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APPLICATION OF ARTIFICIAL NEURAL NETWORK TOWARDS THE
DETERMINATION OF PRESENCE OF DISEASE CONDITIONS IN
ULTRASOUND IMAGES OF KIDNEY
Karthik Kalyan1, Suvigya Jain1, Dr. Ramachandra Dattatraya Lele1, 2*, Dr. Mukund Joshi 3,
Dr. Abhay Chowdhary1
1
Systems Biomedicine Division,Haffkine Institute for Training, Research and Testing (HITRT),
Parel, Mumbai, India, Pincode: 400 012.
2
Nuclear Medicine Department, Jaslok Hospital and Research Centre, Pedder Road, Mumbai, India,
Pincode: 400 026.
3
Ultrasound Department,Jaslok Hospital and Research Centre, Pedder Road, Mumbai, India,
Pincode: 400 026.
ABSTRACT
Ultrasound (US) imaging modality is an important tool for diagnosis of kidney diseases such
as Chronic Kidney disease, Renal Calculus and Cortical Cyst. It is easy to perform because of its
non-invasive nature and lower costs. However due to the use of various ultrasound equipments, the
image of ultrasound is prone to several noises such as ‘Speckle Noise’, which makes the diagnosis of
disease conditions difficult for biomedical specialist such as radiologists. The accuracy of visual
observation depends on the expertise of radiologists; however it is highly subjective. In order to
provide more objective analysis and diagnosis, various features have been extracted from kidney
ultrasound images. In this study many important features of ultrasound kidney images have been
extracted such as Intensity histogram (IH) feature, Invariant moments (IM), Gray level co-occurrence
matrices (GLCM), Gray level run length matrices (GLRLM) and ‘COMBINED’ feature set was
develop from combination of all the four features. In total, 48 features of each image were
calculated. Classification of ultrasonic kidney images is studied utilizing these extracted features by
means of feature extraction methods and then optimal feature amongst them were selected by means
of feature selection using a tool known as Waikato Environment for Knowledge Analysis (WEKA).
Selected features from these methods are used to classify two sets of ultrasound kidney images –
Normal, abnormal (cyst, Chronic Kidney disease, renal calculus). A neural network (ANN) based
pattern recognition tool is employed to evaluate the performance of each feature on their
classification accuracy rate.
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Keywords - Artificial Neural Networks (ANNs), Kidney Ultrasound (US) Image Classification,
Machine Learning Techniques, Medical Image Processing, Specific Disease Condition Applications.
1. INTRODUCTION
Image processing techniques are usually applied in medical images to enhance the quality of
representation of medical image and towards the better understanding of hidden information for
proper objective diagnosis. By using techniques such as feature extraction, image enhancement (part
of medical image processing), it is also possible to extract some parameters or features that will be
very helpful for the diagnosis of the medical images [1].
Diagnostic ultrasound has gained widespread acceptance as an effective diagnostic tool for
imaging organs and soft tissues in human abdominal wall [2]. Well-known facts of abdominal US
imaging such as real-time, non-invasive, non-radioactive and inexpensive properties make it useful
in diagnosing soft tissues [3, 4]. The gray-scale type of display is useful in the detection of
abnormality. One of its important applications within abdomen is kidney imaging. Since ultrasound
images suffer from multiplicative noise forms such as speckle noise, which makes the signal difficult
to differentiate an organ towards its specific pathological changes [2]. When the reflected echoes
from human kidney tissues are displayed as a B-scan image, they form a texture pattern because of
the characteristic of both the imaging system and tissue [3, 5].
Texture is the main feature utilized in medical image processing and computer vision to
characterize the surface and object identification [6]. This indicates the diagnosis of US kidney
images could be achieved by means of interpretation of texture pattern [7] as it could provide some
vital information that may not be inaccessible through visual interpretation of US images [6].
Quantitative evaluations included distribution of gray-level scales of pixels in image to describe
tissue characteristics of kidney, liver etc. [8].
