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Towards an Automated Medical Diagnosis System for Intestinal Parasitosis

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DOI: 10.1016/j.imu.2019.100238

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 Informatics in Medicine Unlocked 16 (2019) 100238

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Informatics in Medicine Unlocked

journal homepage: http://www.elsevier.com/locate/imu

Towards an automated medical diagnosis system for intestinal parasitosis

Beaudelaire Saha Tchinda a, Michel Noubom b, Daniel Tchiotsop a, *, Valerie Louis-Dorr c,
Didier Wolf c
a
Laboratoire d’Automatique et d’Informatique Appliqu�ee (LAIA), IUT-FV de Bandjoun, Universit�e de Dschang-Cameroun, B.P. 134, Bandjoun, Cameroun
b
D�epartement des Sciences Biom�edicales, Facult�e de M�edecine et des Sciences Pharmaceutiques, Universit�e de Dschang-Cameroun, Cameroun
c
Centre de Recherche en Automatique de Nancy (CRAN), UMR CNRS 7039, ENSEM, Universit�e de Lorraine, Nancy, France

A R T I C L E I N F O A B S T R A C T

Keywords Human parasites are a real public health problem in tropical countries, especially in underdeveloped countries.
Intestinal parasites Usually, the medical diagnosis of intestinal parasites is carried out in the laboratory by visual analysis of stools
Wavelet edge detector samples using the optical microscope. The parasite recognition is realized by comparing its shape with known
Hough transform
forms. We offer a solution to automate the diagnosis of intestinal parasites through their images obtained from a
Active contours
microscope connected directly to a computer. Our approach exploits the contour detection based on the multi-
Probabilistic neural network
scale wavelet transform for detecting the parasite. Active contours are combined with the Hough transform to
perform image segmentation and extraction of the parasite. We used principal component analysis for the
extraction and reduction of features obtained directly from pixels of the extracted parasite image. Our classifi­
cation tool is based on the probabilistic neural network. The obtained algorithms were tested on 900 samples of
microscopic images of 15 different species of intestinal parasites. The result shows a 100% recognition rate of
success.

1. Introduction
The parasite is an organism that lives at the expense of its host, which
is also an organism. Intestinal parasites are a form of human parasitosis.
Approximately four billion people are affected in the world [1]. Intes­
tinal parasites are responsible for physical or behavioral disturbances in
children, in immuno-deficient persons, and in worst cases, can cause
death. The diagnosis of intestinal parasites is carried out in the labora­
tory by observing stools samples through an optical microscope. The
parasite identification is done by comparing the shape observed with
known forms. This practice is time consuming and laborious. In addi­
tion, this clinical test is slow and prone to many errors of diagnosis.
There is no reliable quality control. The aim of our research in this
article is to contribute to solving these problems.
In the literature, we found some studies devoted to the medical di­
agnostics of intestinal parasites based upon microscopic image analysis.
Parasitic organisms have at certain stages of its development, well
known morphologies. They therefore lend themselves to pattern
recognition techniques. Various approaches in the literature can be
distinguished either by the parasite species involved in classification, or
by the type of characteristics used by the classifier. In Ref. [2], the au­
thors were interested in identifying human helminthes eggs through
artificial neural networks (ANN). Widmer et al. [3] focused on the
recognition of Giardia cysts and Cryptosporidium oocysts using the
artificial neural network and immunofluorescence microscopy. Using
Bayesian classification, Castanon et al. [4] identified seven species of
Eimeria. Ginoris et al. [5,6] used an artificial neural network to recog­
nize metazoa and protozoa, that are commonly found in the mud.
Dogantekin et al. [7] and Avci et al. [8] used support vector machines
(SVM) and a fuzzy inference system based on an adaptive network, to
recognize helminthes eggs. In Ref. [9], the authors proposed a diagnostic
method for roundworm and whipworm eggs using the parameters of
shape, roundness and dimension. Their classifier is based on a filtering
system with determination of stable thresholds. However, these studies
do not address the identification of human intestinal protozoa, and the
parasites segmentation step is manual. Suzuki et al. [10] proposed a
significant advance towards the automation of parasites diagnosis by
image analysis. Their approach is the first to focus on 15 species of
protozoa and helminthes among the most common in Brazil. The image
analysis method used in Ref. [10] has three main steps: the image

DOI of original article: https://doi.org/10.1016/j.imu.2018.09.004.

* Corresponding author.
E-mail address: daniel.tchiotsop@univ-dschang.org (D. Tchiotsop).

