only reduce
the interference of overlapping spectral bands but also eliminate base-
line drift interference caused by fluorescence background. Quantitative
analysis of chlorophyll content in citrus leaves was performed through
Raman spectroscopy with first derivative of spectra (Yan-de et al.,
2019). SG smoothing eliminates high-frequency noise and improves
spectral signal-to-noise ratio. Zhai et al. (2017) used SG smoothing to
remove spectra from the spectra of salbutamol in fresh muscle tissue
to improve the accuracy. asLS can quickly realize background baseline
deduction without prior information on spectral peak shape and base-
line. The asLS baseline correction method has been used to correct back-
ground noises of microalgae Raman spectra, which originated from
6 S. Weng et al. / Artificial Intelligence in Agriculture 3 (2019) 1–10

Fig. 4. Schematic illustration of: the simultaneous detection of thiram and methamidophos on apple surface based on SERS (a) (Zhang et al., 2014); Bt gene detection procedure using
SERS-barcoded nanotags (b) (Chen et al., 2012); the ‘surface spray’ method to detect the paraquat residues on fruits (c) (Fang et al., 2015); detection of bacteria in skimmed milk
using SERS (d) (Wang et al., 2017).

samples themselves (He et al., 2018). SNV can eliminate the effects of uneven particle distribution and size. Kachrimanis et al. (2007) success-
solid particle size, surface scattering, and optical path changes on spec- fully eliminated the effects of sample preparation and sample inhomo-
tral data. MSC specializes in removing the scattering effects caused by geneity in combination with SNV and MSC. Bian et al. (2011) used

Table 2
Summary of analytes, detection matrix, measurement technique, and limit of detection (LOD)/accuracy.