Sonographic (US) evaluations are made based on the distribution of echogenicity that reflects
tissue characteristics. For better echo visualization, the longitudinal cross section of kidney is taken
to include renal sinus, medulla and cortex regions as suggested by the radiologists. This ensures
better visual interpretation of the normal and diseased kidney. Normal kidney has a bright area
surrounding it, which is made up of Gerota’s fascia and peri-nephric fat.
The periphery of the kidney will appear grainy gray, which is made up of the renal cortex and
pyramids. Sometimes you can see the individual pyramids, but this is not always the case. The
central area of the kidney, the renal sinus, will appear bright (echogenic) and consists of the calyces,
renal pelvis and the renal sinus fat. If the echogenic patterns of the liver and kidney are the same then
it is certainly considered as normal as suggested by radiologists and center of the kidney shows grey
white or white in color, which indicates increased echoes. This is the hilum of the kidney also known
as the central sinus. The kidney diseases are usually categorized as hereditary, congenital or
acquired. The most common disease are frequently performing which detected by US on patients is
chronic kidney disease, cyst and calculi. The most common hereditary disorder is cystic diseases,
which include simple renal cyst and complex renal cyst or poly-cyst, and congenital disease is
medical renal disease.
Picture archiving and communication system (PACS) is relevant to medical imaging
informatics. It is a comprehensive network of digital devices designed for acquisition, data
transmission, storage, display, communication routes to other electronic system and management of
diagnostic imaging studies. PACS are usually based on DICOM standards. Most PACSs handle
images from various medical imaging instruments, including ultrasound (US), magnetic resonance
(MR), positron emission tomography (PET), computed tomography (CT),endoscopy (ES)[18,19].
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Figure 1: Image depicting Normal and Abnormal Kidney Images.
2. METHODOLOGY
The paper aims to classify the normal and abnormal conditions of kidney from the ultrasonic
kidney images using ANNs. First, we performed image-preprocessing techniques such as cropping,
rotation, edge detection and background subtraction to eliminate the disturbance factors from the
images using MATLAB® and image processing toolbox. In order to perform the edge detection
techniques we utilized imageJ software. Secondly, features were extracted from the background
subtracted images by means of 4 feature extraction techniques namely the gray level run length
matrix, intensity histogram, gray-level co-occurrence matrix and invariant moments. These are used
to compute the adequate texture features. Thirdly, feature selection technique was employed using
WEKA software in which optimal features are selected from the four feature extraction methods.
The resultant output from the feature selection phase was stored in ‘.arff file’. Finally, artificial
neural network utilizing a back-propagation algorithm was employed and then used it to classify the
optimal feature set that resulted from the feature selection phase. These techniques are discussed in
further detail within the later sections.
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Figure 2: Workflow of Image Classification Using ANN
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2.1 Image Data Acquisition
The data that was used in our experiments was collected from Jaslok Hospital & Research
Centre, Mumbai. The images used for the analysis are acquired from two types of scanning systems
using curvilinear probe with transducer frequency range of 2 – 5 MHz. The ultrasound images of 47
normal and 47 abnormal with mean age of 55(±15*) were collected, the abnormal images belong to
three categories chronic kidney disease, renal calculus and cortical cyst. Out of these three categories
there are 6 renal calculi, 31 chronic kidney diseases, 10 cortical cysts images. The images of both
right and left kidneys are considered for the analysis. During the image acquisition, sonographer
looks for better visualization of the image in the screen and freezes to store those images within the
PACS. We then retrieve those images from PACS system for further analysis; here the images are
stored in JPG format.
2.2 Image Preprocessing
The image preprocessing methods are used to get the efficient results for further analysis. We
applied four image preprocessing techniques such as Cropping, Rotation, Edge detection and
Background removal to all images: Cropping eliminates the undesirable parts of the image usually
peripheral to the area of interest. The cropping operation is performed in MATLAB® by sweeping
through the images and cutting the image components in horizontal and vertical directions. Rotation
of the cropped image is performed such that the major axis is aligned to zero degrees of image. Edge
Detection is performed using ‘absnake_.jar’ external plugins which is based upon Adaptive active
contours in Image J version 1.46r software [20]. After edge detection, Background removal is
performed to remove the pixels that are present outside the contour region. Those pixels are regarded
as unbounded pixels, whereas the pixels that are enclosed by the contour are considered as bounded
pixel or pixel of interest.