https://doi.org/10.1016/j.imu.2019.100238

Available online 22 August 2019

2352-9148/© 2019 Published by Elsevier Ltd.
B.S. Tchinda et al.
segmentation that locates and delimits objects present in the image; the
description of the forms that extracts the features of the segmented
object; the classification that uses these features to perform the recog­
nition of the species of parasites. These features include the parameters
of roundness, geodesic distances, curvature variance, texture, perimeter,
and area of the parasite. The classifier used in Ref. [10] is based on the
image foresting transform (IFT) method. A performance analysis of al­
gorithms for the identification of intestinal parasites is proposed in
Ref. [11]. In Ref. [12], the authors proposed a system for the identifi­
cation and quantification of pathogenic helminth eggs using a segmen­
tation by the watershed method. Their classification system uses the
nearest neighbor algorithm. This analysis remains limited to the eggs of
two species of helminthes (roundworms and whipworms).
Saha et al. proposed in Ref. [13] the first and partial solution devoted
to the recognition of 9 species of amoebic cysts. In this paper, a complete
system for automated medical diagnosis of human intestinal parasites is
proposed. As well as in Ref. [13], our method is based on the processing
of microscopic images and an artificial neural network system. The steps
of our approach are edge detection, image segmentation and pattern
recognition. One of the main novelties of our method over the existing
techniques is that the step of detection and extraction of parasites in
microscopic images is fully automated. Another difference of our
method over previous methods of parasite diagnosis is the descriptor
type of characteristics that we used. Our features descriptor directly uses
the pixel of the image and does not need to compute other parameters.
Our identification tool uses principal components analysis (PCA) in the
reduction of dimensionality and the probabilistic neural network for
classification. In addition, the varieties of intestinal parasites are
extended to 15 in this work. Also, the results of the different steps of our
system are detailed and the models used are justified here.
In the next section, we present the equipment and methodology used.
This requires image acquisition, segmentation and recognition. In sec­
tion III, the experimental results are provided with detailed discussion.
This is followed by a discussion in section IV and the conclusion in
section V.
2. Materials and methods
The main objective of our system consists in identifying and recog­
nizing the varieties of human parasites in feces slides. For this purpose,
we designed a system whose functioning is given by the block diagram
illustrated in Fig. 1. After acquiring microscopic stools images, our
system makes image segmentation and extracts the parasites. Classifi­
cation features are then extracted from the image. These features are
input to the neural network. After training and testing, the classifier
provides the result of the recognition by displaying the type of parasite
Fig. 1. Flowchart of the proposed system.
2
Informatics in Medicine Unlocked 16 (2019) 100238
detected.
2.1. Acquisition of the microscopic images of stools
The microscope provides a representation of what is not visible to the
naked eye. An optical microscope coupled to an acquisition sensor was
used in our study. It will permit us to access the image of parasites for
recognition. Images of stools are captured via microscope and trans­
ferred to computer for analysis and diagnosis as shown in Fig. 2. As can
be seen in Fig. 2, to acquire stools images, we used glass slides and
microscopy slides; an optical microscope with digital camera eyepiece
and PC plug: “TRAVELER MICROSCOPE”, with its illuminated pen, PC
installation drivers and a video capture program; a laptop: Intel (R)
Pentium (R) M 2.26GHz processor, 504MB RAM, Microsoft Windows XP
SP1, 55GB hard disk with more than 5GB free, a HI color display screen
(1024 � 768 pixels). Note that the characteristics of our computer are
much higher than the minimum required for this microscope namely:
Pentium III 800Mhz or more, recommended for digital video (DV),
256MB RAM or more, Microsoft Windows 98 SE, Windows Me, Windows
2000 or Windows XP; at least 500 MB of available hard disk memory
(4GB is recommended); a True Color or HI color display (1024 � 768
pixels).
The microscopic images of stools that weused were obtained in a
parasitology laboratory of the Public Regional Hospital and in a private
clinical laboratory “Clab-Labo” both in the town of Bafoussam-
Cameroon. More images of parasitized stools were obtained from data­
bases available online [14,15].
2.2. Segmentation and extraction of the parasite
Generally, a microscopic image of stools contains many unnecessary
items for diagnosis. In addition, there are many parasites in a single
image. Then, before its recognition, each parasite must be individually
extracted. The parasite extraction is done through the process of seg­
mentation. Segmentation techniques are either region based or contours
based methods. Firstly, methods based on the region use the intrinsic
properties of objects that are to be extracted. These methods depend
heavily on image characteristics and the shape to be extracted. The
second category of methods is based on the outline that seeks the con­
tours of the objects to be extracted by using the discontinuity of the
image intensity. The edge detection processes either the maxima of
gradient or the zero crossing of the Laplacian of the image intensity
function. In Ref. [16], Tchiotsop et al. have shown that the edge detection
using multi-scale wavelet produces better results than other conven­
tional edge detectors, and particularly when it is applied on microscopic
images of feces. The main advantage of the multi-scale wavelet
Fig. 2. The acquisition materials consisting on a microscope directly connected
to a computer.
B.S. Tchinda et al. Informatics in Medicine Unlocked 16 (2019) 100238

