Archives of Computational Methods in Engineering (2023) 30:2013–2039

https://doi.org/10.1007/s11831-022-09858-w

REVIEW ARTICLE

Advances Towards Automatic Detection and Classification of Parasites

Microscopic Images Using Deep Convolutional Neural Network:
Methods, Models and Research Directions
Satish Kumar1 · Tasleem Arif1 · Abdullah S. Alotaibi2 · Majid B. Malik3 · Jatinder Manhas4

Received: 17 March 2022 / Accepted: 19 November 2022 / Published online: 3 December 2022
© The Author(s) under exclusive licence to International Center for Numerical Methods in Engineering (CIMNE) 2022

Abstract
In the developing world, parasites are responsible for causing several serious health problems, with relatively high infec-
tions in human beings. The traditional manual light microscopy process of parasite recognition remains the golden standard
approach for the diagnosis of parasitic species, but this approach is time-consuming, highly tedious, and also difficult to main-
tain consistency but essential in parasitological classification for carrying out several experimental observations. Therefore,
it is meaningful to apply deep learning to address these challenges. Convolution Neural Network and digital slide scanning
show promising results that can revolutionize the clinical parasitology laboratory by automating the process of classifica-
tion and detection of parasites. Image analysis using deep learning methods have the potential to achieve high efficiency and
accuracy. For this review, we have conducted a thorough investigation in the field of image detection and classification of
various parasites based on deep learning. Online databases and digital libraries such as ACM, IEEE, ScienceDirect, Springer,
and Wiley Online Library were searched to identify sufficient related paper collections. After screening of 200 research
papers, 70 of them met our filtering criteria, which became a part of this study. This paper presents a comprehensive review
of existing parasite classification and detection methods and models in chronological order, from traditional machine learning
based techniques to deep learning based techniques. In this review, we also demonstrate the summary of machine learning
and deep learning methods along with dataset details, evaluation metrics, methods limitations, and future scope over the
one decade. The majority of the technical publications from 2012 to the present have been examined and summarized. In
addition, we have discussed the future directions and challenges of parasites classification and detection to help researchers
in understanding the existing research gaps. Further, this review provides support to researchers who require an effective and
comprehensive understanding of deep learning development techniques, research, and future trends in the field of parasites
detection and classification.

1 Introduction

Parasites are organisms that grow in or on a host and obtain

food from the host. Parasites are too tiny and not visible
clearly with naked eyes however, they can be observed under
a microscope. The parasites community that cause disease
* Satish Kumar in humans includes protozoa, helminths and ectoparasites.
satishkumar@bgsbu.ac.in
It is estimated that 357 million cases of morbidity, mostly
1
Department of Information Technology, BGSB University infected by protozoa, Cryptosporidium, Entamoeba, and
Rajouri, Rajouri, J&K 185131, India Giardia, resulted in 33,900 deaths and the loss of 2.94 mil-
2
Computer Science Department, Shaqra University, Shaqra, lion disability per year [1] and more than 1.4 billion people
Kingdom of Saudi Arabia are infected with helminths [2]. Various other parasites act
3
Department of Computer Sciences, BGSB University as pathogenic and cause diseases also in plants, and other
Rajouri, Rajouri, J&K 185131, India living organisms. They are responsible for causing various
4
Department of Computer Sciences & IT, University deadly diseases like Giardia (through contaminated water),
of Jammu, Jammu, J&K, India toxoplasmosis (spread by cats), malaria etc. [3]. One of the

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Vol.:(0123456789)
2014
helminths parasites globally causes infection in more than
800 million people [4]. In developing countries including
East Asia, South America, Saharan Africa etc. there are
more than 100 human intestinal parasite species that produce
200,000 eggs per day and annually 41,500 human deaths are
reported due to parasitic infections [2, 5]. Infection caused
by these diseases display a wide range of clinical explana-
tions ranging from malnutrition to asymptomatic anaemia
and even cause cancer [6, 7]. Conventional light microscopic
examination remains the gold standard method for diagnosis
of several parasites diseases, such as malaria [8].
There are numerous shortcomings of these methods,
which have serious potential to sway the results of clini-
cal examinations, such as variable sensitivity, resource and
time-consumption. Another drawback of the traditional
clinical parasitology classification and detection is main-
taining staff competency and engagement. The clinical
parasitology laboratory also suffers from two major aspects
firstly, educated technologists increasingly gravitate toward
technology-driven and automated disciplines of laboratory
and secondly, shortage of adequately trained personnel [9]
to keep them staffed. Results based on diagnosis of parasites
are often obtained from clinical signs and symptoms that
are susceptible to human errors which may lead to higher
mortality and buying of unnecessary drugs leading to eco-
nomic burden [10] and despondency. In consequence, alter-
nate methods are required which help to generate quality
diagnosis results. To date, to the best of our knowledge, there
have been no significant technological advancements for the
detection of protozoa in human stool specimens using per-
manently stained slides (e.g., trichrome, modified acid-fast,
and modified safranin).
The objective of this review is to establish the vital aspect
of deep learning in parasite microscopic image classifica-
tion and detection to make it easy for researchers to have a
clear image of deep learning for parasitology from this sur-
vey paper. Further, this systematic review of deep learning
models for microscopic images helps people discover more
about recent growth in this field. In this review, we analysed
deep learning techniques applied in parasitological image
application and in turn made the following contributions:
• We demonstrated that how a pre-trained Convolution
Neural Network (CNN) performance improves by fine-
tuning different layers.
• We demonstrated CNN and transfer learning potential to
detect and classify human parasites taken from images
along with state-of-the-art architectures.
• In this review, we cover challenges faced in deep learning
including small-scale training data, noised image, data
interpretability, and model compression, uncertainty
scaling, over-fitting and vanishing gradient problems.
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S. Kumar et al.
This review provides a broad survey of the most impor-
tant aspects of parasite microscopic image analysis using
deep learning. This review depicted in Fig. 1 is organized
as follows. Section 2 describes the fundamentals concepts
of deep learning, which include convolution layers compo-
nents, methods & models and evaluation metrics. In Sect. 3,
we discuss methodology used to conduct this review includ-
ing research questions, paper retrieval and filtering process.
In Sects. 4 and 5, detailed gist of each machine learning
and deep learning method and model elaborated in selected
research papers has been provided respectively. Summary
of each research paper and their future scope is presented
in the form of tables. In Sect. 6 various results have been
discussed that will provide research directions in parasites
image detection and classifications. Finally, In Sect. 7 con-
clusion and future scope is presented.
2 Background
The following subsections provide a succinct explanation
of various concepts and technologies associated with the
work presented in this paper. Section 2.1 provides an over-
view of Deep Learning, Sect. 2.2 discusses about CNNs
and Sect. 2.3 provides a gist of CNN models and parasite
datasets.
2.1 Deep Learning Overview
In this section, we present the analysis of deep learning
fundamentals that addresses wide range of issues including
medical images detection, segmentation and classification.
The section begins with an introduction to deep learning,
then on to cover various techniques, and concludes with
transfer learning techniques and models built on CNNs to
increase the effectiveness of automatic parasite identification
and categorization. Deep learning is a subfield of machine
learning inspired by the structure and function of the human
brain neural network. In medical diagnosis, deep learning
methods and models operate on large amounts of medical
Fig. 1  Systematic organization of the review
Advances Towards Automatic Detection and Classification of Parasites Microscopic Images… 2015

image data to transfer the given dataset to some specific
labels (Fig. 2).
A large number of artificial neural network layers are used
in the development and design of deep learning, with each
layer carrying out a different evaluation based on the infor-
mation it receives. [11, 12]. Conventional machine learning
algorithms employ various steps to achieve the classifica-
tion tasks like pre- processing, feature extraction, feature
selection and learning. Conversely, Deep learning techniques
automate several tasks of machine learning algorithms [12,
13], as shown in Fig. 1. Deep learning gained popularity in
recent years due to exponential growth of data [14]. Deep
learning methods and models have the potential to enhance
human lives with accuracy in diagnosis including pathogen
detection and classification such as malaria, intestinal para-
site and tuberculosis, etc. In recent times i.e. after the onset
of COVID-19 pandemic, Deep learning (DL) is playing a
vital role in the automatic diagnosis of novel coronavirus
[15]. DL methods and models include Deep Feedforward
Neural Network (DFNN), Convolutional Neural Network
(CNN) [16], Recurrent Neural Network (RNN) and Auto-
encoder. The overview of prominent DL-model architectures
is depicted in Fig. 3, which can be used to enhance the effi-
ciency of automatic parasite classification and detection.
Due to it high accuracy, speed and flexibility deep learning
is being applied in microscopic examination of parasite spe-
cies. The end-results may include classification, detection
and segmentation. Classification task is applied for recog-
nition of multi-parasite species where microscopic images
contain mixed infections. Detection is used to acquire the
position of individual parasites or similar group of parasites.
Segmentation task’s objective is grouping similar regions or
segments of a parasitic image under their respective class.
Classification and detection of microscopic parasites are

Fig. 2  Comparison between

two techniques: a workflow
vs. b deep learning workflow.
Traditional Computer Vision
algorithms employed pre- pro-
cessing, feature extraction, wise
feature selection to achieve the
classification and deep learning
techniques automate the several
tasks of machine learning
algorithms

Fig. 3  Overview of deep learn-

ing models architectures: a
Simple Neural Network with
hidden layers, b Recurrent Neu-
ral Network for sequence and
time series data, c Convolution
Neural Network for computer
vision

