Industrial Crops & Products 146 (2020) 112162

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Industrial Crops & Products

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

Quality classification of Jatropha curcas seeds using radiographic images and T

machine learning
André Dantas de Medeiros*, Daniel Teixeira Pinheiro, Wanderson Andrade Xavier,
Laércio Junio da Silva, Denise Cunha Fernandes dos Santos Dias
Department of Agronomy, Federal University of Viçosa, CEP 36570-900, Viçosa, MG, Brazil

A R T I C LE I N FO A B S T R A C T

Keywords: Efficient seed quality assessment methodologies are important for the seed industry. Advanced seed technology
High throughput analysis research requires the use of high productivity methods that provide detailed information on seed structural
Tissue density integrity and predict its physiological potential quickly and accurately. The aim of this study was to propose a
X-ray imaging method for predicting germination capacity and discriminate Jatropha curcas L. seeds regarding germination
Prediction of seed quality
speed and seedling vigor by combining automatic X-ray analysis and machine learning model. The study was
performed using automated analysis of radiographic images of seeds, obtaining a series of morphological and
tissue integrity descriptors. After the X-ray test, the seeds were submitted to physiological assessments. Based on
all individual seed descriptors, quality classes were created and LDA models were applied. Prediction of seed
viability, germination speed and seedling vigor resulted in an average of 94.36, 83.72 and 89.72% of correctly
classified seeds, respectively. High throughput X-ray image analysis can provide information needed to dis-
criminate individual Jatropha curcas seeds into different classes of quality, i.e., germination capacity, germi-
nation speed and seedling vigor. The methodology proposed can be used to discriminate between seed classes
quickly and robustly.

1. Introduction
Jatropha curcas L. is an oilseed plant that stands out in the scenario
of growing demand for non-petroleum alternative fuels whose pro-
duction does not conflict with global food security (Steinbrück et al.,
2019). Recently, this specie has also been studied for medicinal pur-
poses, presenting potential for the treatment of bacterial infections
(Haq et al., 2019). In addition, J. curcas is resistant to various abiotic
stresses and can be grown on low fertility soils, which are unsuitable for
conventional agriculture (Lama et al., 2018).
Seed propagation is more common in this specie (Silva et al., 2018).
Therefore, the selection of high-quality seeds for the establishment of
crop fields is a fundamental part of the production process. The concept
of seed quality is composed of several attributes, including genetic
purity, health, viability, germination capacity and vigor (ISTA, 2019).
Some of this information related to seed viability, germination, and
vigor is difficult to obtain directly due to time and technological con-
straints (ElMasry et al., 2019).
Noninvasive optical technologies, such as X-ray testing, have been
successfully applied for non-destructive assessment of non-visible seed
traits (Huang et al., 2015; Rahman and Cho, 2016; Xia et al., 2019).
Recent studies have recommended the use of the 2D X-ray technique
combined with software analysis to assess seed physical characteristics
of interest more accurately and faster (Leão-Araújo et al., 2019;
Medeiros et al., 2018, 2019).
However, one of the biggest challenges today is the development of
affordable tools that can determine in advance which seeds are able to
germinate and produce vigorous seedlings, providing fast, non-de-
structive and less subjective diagnosis of individual seeds. Recent ad-
vances in the field of digital image processing and artificial intelligence
have made this kind of approach possible.
Public domain software provides promising perspectives for ad-
dressing this purpose by enabling the automation of seed radiographic
analysis (Medeiros et al., 2019). In addition, machine learning algo-
rithms, especially Linear Discriminant Analysis (LDA) models, have
shown good results for seed classification when combined with imaging
techniques (ElMasry et al., 2019; Sarigu et al., 2019, 2017).
In this sense, the use of automatic analysis of radiographic images
associated with machine learning models may offer a new perspective
for classification of J. curcas seed performance. Thus, the method could

⁎
Corresponding author at: Department of Agronomy, Federal University of Viçosa, Av. P H Rolfs, s/n, Viçosa, 36570-900, MG, Brazil.
E-mail address: andre.d.medeiros@ufv.br (A.D.d. Medeiros).