transform in edge detection is the ability to choose the size of the details 2.2.2. Principle of the hough transform
that will be detected. Nevertheless, the outlines obtained are often split. The Hough transform (HT) is a tool used to determine significant
The Hough transform can extract parametric shapes in an image. It is groups of characteristic points that meet some parametric constraints. It
used in computer vision problems such as the detection of lines, circles, is based on the general principles defined by parametric constraint of the
ellipses or other curves. The Hough transform is successfully used on form of the following equation:
ultrasound images by Golemati et al. [17] to highlight transverse and
f ðX; AÞ ¼ 0 (3)
longitudinal sections of the carotid artery. The form of certain intestinal
parasites such as amoebic cysts is circular. Thus, a circular model of the
where X ¼ ðx1 ; x2 ; :::; xn ÞT is a point of the image and A is a vector of
Hough transform can be easily used for their detection and extraction.
parameters.
Meanwhile, other irregular shapes will not be totally located. The active
The constraints can represent curves (lines, circles, etc.), the surfaces
contours technique, also called the snake model, is another segmenta­
(planes, cylinders, etc.) or the movement trajectories (of translation,
tion approach. It is very effective in contours detection. An imple­
rotation, etc.), depending on the interpretation of the feature point. For
mentation example of this method is presented in Ref. [18]. The high
our case, the feature points are edge pixels obtained from the multi-scale
dependence of active contours to the initial contour is a major disad­
wavelet transform. However, they could also be of the gray level values.
vantage. When the initial outline is near to the target contour, the active
We are interested to the detection of circular shapes in the image. In
contours algorithm converges quickly. The combination of snake model
Cartesian coordinates, the equation of a circle is given as follows:
with the Hough transform is feasible. The Hough transform allows one to
automatically locate the parasite region of interest. This computational ðx aÞ2 þ ðy bÞ2 ¼ r2 (4)
result is then considered as the initial outline for the active contours. In
Ref. [19], this method is successfully utilized in the extraction of human where ða; bÞ represents the coordinates of the center and r is the radius of
parasites on microscopic images of stools. Segmentation uses the outline the circle.
map of the image to separate the parasite from its background. This In the parametric constraints of equation (3), the parameter vector is
image background of the parasite is next deleted using a logic operation. given by equation (5)
Thus, our segmentation algorithm uses the active contours combined
Aða; b; rÞ (5)
with the Hough transform. The multi-scale wavelet transform is used to
detect the edges of the parasites. Here, X ¼ ðx; yÞ is a point of the image.
For each pixel in the contour, we want to know if this pixel belongs to
2.2.1. Principle of the edge detection based on the multi-scale wavelet a circle. Thus we find the place for parameters of that circle. This can be
transform seen from equation (4) that x and y are considered to be fixed points,
It is shown in Ref. [20] that the wavelet transform Wa fðx; yÞ of an while a, b and r are varying. The basic method uses a three-dimensional
image fðx; yÞ is proportional to the first derivative smoothed by a accumulator array A (a,b,r). Each contour element vote for all the circles
convolution kernel θðx; yÞ at a given scale a. This proportional rela­ to which it may belong and the peak of the accumulator array A (a,b,r) is
tionship is given by the following equations: sought. This peak gives the position of the circle and its radius. If it
0 1 happens that we know the radius in advance, we will only need a 2-D
∂
1
!
B ðf *θa Þðx; yÞ C array accumulator. The full version of the Hough transform algorithm
Wa f ðx; yÞ B ∂x C can be found in Ref. [19] and references therein.
Wa f ðx; yÞ ¼ ¼ aB C ¼ arðf *θa Þðx; yÞ (1)
Wa2 f ðx; yÞ @∂ A
ðf *θa Þðx; yÞ
∂y 2.2.3. Contour optimization through the gradient vector flow (GVF) active
� � contours
with. θa ðx; yÞ ¼ 1a θ xa; ay The method of active contours is based on the construction of an
To locate the edges on an image, the wavelet transform module is energy functional that measures the relevance of the outline. The model
first computed. Its local maxima is then determined in the direction of of the Gradient Vector Flow (GVF) is one of the snake models that was
the gradientrðf *θa Þðx; yÞ. The modulus-angle representation of the developed in order to increase the capture range and improve the ability
wavelet transform, at each scale a (a ¼ 2j ;j 2 ℕ) is defined in Refs. [16, of the snake model to move within the limits of concavities. The GVF
20] by the following equation: model addresses these problems by introducing a new external force.
The Gradient Vector Flow field is defined to minimize the following
8 qffi�ffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffi�ffiffiffiffiffiffiffiffiffi�ffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffi�ffiffiffi
> 2 2 energy functional [21]:
> M2j f ðx; yÞ ¼ �w12j f ðx; yÞ � þ �w22j f ðx; yÞ �
>
>
< ZZ n � � o
2
! (2) E¼ μ: u2x þ u2y þ v2x þ v2y þ jrf j2 :jV rf j2 dx:dy (6)
>
> A j f ðx; yÞ ¼ tan 1 w2j f ðx; yÞ
>
>
: 2 1
w2j f ðx; yÞ
where the vector field is V (x,y)¼(u (x,y),v (x,y)), f is the edge map of the
� �
M2j fðx; yÞ is the modulus of the wavelet transform. A2j fðx; yÞis the angle image, rf ¼ fx ; fy is the gradient of the image edge map. The regu­
between the gradient vectorrðf *θ2j Þðx; yÞ and the X-axis of the image larization parameter denoted by μ controls the relative effect of the two
plane (x, y). For the convolution kernel θðx; yÞ, we used the Gaussian terms. μ is set in function to the amount of noise present in the image
function, which offers algorithmic advantages [16]. (the more μ is increased, the greater is the noise level).
The edge detection based on the multi-scale wavelet transform For our case, a value of 0.2 was used for μ. When we minimize the
consists to firstly detect, at each scale, the local maxima of the modulus energy functional of Equation (6), the following Euler independent
of the wavelet transform. For local maxima detection, a hysteresis equations are derived [22]:
threshold is used. This kind of threshold is defined by an interval [TL, 8 � �
TH], with TL ¼ 0.4*TH. Afterwards, these local maxima are chained >
< μ:r2 u ðu fx Þ: fx2 þ fy2 ¼ 0
from the coarser scale (a>1) to the finest scale (a ¼ 1). The goal of the �� � (7)
>
chaining is to solve the location problems caused by the convolution at : μ:r2 v v fy : fx2 þ fy2 ¼ 0
the large scale of the analysis. The full version of the contours detector
based on the multi-scale wavelet transform can be found in Ref. [16]. Equation (7) are resolved by considering u and v as functions of time.
We get:

3
B.S. Tchinda et al.
Vt ¼ ðut ðx; y; tÞ; vt ðx; y; tÞ Þ
with:
8 �
< ut ðx; y; tÞ ¼ μ:r2 uðx; y; tÞ ðuðx; y; tÞ fx ðx; yÞ Þ: fx ðx; yÞ2 þ fy ðx; yÞ2
��
: vt ðx; y; tÞ ¼ μ:r2 vðx; y; tÞ vðx; y; tÞ fy ðx; yÞ : fx ðx; yÞ2 þ fy ðx; yÞ2
where fx and fy denote the derivative of f with respect to x and y
respectively. The gradient vector flow is the solution of the system of
equations (8). Since these equations are decoupled, they can be resolved
separately in u and v, as scalar partial derivatives equations.
After calculating the Gradient Vector Flow, the snake GVF is defined
in Ref. [21] as the parametric curve ψ satisfying the following dynamic
equation:
Xt ðs; tÞ ¼ α:X’’ β:X’’’’ þ k:VðXÞ
Here, X is a function of time t and space s. β Is the rigidity parameter
and α is the tension parameter of the snake. The parameter k controls the
extent to which the GVF field affects the deformation of the curve.
X’’andX’’’’designate the second and fourth derivatives of X with respect
to s, respectively. After its discretization, the dynamic equation (9) is
solved by iteration. From its initial curve, the iterative equations for the
deformation of the snake are given in Ref. [21] by:
�
xt ¼ ðA þ γ:IÞ 1 ðγ:xt 1 þ k:uðxt 1 ; yt 1 Þ Þ
Xt ¼ ðxt ; yt Þ ¼ (10)
yt ¼ ðA þ γ:IÞ 1 ðγ:yt 1 þ k:vðxt 1 ; yt 1 Þ Þ
where x and y denote the coordinates of the vectors of points on the
curve, γ ¼ 1/Δt is the step size of the iteration, I is an identity diagonal
matrix and A is a pentadiagonal matrix with boundary conditions
established for the snake used for longitudinal images. The snake is
dynamically reparameterized after each iteration to maintain a separa­
tion point in the limit of 0.5–1.5 pixels [22].
The outlines search procedure by the snake method depends on other
mechanisms such as interaction with a user or mechanism of high-level
vision of the computer. First, the snake is placed near the contour of the
region of interest. To achieve this first step, we used the Hough trans­
form to automatically find the initial curve of the snake. The second step
is the deformation of the initial curve (circle given by HT). This initial
curve is considered as a snake that uses the GVF field as the external
force. Details of the extraction algorithm is given in Ref. [19].
2.3. The feature extraction using principal components analysis (PCA)
The principal components analysis (PCA) is a conventional linear
method of feature extraction. It is based on the second order statistical
analysis of the data, and in particular the analysis of eigenvalues of the
covariance matrix. The basic idea is that in many such measures, the
mobservational variables ðx1 ; x2 ; :::; xm Þ can be well represented by a
parametric surface of n dimensionðy1 ; y2 ; ::: ; yn Þ, with n smaller than
m.
PCA has been used in the dimensionality reduction of the multi-
variable data [23–25]. It consists of projecting the data in the di­
rections of their maximum variability. Thus, a family of variables is
replaced by new variables of maximum variance, uncorrelated and
which are linear combinations of the original variables. The principal
components are basis vectors of the directions in descending order of
variability. The basic vector for the direction of the highest variability is
provided by the first principal component. The second principal
component gives the basis vector for the next direction orthogonal to the
first principal component, and so on. The calculation of the principal
components requires computation of the covariance matrix, and calcu­
lation of eigenvalues, with storage of eigenvectors according to the
descending order of eigenvalues. For the reduction of features, only the
n (with n � m) first eigenvectors will be selected, corresponding to the
Informatics in Medicine Unlocked 16 (2019) 100238
largest eigenvalues. The projection of the data in the new basis defined
by the principal components is carried out by the scalar product of
original data with the arranged eigenvectors.
� Practically, the PCA consists to look for a transformation of matrix W
that corresponds to each characteristic vector CX defining in the set X
�
another vector of characteristics CY for the set Y, such that the covariance
matrix of the elements in Y is diagonal. This transformation is linear and
(8)
is defined as follows:
CY ¼ CX W T (11)
The matrix W can be found by solving the following equation:
Σ X wi ¼ λi wi ; (12)
λi defines the eigenvalues and wi defines the eigenvectors. Σ X Is the
covariance matrix of X.
Since the eigenvectors wi are known, the transformation matrix Wis
(9)
obtained by considering the wi as its columns. For the reduction of the
characteristics, W is a matrix of dimension m � n, containing n eigen­
vectors (wi ;i ¼ 1:::n) which correspond to the n largest eigenvalues. For
our case, m ¼ 144 and n ¼ 2.
2.4. Principle of the recognition and classification using the probabilistic
neural network
The artificial neural networks (ANN) are very popular tools for
pattern recognition. Probabilistic neural networks (PNN) are a special
type of radial basis neural network. It is an alternative of radias basis
networks for classification problems. the learning easiness and its
instantaneousness process are the main advantages of PNN [26–29].
In our work, we used a probabilistic neural network. Its architecture
is given in Fig. 3. At the entrance of the network, there is a column vector
P of R lines. The radial inner layer subtracts the input vector from the
weight vector W of this layer, and we obtain W–P. The resulting vector is
next multiplied element by element with the bias vector b. The obtained
output S1 is used as the argument of the radial function “radbas”; thus
we obtain a. The activation function in the radial inner layer is defined
�
by radbasðnÞ ¼ exp n2 . The output a is multiplied by the weight
matrix of the competitive layer LW, and S2 is obtained. The output S2
serves as an argument for the competitive function C. The competitive
layer directs each entry in one of the K classes used in the learning step.
The output S of the competitive function is a column vector of K lines.
The competitive functionC produces a 1 corresponding to the largest
component of S2, and 0 otherwise.
For training and testing the probabilistic network, the reduced
characteristics are applied to the input. In our case, a total of 1800 im­
