2015 4th International Conference on Instrumentation, Communications, Information Technology, and Biomedical Engineering (ICICI-BME)

Bandung, November 2-3, 2015

Extraction and Classification Texture of

Inflammatory Cells and Nuclei in Normal
Pap smear Images
Dwiza Riana1, Dwi H. Widyantoro2 and Tati L Mengko2
1
Information System
STMIK Nusa Mandiri, Jakarta, Indonesia
(Tel: +62-817-771-998; E-mail: dwiza@bsi.ac.id)
2
School of Electrical Engineering & Informatics
Institut Teknologi Bandung, Bandung, Indonesia
(Tel: +62-22-2502260; E-mail: dwi@stei.itb.ac.id; tmengko@itb.ac.id)

Abstract- The presence of inflammatory cells complicates the
process of identifying the nuclei in the early detection of cervical
cancer. Inflammatory cells need to be eliminated to assist
pathologists in reading Pap smear slides. The texture of Grey-
Level Run-Length Matrix (GLRLM) for inflammatory cells and
nuclei types are investigated. The inflammatory cells and nuclei
have different texture, and it can be used to differentiate them. To
extract all of the features, firstly manual cropping of
inflammatory cells and nuclei needs to be done. All of extracted
features have been analyzed and selected by Decision Tree
classifier (J48). Originally there have been eleven features in the
direction of 135º which are extracted to classify cropping cells into
inflammatory cells and nuclei. Then the eleven features are
reduced into eight, namely low gray level run emphasis, gray level
non uniformity, run length non-uniformity, long run low gray-
level emphasis, short run high gray-level emphasis, short run low
gray-level emphasis, long run high gray-level emphasis and run
percentage based on the rule of classification. This experiment is
applied into 957 cells which were from 50 images. The
compositions of these cells were 122 cells of nuclei and 837 cells of
inflammatory. The proposed algorithm applied to all of the cells
and the result of classification by using these eight texture features
obtains the sensitivity rates which show that there are still nuclei
of cells that were considered as inflammatory cells. It was in
accordance with the conditions of the difficulties faced by the
pathologist while the specificity rate suggests that inflammatory
cells detected properly and few inflammatory cells are considered
as nucleus.
Keyword: Classification, Cells Pap Smear, inflammatory cells,
Texture, GLRLM, Decision Tree.
I. INTRODUCTION
Global Mortality per annum of cervical cancer are still very
high. It is a threat to the woman's life [1]. Early prevention of
cervical cancer can be done with a Pap test, which is a key
stage of the accuracy of the identification of the cell nucleus
[2].
Pap smear cell research is focused on identifying the nucleus
[3] - [10]. Mustafa N. et al [11] use the feature perimeter, red,
green, blue, intensity1, intensity2, and saturation, which are
grouped into classes of normal cervical cells, cell LSIL and
HSIL to classify the cell nucleus. Plissiti, et al [10] use three
features, namely texture, shape and intensity to classify the cell
nucleus. None of those researches has observed about
identification of inflammatory cells.
Many methods identify the location of nucleus in each
image. In Garrido et al., [6] a method which affects the excess
of edge points or overlapped objects in complex images was
proposed. In addition, genetic algorithms by Lassouaoui et al,
[7], pixel classification (Baak et al, [8]), region growing (Mat
Isa, [9]) and combining shape, texture and intensity features for
cell nuclei extraction in pap smear images, Plissiti et al., [10]
were also proposed. All images were no deal with the existence
of inflammatory cells in Pap smear images.
The presence of inflammatory cells in the background is a
common feature of conventional Pap smear images. There are
plenty of methods proposed in the literature for the analysis of
Pap smear images. The problem of inflammatory cell
identification has been addressed by several methods.
The extraction and classification of inflammatory cells and
the nucleus have been investigated in several studies.
Muhimmah, et all [12] proposed method for the automated
detection of cervical epithelial cell numbers in Pap smear
images, which may contain overlapping nuclei and
inflammatory cells.
Riana [13] proposed method for extraction of inflammatory
cells with a combination of gray level thresholding and
definitions of distance rule.
In this paper we investigate texture features of inflammatory
cells and nuclei. The proposed features are Grey-Level Run-
Length Matrix (GLRLM) which consists of 11 texture features.
These features were applied in identification of inflammatory
cells and nuclei.
Eleventh texture features are used for classification into two
categories of inflammatory cells and nucleus by using Decision
Tree Learning algorithm (J48).
This paper is divided into several sections. In the section II,
it discusses about the material and methods used in this study
such as data sets, features texture extraction, and inflammatory
cells and nuclei classification. Implementation of data test is in
Section III. Furthermore, the result and discussion are in
section IV, and the conclusion is drawn in Section V.