13
2016 S. Kumar et al.

usually performed by CNN and RCNN series models [48, of the input image. It is a technique to maintain the size
70]. of image that reduces as a result of strides. Consider the
input parasitic image of size H×H×C, suppose F implies
2.2 Convolutional Neural Networks (CNN) number of filters, S implies stride, and P for padding.
The following formula can used to determine the output
CNN structure perform computations based on the structure image size:
of human visual cortex and is a popular choice for automatic
H − F + 2P
extraction of relevant features from large amounts of data Iout = +1 (2)
S
[17]. A CNN is designed with a sequence of convolution
layers, sampling layers followed by fully connected layer as   The output size of parasitic image will be
shown in Fig. 3a. Input layers of CNN model is arranged in Iout × Iout × Cout
the 3-dimensions (height, width, and depth), m × m × r. The b. Pooling Layer: Pooling is another important component
depth (r) represents the number of channels [14]. In each in CNN architecture to reduce the dimensionality of the
convolutional layer, several filters are applied and these fil- feature map. This approach shrinks the large joint fea-
ters are also organized in 3D, (n × n × q), but values of both ture representation size into small valuable information.
n and q are smaller than m and r respectively. The convolu- The same process of convolution layer is applied in the
tional layer evaluates the product of inputs and weights, as pooling layer. There are different types of pooling meth-
shown in Eq. 1. ods that are applied to different pooling layers. These
are min pooling, max pooling, average pooling, global
(h)k = f W k ∗ x + bk (1)
( )
average pooling, global max pooling and tree pooling.
Three familiar pooling operations are shown in Fig. 4.
To accelerate the training process and to handle the over-
c. Activation Function: Activation functions are nonlinear
fitting of a model, the down-sampling is applied to layers to
functions and neural networks utilize different activation
extract features. Finally, mid and low-level features are fed to
functions to map the input values to output. The input to
fully connected layers to obtain the high-level of abstraction.
activation evaluate by summation of the dot product of
weights and inputs along with bias.
2.2.1 CNN Layers
d. Loss Function: In CNN architecture the final classifica-
tion is obtained from the output layer. CNN model uti-
This subsection discusses each layer of CNN basic architec-
lizes several loss functions in the output layer to evaluate
ture along with their functions to deal with parasitic image
the error predicted during training. Next, this error is
classification and detection as elaborated below.
applied to optimize the CNN learning process. Literally,
the loss function is calculated by two parameters. First is
a. Convolution Layer: Every CNN architecture includes an
the predicted output of the CNN model and the second
important component called convolution layer and each
parameter is the actual output
CNN layer is comprised of several filters (kernels). Over
N-dimensional metrics of an input image, convolution
operations are performed with these kernels to obtain
output features. Firstly, the filters are convolved over the
entire input image horizontally and vertically during the
forwarding pass, then, the product of input images and
the filters is determined. It generates a two dimensional
visual of image that shows the output of filters at spatial
location of the image. The entire process is repeated for
input images until there is no possibility of sliding.
  Stride is a component of convolutional neural net-
works that is streamlined for image data compression.
Stride is a CNN filter parameter that regulates the
amount of movement all over the image. For instance,
if the stride of a neural network is set to 1, the filter will
move one pixel at a time. Since the filter size influences
the encoded output volume, stride is frequently set to a
whole integer rather than a fraction or decimal. Padding
is also applied to determine the border size information
Fig. 4  Pooling layers operations

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Advances Towards Automatic Detection and Classification of Parasites Microscopic Images…
2.2.2 Evaluation Metrics
Evaluation metrics play a major role in achieving the opti-
mized classifier to detect and classify the parasite species
using deep learning. The performance metrics for parasitic
image classification generally include Accuracy, Sensitivity
or Recall, Specificity, Precision, F1-Score, J Score, False
Positive Rate (FPR) and Area Under the ROC Curve. The
evaluation metrics of parasitic egg detection include average
precision (AP), precision recall curve, mean average preci-
sion (mAP) and area under curve (AUC). The Accuracy is
the relationship between the predicted value and the target
value. Accuracy evaluates how close the predicted value is
to the target value. Sensitivity calculates the predicted output
with respect to the change in input, which means sensitiv-
ity shows the ratio of the true positives that are correctly
identified. In contrast specificity, which calculates the ratio
of true negatives that are correctly identified. TN and TP are
the number of negative and positive instances, respectively,
for successfully classification and detection of parasites.
Further, FN and FP are defined as the number positive and
negative instances respectively, for misclassification. The
parasitic images classification and detection based on deep
learning are measured with the help of following formula:
a. Accuracy measures the ratio of correct predicted value
to the total number of instance evaluated.
TP+TN
Accuracy =
TP + TN + FP + FN
b. Sensitivity or Recall measures the fraction of positive
values that are correctly classified
Sensitivity =
TP
TP + FN
c. Specificity measures the fraction of negative values that
are correctly classified.
TN
Specificity =
FP + TN
d. Precision measures the positive values that are correctly
predicted by all predicted values in a positive class.
TP
Precision =
TP + FP
e. F1-Score measures the harmonic average between recall
and precision rates.
Precion*Recall
F1-Score = 2*
Precion+Recall
f. J Score also called as Youdens J statistic.
2017
J-Score = Sensitivity + Specif icity − 1 (8)
g. False Positive Rate (FPR) measures the possibility of a
false alarm ratio
FPR = 1 - Specif icity (9)
h. Area Under the ROC Curve (AUC) is used to measure
comparisons between learning algorithms, as well as
to construct an optimal learning model. The following
equation is used to measure the AUC value for two-class
problem.
sp − np (np + 1)2
AUC = (10)
np nn
2.3 CNN Models and Parasite Datasets
Over the last two decades, numerous CNN models have
been proposed to perform different tasks [35]. CNN archi-
tecture has been updating from time to time from 1989 up
to this day. Updating in CNN includes regularization, struc-
tural reformulation, parameter optimizations and more. In
this subsection, the authors discuss the most popular CNN
models starting from the AlexNet model to the EfficentNet
model, as shown in Fig. 5. The overview of popular CNN
architectures along with model depth, dataset used, param-
eter error rate and input size are presented in Table 1.
(3)
2.3.1 Parasite Datasets
In order to enhance the deep learning method and models to
diagnose the parasitic diseases using microscopic images,
(4) various parasite datasets have been used which are sum-
marized and described in Table 2. The Table includes the
dataset of Plasmodium, Toxoplasma and Intestinal parasites.
This review contains some important datasets of other para-
sites also, such as Leishmania, Babesia and Trichomonad.
These datasets are mostly used for classification and detec-
(5)
tion tasks. Some publicly available microscopic images of
parasites from representative datasets for deep learning are
shown in Fig. 6.
(6)
3 Survey Methodology
To organize a systematic review, first, we frame the research
questions for conducting this research and then present our
analysis of the relevant deep learning-based research papers
(7) in the concerned domain, in chronological order. Next, we
demonstrate the summary of existing methods and models
along with the results based on the review of some poten-
tial techniques. Finally, we introduce the future directions
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2018 S. Kumar et al.

Fig. 5  Overview of CNN

architectures over a timeline
(1998–2020)

Table 1  An overview of CNN architectures with brief detail

Model Main finding Depth Dataset Parameters (M) Error rate Input size References

AlexNet Used Dropout and ReLU 8 ImageNet 60 16.4 227 × 227 × 3 [17]
VGG Increased depth, small 19 ImageNet 138 7.3 224 × 224 × 3 Simonyan and Zisserman
filter size [18]
GoogLeNet Increased depth, different 22 ImageNet 4 6.7 224 × 224 × 3 Szegedy et al. [19]
filter size, concatenation
Inception-V3 Utilizes small filter size, 48 ImageNet 23.6 3.5 229 × 229 × 3 Szegedy et al. [20]
better feature represen-
tation
Inception-V4 Divided transform & 70 ImageNet 35 3.08 229 × 229 × 3 Szegedy et al. [21]
integration concepts
ResNet Robust for over-fitting 152 ImageNet 25.6 3.57 224 × 224 × 3 He et al. [22]
Inception-ResNet-v2 Use residual links 164 ImageNet 55.8 3.52 229 × 229 × 3 Szegedy et al. [21]
Xception Convolution followed by a 71 ImageNet 22.8 0.05 229 × 229 × 3 Chollet [23]
point wise convolution
DenseNet Used blocks of layers 201 ImageNet, 25 3.46, 5.54 224 × 224 × 3 Huang et al. [24]
CIFAR-
100,
MobileNet-v2 Inverted residual structure 53 ImageNet 1.677 – 224 × 224 × 3 Sandler et al. [25]
HRNetV2 High-resolution represen- – ImageNet 45.2 5.4 224 × 224 × 3 Ke Sun et al. [26]
tation

and outline prominent challenges in parasites detection
and classification. We reviewed 70 related technical papers
from 2012 to the present. This work will act as a guide to
researchers for a comprehensive understanding of the pre-
sent state-of-the-art, future challenges and trends in the
research area of parasites detection and classification.
3.1 Research Questions
This review aims to provide insights into cutting-edge
machine learning and deep learning methods for parasite
detection and classification based on microscopic images,
as well as an analysis and summarization of previous work
on deep computer vision. From that perspective, the authors
develop the research questions to be addressed through the
research methodologies implemented by researchers. These
research questions are shown in Table 3. In the end, this sys-
tematic review paper also responds to these research ques-
tions posed here.
3.2 Paper Retrieval and Filtering Process
By applying deep learning, we have conducted a potential
investigation in the field of image detection and classifica-
tion of various parasites. As shown in Fig. 7, online data-
bases and digital libraries were searched in order to collect
sufficient relevant or related paper collections. The focus
was to collect papers from the most reputed publishers, such
as ACM, IEEE, ScienceDirect, Springer, and Wiley Online
Library.
The search and filtering process of papers involved in this
review is shown in Fig. 8. In the papers retrieving stage, we