ages of microscopic parasites are used. These samples were divided into
two sets of 900 images each. The first set, constructed from 60 images for
each of the 15 types of parasites, was used for training. The second set of
900 images was considered for testing, with the same allocation by type
of parasite. The weight matrix W of the radial inner layer is a Q � R
matrix formed from training samples. W contains in each line R principal
components of a training sample. 900 samples are available for training
pffiffiffiffiffiffiffiffiffiffiffiffiffiffiffi
in this work, thus Q ¼ 900. The radial layer bias are all set to ln 0:5=s,
where s denotes the network spread constant. In our case, the spread
constant has been adjusted to 0.4 by experience. This is the value that
yielded an improved classification rate. The weight matrix of competi­
tive layer LW is set to a K � Q matrix of Q vectors of target class. K is
equal to 15 in our case.
3. Results
For our experimentation, we used microscopic images with a
magnification of � 400 for helminthes eggs and � 1000 for amoeba
cysts. The image format is JPEG and the size is 360 � 400.
An example of a microscopic image of feces is showing in Fig. 4. This
4
B.S. Tchinda et al.
Fig. 3. Architecture of the probabilistic neural network.
image contains the parasitic elements and many other insignificant
items. In this image, there is a round egg shape of a tapeworm. This egg
has about 30 μm in size. A second egg found, of ovoid form, is from the
whipworm, having a size of about 50 μm. One can also note the presence
of food debris. Our goal is to detect the parasite, then extract and
recognize it. Before the recognition phase, we need another important
intermediate step, which is feature reduction. Its role is to facilitate the
recognition step by reducing the number of entries in the classification
system.
3.1. Results of the parasite detection
We applied the proposed edge detector to a large number of micro­
scopic images of feces containing human parasites. Here the results
obtained on some of these images were presented. Fig. 5 shows the re­
sults obtained by applying the edge detection algorithm on the micro­
scopic image of stools described above in Fig. 4. We can note in Fig. 5
that the variation of the analysis scale of the wavelet transform reveals
the different structures present in the stools image. For example, as can
be seen in Fig. 5, on the images (A) and (E), for the two thresholding
values used ([0.08, 0.2] and [0.12, 0.3]), the results obtained at scale 1
of the wavelet transform are still confused and contain many unnec­
essary edges. However, in image panels (C), (D) (G) and (H), the results
obtained at scales 6 and 8 with the same thresholdings correctly locate
almost all desired edges (D). Thus, in this case, the scales 6 and 8 are
better than scale 1 for the edge detection of parasites on the considered
image. The threshold variation and the variation of analyzing scale can
Fig. 4. Microscopic image of stool. This image contains a tapeworm egg, an egg
of whipworm, yeast and other insignificant items such as food debris.
5
Informatics in Medicine Unlocked 16 (2019) 100238
therefore reveal the various characteritics of the parasite. Other results
of the application of the multi-scale wavelets transform, and its perfor­
mance on the edge detection of intestinal parasites in stools microscopic
images, can be found in Ref. [16]. These results of the edge detection
show the effectiveness, and justify the choice of this algorithm in the
parasite detection phase.
3.2. Results of the parasite extraction
We applied our segmentation algorithm based on the Hough trans­
form and active contours on microscopic images of stools containing
parasites, in order to detect and extract the parasites. Fig. 6 shows the
extraction of various parasite cysts of Entamoeba coli. These cysts can
have a spherical or ovoid form, and are about 15–25 μm in diameter,
depending upon maturity. Fig. 6 (A) shows an image with 7 cysts. In the
images (B), (C), (D) and (E) of this figure, the parasites are extracted
individually after the adjustment of analysis parameters (scale,
threshold and radius of the circular Hough transform). Fig. 6 (F) shows
all four extracted parasites, colored on the same initial image. By
varying the analysis parameters, all cysts present in this image can be
extracted. In Fig. 7, we can also observe other parasites extracted
automatically from an initial outline obtained through the Hough
transform. The images (A-B- ... G) are the microscopic images of feces to
analyze. the images (A1-B1 …- G1) show the edge images obtained from
the multi-scale wavelet process (in black on the figure), on which are
superimposed the initial contour given by the Hough transform (blue).
They are obtained respectively with the scale, high threshold TH and
radius parameters of (4, 0.6, 50 pixels) for A1; (2, 0.5, 40 pixels) for B1;
(8, 0.75, 75 pixels) for C1; (6, 0.65, 80 pixels) for D1; (8, 0.4, 35 pixels)
for E1; (8, 0.6, 60 pixels) for F1 and (8, 0.6, 35 pixels) for G1. The
extracted parasite resulted from the convergence of the active contours
is given in the images (A2-B2- … -G2) of the same figure. The analysis
radius used by the Hough transform is related to the size of the parasite.
It is expressed in pixels. It also depends on the resolution of the camera
used, and the magnification of the microscope. Thus, a specific type of
parasite can be searched automatically using its size.-
3.3. Result of the features extraction and dimensionality reduction
For the complexity reduction of the classification and recognition
phase, the features using as input need to be reduced. The image of the
extracted parasites are first resized. The image dimensions of the
extracted parasite have been reduced to the 12 � 12 size. The resizing
uses the Bicubic interpolation method. With this method, the output
pixel value is a weighted average of pixels in the nearest 4-by-4 neigh­
borhood. The PCA is subsequently used for projecting the characteristics
of 12 � 12 pixels in a new space. The role of PCA is to reduce the size of
the initial data space to the smallest intrinsic dimension. The obtained
features space are sufficient to economically and efficiently describe the
B.S. Tchinda et al. Informatics in Medicine Unlocked 16 (2019) 100238