https://doi.org/10.1016/j.indcrop.2020.112162
Received 18 September 2019; Received in revised form 20 January 2020; Accepted 22 January 2020
0926-6690/ © 2020 Elsevier B.V. All rights reserved.
A.D.d. Medeiros, et al. Industrial Crops & Products 146 (2020) 112162

be included in the production chain of this oilseed, saving time and
resources, especially in the seed production process.
Thus, the main objective of this study was to propose a method to
predict J. curcas seed germination capacity and discriminate seeds re-
garding germination speed and seedling vigor by combining automatic
X-ray analysis and machine learning model.
2. Materials and methods
2.1. Local and plant material
The plant material consisted of Jatropha curcas seeds harvested in
the 2018/2019 crop season in an experimental field located in Viçosa,
Minas Gerais State, Brazil (20° 46′01.7″S 42° 52′05.6″ W). At least 20
adult plants were randomly selected, and their fruits were harvested.
The seeds were extracted manually from the fruits and placed to dry
naturally in an uncontrolled environment (25 °C and 40 RH%) until
reaching the equilibrium moisture content (approximately 8%).
TXT format.
2.3. Physiological analysis
After obtaining the radiographic images, the seeds were evaluated
for their physiological quality. For this, the germination test was con-
ducted on germination paper rolls (Germitest®) moistened with water
equivalent to 2.7 times the dry paper mass and kept in a germinator
(Mangelsdorf) at 25 °C for 12 days (Oliveira et al., 2014). The 800 seeds
were analyzed individually and daily for germination. Germinated
seeds were considered those with radicle greater than 2 mm. In the last
count, the seeds were classified into germinated seeds and non-germi-
nated seeds (those without root protrusion up to 12 days of assessment
and / or not viable). The seedlings generated were classified as normal
(those that presented all well-developed structures) and abnormal
(seedlings poorly developed or defective).
2.4. Seed classes

2.2. Digital X-ray acquisition and analysis
The seeds were submitted to internal morphology analysis by X-ray
technique. In total, 800 seeds were fixed on adhesive paper, in groups of
six seeds, in an orderly and equidistant manner. This procedure was
performed to allow individual identification of each seed in subsequent
analyses, and each seed was analyzed individually.
Radiographic images were generated by a Faxitron MX-20 model
(Faxitron X-ray Corp. Wheeling, IL, EUA). The equipment was adjusted
to a voltage of 23 kV and the seeds were exposed to radiation for 10 s at
a focal length of 41.6 cm. Image contrast has been calibrated to 16383
(width) x 3124 (center). The images were saved in Tagged Image File
Format (TIFF) files and then analyzed.
Automated image analysis was performed using the PhenoXray
macro (Medeiros et al., 2019) developed for the software ImageJ®
(https://imagej.nih.gov/ij/download.html) (Schindelin et al., 2015).
The sequential analysis performed by the macro consisted of scale ca-
libration (39,6003 pixels / mm), segmentation and extraction of dif-
ferent morphometric and tissue integrity descriptors of each seed con-
tained in each image.
In more detail, each opened image was duplicated and segmentation
was done on the image copy. ImageJ® Threshold mode was used and
the Yen's automatic multilevel thresholding method was selected (Yen
et al., 1995) for segmentation. Then the selections in the binary image
were redirected to the original image. Finally, the area of interest
(seeds) was analyzed using the “analyze particles” command, gen-
erating 15 descriptors listed in Table 1. After processing, the analysis
results were stored in a pivot table and automatically saved to a file in
According to the data obtained from the germination test, J. curcas
seeds were classified into different categories based on: i) germination
capacity; ii) germination speed and viability; and iii) seedling vigor.
Based on germination data, seeds were classified into two groups:
Class 1 – germinated seeds; and Class 2 – non-germinated seeds. In addi-
tion, in a second classification, the germinated seeds were divided ac-
cording to the germination speed (time required to initiate root pro-
trusion). Then, three classes were tested: Class 1: rapid germination –
root protrusion up to 96 h after initiation of imbibition; Class 2: slow
germination - root protrusion after 96 h after initiation of imbibition;
and Class 3: non-germinated seeds. The period of 96 h was defined based
on the accumulated germination curve for this experiment. At this time,
approximately 80% of the seeds were geminated. Finally, according to
seedling vigor, the germinated seeds were classified into two classes:
Class 1: normal – seeds that generated well-developed seedlings; and
Class 2: abnormal – seeds that generated seedlings showing absence,
underdevelopment or deformation of some essential structure (cotyle-
dons, primordial leaves, roots).
For the analyses, the data set (800 seeds) was divided into two
subsets: a training set (n = 635 seeds), used to develop the dis-
crimination models, and a validation set (n = 165 seeds), for validate
the models developed (Table 2).
2.5. Multivariate data analysis and machine learning
Principal Component Analysis (PCA) was applied as a multivariate
exploratory analysis technique to identify the hidden patterns in the
data obtained from X-ray analysis. Thus, the data obtained from