Classification Analytes Matrix Measurement LOD/accuracy References

technique

Adulteration Calcium oxalate hydrate Urinary stones RS 0.6 mol Kontoyannis et al., 1997
Adulteration Margarine Butter RS 0.968 Uysal et al., 2013
Adulteration High-fructose corn syrup and maltose syrup Honey RS 0.844 S. Li et al., 2012; Y. Li et al., 2012
Crop diseases Citrus Huanglongbing Sweet orange RS 0.892 Pérez et al., 2016
Crop diseases Yellow leaf curl Sardinia virus Tomato RS N0.70 Mandrile et al., 2019
Crop diseases Spotted wilt virus Tomato RS N0.85 Mandrile et al., 2019
Farm chemicals Thiram Apple SERS 4.6 × 10−7 M Zhang et al., 2014
Farm chemicals Methamidophos Apple SERS 4.4 × 10−4 M Zhang et al., 2014
Farm chemicals Flusilazole Pear SERS 0.1 μg/g Zhao et al., 2018
Farm chemicals Chlorpyriphos Rice SERS 0.506 mg/L Huang et al., 2015
Farm chemicals Tricyclazole Rice SERS 0.002 mg/L Tang et al., 2012
Farm chemicals Ediphenphos Rice SERS 0.1 mg/L Weng et al., 2018a, 2018b
Farm chemicals Omethoate Peach SERS 0.01 mg/kg Yaseen et al., 2018a, 2018b
Additives Sudan-1 Chili powder SERS 10−4 mol/L Cheung et al., 2010
Additives Melamine Milk SERS 0.17 mg/L Giovannozzi et al., 2014
Additives Rhodamine B Chili powder SERS 10−6 g/g Lin et al., 2015
Additives Methylene blue Fish muscles SERS 10 ng/g C. Li et al., 2016; X. Li et al., 2016
Toxins Deoxynivalenol Corn SERS 10−6 M Yuan et al., 2017
Toxins Deoxynivalenol Kidney beans SERS 10−6 M Yuan et al., 2017
Toxins Deoxynivalenol Oats SERS 10−4 M Yuan et al., 2017
Toxins Aflatoxin Maize SERS 13 μg/kg Lee et al., 2014
Toxins Ricin B toxin SERS 0.32 pM Zengin et al., 2015
Toxins Microcystin-LR Tap water SERS 10−6 mg/L He et al., 2019
Toxins Saxitoxin SERS 11.7 nM Cheng et al., 2019
Toxins Ephedrine Slimming dietary supplements SERS 0.01 mg/L Lv et al., 2015
Biological Insecticidal proteins Gene-transformed rice SERS 0.1 pg/mL Chen et al., 2012
molecules
Biological Crude protein Soybeans SERS 0.916 Lee et al., 2013
molecules
Biological Oil content Soybeans SERS 0.872 Lee et al., 2013
molecules
 S. Weng et al. / Artificial Intelligence in Agriculture 3 (2019) 1–10
MSC to pretreat the spectra of metabolites in urine. The correlation co-
efficient between the predicted and real concentration was up to 0.96.
WT can perform spectral smoothing, denoising, and compression pro-
cessing to reliably distinguish and detect useful analytical signals from
interfering signals. Hu et al. (2007) used WT to denoise the Raman spec-
tra of gastric cancer tissue, performed wavelet multi-scale analysis on
the filtered spectra, and obtained baseline corrected information
through wavelet reconstruction. All these methods can effectively de-
duct the fluorescence background, eliminate the interference of noise
and baseline drift, and retain the effective information of spectra,
thereby improving the analytical capability and robustness of qualita-
tive and quantitative models. Among these methods, (SG) smoothing
can eliminate the noise signal superimposed in the Raman spectrum,
asLS can deduct the fluorescent background without changing the
Raman signal and realize the automatic correction of the spectrum.
MSC, SNV, and WT can effectively deduct the fluorescent background
and eliminate noise interference, but these methods need to adjust
the relevant parameters to get better processing results.
Spectra measured by Raman spectrometer are generally of hundreds
or thousands of dimensions. Thus, redundant and irrelevant informa-
tion is unavoidable. Feature extraction and variable selection methods
are normally used to extract main information and reduce the spectral
dimension. Feature extraction aims to decompose or transform the orig-
inal spectrum and obtain the main components according to certain
rules, Variable selection aims to select important characteristic range.
The two methods are greatly different in the principle, but the effects
are similar. The feature extraction methods include principal compo-
nent analysis (PCA) (Hasegawa et al., 2000), locally linear embedding
(LLE) (Roweis and Saul, 2000), discrete cosine transform (DCT)
(Phamila and Amutha, 2014), and nonnegative matrix factorization
(NMF) (Lee and Seung, 1999). PCA is the most widely used feature ex-
traction algorithm, which is a multivariate statistical analysis method
that combines multiple previously correlated variables in the data into
a new set of unrelated comprehensive variables in the form of linear
combination to reduce the number of new variables and contain many
information (Wold et al., 1987). Zhang et al. (2015) used PCA, DCT,
and NMF to extract features of thiram SERS spectra and established par-
tial least squares regression (PLSR) and support vector machine (SVM)
regression models. The results showed that PCA and NMF had the best
effect in PLSR and SVM models, respectively. By combining NMF with al-
ternate least squares, Hong et al. (2017) successfully realized the trace
detection of antibiotics and their metabolites in water.
The simplest variable selection method is manual interception, but it
relies on experience and existing spectral libraries. Correlation coeffi-
cient, stepwise regression, spectral peak identification, genetic algo-
rithms (GA) (Gen and Lin, 2007), uninformative variable elimination
(UVE) (Koshoubu et al., 2000), competitive adaptive reweighted sam-
pling (CARS) (Li et al., 2009), successive projection algorithm (SPA)
(Pontes et al., 2005), and interval partial least squares (iPLS)
(Norgaard et al., 2000) are the frequently used automatic selection
methods. Lavine et al. (2001) used GA to extract the characteristics of
the Raman profile of each wood type and achieved rapid classification
of different woods. Li et al. (2015) used SPA to extract the Raman char-
acteristic wavenumbers of lead chrome green in tea, greatly simplifying
the model. In the quantitative analysis of furfural oil soluble substances,
Chen et al. (2018) utilized CARS to select the optimal combination of
spectroscopy that mostly reflects the chemical operations of concern.
UVE and iPLS were employed to obtain the informative variables of
azithromycin tablets from Raman spectrum for improving the model
performance, achieving a classification accuracy of up to 0.96 (Li et al.,
2011).
After noise reduction, feature extraction, or variable selection, the
modeling algorithms are then adopted to build the classification and re-