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Advances Towards Automatic Detection and Classification of Parasites Microscopic Images… 2019

Table 2  Represent publicly available microscopic image datasets of protozoan parasites

Parasite types and image number Descriptions Dataset source References

Plasmodium falciparum-2703 Annotated image dataset with bounding https://​air.​ug/​micro​scopy/ [27]

Plasmodium-15,927, Babesia-1100
Toxoplasma gondii-8,156 with 400×, 6969 This FCGAN dataset also includes 4979
with 1000×
Chula-ParasiteEgg-11 1000 and 250
images/class for training and testing
boxes of 50,255 parasites. The dataset
also contains 1182 thick blood smear
images with bounding boxes of 7245
parasites
This dataset contains totally 23,463 micro- https://​github.​com/​senli​2018/​DTGCN_​ [28]
scopic images of multi-stage Plasmo- 2021
dium, Babesia and host cells (RBCs
and Leukocytes) under ×1000 magnifica-
tion
https://​github.​com/​senli​2018/​FCGAN/b [29]
host cell images at ×400 and 8023 host
cell images at ×1000 magnification
Chula-ParasiteEgg-11 training dataset https://​icip2​022ch​allen​ge.​piclab.​ai/​datas​et/ [30]
contains 11 types of parasitic eggs from
faecal smear samples Each category has
1000 images

Fig. 6  Three different datasets

of publicly available protozoan
parasite for deep learning. a
Intestinal parasitic dataset [29].
The dataset contains 11 types
of parasitic eggs from faecal
smear samples. Each category
has 1000 images. b Depict the
parasites images from dataset
[38]. This dataset includes
six types of parasites species
images (Toxoplasma, Leish-
mania, Babesia, Plasmodium,
Trichomonad, Trypanosome)
and RBCs and Leukocyte host
cells in the cropped patches. c
The dataset contains Plasmo-
dium falciparum cropped image
patches from parasitized and
uninfected RBCs [17]

Table 3  Research questions

Q1 What suitable domain knowledge exists for the diagnosis and treatment of human parasites diseases?
Q2 What are the DL based methods and models applied by researchers for parasites image detection and
classification?
Q3 What are the various measures applied to evaluating the performance of DL models?
Q4 How has the CNN based transfer learning techniques based developed over time?
Q5 What are the challenges and future direction in parasitology with DL?