Table 1
List of descriptors generated by the analysis of radiographic images of seeds.
Abreviation Name descriptor Description

Area Area (mm2) Area inside the polygon defined by the perimeter.
Mean Mean Gray (gray·pixel−1) Average gray value within the selection.
StdDev Standard Deviation Standard deviation of the gray values.
Perim. Perimeter (mm) Length in millimeters of the outer limit of the selection.
Width Width (mm) Width of the smallest rectangle that encompasses the selection.
Height Heigth (mm) Height of the smallest rectangle that encompasses the selection.
Circ. Circularity Circularity = 4·π·Area/Perimeter2
IntDen Integrated density (gray·mm·pixel−1) The sum of the greyscale values in the particle
Median Median Median greyscale
Skew Skewness The third order moment about the mean
Kurt Kurtosis The fourth order moment about the mean
%Area Seed filling (%) Determined by dividing the area effectively filled with high-density tissue (grey levels above the initially defined threshold)
by the total area of each seed
AR Aspect ratio Aspect ratio = major axis/minor axis
Round Roundness Round = 4·Area/(π·major axis2)
Solidity Solidity Solidity = Area/ConvexArea

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A.D.d. Medeiros, et al. Industrial Crops & Products 146 (2020) 112162

Table 2 and gray level of the images (e.g. Mean, IntDen, Median, %Area, Skew,
Final number of seeds for each class used in the training and validation data Kurt). Except for the asymmetry, the other descriptors related to the
sets. gray level of the radiographs tended to have the highest averages as-
Classification type Training set Validation set sociated with Class 1 (Germinated) seeds and the lowest averages as-
sociated with Class 2 (Non-germinated) seeds. This trend was main-
Class 1 Class 2 Class 3 Class 1 Class 2 Class 3 tained in the classifications based on germination speed and seedling
vigor, where seeds with better performance, i.e., Class 1 seeds, had
Germination 468 167 – 129 36 –
Speed of germination and 377 91 167 91 38 36 higher averages for the descriptors.
viability
Seedling Vigor 414 221 – 108 57 –
3.2. Viable and non-viable Jatropha curcas seeds overview

radiographic analysis for all seeds were arranged in an X matrix
(800 × 15), where the rows represented the observations (seeds) and
the columns represented the variables.
Then, descriptors obtained from seed radiographs were used to
develop multivariate discrimination models for classifying seeds into
different categories based on their germination and seedling data. The
seeds were divided into training and validation sets (Table 2), and the
Linear Discriminant Analysis (LDA) classification models were devel-
oped using the training set and the obtained models were validated
using the independent validation set, which was not used during the
construction of the models. For the development of the models using
the LDA method, the data obtained from the radiographic images were
arranged in an X matrix (the predictors) and the data resulting from the
Y vector germination test (response variable). In this study, the accu-
racy of the LDA models was assessed by the percentage of correctly
classified seeds. All statistical analyses were performed using the soft-
ware R 3.6.1 (R Core Team, 2019).
3. Results
3.1. Seed internal morphology and physiological data
The averages of the morpho-anatomical parameters obtained
through the automated analysis of the seed radiographs for each clas-
sification type are presented in Table 3. For germination-based classi-
fication, major differences in the averages between classes were ob-
served for most descriptors, especially those related to the distribution
The morphometric and tissue integrity data, obtained from the
analysis of radiographic images of the seeds, were submitted to PCA
analysis (Fig. 1). The first three main components explained 79.88% of
the original variation between seed descriptors with 45.36, 26.51 and
8.01% for PC1, PC2 and PC3, respectively. As presented in the PCA
scores, there was seed separation according to germination in the ger-
minated (yellow) and non-germinated (blue) classes. These data show
that, from the assessment of the internal morphology of the seeds, it is
possible to infer about their germination capacity. The parameters that
most contributed to the constitution of the first dimensions of the
components were seed filling and tissue integrity (e.g. seed filling, gray
median, gray mean, skewness – supplementary material), which de-
monstrates the relationship of these characteristics with the physiolo-
gical quality of seeds. However, some non-germinated seeds were
grouped with germinated seeds and vice versa (Fig. 1).
3.3. Discrimination models for seed classification
Three different models were developed based on Linear
Discriminant Analysis (LDA) aiming to classify seeds into different
classes, based on germination capacity, germination speed and viability
and seedling vigor. The classifications were stored in the Y vector, and
the data obtained from the automatic analysis of digital seed radio-
graphs were stored in the matrix X.