978-1-4673-7800-0/15/$31.00 2015 IEEE 65

2015 4th International Conference on Instrumentation, Communications, Information Technology, and Biomedical Engineering (ICICI-BME)
Bandung, November 2-3, 2015

II. MATERIAL AND METHODS is the number of different run lengths. Figure 2 is a
A brief description of the experimental data sets are given. representation of matrix GLRL (Grey-Level Run-Length) at 0º
The data is used in this case study in order to prove the validity direction [P (i, j | = 0º)]. In addition, the direction of 0º,
of the proposed approach. GLRL matrix can be also obtained in the direction of 45º, 90º,
A. Data Set or 135º.
In our experiments, we used 117 cytological images of
conventional Pap smears. For the construction of the training
set we had selected 67 images and data test of 50 images. The
training set for texture extraction and establishment of
classification rule used the data as many as 169 cells which
consist of 83 nuclei and 86 inflammatory cells that derived
from a Pap smear slide. The data were taken from 67 images Fig. 2. Directions are available on the GLRL
Pap smear. We used the data test for implementation
TABLE I
performance of 50 images. These images contain 957 candidate EQUATIONS TO CALCULATE THE GLRM FEATURES
of nucleus which namely 122 nuclei and 837 inflammatory
cells. GLRM features Equation
The methods consist of manual nucleus and inflammatory 1. Short Runs Emphasis m n
cells cropping. These cropping were taken from conventional (SRE) SRE = 1/nr ! ! p(i,j) / j
2
Pap smear images with inflammatory cells. The nucleus and
i=1 j=1
inflammatory cells cropping aimed to obtain a separate image
of the inflammatory cells and nucleus. The image of nuclei and 2. Long Runs Emphasis m n
inflammatory cells cropping was taken manually, as illustrated (LRE) LRE = 1/nr ! ! p(i,j) * j
2
in Figure 1.
i=1 j=1

3. Gray Level Non m n

2
uniformity (GLN). GLN = 1/nr ! ( ! p(i,j) )
i=1 j=1

4. Run Percentage (RP) RP = nr / ( p (i,j) * j)

5. Run Length Non- n m

2
uniformity (RLN) RLN = 1/nr ! ( ! p(i,j) )
j=1 i=1

6. Low Gray Level Run m n

2
Emphasis (LGRE) LGRE = 1/nr ! ! p(i,j) / i
i=1 j=1

7. High Gray Level Run m n

Inflammatory cell nucleus HGRE = 1/nr ! ! p(i,j) * i
2
Emphasis (HGRE)
Fig. 1. The example of conventional Pap smear image with inflammatory cells i=1 j=1
and manual cropping
8. Short Run Low Gray- m n
B. Features Texture Extraction 22
Level Emphasis SRLGE = 1/nr ! ! p(i,j) / i j
Each image of 83 nuclei and 86 inflammatory cells from (SRLGE) i=1 j=1
manual nucleus and inflammatory cells cropping (Fig.2) have
RGB color. At this stage all RGB images are converted to 9. Short Run High Gray- m n
grayscale by using rgb2gray function. The grayscale value was Level Emphasis SRHGE = 1/nr ! ! ( p(i,j) i2)/j2
obtained by forming a weighted sum of the R, G, and B (SRHGE) i=1 j=1
components as given in (1).
10. Long Run Low Gray- m n
0.2989R + 0.5870 G + 0.1140 B (1) Level Emphasis LRLGE = 1/nr ! ! ( p(i,j) j2)/i2
(LRLGE) i=1 j=1
The next process is analysis of texture using Grey-Level
Run-Length Matrix (GLRLM). Matrix Gray-Level Run-Length 11. Long Run High Gray- m n
is a two-dimensional matrix in which each element p (i, j | ) is Level Emphasis 22
SRHGE = 1/nr ! ! p(i,j) j i
the intensity i to j number of elements. In the direction , and nr (LRHGE.
i=1 j=1

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 2015 4th International Conference on Instrumentation, Communications, Information Technology, and Biomedical Engineering (ICICI-BME)
Bandung, November 2-3, 2015