Fig. 5. Analysis scale variation and edge detection by the wavelet transform. (A) Contours analysis at scale 1 with a thresholding of [0.08, 0.2]; (B) Contours at scale
4 with a threshold of [0.08, 0.2]; (C) Contours at scale 6 with a thresholding of [0.08, 0.2]; (D) Contours at scale 8 with a threshold of [0.08, 0.2]; (E) Contours at
scale 1 with a threshold of [0.12, 0.3]; (F) Contours at scale 4 with a thresholding of [0.12, 0.3]; (G) Contours at scale 6 with a threshold of [0.12, 0.3]; (H) Contours
at scale 8 with a threshold of [0.12, 0.3].

Fig. 6. Extraction of different parasites by varying the analysis parameters. (A)

Original image. Extraction results of the parasite: (B) at the scale 4, with the
threshold of [0.06, 0.15], and the radius of 43 pixels; (C) at the scale 4, with the
threshold of [0.06, 0.15], and the radius of 51 pixels; (D) at the scale 6, with the
threshold of [0.07, 0.18], and the radius of 44 pixels; (E) at the scale 8, with the
threshold of [0.06, 0.15], and the radius of 41 pixels; (F) all four extracted
parasites colored on the same initial image.

data. For this goal, the dimension of the space of the new features is
selected according to the classification accuracy. It also depends upon
the system complexity.
Fig. 8 shows a matrix containing a set of 300 images of parasites. We
can distinguish 15 species of parasites. For each species, there are 20
samples. These samples are used to configure our system. Table 1 shows
the result of the implementation of the PCA on this set of parasites.
Those are the first three principal components (PCA1, PCA2 and PCA3). Fig. 7. Initial contours and parasites extracted. (A-B ... F) are microscopic
The values in this table are the average and the maximum deviation images of feces for analysis. (A1-B1 … F1) are the outlines obtained from the
obtained on the 20 samples of each class (A, B, C, D, E, F, G, H, I, J, K, L, multi-scale wavelet transform, which are superimposed on the initial contours
M, N, O). To facilitate classification, a good feature reduction should given by the Hough transform. (A2-B2 … F2) are the images of the para­
provide a set of new features with close values for the same classes, and sites extracted.
dispersed values for different classes. To evaluate our features reduction
tool, independent component analysis (ICA) was also applied to the upon the ICA method (Table 2). For the PCA, the values of the same class
same image samples. The ICA is a non-linear method of feature reduc­ are fairly close together (Table 1). This observation can also be shown in
tion [30]. Table 2 shows results for ICA. Also, 3 components are retained Figs. 9 and 10. In Fig. 9, which provides the values of the first two
(ICA1, ICA2 and ICA3). When analyzing these tables, we can see the components, for every 300 samples of 15 classes for the ICA, there is no
wide disparity of values for the same species of parasite, when it is based parasite class regrouped. The dispersion rate is very high. For the PCA,

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B.S. Tchinda et al. Informatics in Medicine Unlocked 16 (2019) 100238

Table 2
Average values of the first three components of the ICA obtained for 15 classes of
20 samples of parasites. Different mean values are added to the maximum
dispersion of these values compared to the average. In this case, we can see that
these differences are high compared to the value considered. Similarly, there are
very small differences or overlaps between the different average values. This
complicates the classification phase.
Features

ICA1 ICA2 ICA3

Classes A 0.502 � 1.760 0.566 � 1.717 0.960 � 0.377

B 0.469 � 1.584 0.007 � 1.284 0.028 � 1.450
C 0.370 � 1.536 0.251 � 1.370 0.686 � 1.776
D 0.944 � 0.772 0.183 � 1.394 0.429 � 1.605
E 1.036 � 0.234 0.009 � 1.297 0.659 � 1.716
F 0.982 � 0.205 0.330 � 1.451 0.495 � 1.719
G 0.963 � 0.816 0.144 � 1.371 0.681 � 1.732
H 0.991 � 0.339 0.427 � 1.619 0.024 � 1.290
I 1.020 � 0.223 0.470 � 1.436 0.444 � 1.579
J 0.499 � 1.642 1.033 � 0.414 0.478 � 1.729
K 0.477 � 1.724 0.516 � 1.776 0.013 � 1.246
L 0.558 � 1.639 0.006 � 1.265 1.064 � .1840
M 0.072 � 1.261 0.595 � 1.650 0.844 � 1.569
N 0.930 � 0.396 1.030 � 0.293 0.516 � 1.633
O 0.548 � 1.543 0.033 � 1.475 0.029 � 1.333