Table 3
Averages followed by the standard deviation obtained for morpho-anatomical descriptors of Jatropha curcas seeds in different classes, based on germination capacity,
germination speed and viability and seedling vigor.
Classification type Descriptor

Class Area Mean StdDev Perim. Width

Germination 1 153.5 ± 11.28 169.6 ± 17.57 70.4 ± 6.03 59.4 ± 12.27 10.9 ± 0.45
2 140.4 ± 14.07 99.3 ± 33.04 66.6 ± 9.69 59.6 ± 9.22 10.1 ± 0.73
Speed of germination and viability 1 155.1 ± 10.86 173.2 ± 13.76 70.6 ± 5.78 60.9 ± 13.06 10.9 ± 0.44
2 147.9 ± 11.01 156.8 ± 23.1 69.4 ± 6.79 53.7 ± 6.19 10.7 ± 0.45
3 140.4 ± 14.07 99.31 ± 33.04 66.6 ± 9.69 59.6 ± 9.22 10.1 ± 0.73
Seedling Vigor 1 154.3 ± 10.94 172.3 ± 14.54 70.4 ± 5.74 60.0 ± 12.58 10.9 ± 0.44
2 142.6 ± 14.04 113.2 ± 38.51 67.5 ± 9.31 58.3 ± 9.3 10.3 ± 0.74
Height Circ. IntDen Median Skew
Germination 1 17.7 ± 0.84 0.59 ± 0.15 26114 ± 3606 195.1 ± 21.8 −0.91 ± 0.21
2 18.2 ± 1.22 0.52 ± 0.12 14231 ± 5794 98.6 ± 46.27 0.21 ± 0.57
Speed of germination and viability 1 17.8 ± 0.83 0.57 ± 0.15 26881 ± 2915 199.3 ± 17.46 −0.94 ± 0.17
2 17.4 ± 0.81 0.66 ± 0.09 23330 ± 4423 180.1 ± 28.4 −0.79 ± 0.26
3 18.2 ± 1.22 0.52 ± 0.12 14231 ± 5794 98.6 ± 46.27 0.21 ± 0.57
Seedling Vigor 1 17.7 ± 0.82 0.58 ± 0.15 26626 ± 3130 198.2 ± 18.23 −0.93 ± 0.17
2 18.0 ± 1.19 0.55 ± 0.13 16474 ± 6615 118.9 ± 54.21 −0.04 ± 0.66
Kurt %Area AR Round Solidity
Germination 1 −0.29 ± 0.37 97.9 ± 2.12 1.63 ± 0.07 0.61 ± 0.03 0.99 ± 0
2 −0.69 ± 0.67 90.0 ± 6.95 1.79 ± 0.15 0.56 ± 0.05 0.98 ± 0.01
Speed of germination and viability 1 −0.24 ± 0.35 98.3 ± 1.25 1.63 ± 0.07 0.61 ± 0.03 0.99 ± 0
2 −0.45 ± 0.38 96.6 ± 3.61 1.63 ± 0.08 0.62 ± 0.03 0.99 ± 0
3 −0.69 ± 0.67 90.0 ± 6.95 1.79 ± 0.15 0.56 ± 0.05 0.98 ± 0.01
Seedling Vigor 1 −0.25 ± 0.35 98.2 ± 1.34 1.63 ± 0.07 0.61 ± 0.03 0.99 ± 0
2 −0.66 ± 0.61 91.5 ± 6.86 1.75 ± 0.15 0.58 ± 0.05 0.98 ± 0.01