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2020
Fig. 7  Search and filter information
firstly explore an arbitrary collection of the successive words
or phrases in ACM, IEEE, ScienceDirect, Springer, and
Wiley Online Library: “machine learning or parasites” and
“deep learning or parasites”, “CNN or microscopic images”
along with detection, classification, where 298 papers were
retrieved. We gathered an additional 50 papers from the ref-
erences of the retrieved papers. In total, we collected 348
papers in the searching stage. We remove collected papers
in two steps during the filtering stage. In the first step, we
filtered papers by checking whether the paper was dupli-
cated or not, 21 papers were excluded on this account. In
Fig. 8  The search and filter
process of papers
13
S. Kumar et al.
step two, 54 papers were selected for traditional machine
learning, 48 papers for deep learning, 15 for both classical
image processing and traditional machine learning and 10
papers are related to potential methods, which include visual
transformer-based methods.
4 Traditional Machine Learning Based
Methods and Models
In recent decades, traditional ML methods have gained pop-
ularity as a research area and have been applied in a vari-
ety of fields, including Natural Language Processing (spam
detection, text mining), Computer Vision (Face Recognition,
picture deletion and classification), and others. The major-
ity of ML-based techniques and models used today are for
object recognition. Related efforts on parasite identification
and classification using ML are chronologically discussed
in Sect. 4.1.
4.1 Machine Learning Related Works in Proposed
Field
This section demonstrates related works on parasite detec-
tion and classification based on ML, including methods,
models, results, and experimental data collection.
Advances Towards Automatic Detection and Classification of Parasites Microscopic Images…
In the year 2001, Yang et al. [31] proposed a framework
based on an artificial neural network classifier and digital
image processing techniques for automatic detection of
helminth eggs of humans on microscopic faecal speci-
mens. Digital image processing techniques were applied to
extract the morphometric characteristics of eggs of human
parasites in faecal specimens from microscopic images. The
dataset contained 82 microscopic images of seven common
human helminth eggs, which were used to train the pro-
posed model. The proposed ANN model performed identi-
fication of human helminth eggs in two stages. In stage first,
ANN-1 isolated eggs from confusing artefacts and in stage
two, ANN-2 classified eggs by species, as shown in Fig. 9.
In the same year, Tchinda et al. [32] presented a machine
learning technique to recognize intestinal parasite cysts from
microscopic images. Probabilistic neural network approach
trained by using image pixels feature was employed. It is an
effective machine learning approach for classification prob-
lems. In this approach parasites separated from microscopic
images and then resized to 12 × 12 pixels images. Principal
component analysis basis projection is used to reduce the
dimensionality. The proposed model was trained on 540
human parasite cyst images. The trained model successfully
classified intestinal parasites into 9 different kinds.
In year 2002, K. W. Widmer et al. [33] proposed a ANN
based system for Cryptosporidium parvum oocysts detection
to reduce the analysis time and achieve the high accuracy of
diagnostic process. A total of 525 images of labelled oocysts,
fluorescent microspheres, and other miscellaneous nonoo-
cyst images were collected and employed in the training of
the ANN. Each type of digital images were separated into
20% for training datasets and 80% for test datasets. Result
shows that the correct identification of authentic oocyst
images ranged from 80 to 97%, and the correct identification
of nonoocyst images ranged from 77 to 82%, on test dataset.
Fig. 9  Overall processing steps
of proposed ANN-based models
for both isolation and classi-
fication of helminth eggs. For
localization and classification
of helminth eggs from obtained
images. a Digital image pro-
cessing methods are applied
to get meaningful entities and
extract their features. b Two
stage ANN applied to classified
them based on their features
2021
Widmer et al. [34] developed an ANN-based model
for automatic identifications of Cryptosporidium oocyst
and Giardia cyst digital images. The digital images were
captured using a camera at ×400 magnification and con-
verted into a binary array. The ANN for Cryptosporidium
oocyst was trained with 1,586 images whereas the ANN for
Giardia cyst was trained with 2,431 images. After training
these networks were validated with unseen 500 images (250
positives, 250 negatives) of Cryptosporidium oocyst and 282
(232 positives, 50 negatives) images of Giardia cysts. Exper-
imental result of proposed model shows that the ANNs cor-
rectly identify the Cryptosporidium oocyst and Giardia cyst
images with an accuracy of 91.8% and 99.6% respectively.
Chen et al. [35] proposed a model based on machine
learning that performed classification and counting of bacte-
rial colonies from Petri dish images. This model recognized
both achromatic and chromatic images effectively. Support
Vector Machine approach was used for classification based
on morphological features. Two types of Petri-dish were
used for experiment. The proposed model predicted com-
parable performance to accomplish automation of the bacte-
rial colony. The proposed machine learning model achieved
96% accuracy level, For 75 achromatic images 97% accuracy
obtained and for 25 chromatic images 95%.
An automatic and rapid detection model based on neural
network was developed by Kumar et al. [36] for pathogens
in foods. The proposed model involved identification in two
stages. In stage first, background correction is applied to dis-
tinguish the treated image from the image background using
better approaches. In stage second, collecting the images of
the local region. Thereafter textural, optical and geometrical
features of processed pathogen images are collected. Finally,
the proposed model based on Probabilistic Neural Network
applied to classify the microorganisms from collected.
Osman et al. [37] developed a model based on image pro-
cessing and genetic neural network techniques for automatic
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2022
detectioin of Mycobacterioum tuberculosis in tissues. The
proposed model is divided into two steps: step one invoved
K-means clustering methods for image segmentation and
step second involved GANN method for feature selection,
classification and feature extraction purposes. After applying
a genetic algorithm to select features, a multilayer percep-
tron was trained for the final classification of bacteria (true
TB and Possible TB). Dataset collection includes 960 total
object images of which 360 for true TB and 600 for possible
TB. The proposed model was trained on 400 images and the
rest of 280 images used for testing purposes. Experimental
results demonstrated that proposed approach able to produce
84.9% accuracy with fewer input features.
Hiremath et al. [38] presented identification and clas-
sification of a bacterial cell of cocci data collection using
machine learning technique. The proposed model was devel-
oped using 3α, KNN classifiers and a selected neural net-
work to recognize the pattern of cocci bacterial cells. The
data is processed by applying a neural network pipeline that
includes inputs layers, output layers, gradient descent and
backpropagation function. In this experiment 500 different
types (sarcinae, streptococci, diplococci, cocci and tetrad)
of digital bacterial images were used. Using the proposed
model up to 94% level accuracy was achieved based on the
3α classifier. With KNN classifier where k = 1, 75% to 100%
accuracy achieved and up to 100% accuracy achieved with
Neural Network classifier.
A ML based approach was implemented by Ghazali et al.
[39] for human fecal parasite detection based on comput-
erized image analysis. The presented model contains three
stages as shown in Fig. 10. In stage first, the pre-processing
techniques were applied to enhance features. In stage sec-
ond, a features extraction mechanism was used with three
Fig. 10  Overview of three different Pre-processing methods: (Pre-method 1) Content noise reduction with median filter, (Pre-method 2) Content
edge detection using canny filter and (Pre-method 2) Content edge enhancement using unsharp filter
13
S. Kumar et al.
characteristics (shape, shell smoothness and size). In stage
third, filtration with Steady Determinations Thresholds Sys-
tem method was used to identify and classify the types of
parasites based on features values. The final result predicted
success rates of Ascarislumbricoides and Trichuristrichiura
almost 93% and 94% respectively.
In [40] developed a model based on machine learning
for automatic classification and segmentation of human
intestinal parasites. The proposed model classifies into two
stages, in stage first segmentation process was performed
using image transformation, quantization border enhance-
ment and ellipse matching, as seen in Fig. 11. In the second
stage, classification was performed with different ML algo-
rithms like ANN-MLP cum Adaboost, optimum path forest
classifier, SVM and SVM cum Adaboost. After investigating
the performance of different ML algorithms, the optimum
path forest classifier prediceted a good result for classifica-
tion images. The experiment result shows that the proposed
Fig. 11  Overview segmentation pipeline include operation like Quan-
tization for colored conversion, Border enhancement for quantized
image border with Sobel Gradient operator, and Ellipse matching:
objects having higher degree of ellipse matching considered as para-
site candidate
Advances Towards Automatic Detection and Classification of Parasites Microscopic Images…
ANN based model classify 155 images from the test dataset
with 98.22% accuracy.
Nugroho et al. [41] developed a model based on image
processing techniques to recognize three phases of malaria
parasite cell host in microscopic images i.e. schizont, tropho-
zoite and gametocyte plasmodium falciparum. The proposed
model develops in two phases. In phase first image pre-pro-
cessing was implemented with median filter and contrast
stretching. In phase second k-means method was applied for
image segmentation. Finally, a multilayer perception back-
propagation technique was employed for classification. The
data collection contained 60 images of trophozoite, game-
tocyte and schizont. The proposed model achieved accuracy
level of 87% with specificity 90% for detection.
In the year 2016, Seo et al. [42] developed a machine
learning model for classification of staphylococcus species.
In this experiment, the authors used five different types of
species of staphylococcus bacteria namely aureus, haemo-
lyticus, hyicus, sciuri and simulans. Mahalanobis distance
method was applied to eliminate the outliers, after that wave-
length selection performed using correlation coefficient. The
proposed model classified the staphylococcus bacteria spe-
cies using Partial least square discriminant analysis and sup-
port vector machine. With the proposed model 89.8% accu-
racy was achieved using Support Vector Machine and 97.8%
accuracy using Partial least square discriminant analysis.
In [43] purposed an approach that utilized the multi-scale
wavelet counter detection to detect the parasites. Jointly
active contours and Hough Transform were used to perform
detection and segmentation of parasites images. The pro-
posed model involved Principal Component Analysis and
Probabilistic Neural Network. Principal Component Analy-
sis was used to extract and reduce the features acquired from
parasites images pixels and a probabilistic neural network
model was used for the classification task. This model is
tested on 15 intestinal parasites species with 900 microsco-
pies images. Using this approach, the correct rate of clas-
sification obtained was 100%.
Nkamgang et al. [44] has purposed neuro-fuzzy approach
to automatic detection and classification of human intestinal
parasites. This model is based on segmentation and training
of classifier. In this approach, parasites were localized using
circular Hough transform and after that distance regularized
level was initialized for segmentation. Finally, classification
was performed by applying a trained neuro-fuzzy classifier.
The proposed model has been applied for identification and
classificatoin of 20 type’s human intestinal parasites. For
every 20 classes of intestinal parasites satisfactory classi-
fication result was obtained and 100% recognized rate was
achieved.
Vakilian et al. [45] developed a model based on image
processing techniques and an artificial neural network for
recognizing two types of fungi that are responsible for
2023
spreading infection in cucumber plant leaves. The proposed
scheme contained total 300 images of healthy and infected
plants. Among these, 250 images were used for training
ANN model and the remaining were used for inspection. In
this experiment, the training dataset indicated good fit. The
relationship between the outputs and the inputs for validation
and test dataset was 0.9.
Liu et al. [46] focused on KNN classifier to classify the
morpho type bacterial species based on morphological fea-
tures. Total 1937 digital images were collected for the pro-
posed system. Among these, 1271 cells images were applied
to train the classifier which exhibits 96% accuracy and 466
test cell images exhibit 97% accuracy.
Inayah et al. [47] worked on a Randomly Wired Neural
Network for recognize the parasites from red blood cells.
Secondary data set is used in this model collected from the
National Library of Medicine (NLM). In this model total
of 27,558 images of red blood cells were used as data. The
proposed model worked on feedforward and backpropaga-
tion techniques. Using this model, average accuracy 95.08%
was achieved in fivefold cross-validation.
4.2 Summary
In the past two decades, traditional ML methods for parasite
detection and classification have been updated from time to
time. Table 4 displays the related research works, including
references, publication date, methods, objectives, species
categories, and data details evaluation metrics, limitations,
and future scope.
5 DL Based Methods and Models
In recent years, high-stake applications have been imple-
mented using deep learning methods and models for micro-
scopic image diagnosis. An extensive literature review and
study is carried out for the proposed topic of convolutional
neural network techniques based on deep learning for detec-
tion and interpretation using clinical intestinal protozoa
microscopic images. In this section, an overall reviewed
summary of methods and models of related subjects is
prepared.
5.1 DL Related Works in Proposed Field
Hung et al. [48] presented the task of detection of individual
cells and their respective classes using Faster Region-based
Convolutional Neural Network (Faster R-CNN). The pro-
posed model contains two sub-module, as seen in Fig. 12.
Sub-module first apply Faster R-CNN to detect individual
cells from the image by generating a bounding box around
cells like red blood cells or non-red blood cell and in
13
 Table 4  Summary of reviewed research works on traditional machine learning methods and models as applied for detection and classifications used objective, dataset details which include class
2024

(C), total images (T.I), training (Tr.), test (Ts.) and evaluation metrics which include accuracy (Acc.), precision (Pre.), recall (Rec.), sensitivity (Sn.), specificity (Sp.)
References Date Method Type of features Objective Parasites (species) Dataset details Evaluation metrics Limitations Future scope

13
[31] 2001 ANN Pixel intensity Automatic detection Helminth eggs C=2 Acc. = 86.1% Small dataset An enhanced model
of human helminth T.I = 82 proposed to classify
eggs helminth eggs
[32] 2001 ANN Pixel intensity Automatic Identifica- Helminth Eggs C=7 Det. = 86.1% Small dataset To improve results
tion of human T.I = 82 large dataset may
helminth eggs be used
[34] 2005 ANN Shape feature Classification of Giardia cyst and C=2 Acc.(GC) = 91.8 Insufficient dataset More tests from food
Giardia cyst (GC) Cryptosporidium Tr. = 2431(GC), Acc.(CO) = 99.6 matrices need to be
and Cryptosporid- oocyst 1586(CO) continued to validate
ium oocyst(CO) Ts. = 100 & confirm HMI
methods
[35] 2009 SVM Shape feature automated bacterial Bacterial colony C=2 Acc = 96% Clustered colonies of Model may improve
colony counting T.I = 100 Pre. = 0.97 bacteria’s are not for better classifica-
and classification Rec. = 0.96 distinguishes tion
F1-Score = 0.96
[36] 2010 ANN Shape feature Rapid detection of Microorganisms C=5 Acc. = 100% Small dataset
microorganisms TI = 1
[37] 2010 GA-NN Shape feature GA-neural network mycobacterium C=2 Acc. = 89.64% In sufficient Evalua- Improving the
approach for myco- tuberculosis T.I. = 960 tion Criteria performance of the
bacterium tubercu- Tr. = 400 bacteria colony clas-
losis detection Ts. = 280 sification
[38] 2011 K-NN, ANN Geometric features Identification and cocci bacterial cells C=6 Acc. = 99% Over lapped cells Improving the limita-
classification of T.I = 350 not considered in tion of proposed
cocci bacterial purposed model model
cells
[39] 2013 F-SDTS Shape feature Automated system Ascaris lumbri- C=2 Acc.(ALO) = 93% limited to the basic An enhanced model
for diagnosis intes- coides (ALO), T.I (ALO) = 100 Acc.(TTO) = 94% diagnosis parasitic proposed to diagno-
tinal parasites by Trichuris trichiura T.I (TTO) = 100 worms sis parasite worms
ova (TTO)
[40] 2013 ANN,SVM Shape feature Classification of Human intestinal C = 16 Sn. = 90.38% Insufficient dataset Improve conventi onal
human intestinal parasites TI = 5763 Sp. = 98.22% slides impurities, by
parasites Tr. = 2881 applying parasite-
Te. = 2 ological techniques
[42] 2016 SVM Shape feature Identification of Staphylococcus C=5 Acc. = 97% Insufficient dataset Size of dataset may
Staphylococcus species be increased for
species validation
[41] 2015 ANN Shape feature Classification for Trophozoite, schiz- C=3 Acc. = 8708% Insufficient dataset Increase
detection malaria ont, and gameto- T.I = 180 Sn. = 81.7% classification with
parasites cyte Sp. = 90.8% more feature extrac-
tion methods
for identification
S. Kumar et al.
 Advances Towards Automatic Detection and Classification of Parasites Microscopic Images… 2025

submodule second AlexNet model was used for further clas-

and classify different

classify other para-

upgraded to obtain

working efficiency
improved to detect

cantly improve the

sification of cells from images. The data collection contain

types of parasites

better result and

DL model signifi-
Model may be 1300 images and after pre-processing these images contain