3.4. Results of the parasite recognition

We used 15 different species of intestinal parasites. Microscopic

images of each of these parasites is given in Fig. 11. In the list, there are 9
Fig. 8. Parasite images of 15 classes and 20 samples each. For each image of types of protozoan cysts: Giardia lamblia, Entamoeba hartmanni,
parasites extracted, other images are generated by introducing noise. Other
Entamoeba polecki, Entamoeba histolytica, Entamoeba coli, Endolimax
images are also generated by projecting the image on itself from any angle.
nana, Balantidium coli, chilomastix mesnili and Iodamoeba Butschlii. One
can also distinguish 6 types of helminthes eggs: Ascaris, Tapeworm,
Table 1 Schistosoma mansoni, Schistosoma intercalatum, Schistosoma japonicum,
Average values of the first three components of the PCA obtained for 15 classes and whipworm.
of 20 samples of parasites. Different mean values are added to the maximum All of these images were subjected to rotations of 0� –150� at the step
dispersion of these values compared to the average. In this case, we can see that rate of 30� ; we used five different scales. In addition, four types of noise
the differences are quite small relative to the value considered. Similarly, there were added separately to these images with an algebraic addition
are significant differences between the different average values. This facilitates operation (“Gaussian noise”, “Poisson noise”, “salt & pepper noise”,
the classification phase. “speckle noise”). For each parasite type, we used 120 microscopic im­
Features ages, a database of 1800 images in total. For training the network, half
PCA1 PCA 2 PCA 3
randomly selected from this database was used. The other half of the
database was used for testing; hence 60 images for each class of parasite.
Classes A 1155.99 � 5.13 376.39 � 5.69 757.75 � 9.74
The training phase performed well. Table 3 provides the test confusion
B 1642.90 � 18.67 169.71 � 13.93 962.86 � 22.82
C 1402.45 � 15.46 460.36 � 8.88 853.47 � 17.70 matrix of our recognition system. According to this table, all of the
D 1342.67 � 25.86 107.49 � 14.34 936.07 � 23.24 fifteen types of parasites were classified with a 100% correct recognition
E 1304.05 � 15.59 153.23 � 8.88 975.45 � 14.66 rate. This shows the efficacy of the type of features descriptor used
F 1657.73 � 22.97 359.52 � 12.67 966.03 � 9.06
(PCA), as well as the probabilistic neural network in a recognition sys­
G 1453.31 � 25.06 268.39 � 11.06 928.81 � 32.05
H 1590.69 � 22.97 76.27 � 5.73 966.88 � 15.91
tem of intestinal parasites. Indeed, the success rate can be predicated
I 1512.48 � 11.91 239.84 � 9.54 1007.37 � 8.29 from the feature extraction results which previously regrouped the same
J 1324.56 � 7.67 83.80 � 12.22 896.10 � 28.87 classes and separated it from the others. When these classes are sepa­
K 1853.33 � 4.62 74.74 � 7.35 760.68 � 14.03 rated, it becomes easy to classify by the neural network insofar as the
L 1694.12 � 3.24 212.24 � 11.57 889.07 � 39.70
boundary of class separation will be well defined. As can be seen on the
M 1837.82 � 6.56 463.67 � 12.61 888.28 � 16.96
N 1512.66 � 10.69 455.31 � 14.21 988.66 � 9.14 feature extraction results in Fig. 10, the boundary of class separation is
O 1506.06 � 5.18 337.11 � 10.90 1028.40 � 13.09 not linear. The success of the recognition phase is also justified by the
fact that the probabilistic neural network proceeds by defining the
center and the radius of each class in its radial input layer. Subsequently,
shown in Fig. 10, we can distinguish the fifteen types of parasites, each its competitive output layer is responsible for directing the entrance to
by a mode of representation. In addition, as shown in this figure, para­ the class closest to it following this center and this radius.
sites of the same species are grouped together and are distant from other
species. The capacity of the new features for the discrimination of the 15 4. Discussion
classes can thus be evaluated qualitatively. The separation boundaries of
the different classes of parasites can be readily obtained. In this paper, we proposed a method for automatically diagnose in­
Thus, our choice was focused on principal components analysis. The testinal parasites with the aid of digital image processing and pattern
first two principal components were used. We utilized a transformation recognition. The process performs via the following steps: parasite
ðf : ℝ144 →ℝ2 Þof matrix W to obtain the values of the features in the new detection, parasite segmentation and extraction, recognition of the
coordinate system. parasite. We have performed and evaluated all steps in order to obtain

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B.S. Tchinda et al. Informatics in Medicine Unlocked 16 (2019) 100238

Fig. 9. ICA projection in two dimensions. Each of the points on this figure corresponds to the representation of the two characteristics obtained for a parasite image.
We note that for the images of the same class, the points are widely dispersed. In this case, the network discrimination function of classification is difficult to obtain.

Fig. 10. PCA Projection in two dimensions. Each of the points on this figure corresponds to the representation of the two characteristics obtained from a parasite
image. We note that, for images of the same class, the points are grouped separately from those of other classes. In this case, the network discrimination function of
the classification is easy to obtain.

the choice which contributes to the best diagnostic. The particularity of
the microscopic images of stools is that it contains enough noise, and
many other elements not need for the parasite detection. For the first
step, we need to detect the edge of the parasite. We used the multi-scale
wavelet transform. In Ref. [16], it is shown that the multi-scale wavelet
transform performs well for edge detection of intestinal parasites. The
main advantage of this edge detection method is the scale of the anal­
ysis. As can be seen in Fig. 5, the image is analyzed on many scales and
the retained result reveals the contours of the intestinal parasite and
rejects the contours of undesirable elements. The second step uses the