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A.D.d. Medeiros, et al.
Fig. 1. PCA biplot obtained for seed morphometric data (n = 800) of Jatropha curcas showing two seed classes (germinated and non-germinated).
3.4. Discrimination between germinated and non-germinated seeds
The discrimination model developed to classify seeds into germi-
nated and non-germinated was established to identify whether the in-
dividual seed had internal characteristics (assessed from images ob-
tained in the X-ray spectral range) that affected its viability and
germination capacity. The results of the prediction of seed participation
in the classes and the correctness general classification of the model are
presented in Table 4 for the training data and the independent vali-
dation.
The LDA model obtained was highly accurate to distinguish ger-
minated and non-germinated seeds, with an accuracy of 94.8, 93.93%
for training and independent validation data sets, respectively.
3.5. Seed discrimination based on germination speed and seed viability
Seeds were classified according to germination speed and seed
viability into three groups: seeds that germinated up to 96 h (rapid
germination); seeds that germinated after 96 h (slow germination); and
non-germinated seeds (not viable).
The LDA model obtained allowed to discriminate between these
three classes with accuracy of 85.03 and 82.42%, for training and va-
lidation data, respectively (Table 5). It was observed that the model
accuracy was higher for distinguishing fast germinating seeds and non-
germinated seeds compared to slow germinating seeds (61.02% and
Table 4
LDA Confusion Matrices for participation in 'Germinated' and 'Un-germinated' Jatropha curcas seed classes in training and validation sets.
Feature Training set (n = 635)
Germinated Non-Germinated
Germinated 463 28
Non-Germinated 5 139
Overall correct classification (%)
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Industrial Crops & Products 146 (2020) 112162
76.00% accuracy, for training and validation data, respectively).
Based on the first two discriminant factors (LD1 and LD2), which
explained 95.52% and 4.48% of the total variance, respectively, the
seeds were grouped according to the three classes (Fig. 2A). Non-ger-
minated seeds, which were located in the negative LD1 scores, were
mostly separated and well differentiated from the classes Fast germi-
nation and Slow germination. It is important to emphasize that the dif-
ference between seeds germinated rapidly and germinated slowly is
very subtle, as these two classes comprises seeds that germinated. Thus,
there were greater interactions between the classes Fast germination and
Slow germination due to the low variation between individual seeds in
terms of their physical properties. Thus, the model is efficient to dis-
tinguish seeds with germination potential from non-viable seeds, based
on the physical characteristics assessed by automatic analysis of
radiographic images.
The discriminant function included 15 descriptors. In Fig. 2C, the
first three columns show the averages of each descriptor by category.
Higher averages are shaded in blue and lower averages in red, with
significant values at the 5% level in bold. The R-Squared column shows
the proportion of variation within each row that is explained by the
descriptor. In this measure, the five most discriminating descriptors
were mean (gray mean), median (gray median), skewness (asymmetry),
IntDen (integrated density) and %Area (seed filling). Seeds with fast
germination, in general, presented higher averages in the dis-
criminating factors listed, except Skewness, which presented negative
Validation set (n = 165)
%Correct Germinated Non-Germinated %Correct
94.30 124 5 96.12
96.53 5 31 86.11
94.8 93.93
A.D.d. Medeiros, et al. Industrial Crops & Products 146 (2020) 112162

Table 5
LDA Confusion Matrices for participation in Jatropha curcas seed classes based on germination speed and viability in training and validation sets.
Feature Training set (n = 635) Validation set (n = 165)

Fast Slow Non-Germinated %Correct Fast Slow Non-Germinated %Correct

Fast 366 53 15 84.33 87 16 3 82.08

Slow 9 36 14 61.02 3 19 3 76.00
Non-Germinated 2 2 138 97.18 1 3 30 88.24
Overall correct classification (%) 85.03 82.42

Fig. 2. LDA graph obtained from Jatropha curcas seeds morpho-anatomical data and classification according to germination speed. LDA ordination diagram with the
arrangement of individuals in their respective groups (A). LDA biplot with predictors and the centroid of the inserted classes (B). Averages, contribution and
significance of the descriptors for class differentiation (C). The training data were used to draw the graph.