Model may be
Future scope

100,000 labelled cells. Experimental results predicted an

sites too
accuracy of 98% for the proposed model.
M. Górriz et al. [49] used U-Net, a deep convolution
neural network to classify and segment the Leishmanio-
sis Parasite, which causes thousands of deaths in some
Insufficient dataset
Imbalance dataset

undeveloped countries annually, as shown in Fig. 13. The

number of images used in this task includes 45 having
Limitations

size 1500 × 1300pixels captured with light microscopic

with the magnification of ×50 to facilitate image analysis.
F1-Score = 95.05% Evaluation of F1-Score based on pixel-wise classification
of classes Background, Cytoplasm, Nucleus, Promastig-
Evaluation metrics

Rec. R. = 100%

ote, Adhered and Amastigote is 0.980, 0.896, 0.950, 0.491,

Acc. = 95.08%

Rec. = 96.44%
Pre. = 93.62%
C.R = 100%

0.457, 0.777respectively. Jaccard Index (j) is used to auto-

matic detection of class Promastigote, Adhered and Amas-
tigote and their evaluation when j > 0.75 is 0.50, 0.12, 0.55
respectively.
Viet et al. [50] developed an automatic Parasite worm
Dataset details

egg detection and classification model by applying the deep

T.I = 27,558

learning Faster R-CNN method in microscopy stool images.

Ts. = 1200
T.I = 1800

T.I = 1800

Ts. = 900
Tr. = 600

Tr. = 900

Faster R-CNN uses RPN (a fully CNN) network to generate

C = 20

C = 15

proposal regions that simultaneously predicts object bounds

and object scores at each position. RoI Pooling layer draw
Falciparum parasite
Intestinal parasites
Parasites (species)

interests region along with convolutional features as input to

Automated detection Human intestinal

generate the bounding box around objects. The experiment

parasites

result shows that the Faster R-CNN model performs better

with an accuracy 97.67%.
Yang et al. [51] worked on a model that recognized the
parasites in microscopic images of blood smear. The author
of human intestinal

Classification of fal-
for intestinal para-
Automated medical
and classification

diagnosis system

ciparum parasite

divided this model into two parts, first to detect the parasites
entities Iterative Global Minimum Screening technique used
parasites

and second, the authors used a customized Convolutional

Objective

sitosis

Neural Network to classify each entity from images of either

parasites or background. For this model, the authors col-
lected 1819 thick smear digital images from 150 patients.
The proposed model gave an accuracy of 93.46% and an
Shape and texure
Type of features

AUC of 98.39%.
Shape feature

Khoa Pho et. al [52] proposed a model based on trans-

feature

fer learning and data augmentation techniques to detect and

identify the images of systs and oocysts of various species
–

like Iodamoeba butschilii, Toxoplasma gondi, Giardia lam-

Neural Network

blia, Cyclospora cayetanensis, Balantidium coli, Sarco-

2018 neuro-fuzzy clas-

2020 Randomly Wired

cystis, Cystoisospora belli and Acanthamoeba, which have

round shapes in common and affect seriously to human and
Method

sifier

animal health. The proposed modedl RetinaNet automati-

2018 ANN

cally detect and identify the protozoa’s. Even though there

Table 4  (continued)

were lack of data in the training data, the proposed model

Date

still achieves good accuracy.

Mathison et al. [53] used a deep convolution neural
References

network for detection of intestinal protozoa in Trichrome-

[44]

[43]

[47]