Figure 3: Workflow depicting the Kidney Image preprocessing; Step - a).Image after cropping
operation; Step - b).Image after rotation; Step - c). Image after edge detection and Step - d).Final
image after background subtraction
2.3 Feature Extraction
After pre-processing of the images, which represents the data-cleaning phase, features
relevant to the classification are extracted from the cleaned images by means of techniques such as
Intensity Histogram features, Gray Level Co-occurrence Matrix (GLCM), Gray Level Run Length
Matrix (GLRLM) and Rotation Invariant Moments
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2.3.1 Intensity Histogram (IH) Features
Intensity Histogram texture measures are calculated from the original image values and it
falls under the category of first-order statistics. They do not consider the relationships with
neighborhood pixel. Features derived from this approach consist of mean, variance average energy,
entropy, skewness and kurtosis [9].
2.3.2 Gray level co-occurrence matrix (GLCM)
The gray tone spatial dependence approach characterizes texture by the co-occurrence of its
gray tones [10]. The gray-level co-occurrence matrix (GLCM) or gray-level spatial dependence
matrix, a frequency matrix based calculations that fall under the category of second-order statistics.
GLCM is a useful method for enhancing texture details and is used as an aid for interpretation of an
image, which can be extracted from the co-occurrence matrix. The GLCM is a tabulation of how
often different combinations of pixel brightness values occur in an image [11, 10].
We can calculate the following statistics elements as texture features: Autocorrelation,
Contrast, Difference variance, Entropy, Correlation, Cluster Prominence, Cluster Shade,
Homogeneity, Maximum probability, Sum of squares, Dissimilarity Energy, Sum average,
Information measure of correlation, Sum variance, Sum entropy, information measure of correlation,
Inverse difference normalized.
2.3.3 Gray level Run length matrix (GLRLM)
The gray level run length matrix is another method of extracting the higher order statistics of
the texture of image and has been a major descriptor of regularity and periodicity of the texture
pattern. GLRLM characterizes coarse textures as having many pixels in a constant gray tone run and
‘fine textures’ as having few pixels in a constant gray tone run [12]. A gray level run length primitive
is a maximal collinear connected set of pixels all having the same gray tone [10].
We can calculate the following statistics as texture features from image: Short Run Emphasis
(SRE), Long Run Emphasis (LRE), Gray-Level Non-uniformity (GLN), Run Length Non uniformity
(RLN), Run Percentage (RP), Low Gray-Level Run Emphasis (LGRE), High Gray-Level Run
Emphasis (HGRE), Short Run Low Gray-Level Emphasis (SRLGE), Short Run High Gray-Level
Emphasis (SRHGE) Long Run Low Gray-Level Emphasis (LRLGE), Long Run High Gray-Level
Emphasis (LRHGE).
2.3.4 Rotation Invariant Moments (IM)
There are many applications for texture analysis in which rotation-invariance is important,
but the problem is that many of the existing texture features are not invariant with respect to the
rotations. Hu’s 7 moment invariants are invariant under translation, changes in scale, and also
rotation [13, 14]. It describes the image inspite of its location, size, and rotation. The moment
invariants are generally specified in terms of normalized central moments [15].
In order to evaluate the efficiency of the texture features, we use four feature extraction
module’s namely Intensity histogram feature, GLCM feature, GLRLM feature and Invariant
Moments Features were extracted from each of the total 94 preprocessed images of kidney in
MATLAB® using their module. Invariant moments include 7 features, GRLM includes 11 features,
GLCM includes 22 features, and Intensity Histogram includes 6 features, therefore total: 6 + 22 + 11
+ 7 = 46 features were extracted for each image and four features were extracted from each image
therefore a total of 376 feature files were extracted each image. In total, 4324 features were
extracted from all the images.