values (Table 3). The opposite was observed for non-viable seeds.
3.6. Discrimination between normal and abnormal seedlings
The LDA model constructed to classify J. curcas seeds capable of
producing normal seedlings and seeds that produced abnormal seed-
lings revealed high accuracy. The results demonstrate an overall clas-
sification accuracy of 89.76 and 89.69% in training and validation
datasets, respectively (Table 6). These results point to a direct re-
lationship in the internal morphology of the seeds and the ability to
generate well developed seedlings.
From the data of the morpho-anatomical parameters of the seeds
(Table 3), it can be observed that the seeds that originated normal
seedlings presented higher averages in the descriptors related to the
gray level of the images, that is, the images of the seeds had higher
radiopacity.
4. Discussion
Changes in morpho-anatomical properties of Jatropha curcas seeds
may occur due to several factors such as physiological disturbances
during maturation, insect predation, tissue deterioration, incidence of
pathogens, damage caused by improper storage conditions, among
others (Moncaleano-Escandon et al., 2013; Silva et al., 2018; Suresh
et al., 2019). Optical technologies, able to non-destructively access
these changes, generate time and resource savings (Rahman and Cho,
2016). The 2D X-ray technique is well-established for seed analysis,
indicated by the International Seed Testing Association (ISTA, 2019),
and for its simplicity of execution and lower cost can be considered
attractive from a practical standpoint compared to other methods more
advanced, that is, magnetic resonance imaging, microtomography, high
cost multispectral equipment.
However, when the analysis of 2D X-ray images is performed vi-
sually, the risks of error increase considerably due to the subjective
interpretations of analysts, in addition to the great time spent on the
analysis (Xia et al., 2019). The high-performance x-ray analysis pro-
posed in this paper is a valuable alternative to reduce these difficulties.
Some descriptors generated from the automated analysis of radio-
graphic images proved to be important in the discrimination between
seed classes regarding physiological quality, such as mean and median
of gray, integrated density, asymmetry and filling. These parameters
were correlated with the physiological quality of seeds of other species,
such as Brachiaria ruziziensis (Medeiros et al., 2019) and Leucaena leu-
cocephala (Medeiros et al., 2018).
The variations observed in the descriptors in the range of the X-ray
electromagnetic spectrum between individuals are attributed to
changes in seed morphological and anatomical properties. Compared to
the higher quality seeds (germinated, fast germinating and well-formed

Table 6
LDA Confusion Matrices for partition into Jatropha curcas seeds classes that originated normal and abnormal seedlings.
Feature Training set (n = 635) Validation set (n = 165)

Normal Abnormal %Correct Normal Abnormal %Correct

Normal 164 8 95.35 45 5 90.00

Abnormal 57 406 87.69 12 103 89.57
Overall correct classification (%) 89.76 89.69