Stained stool specimens from scan digital microscopic

13
2026
images. Traditionally, the ova-and-parasite (O&P) inspec-
tion method is used to manually microscopic evaluation
of stool. It is a resource and time-consuming method. The
purpose of this research is to develop a novel CNN model
along with scan high-resolution digital side images to rec-
ognize intestinal parasites from stool, as shown in Fig. 14.
The whole task is divided into three parts. Part I, collect the
digital scan microscopic images of intestinal protozoa con-
taining target classes. Part II, input the collected microscopic
images into CNN model for training so as to detect defined
classes. Part III, perform the validation and prediction of
the trained model. The author collected and prepared one
Fig. 12  Detail of how proposed two stage deep learning model for
recognition and classification is applied to images during test phase.
a An original image is fed into Faster R-CNN model to recognize
Fig. 13  Overview of the
proposed model for detecting
Leishmaniasis Parasites
Fig. 14  Workflow of training
for CNN
13
S. Kumar et al.
hundred twenty-seven slides of 11 categories of protozoa
to train the model. During the model development, various
training steps were executed and analysis of model perfor-
mance was evaluated with the resulting metrics. All images
were resized to 250 by 250-pixel images, of which 10% of
label images of all classes were used for validation of CNN
after training. The proposed intestinal detection model archi-
tecture is RGB CNN based on the SSD Inception V2 trans-
fer learning model. The based model pertained with COCO
image dataset. The trained model was shown the collection
of 250 by 250-pixel images scenes to recognize the parasites.
The model created a label image box to detect the parasite.
objects and label them as RBC or other. b The labelled objects as
other are sent to AlexNet model to undergo more fine-grained clas-
sification
Advances Towards Automatic Detection and Classification of Parasites Microscopic Images…
The precision recall plot were used to view the model per-
formance on the basis of per labelled parasite image box.
The slide-level agreement is used to calculate the accuracy
of the model, the positive agreement achieved was 98% and
the negative was 98.11%.
Baek et al. [54] developed a model with Fast Regional
Convolutional Network (Fast R-CNN) based on DL to
quantify and classify five cyanobacteria. The proposed Fast
R-CNN model includes two stages, in stage first classify
cyanobacteria species taken from microscopic images using
the fast R-CNN method and in step second CNN technique
is used to quantify the cyanobacteria cells. The dataset col-
lection covered 200 images of five species of cyanobacteria
(Microcystiswesenbergii, Microcystis aeruginosa, Dolichos-
permum, Aphanizomenon and Oscillatoria). Experiment
results show that the Fast R-CNN based model was able to
achieve a reasonable accuracy for classification and yielding
average precision (AP) values of 0.929, 0.973, 0.829, 0.890,
and 0.890 for respective species.
Kang et al. [55] purposed an expensive deep learning net-
work which utilized 1D CNN, Long-Short Term Memory
Network (LSTM) and Deep Residual Network (ResNet). The
proposed hybrid deep learning model define as Fusion-Net
perform the classification of foodborne bacteria at a sin-
gle-cell level. The Fusion-Net formation was performed in
three parts comprising hyper parameter optimization, mul-
tiple deep learning architecture selections, and Fusion-Net
Fig. 15  MCellNet architecture
includes a convolutional layer,
six inverted residual blocks, one
flattened layer, and one fully
connected layer. The input to
MCellNet model is Crypto-
sporidium and Giardia images
of 120 × 120 pixels, and the
output is the probability of each
class
2027
construction. The dataset was prepared by collecting 5000
bacterial cells images of five foodborne bacterial cultures, of
which 72% are used for training, 18% are used for validation
and10% are used for the test dataset. Results show that the
proposed model yields classification accuracy up to 98.4%.
Luo et al. [56] report a deep learning-based model for
predicting Cryptosporidium and Giardia in drinking water.
The proposed system merged imaging flow cytometry with
MCellnet an efficient neural network. Figure 15 shows the
architecture of MCellNet. The dataset collection included
millions of raw images of which 80,146 images were
selected for the final image database and each image from
the database was patched to 120 × 120 pixels. 13 classes of
Cryptosporidium (2082 images), Giardia (3569 images)
were included in the dataset. The image data set is randomly
split into a training data set (38,469 images), a validation
data set (9618 images) and a test data set (32,059 images)
that contained 48%, 12%, and 40% images respectively. The
proposed model for multiclass and binary classifications
achieves accuracies of 99.69% and 99.7%, respectively.
Nakasi et al. [57] evaluate the performance of the
AlexNet and GoogleNet model based on transfer learning
for the diagnosis of scan digital intestinal parasites stool
microscopic images. The authors compared these two mod-
els with trained Convolution Neural Network for the same
work. Models are evaluated on the system having low speci-
fication which shows that models can be deployed to tackle
13
2028
real word diagnostics problems. A total of 6500 (10.9% posi-
tive) image patches were applied in AlexNet, 6461 image
patches (11% positive) applied in GoogleNet and 2071
image patches (30.5% positive) applied in Custom CNN.
From proposed models, the AlexNet attained accuracy ROC
AUC of 1.00 and GoogleNet attained ROC AUC of 99.
Lee et al. [58] developed a Helminth Egg Analysis Plat-
form (HEAP) that help medical technicians to diagnosis
parasite infections. The authors integrated the various deep
learning techniques (SSD, Single Shot MultiBox Detector,
U-net, and Faster R-CNN, Faster Region-based Convolu-
tional Neural Network) to recognize the helminth egg speci-
mens as shown in Fig. 16. The proposed model also includes
pixel level based methods image binning and egg-in-edge
algorithm to improve performance. HEAP exhibit effective
performance in counting and recognizing the helminth eggs
from digital images.
Litjens et al. [59] investigated a deep convolution neural
network to improve the efficiency and accuracy of cancer
diagnosis in H and E images. This model is used to perform
two different tasks, first prostate cancer recognition from
biopsy samples, and second breast cancer recognition from
sentinel lymph nodes. Pre-processing pipeline of the model
consists of 4 convolution layers for features extraction, 3
max-pooling layers to reduce the dimensionality and a dense
layer for classification. Dataset for prostate cancer includes
225 glass slides of which 100 are selected for training, 75
for testing and remaining for validation. Dataset collection
for breast cancer sentinel lymph nodes for the experiment
includes 271 slides of which 98 for training, 33 for validation
and remaining for testing the model. Optimal percentiles
were obtained using the validation set for both ROC curves
and the highest specificity that was the median and 90th
percentile for both.
Panicker et al. [60] work on end to end selective auto-
encoder approach based on convolution neural network to
recognize complex soybean cyst nematode eggs from micro-
scopic images. The soybean cyst nematode eggs training
patches were used to train the proposed convolutional neural
Fig. 16  Functionality of HEAP-assisted parasite egg investigation. In
stage first, all the specimen preparation measures are applied. Then,
an automatic microscope image system was used to digitalize the
specimen slides. Multiple focusing planes were required to gather all
13
S. Kumar et al.
network. The trained model was validated with validation
images. Figure 17 depict the architecture of the proposed
Convolution auto-encoder model. The dataset collection
included 644 nematode microscopic images that were used
to investigate soybean cyst nematode eggs. 80% of images
were used to train the model and the rest of the images were
used for validation. Experimental results predicted accuracy
of 94.33% for the proposed model.
Tahir et al. [61] develop a Convolution Neural Network
based on deep learning for the detection and classification of
five different types of fungus spores and dirt. Around 40,800
annotated RGB images of 6 classes were developed for fun-
gus detection and classification. The model was trained on
30,000 fungus images and each class contain 5000 images.
The test set comprises 10,800 fungus images with 800
images per class. The accuracy achieved by the purposed
model is 94.8%.
Oomman et al. [62] developed an automatic approach
based on deep convolution neural network for the detection
of Tuberculosis bacilli from microscopic images. The pro-
posed model was developed in two stages, stage first done
image binarisation with Otsu threshold algorithm and in sec-
ond stage classification of detected regions done using a con-
volutional neural network. The dataset collection included
120 images along with ground truth, each image in the data-
set has 2816 × 2112 pixel resolution. For CNN training and
testing the images were cropped to 900 negative patches and
900 positive patches. From the total of 1800 patches, 80%
were used for training purposes and 20% used for testing.
Experimental results show that the proposed model achieved
a recall of 97.13%, a precision of 78.4% and an F-score of
86.76%.
Treebupachatsaku et al. [63] purposed a method based
on deep learning for the detection of a genus of a bacte-
rium from microscopic bacterial images using the Tensor-
flow framework. More than 800 sample images of S. aureus
and L. delbruekii datasets were collected. Eighty percent of
images from both datasets were applied to train the proposed
the images. HEAP carried out the egg recognition and egg counting
using cloud computing. Finally, medical expert verify the model pre-
diction result using computer client on internet
Advances Towards Automatic Detection and Classification of Parasites Microscopic Images…
Fig. 17  Convolutional auto-encoder architecture to recognize complex soybean cyst nematode eggs from microscopic images
model and the remaining images were used for testing. The
proposed model achieved 96% of validation accuracy.
Pedraza et al. [64] worked on deep learning-based neu-
ral to check the diatom detection from water. The authors
determined the diatom detection with two popular transfer
learning techniques i.e. RCNNs (Region-based Convolu-
tional Neural Networks), which applies convolution opera-
tion on candidate region and YOLO (You Only Look Once)
which applies a neural network over the whole image. These
two methods were trained on 11,000 microscopic images of
diatom from 10 species. Diatom detection results of RCNN
and YOLO are depicted in Fig. 18. The experimental result
shows that the YOLO model performs better with 84%
F-Measure than RCNN.
Sajedi et al. [65] proposed a model to recognize bacte-
rial species from solid culture plates. Two methods based
on deep learning were applied to detect action bacterial
strains. In the first method, a two-level wavelet transform
was utilized on action bacterial strains images. In the sec-
ond method, two operations are performed i.e. data augmen-
tation for blurring, cropping, and horizontal rotation and
Fig. 18  Detection results of the
proposed model. Left column:
a with false positive regions;
Centre column: b with false
negative regions; Right column
c YOLO evaluation
2029
classification using transfer learning technique ResNet. The
dataset collection was prepared from UTMC.V1.DB and
UTMC.V2.DB databases containing 703 images from 55
different classes and 1303 images from 97 different classes
from respectively. The experimental result exhibits that the
former method acquired an accuracy of 80.81% and 84.81%
on both datasets. The secondary method acquired accuracy
of 90.24% and 85.96% on both datasets.
Zhou et al.[66] implemented a model by applying a
transfer learning approach based on a convolution neural
network to automatic analyses diatom from digital whole-
slide images. The proposed model applied the GoogLeNet
Inception-V3 transfer learning technique for training to rec-
ognize the diatom, as shown in Fig. 19. The dataset collec-
tion comprised 53 digital whole-slide images of which 43
slides were selected for training and 10 slides for validation.
Experimental results show that the transfer learning model
using the augmented database achieved accuracy of 97.67%
and AUC: 99.51%.
Qian et al. [67] demonstrated a novel multi-target deep
learning framework developed with Faster R-CNN for algae
13
2030
Fig. 19  The CNN architecture
implemented with the Goog-
LeNet Inception-V3 CNN
detection and classification. The proposed extensive model
was trained on a large-scale coloured microscopic algae
dataset, as depicted in Fig. 20. The dataset collection was
prepared with 1859 images of 37 algae as well as anno-
tations of genera and classes. In this experiment, 80% of
images of genera were collected in the training set to train
the model and the remaining were collected for the testing
set. The experimental result show that the successful identi-
fication rate achieved at genus level by the proposed model
was 74.64% and at class level it was 81.1%
Salido et al. [68] focus on mitigating the Diatom detection
for specimen counting and sample classification challenge
with the YOYO and SegNet network based on deep learn-
ing. The dataset prepared collects microscopic images of
80 species of diatoms and each species contain hundreds of
images. Detection of diatoms for faster diatom counting by
using YOLO for on-time inferences with an average sensitiv-
ity of 84,6%, specificity of 96.2%, and precision of 72.7%.
Holmström et al.[69] focuses on deep learning methods
for accurate and fast detection of helminths and Schistosoma
haematobium. The author used 8,342,769 echocardiograph
images of 276 patients. 80 images were used to train the
Fig. 20  Model architecture depicts 3 branches simultaneously out-
puts the genus, bounding box, and a biological class of the algae and
orange component extended classification branch. Branch-1 is used to
13
S. Kumar et al.
model and the remaining were used for testing and validation
of the model. Train model showed 97% accuracy without
any over-fitting. The model achieved the same test accuracy
on low-resolution images among 15 views. Evaluation repre-
sented using confusion matrices also detect similarities and
classification based on relevant image features.
Peixinho et al. [70] proposed a deep learning-based
approach ConvNet that recognize the image features effec-
tively for human intestinal parasite images. Random kernels
are defined for hyper-parameters optimization CNN archi-
tecture. For the experiments, the dataset contained 16,437
objects including the 15 most common species of human
intestinal parasites. Using the proposed approach effective
accuracy was obtained for the classification of human intes-
tinal protozoa’s and eggs.
López et al. [71] implement a model based on CNN to
detect the mycobacterium tuberculosis (MT). Dataset consist
of 9770 positive and negative smears patches prepared from
492 digital images. Three types of patches (grey-scale, RGB,
R-G) were used to train the proposed CNN based model.
The proposed model includes three layers to perform the
predict the genus of algae. Branch-2 is used for algal detection and
localization. Branch-3 is used to predict the class of algae
Advances Towards Automatic Detection and Classification of Parasites Microscopic Images… 2031