gression models for category identification and quantity determination
of analytes. The spectral classification methods include K-means clus-
tering algorithm (KCA), k-nearest neighbor method (KNN), Linear
7
discriminant analysis (LDA), soft independent modeling of class analogy
(SIMCA), SVM, random forest (RF), naive Bayes (NB), and artificial neu-
ral network (ANN). Li et al. (2019) used KCA method in the analysis of
pathological progress after spinal cord injury by confocal Raman
microspectral imaging to highlight biochemical and structural varia-
tions after tissue damage and they obtained good results. Koljenović
et al. (2005) established a classification model of dura and tumor tissue
on the basis of LDA with an accuracy of 100%. PCA and KNN were
employed to develop diagnosis models for the Raman spectrum of
colon cancer, and the accuracy was improved to 91% (C. Li et al., 2016;
X. Li et al., 2016). SERS spectra of 7 food and waterborne viruses were
analyzed by SIMCA for identifying viruses with and without envelope,
achieving an accuracy of higher than 95% (Fan et al., 2010). Yan et al.
(2011) established an SVM model of the Raman spectra of neoplasms
in the parotid gland and successfully identified normal parotid gland
and parotid gland tumors. Kinalwa et al. (2011) used RF to determine
protein folding categories from Raman spectrum and correctly classified
33 of 44 proteins. Zhang et al. (2018) established a silicate prediction
model of drug-induced respiratory toxicity by using the NB classifier
with an overall prediction accuracy of 91.8%. Ozbalci et al. (2013) used
ANN to analyze the spectral characteristics of four sugars in honey and
predicted their contents with high accuracy.
Among these methods, SVM and RF can also be used for regression
analysis. Multivariate linear regression (MLR), principal component re-
gression (PCR), and PLSR were applied for regression analysis. PLSR and
MLR were used to establish a predication model for chloramphenicol
and crystal violet, and R2 values of chemometric models ranged from
0.82 to 0.87 (Lai et al., 2011). Guimaraes et al. (2018) adopted PCR to
quantitatively analyze dipyrone in oral solutions with a prediction
error of 0.013. Weng et al. (2018a, 2018b) used RF to develop the quan-
titative analysis models of fenthion with the root mean square error of
cross-validation of 0.0101 mg/L. Fan et al. (2015) quantified carbaryl
residues by using PLSR and SVM models. The results showed that the
carbaryl levels in apples can be predicted by PLSR (R2 = 0.983) or
SVM (R2 = 0.986) with low root mean square errors (0.48 μg/g or
0.44 μg/g) and a high ratio of performance to deviation value (7.71 or
8.11).
Deep learning methods, such as recurrent neural network,
stacked auto encoder, deep belief network, convolutional neural
network (CNN), and multi-layer perceptron (MLP), have achieved
great results in speech recognition, visual object recognition, and
object detection (LeCun et al., 2015). Nowadays, many of these
methods are applied to analyze Raman spectrum. Dong et al.
(2019) proposed a practical CNN model to discriminate the
Raman spectra of human blood and animal blood. The classification
accuracy for the calibration set and the test set was 100% and
96.33%, respectively. A novel approach entitled deep learning-
based component identification (DeepCID) was proposed to iden-
tify the mixtures. CNN models were established to predict the pres-
ence of components in mixtures. The studies DeepCID can learn
spectral features and identify components in both simulated and
real Raman spectral datasets of mixtures with high accuracy (Fan
et al., 2019). Among these modeling algorithms, the linear methods
include MLP, PLSR, PCR, LDA, and NB, and the nonlinear methods
include ANN and CNN. In addition, machine learning methods are
generally suitable for analyzing small-scale data, while deep learn-
ing is an effective and simple method for analyzing large-scale
data. Therefore, appropriate modeling methods can be selected ac-
cording to the size of the data during data processing.
In summary, the different analysis methods have different ef-
fects, and the selection of suitable analysis methods for the ob-
tained spectra is important. In regard to the analysis of a large
amount of SERS spectra, the deep learning methods may show su-
perior performance. However, with the aid of lightweight deep
learning networks, good results can still be obtained for routine
spectral analysis.
8 S. Weng et al. / Artificial Intelligence in Agriculture 3 (2019) 1–10
5. Conclusions
Recently, RS and SERS have become powerful analytical tools in ag-
riculture, food, and biosystems. This review aims to discuss the recent
advances in RS and SERS, including technical evolution, application
and challenges, and spectral processing methods. First, the origin, prin-
ciple, and defect of RS were introduced, and many signal enhancement
techniques in RS, such as RRS, CARS, TERS, and SERS were further
discussed. Then, the applications and existing problems of RS and
SERS in agriculture, food, and biosystems were described, and some fea-
sible solutions were proposed for the above problems. Moreover, the
spectral analysis methods of noise reduction, feature extraction or vari-
able selection, and modeling were analyzed in detail, which can realize
the automatic and intelligent analysis of spectra without relying on pro-
fessionals. In summary, both RS and SERS have certain limitations. RS
cannot achieve trace detection due to its low sensitivity, while SERS is
susceptible to signal interference from other components in the sample,
and the performance is poor in terms of stability and sensitivity. How-
ever, with the development of optics, nanotechnology, and instruments,
Raman technology presents wide potential application in agriculture,
food, and biosystems.
Acknowledgements
This study is supported by Anhui Provincial Major Scientific and
Technological Special Project (No. 17030701062), National Natural Sci-
ence Foundation of China (Nos. 3170123 and 61672032), National Key
Research and Development Program (No. 2016YFD0800904), and Open
Foundation of Laboratory of Quality and Safety Risk Assessment on Ag-
ricultural products (Beijing), Ministry of Agriculture (No. KFRA201802).
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