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A.D.d. Medeiros, et al.
seedlings), the lower quality seeds had lower resistance to X-ray pas-
sage generating images with lower gray levels (Table 3). The mean gray
level of the seed is directly related to its tissue density (Medeiros et al.,
2018), higher gray means are related to seeds with higher amounts of
reserves, lower incidence of physical damage and higher physical in-
tegrity of the tissue. In addition to the gray mean, other descriptors
studied as% Area and IntDen are closely related to the filling and
density of tissue of reserves available in J. curcas seed. These char-
acteristics are physiologically important, linked to a good initial seed-
ling establishment in the field (Finch-Savage and Bassel, 2016) and
related to other properties of interest to the industry, such as oil content
(Pinto et al., 2018).
It is important that the proposed method for seed quality assessment
is efficient in distinguishing high quality seed from low quality seed
(Huang et al., 2015; Kotwaliwale et al., 2014; Rahman and Cho, 2016).
In this sense, the focus of the present work was to use the information
extracted from radiographic images of seeds to predict the capacity of
these seeds to germinate and produce normal seedlings. The LDA
models developed in this research for the different J. curcas seed classes
showed a high degree of discrimination between them, as can be seen
briefly in Fig. 3.
The results revealed that the method is highly satisfactory to predict
germination capacity and to explore the possibility of discriminating
the vigor of individual seedlings. In general, the classical statistical
approach of LDA achieves maximum class discrimination by calculating
the optimal transformation that minimizes distance within the class and
maximizes the distance between classes simultaneously (Maione and
Barbosa, 2018). However, we inquired that other machine learning
models (e.g. artificial neural networks) could be examined in future
research to increase overall classification accuracy, especially for ger-
mination rate related classes. It is important to emphasize that this is a
pioneering work, combining high yield analysis technique of radio-
graphic images with machine learning models to predict seed physio-
logical quality.
Recent research using seed X-ray image analysis has found a good
correlation between the descriptors of seed filling and tissue integrity
with seed germination and seedling length in Brachiaria ruziziensis
(Medeiros et al., 2019), Campomanesia adamantium (Leão-Araújo et al.,
2019), Leucena leucocephala (Medeiros et al., 2018), among other
works. In this sense, descriptors generated using the PhenoXray macro
in digital radiographs were correlated with physiological attributes of
brachiaria seeds (Brachiaria ruziziensis). The results revealed high cor-
relations (r > 0.94) between the physical descriptors of the radio-
graphic image with physiological quality aspects, and that seed lots
with lower physiological quality presented lower gray levels (called
relative density) than the good quality lots (germination > 60%)
(Medeiros et al., 2019). Other imaging techniques have also been ap-
plied in previous work in combination with machine learning models
Fig. 3. Accuracy of LDA models developed for different classification scenarios
of Jatropha curcas seeds in classes, based on germination and development
parameters of seedlings, using morpho-anatomical parameters of seeds.
6
Industrial Crops & Products 146 (2020) 112162
for seed classification. In cowpea, using single-seed spectral signatures
extracted from VideometerLab3® multispectral images, different linear
discriminant analysis (LDA) models classified seeds for germination
with a precision percentage greater than 96% (ElMasry et al., 2019).
Seeds with rapid germination speed and vigorous seedlings are ex-
tremely important for the agricultural system. These seeds and seed-
lings are less subject to biotic and abiotic stresses, which ensures proper
establishment of the plant stand in the field (Finch-Savage and Bassel,
2016). Thus, finding a good relationship between easily measurable
descriptors and complex attributes of physiological quality are valuable
findings for the advancement of seed science. As observed in the present
work, descriptors of J. curcas seed internal morphology were efficiently
used in the elaboration of seed quality prediction models. Seed com-
panies can use these descriptors to make decisions regarding the des-
tination and disposal of seed lots, which saves time and resources
during processing and quality control of seed production.
Fig. 4 highlights the gray levels assessed in the seed radiographs as
being associated with physiological characteristics related to viability
and vigor of J. curcas seeds. It shows the original radiographic image,
the seed gray histogram and the color 3D representation of the tissue
density in gray per pixel. Warm colors are associated with high-density
regions, while cool colors are associated with low-density regions.
Seeds of higher physiological quality (Fig. 4D) have higher gray values,
which means higher tissue density, and give rise to better developed
seedlings. On the other hand, seeds with lower gray values give rise to
abnormal seedlings (Figs. 4B and C) or do not have the ability to ger-
minate (Fig. 4A), as observed in this experiment. This representation
only visually reinforces what has been observed in previous results,
which point to a strong link between these characteristics.
Thus, the present work presented promising results on the re-
lationship between seed physical characteristics and physiological
quality, but this relationship cannot always be easily visualized, since
seeds as biological objects are multi-parametric and multicomponent
nonlinear complex systems (Arkhipov et al., 2019), which are influ-
enced by other factors, mainly environmental. However, this work of-
fers new perspectives for further study of the association of imaging
techniques with physiological, biochemical and genetic processes in
seeds.
High-throughput analysis of J. curcas seed radiographs combined
with LDA machine learning models proved to be a fast, non-destructive,
non-subjective and highly accurate method for classifying seeds for
viability and vigor.
5. Conclusion
High throughput X-ray image analysis provides information needed
to discriminate Jatropha curcas individual seeds into different quality
level classes quickly and robustly. LDA-based machine learning models
were adequate to discriminate seed classes with high accuracy.
CRediT authorship contribution statement
André Dantas de Medeiros: Methodology, Formal analysis,
Writing - original draft. Daniel Teixeira Pinheiro: Conceptualization,
Data curation. Wanderson Andrade Xavier: Data curation. Laércio
Junio da Silva: Supervision. Denise Cunha Fernandes dos Santos
Dias: Project administration.
Declaration of Competing Interest
The authors declare that they have no known competing financial
interests or personal relationships that could have appeared to influ-
ence the work reported in this paper.
A.D.d. Medeiros, et al.
Fig. 4. Radiographs of Jatropha curcas seeds with their respective histograms and 3D color representation of the gray levels of each pixel. Non-germinated seed (A),
slow germinating seed and abnormal seedling (B), embryo-damaged seed and abnormal seedling (C) and fast germinating healthy seed and normal seedling (D).
Acknowledgment
The authors are grateful to the Coordenação de Aperfeiçoamento de
Pessoal de Nível Superior, Brasil (CAPES), Finance Code 001, Conselho
Nacional de Desenvolvimento Científico e Tecnológico (CNPq) and
Fundação de Amparo à Pesquisa do Estado de Minas Gerais (FAPEMIG)
for the financial support.
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