classification of patches into two classes i.e. positive or neg- to increase the size of the dataset. From this dataset, 70%
ative MT. The proposed model accomplished 96% accuracy of images were used to train the model and 30% were used
level. for validation. The proposed model obtained experimental
Zieliski et al. [72]developed a hybrid deep learning model results with 88.59% accuracy.
for the classification of bacterial species from digital images. In [77] presented a deep learning-based approach to clas-
In the proposed model deep convolutional neural network is sify bacterial colonies. The authors used Deep Convolutional
used to recognize image descriptors, subsequently features neural network (CNN) to obtain image descriptors and sup-
vectors are generated with the pooling encoder method and port vector machine (SVM) and Random forest for classifi-
finally Support Vector Machine was used for classification. cation, as shown in Fig. 21. Features based on shapes namely
The dataset used in this model includes 33 bacteria spe- spiral, cylindrical and spherical were extracted. The dataset
cies with 20 digital images of each bacterium. The proposed consisted of 660 images with 33 different genera and species
model used 50% data of the dataset for training purposes of bacteria. The experimental results predicted the accuracy
and 50% for testing. The results exhibit that the proposed of recognition to be 97.24%.
DL based model is 96.82% accurate in the classification of Hay et al. [30] presented a convolutional neural network-
bacterial species from digital images. based tool for differentiating bacteria images from non-
Wahid et al. [73] implement a model by using a transfer bacterial images using three-dimensional microscopy data
learning technique to automate the classification and rec- of gut bacteria found in larval Zebrafish. The authors used
ognition task using a deep convolution neural network. The TensorFlow framework to implement 3D convolutional neu-
proposed inspection DCNN model was trained using 500 ral network and compared the performance of the model
digital microscopic images of five bacterial species. The with support vector machine and random forest classifiers.
dataset was split into the training (80% images) and testing The proposed model performed better with 89.3% accuracy
(20% images) parts. The detection and classification rate of whereas random forest classifier and support vector machine
the proposed model is 85% classifiers achieved accuracy of around 78.5% and 83.1%
Ahmed et al. [74] Implemented a hybrid approach to respectively.
classify microscopic bacterial images using the SVM and In [78] developed a CNN based model using transfer
Inception-V3 model. In the proposed model image pro- learning approaches for automatic classification of parasites
cessing techniques like image cropping, converting images with low quality microscopic scanned images, as shown in
from grayscale to RGB, image flipping, image translation
and feature extraction by Inception-V3 Deep CNN method
were used. The SVM was used to classify the microscopic
bacterial images into defined classes. The authors used 800
bacterial images to train the proposed model and 200 images
for testing. Based on the proposed model 75% accuracy in
the classification of bacterial species from digital images
was achieved.
In [75] performed an experiment on datasets of In Situ
plankton images using deep learning techniques. Proposed
model extract features from various planktonic images data-
sets i.e. Imaging Flow Cytobot (IFCB), Scripps Plankton
Camera System (SPC) and Situ Icthyoplankton imaging sys-
tem (ISIIS). The authors train CNN model by using IFCB
and ISIIS plankton images datasets. The dataset SPC was
small in size and so it was used for testing purposes. To train
the proposed CNN model images of plankton were resized
to 256 by 256. Experimental results of the proposed model
work well on the feature extraction from planktonic images
using CNN.
In [76] determined the classes of microalgae using convo-
lution neural network technique of deep learning. FlowCam
practical analyser used to extract microalgae images from
water extracted from South Atlantic Ocean. The dataset con-
tained 29,449 microalgae images that are further classified Fig. 21  Flowchart of deep learning-based approach to classify bacte-
into 19 classes. The data augmentation technique was used rial colonies

13
2032
Fig. 22. The patches based technique was used to search
the location of eggs from images. The dataset collection
contained ×10 magnification microscopic images of four
different types of parasites i.e. Ascarislumbricoides (67
images), Hymenolepisdiminuta (27 images), Fasciolopsis-
buski (32images) and Taeniaspp. (36 images). Before apply-
ing data augmentation and the patch overlapping, grayscale
conversion and contrast enhancement are performed on the
parasite egg image collection. The grayscale conversion
operation decreases the depth of the input parasite image
from three channels of RBG to one channel of grayscale.
Further, the visualisation of low magnification of images is
enhanced with contrast enhancement. Each parasitic image
was split into small patches, which allowed the model to
extract features from the image by examining the local areas.
In order to encapsulate the mentioned parasites, patch size
set to 100 × 100 pixels. The data augmentation technique
was applied to increase the size of the dataset, approxi-
mately 10,000 patches per egg type. In order to implement
the proposed framework, a transfer learning technique was
employed with fine-tuning pretrained models. These models
have been trained on large dataset of images collected from
different specific applications. The last two layers of these
models were replaced with a fully connected layer and a
softmax layer to classify images into five classes. Grayscale
conversion operation decreases the depth of the input para-
site image from three channels of RBG to one channel of
grayscale. Further, the visualisation of low magnification of
images is enhanced with contrast enhancement. Each para-
sitic image was split into small patches, which allowed the
model to extract features from the image by examining the
local areas. In order to encapsulate the mentioned parasites,
Fig. 22  Overview of the pro-
posed architecture for training
and testing CNN model. In
stage first, model trained on the
pre-processed collected speci-
men images. In stage second,
testing is performed on trained
model with test data set
13
S. Kumar et al.
patch size set to 100 × 100 pixels. The data augmentation
technique was applied to increase the size of the dataset,
approximately 10,000 patches per egg type. In order to all
implement the proposed framework, a transfer learning
technique was employed with fine-tuning pertained models.
These models have been trained on large dataset of images
collected from different specific applications. The last two
layers of these models were replaced with a fully connected
layer and a softmax layer to classify images into five classes.
For object detection, AlexNet is a cutting-edge model that
improved CNN execution performance, whereas ResNet50
is a more sophisticated architecture that performs better
for image classification tasks. The dataset of parasite egg
images was split into two parts, part first contained 60% of
the images for training purposes, and the second contained
40% of the images for testing purposes. Based on the pro-
posed framework, experiment results represented state-of-
the-art parasitic egg detection and classification task. Based
on the proposed framework, experiment results represented
state-of-the-art parasitic egg detection and classification.
Quinn et al. [27] authors purposed a framework based
on Deep CNN to evaluate the performance with differ-
ent microscopy tasks i.e. intestinal parasite eggs in stool
samples, tuberculosis in sputum samples, and diagnosis of
malaria in thick blood smears. The experts mark bounding
boxes around each interested entity in all images. Finally,
prepared, plasmodium was annotated (7245 entities in 1182
images) in thick blood smear images, tuberculosis bacilli
were annotated (3734 entities in 928 images); in sputum
samples, and, the eggs of hookworm, Taenia and Hymeno-
lepsis nana were annotated (162 entities in 1217 images)
in stool samples. The proposed model is trained on the
Advances Towards Automatic Detection and Classification of Parasites Microscopic Images…
collected images. After training the resulting model was
applied to the test set: plasmodium detection set, which con-
tains 261,345 test patches, tuberculosis set contain 315,142
test patches and hookworm set contains 253,503 patches. In
all cases, experiment results show that accuracy was higher
and better than traditional medical imaging techniques.
Butpoly et al. [75] proposed DL based method for clas-
sification of Ascaris lumbeicodes parasites images. The pro-
posed model recognize three types of eggs of Ascaris lumbe-
icodes with effective approach of deep learning. The dataset
collection included training and testing data. Both training
and testing dataset included three types Ascaris lumbeicodes
eggs namely infertile eggs, fertile eggs and decorticate eggs.
For this experiment the training dataset consist of 200 of
each type (total images 600). Experimental results predicted
93.33% classification accuracy of the parasites eggs.
Avic et al. [76] implemented methodology based on
multi-class support vector machine for classification of
human parasites eggs from digital microscopic images. The
proposed model consists of four steps. These steps are pre-
pre-processing feature extraction, classification and testing.
In pre-processing step, the image processing methods, such
as contrast enhancement, thresholding, noise reduction are
applied. In second step i.e. feature extraction, the invariant
moments of parasites images obtained in step first are evalu-
ated. In classification step, the multi-class support vector
machine was applied to classified feature collected in feature
extraction step. The proposed model was tested with test
data. The proposed approach achieved average accuracy of
97.70% for classification of human parasites.
5.2 Summary
In the past two decades, traditional deep learning methods
for parasite detection and classification have been updated
from time to time. Table 5 displays the related research
works, including references, publication date, methods,
objectives, species categories, data-details evaluation met-
rics, limitations, and future scope.
6 Discussion
We compiled traditional machine learning and deep learn-
ing-based methods for microscopic image classification and
detection of various parasites in this paper. All the research
studies discussed here show that both ML and DL methods
and models are effectively used by researchers. Traditional
machine learning methods and models include, as stated in
the review, k-NN, SVM, ANN, GA-NN, and Neuro-fuzzy
classifier. An overview of the processing flow of traditional
machine learning detection and classification algorithms is
shown in Fig. 23. In this review, we found that the most
2033
potential model of machine learning used for microscopic
parasite image classification and detection is the Support
Vector Machine. SVM is a supervised algorithm used for
both linear and non-linear data. It defines the classification
by constructing the set of hyperplanes in feature space [79].
In SVM, kernel functions are used to perform the transfor-
mation in the hyperplane. The most commonly used kernel
functions are linear, polynomial, sigmoid, and radial basis
functions. A better classification is achieved with the hyper-
plane maximum distance to the nearby training data point of
classes [80]. However, this model is not effective for multi-
ple species classification and detection.
The deep learning methods and models surveyed in this
paper are playing a major role in parasitological research.
Furthermore, it supports tackling similar problems within
several other subdomains. Deep learning models handle
more complex tasks than traditional machine learning, such
as object detection, image segmentation, image recognition,
and classification. Figure 24 shows CNN-based transfer
learning models used in parasite classification and detec-
tion. Popular classical deep learning models, such as CNN
and its offspring methods and models, are constantly used in
the task of parasite classification and detection, such as CNN
mentioned in [60, 61, 70], AlexNet and GoogleNet men-
tioned in [57], AlexNet and ResNet50 mentioned in [78],
Faster R-CNN mentioned in [50], and R-CNN mentioned
in [54]. According to the survey on deep learning methods
and models for parasites, the most popular detection and
classification model is Faster R-CNN. In [50, 51] Faster
R-CNN is mentioned. In comparison to R-CNN, Faster
R-CNN implemented with the Regional Proposal Network
(RPN) technique performs better because in Faster R-CNN,
RPN improves the performance and accuracy of detection.
Moreover, it also exhibits end-to-end detection [81]. The
main limitations of Faster R-CNN are that it cannot detect
objects in real time and that it performs large amounts of
computations due to the RPN extraction method.
7 Conclusion and Research Directions
In this systematic review, we demonstrated a significant
investigation of parasites microscopic image detection and
classification methods and models based on traditional
machine learning and modern deep learning technologies.
In Sect. 1, we discussed certain fundamentals to understand
parasites along with diseases and diagnosis approaches,
including motivation and research position. In Sect. 2, we
outline the basic concepts of deep learning, which include
CNN models for visual recognition. In Sect. 3, we have out-
lined the research progress of traditional and modern meth-
ods and models of parasite detection and classification in
chronological order. In Sects. 4 and 5, we have organized
13
 Table 5  Summary of reviewed research works on deep learning methods and models as applied for detection and classifications used objective, dataset details which include class (C), total
2034