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B.S. Tchinda et al. Informatics in Medicine Unlocked 16 (2019) 100238

automatically to find and extract a parasite in the microscopic images of

stools. However, to facilitate searching, the dimension of the parasite
can be provided to the system. For the last step, the extracted parasite is
recognized via an artificial neural network. The dimension of the
parasite image is enough to serve directly as the input features vector of
the classification tool. We reduced this dimension by using principal
components analysis (PCA). PCA extracts a features vector from the
image of parasite. The PCA results are presented in Fig. 10. In this figure,
we can see that the same classes of parasites are grouped together, and
different classes are separated. This is a good thing because the sepa­
ration curves of the classification tool will be obtained easily. The arti­
ficial neural network (ANN) is a classification tool which imitates the
activity of the neurons in the human brain. We choose the probabilistic
neural network type for the simplicity of its structure and the easiness of
the training phase. The results of the recognition step are presented in
Table 3. The concerned parasites are showing in Fig. 11. We used 15
types of intestinal parasites (9 amoeba cysts and 6 helminth eggs). We
obtained a 100% of correct classification rate.

5. Conclusions

We presented in this paper a microscopic image processing system

Fig. 11. Microscopic images of each of the 15 types of parasites to recognize. A:
Balantidium coli cyst; B: Endolimax nana cyst; C: Entamoeba coli cyst; D:
Entamoeba hartmanni cyst; E: Entamoba histolytica cyst; F: Entamoeba polecki cyst;
G: Giardia lamblia cyst; H: Iodamoeba butschlii cyst; I: Chilomastix mesnili cyst; J:
Ascaris egg; K: Tapeworm egg; L: Schistosoma mansoni egg; M: Schistosoma
Intercalatum egg; N: Schistosoma japonicum egg; O: whipworm egg.
edge detection result to provide segmentation and extraction of the
parasite. For this step, we need to extract individually each parasite and
separate it from its background before the recognition. We used the
combination of the circular Hough transform and the active contours
methods. The efficacy of this combination has been shown in Ref. [19].
The Hough transform method uses the image edge to reveal by vote the
existing parametric forms in the image. Certain forms of intestinal par­
asites such as cysts are circular. Others are ovoid. For the first case, the
circular Hough transform well detects the external contour of the
parasite. For the ovoid forms of parasites and other closely related forms,
the circular Hough transform partially locates the contour of the para­
site. This partial contour serves as an initial contour for active contours
models. We know that the success of the active contours method de­
pends strongly on the initial contour. For our case, this initial contour is
obtained automatically. With the external contour of the parasite, we
just need to perform a logic operation to extract the parasite image and
reject its background. As can be seen in Fig. 6, our system performs
for medical diagnosis of intestinal parasites. This image processing
technique includes the detection of the parasite, its extraction and
recognition. The wavelet transform has allowed us to detect the parasite
contours. The contours obtained were subsequently exploited, to
segment the image and highlight the parasite. Our segmentation tool
uses a snake technique initialized by the Hough transform. This hybrid
method is confirmed to have high performance in the extraction of in­
testinal parasites. In addition, it allows automatic and individual
extraction of the parasite prior to the identification. The probabilistic
neural network has proven to be suitable for the recognition of the
parasites extracted. In addition to its simple structure, the training of the
probabilistic neural network is fast. Unlike previous work, vectors of
12 � 12 size features were obtained directly from the image pixels.
These features have been projected in a base of principal components
analysis for the reduction of dimensionality. The reduced features vector
served as input to the network. The results indicate that the feature
vector, consisting of the gray levels of the image pixels, is achievable. In
addition, this type of features provides remarkable performances when
we use a probabilistic neural network classifier, after reducing the
dimensionality of the features by projection on a base of principal
components analysis. Our system can automatically recognize an in­
testinal parasite through feces microscopic images loaded from a digital
camera or scanner. We obtained some very interesting results. We
believe that a significant step has been taken towards the development

Table 3
Confusion matrix of the classification system: 60 samples of parasites per class; the test gives a rate of 100% correct recognition (60/60) for all of the 15 parasite classes
considered.
Target classes

Classes A B C D E F G H I J K L M N O

current classes A 60 0 0 0 0 0 0 0 0 0 0 0 0 0 0
B 0 60 0 0 0 0 0 0 0 0 0 0 0 0 0
C 0 0 60 0 0 0 0 0 0 0 0 0 0 0 0
D 0 0 0 60 0 0 0 0 0 0 0 0 0 0 0
E 0 0 0 0 60 0 0 0 0 0 0 0 0 0 0
F 0 0 0 0 0 60 0 0 0 0 0 0 0 0 0
G 0 0 0 0 0 0 60 0 0 0 0 0 0 0 0
H 0 0 0 0 0 0 0 60 0 0 0 0 0 0 0
I 0 0 0 0 0 0 0 0 60 0 0 0 0 0 0
J 0 0 0 0 0 0 0 0 0 60 0 0 0 0 0
K 0 0 0 0 0 0 0 0 0 0 60 0 0 0 0
L 0 0 0 0 0 0 0 0 0 0 0 60 0 0 0
M 0 0 0 0 0 0 0 0 0 0 0 0 60 0 0
N 0 0 0 0 0 0 0 0 0 0 0 0 0 60 0
O 0 0 0 0 0 0 0 0 0 0 0 0 0 0 60

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B.S. Tchinda et al.
of a medical system for the automatic diagnosis of human intestinal
parasites.
Funding and competing interests
There are no conflicts of interest associated with this publication and
there has been no significant financial support for this work that could
have influenced its outcome.
Ethical approval
This article does not contain any studies with human participants
and/or animals performed by any of the authors.
Acknowledgments
Declared none.
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