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2.4 Feature Selection
All features were extracted from image and the resultant data contains
many redundant or irrelevant features. Features selection technique is used to remove those
redundant and irrelevant features and to find the significant features, which are useful in further
analysis.
Feature Selection was performed using Waikato Environment for Knowledge Analysis
(WEKA) [16] software Version 3.6.9. WEKA is compatible with and recognizes only ‘.arff’ data
files. Therefore ‘.arff’ file was generated which contains the value of features, that were extracted
(including both normal as well as abnormal).
Feature Extraction Method
No. of selected feature/total feature
Intensity Histogram features
3/6
GLCM features
11/22
GLRLM features
5/11
Invariant Moments
3/7
Combined Features
14/48
Table 1: Optimal Features selected in each Texture Algorithm
2.5 Training and Testing Of ANN
After feature selection in order to classify both abnormal and normal conditions of kidney
from optimized feature set neural network pattern recognition tool (nprtool) was used in MATLAB®
[21]. A two-layer feed-forward network, with sigmoid hidden and output neurons was used. The
samples were divided into training, validation and testing data on the basis of performance of each
set and then we decide the final percentage of each sample. The samples were divided into 70% of
Training, 15% of validation and 15% of Testing for this study. Number of hidden neurons present in
the hidden layer is very important in the training of the dataset. For selecting hidden neuron there is
no algorithm as it is based upon trial and error method [17]. On the basis of that, training trials were
performed for selecting the hidden neuron members for various feature extraction method (see table
no. 2).
Figure 4: Screenshot demonstrating the architecture of ANN
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The network was trained for 1000 number of epochs to classify the inputs according to the
targets. Scaled conjugate gradient Back-propagation (trainscg) algorithm was used to train network
then. There are two parameters Mean Squared Error (MSE) and percent error which tell us about
how good our data is in terms of classification by seeing that value.
Features
Number of Hidden Neurons
Intensity Histogram
2
GLCM
11
GLRLM
5
Invariant moments
4
Combined Features
13
Table 2: Number of hidden neuron for each feature extraction
3. RESULTS AND DISCUSSION
In general, measures of quality of classification are built from a confusion matrix which
records correct and incorrect recognition, such as the true positive (TP), false positive (FP), false
negative (FN) and the true negative (TN). In neural network, the diagonal cell shows the number of
classes that were correctly classified and the off diagonal cells show the misclassified cases. The blue
cell in the bottom right shows the total percent of correctly classified cases in green and the total
percent of misclassified cases in red. The results show very good recognition. The ROC curve can
manifest the relationship between the true-positive rate (TPR) and false-positive rate (FPR) with the
variations in decision threshold.
If curve is on diagonal or off diagonal then the diagnostic system is not considered to be
effective. If the curve is near the axis of true positive rate or it touches to axis completely then the
diagnostic system is considered to be excellent. If the curve exists between diagonal or in the middle
axis of that then it is considered to be a good diagnostic system. To investigate the performance of
classification of selected feature’s, performance measures such as accuracy, sensitivity, specificity
and false negative rate were computed.
Figure 5: Image depicting Confusion Matrix and ROC plot of Intensity histogram feature of training
data
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Figure 6: Image depicting Confusion Matrix and ROC plot of INVARINTS MOMENTS feature of
training data
Figure 7: Image depicting confusion matrix & ROC plot of GRLRM of training data
Figure 8: Image depicting confusion matrix & ROC plot of GLCM feature of training data
Figure 9: Image depicting Confusion Matrix and ROC plot of COMBINED feature of training data
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Performance measures were computed from confusion matrix of COMBINED features as
seen in table 3. The classification accuracy of COMBINED feature was 100 percent at the time of
training and 87.5 percent at the time of testing, which is better than that of other feature extraction’s
accuracy. The sensitivity and specificity values were 1 and 1 of training, respectively, which were
also better than those of the other features. Specificity of COMBINED feature at testing was 0.75,
which was not better than GLRLM feature. Specificity of GLRLM feature was 0.8, and as a result of
it large difference between the two values cannot be observed.