images (T.I), training (Tr.), validation (V), test (Ts.) and Evaluation metrics which include accuracy (Acc.), precision (Pre.), recall (Rec.), area under the ROC curve (AUC), mean average preci-
sion (mAP), sensitivity (Sn.) and specificity (Sp.)

13
References Date Types of features Method Objective Parasites (species) Dataset details Evaluation Limitations Future scope

[48] 2015 Deep features Faster R-CNN Object detection on Plasmodium vivax –- Acc. = 98% Validation of our model Intend to test the
malaria images jane needs to be done model on more
reliable ground
truth and test for
robustness by
testing on samples
prepared in a dif-
ferent lab
[70] 2016 Deep features CNN Diagnosis of human Intestinal parasites C = 15 Acc. = 0.9649 ± 0.0043 Clinical laboratory Intend to further
intestinal parasites T.I = 16,437 validation was not extend the work to
employed diagnosis of para-
sites in animals
[71] 2017 Deep features CNN Classification of Mycobacterium tuber- C=2 AUC = 96% Insufficient data The proposed model
Mycobacterium culosis T.I = 9770 can be used in
tuberculosis sliding for detect-
ing the parasite in
full smear micros-
copy images
[75] 2017 Deep features AlexNet Deep feature extraction Planktonic images T.I = 30,336(ISIIS),53,239 Qualitative Small set of classes Include more
for planktonic images (IFCB) image data from
plankton domains
to improve classi-
fication accuracy
[60] 2018 Deep features CNN Automatic detection of Tuberculosis bacilli C=2 Rec. = 97.13% Insufficient dataset An enhanced model
Tuberculosis bacilli T.I = 1800 (900 + ve & 900 –ve Pre. = 78.4% proposed to
patches) F-score = 86.76% diagnosis
tuberculosis bacilli
[49] 2018 Deep features U-net model Leishmaniasis parasite Promastigote C=3 Promastigote (J > 0.54) Imbalance dataset Results that could
segmentation and Adhered T.I = 45 Adhered(J > 0.82) be improved using
classification g Amastigote Amastigote(J > 0.88) larger databases
[61] 2018 Deep features CNN Fungus detection Fungus species C=5 Acc. = 94.8% Evaluation details are explore regional
T.I = 40,800 not described convolutional
Tr. = 10,800 neural network
Ts. = 5000 and transfer learn-
ing for the fungus
detection
[63] 2019 Deep features LeNet CNN Bacteria classification S. aureus and L. C=2 Acc. = 96% Small dataset limited to Apply another CNN
using DL delbruekii T.I = 800 only two species of methodology
bacteria for comparison
such as ResNET,
AlexNET
[50] 2019 Deep features Faster R-CNN Parasite worm egg Parasite species C=8 mAP = 97.67% Less dataset details Advanced tech-
automatic detection mentioned niques
applied for
better results
[53] 2020 Deep features D-CNN Detection of intestinal Intestinal Protozoas (10 T.I = 910 Rec. = 98% Clinical laboratory Collection of addi-
protozoa Catg.) validation was not tional slides in
employed order to enrich the
data set and refine
the model
S. Kumar et al.
 Table 5  (continued)
References Date Types of features Method Objective Parasites (species) Dataset details Evaluation Limitations Future scope

[54] 2020 Deep features R-CNN Identification and Cyanobacteria species C=5 AP = 0.929, 0.973, Less dataset details Research recom-
enumeration of 0.829, 0.890, and mentioned mended to
cyanobacteria species 0.890 for five classes improve the cell-
count accuracy
[55] 2020 Deep features Fusion-Net Single-cell classifica- Pathogens C=5 Acc. = 98.4% Insufficient dataset Collection of images
tion of foodborne in order to enrich
pathogens the data set and
refine the model
[57] 2021 Deep features AlexNet & GoogleNet Intestinal parasite Intestinal parasite – AlexNet AUC = 1.00 No details about quan- Transfer learning
detection in GoogleNet = 0.99 tity of database could be used to
analyze the data
further to under-
stand why
[51] 2019 Deep features Faster-RCNN Parasite detection in Parasites T.I = 2967 Detection rates on Evaluation details Focus on reducing
thick blood smears image and patient are not described false positives
based level = 96.84% &
96.81%, respectively
[69] 2017 Detection of soil- Helminths and Schisto-
transmitted helminths soma haematobium
and Schistosoma
haematobium
[56] 2021 Deep features MCellNet Deep learning- Cryptosporidium and C=2 Acc. = 99.0% Insufficient dataset High-quality
(CNN) enabled predicting Giardia Tr. = 38,469 Pre. = 98.66% training data,
Cryptosporidium and Ts. = 32,059 F1-Score = 99.09% MCellNet could
Giardia in drinking Val. = 9618 be extended to
water detect other types
of bioparticles in
high speed
[58] 2021 Deep features Single Shot Detector Helminth egg Helminth egg C = 17 Qualitative Evaluation details Model improved
(SSD), U-net and identification and are not described by integrating
Faster R-CNN quantification based increasing number
Advances Towards Automatic Detection and Classification of Parasites Microscopic Images…

on the integration of of human vali-

deep learning dated samples
[78] 2021 Deep features AlexNet and ResNet50 Parasitic egg detec- Ascaris lumbri -coides C=4 Acc. = 87.69 (AlexNet) The poor-quality micro- Enhance the model
tion using transfer (AL), Hymenolepis T.I = (AL), 27 (HD), 32 (FB) & scopic image with to learn more
learning diminuta (HD), Fas- and 36(Tn) 90.77(ResNet50) insufficient detail complex features
ciolopsis buski (FB) of the parasite
and Taenia spp. (Tn) eggs

13
2035
2036 S. Kumar et al.

various methods and models of traditional machine learn-

ing and deep learning, respectively. Finally, in Sect. 6,
i.e., the discussion part, we analyse the two categories of
methods and models and further present the performance
of each method. After a detailed review on parasites detec-
tion and classification using deep learning, the experimental
results show that deep learning is a better and more effortless
approach than the traditional machine learning approach that
employs hand-engineered features, which is a challenging
and time-consuming task. Several deep learning methods
and models have been extensively used for the detection and
classification of parasite microscopic images. Some of the
state-of-the-art techniques in the deep learning framework
Fig. 23  Overview of a processing flow of traditional machine learn-
are CNN, F-RCNN, VGG-Net for detection and classifica- ing detection and classification algorithms
tion purposes. The native paper researchers hardly examined
a few species of parasites due to the limited size of the data
collection. The performance of methods and models falls
short of expectations due to the scarcity of datasets. Deep
learning methods and models achieve sophisticated develop-
ment and produce better results than the traditional machine
learning methods on various benchmarks. In spite of this,
deep learning techniques are too immature in the field of
visual recognition. Based on the analysis of deep learning
techniques in Sect. 5, the authors found some major gaps,
which are outlined as future directions for further enhance-
ment for parasites detection and classification based on
microscopic images. The summary of all CNN based meth-
ods and models along with their best scores and datasets is
mentioned in Table 5. The AlexNet and Fast R-CNN models
yield the best results for the detection and classification of
parasites in digital images. They are followed by R-CNN, Fig. 24  CNN based transfer learning models used in parasites clas-
GoogleNet, LeNet, and U-Net models. Moreover, fine-tun- sification and detection. The horizontal line in the middle shows time
ing of concerned methods also outperforms whatever the line. One-stage detection models are lie above the time line, and two-
Stage detection models shown below the time line
network model may be. This approach provides a significant
improvement in multiclass datasets.
The future development trends and challenges in deep parasite images data collection, and high processing costs,
learning are predicted on the basis of the development of which affect generating good quality datasets.
parasites classification and detection methods and models.
To detect and classify parasitic species in deep learning, the
Funding No funds, Grants, or other support was received.
most promising development could be to combine existing
transfer learning techniques. Due to the successful applica-
Declarations
tion of transfer learning-based models in computer vision,
at present, many researchers are applying transfer learning Conflict of interest On behalf of all authors, the corresponding author
to detect and classify objects from microscopic images. states that there is no conflict of interest.
Combining transfer learning models with others can result
in improved parasite detection and classification perfor-
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