In addition, an effective classification method should decrease the possibility of
misclassification, especially for the false-negative rate. A high false-negative rate represents the risk
of underestimating the disease severity in a patient when the clinicianis making of use the
classification system. Therefore, the false-negative rate may be considered as an index for evaluating
the performances of the features [9]. On the basis of that the value of false negative word (FNR) of
COMBINED feature was zero, which was also better from other feature extraction methods.
FEATURE
Training
Accuracy TNR
Testing
TPR
FNR Accuracy TNR TPR FNR
Intensity Histogram
0.8298
0.8511 0.8085 0.1489
0.825
0.85
0.8
0.2
Invariant Moments
0.5426
0.2766 0.8085 0.7235
0.475
0.75
0.2
0.8
GLRLM
0.0898
0.8085 0.8511 0.1915
0.85
0.85
0.9
0.1
GLCM
0.8298
0.8085 0.8511 0.1915
0.825
0.85
0.8
0.2
Combined Feature
1
0.875
0.75
1
0
1
1
0
Table 3: Performance measure of all feature extraction methods
4. CONCLUSION
The study was undertaken to evaluate which of the different feature extraction methods give
high recognition rate and for classifying abnormalities in US kidney images using Artificial neural
network. The Intensity Histogram feature, GLCM feature, GLRLM feature, Invariant moments
feature and COMBINED feature were considered for performance evaluation. According to the
results (see table 3) obtained, it is difficult to make a claim between GLRLM and COMBINED sets,
as to which individual feature is superior because the specificity value of COMBINED feature of
testing is less than that of GLRLM. By considering other parameters such as sensitivity, false
negative rate and total accuracy rate of training and testing which are far better than that of GRLRM
features from that it provides conclusive evidence that COMBINED feature performs well and high
recognition rates have been achieved as compared to other feature extraction methods.
COMBINED feature reached a 100% accuracy rate in training datasets. It correctly classified
94 instances from 94 instances. On testing datasets it correctly classified 35 instances out of 40 with
an 87.5% accuracy rate. This revealed that the usage of COMBINED feature was relatively effective
in abnormal classification of kidney.
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5. ACKNOWLEDGEMENTS
We gratefully acknowledge Mr. Sandeepan Mukherjee (Scientific Officer from HITRT) and
Mr. Samrit Maity (Senior Technical Officer from CDAC Pune) for their thoughtful reviews of this
paper.
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AUTHORS PROFILE
1. Karthik Kalyan: He currently works as a Scientific Officer at Systems Biomedicine
Division, Haffkine Institute for Training Research and Testing (HITRT) in Mumbai. His
research interests include Hi Performance Computation, Agent Based Modelling and
Simulation (ABMS), Complex Adaptive Systems, Bio-Complexity, Intelligent Software
Systems Development, Artificial Neural Networks, Bio-Medical Image Processing, Complex
Systems and Emergence and Decision Making.
2. Suvigya Jain: He is a Short Term Research (STRIP) Intern at Haffkine Institute for
Training Research and Testing (HITRT) in Mumbai. His research interests include Artificial
Neural Networks, Medical Image Processing, and Sequence Analysis.
3. Dr. Ramachandra Dattatraya Lele: He is the Chairman of Research Advisory
Council at Haffkine Institute for Training Research and Testing and Hon. Chief Physician
and Director of Nuclear Medicine at Jaslok Hospital and Research Centre. His research
interests include Bioinformatics, Biomedical Imaging, Nuclear Medicine and Medical
Informatics.
4. Dr. Mukund Joshi: He is the Head of the Department of Ultrasound Department at
Jaslok Hospital and Research Center in Mumbai. His research interests include Pediatric
Urology, Prostrate Imaging, Newer Trends in Breast Ultrasound, Newer Trends in Prostratic
Ultrasound, Acoustic Radiation Force Impulse Imaging (ARFI), Elastographic Studies.
5. Dr. Abhay Chowdhary: He is the Director of Haffkine Institute for Training Research
and Testing (HITRT) in Mumbai. His research interests include Medical Virology and
Vaccinology.
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