The GLRLM features were applied in inflammatory cells and image bounding box. Bounding box > 50x50 pixels is to get
nuclei. The complete equation of all statistical measures is as candidate of nucleus. The unsharp masking is used in the
parameter texture analysis by Xu et al., [14], shown in Table I. image sharpening step.
The next phase is creating GLRLM size 8x8 pixel matrix
C. Inflammatory cells and nuclei classification. and calculating the 11 properties GLRLM (grayRLprops) for
The classification process uses decision tree (J48) classifier. direction of 135º. After the texture is obtain, so it is classified
The value of each parameter matrix will be processed for the by using the rule texture of decision tree (J48) for
classification of cell nuclei and inflammatory cells. Figure 3 is inflammatory cells and nuclei classification (Fig.3).
the result of the algorithm decision tree (J48). The rule shows In the last phase, every inflammatory cell color which is
that only 8 texture features were used, namely LGRE, GLN, identified will be changed into the color which is similar to
RLN, LRLGE, SRHGE, SRLGE, LRHGE, and RP. The cytoplasm color whereas nuclei which succeed to be identified
classifications were tried in direction of 0º, 45º, 90º, and 135º, will have unchanging color. Table II shows the algorithm for
and a representation of matrix GLRL in direction of 135º is the feature extraction and classification inflammatory cell and
best result. This result is using the Decision Tree (J48) with nuclei in normal Pap smear images.
Weka Correctly Classification Instances (CCI) and Kappa
Coefficient classification CCI value which indicates TABLE II
ALGORITHM FOR FEATURE EXTRACTION AND CLASSIFICATION
performance of 96.4497% with incorrectly classified Instances INFLAMMATORY CELL AND NUCLEI IN NORMAL PAP SMEAR IMAGES
of 3.5503% with Kappa statistic 0.9289.
J48 pruned tree Pseudo-code
------------------- Input : Pap smear image with inflammatory cells and
LGRE <= 0.273168 Nucleus.
GLN <= 41.814242 : nucleus (47.0/1.0) Output: Pap smear image with inflammatory cells eliminated
GLN > 41.814241
and nucleus detected.
RLN <= 198.044898 : inflammatory (12.0/3.0)
RLN <= 198.044898
1. Convert image from RGB to grayscale.
GLN <= 92.526154 : nucleus (2.0) 2. Improve the image of the adjustment and filter unsharp.
GLN > 92.526154 : inflammatory (4.0/1.0) 3. Use the global threshold 0.07 to get the image bounding
LGRE > 0.273168 box.
LRGE <= 3.868303 4. if bounding box> 50x50 pixels then the candidate
SRHGE <= 64.026621 nucleus.
SRLGE <= 0.051582 5. Create GLRLM size 8x8 pixel matrix.
LRHGE <= 8011.635671 : nuclei (6.0/1.0)
6. Calculate the 11 properties GLRLM (grayRLprops) for
LRHGE > 8011.635671 : inflammatory (5.0)
SRLGE > 0.051582 : nucleus (5.0)
direction of 135º.
SRHGE > 64.026621 : inflammatory (8.0) 7. Use the rule texture of decision tree (J48) for
LRGE > 3.868303 inflammatory cells and nuclei classification.
RP <= 1.1125 8. Define nuclei and eliminate inflammatory cells with
SRHGE <= 41.59111 : inflammatory (9.0) changing their color into a color that is similar to the
SRHGE > 41.59111 color of the cytoplasm.
SRHGE <= 52.54535 : nucleus (3.0)
SRHGE > 52.54535 : inflammatory (2.0) IV. RESULST AND DISCUSSION
RP > 1.1125 : inflammatory (48.0)

Number of Leaves : 12 Numerical evaluation is carried out for texture analysis on

Size of the tree : 23
Fig. 3. The rule texture of decision tree (J48) for inflammatory cells and nuclei.
IV. IMPLEMENTATION OF DATA TEST
The first stage in implementation of data test is converting
the RGB image to grayscale without changing the contrast of
the original image. At this stage the conversion result image
has low contrast, and further complicates the process. Each
image has a different size and it has each RGB color. At this
stage all RGB images are converted to grayscale using
rgb2gray function.
In the second phase, image adjustment and filtering are used
to enhance the contrast of the image, resulting in cell
boundaries that are clearly distinguishable from the
background of the image with global threshold 0.07 to get the
inflammatory cells 86 and 83 nuclei. In the process of object
recognition inflammatory cells and cell nuclei obtained 8
GLRM features that can distinguish among them. These
features are LGRE, GLN, RLN, LRLGE, SRHGE, SRLGE,
LRHGE, and RP while the other three features GLRM which
are namely SRE, LRE and HGRE were not used.
The three features that are not used can be analyzed that for
the value of SRE and LRE, inflammatory cells and nuclei
cannot be distinguished from the value of which depends on
the short runs and long runs structure of the rough structure.
The mean value of SRE for both groups of data are an
average of 0.18. Mean value and standard deviation of SRE on
nucleus group are 0.18 ± 0.07. This value is almost equal to the
mean value of SRE on inflammatory cells of 0.18 ± 0.05.

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2015 4th International Conference on Instrumentation, Communications, Information Technology, and Biomedical Engineering (ICICI-BME)
Bandung, November 2-3, 2015

TABLE III The dataset used in feature extraction and making rule
THE TEXTURE OF NUCLEI
classification phase is different from classification phase. This
GLRLM Mean St Dev Range Min Max is conducted to test the robustness of the features used for the
Features new data. We tested the classification stage on 50 images.
SRE 0.18 0.07 0.3 0.05 0.35 These images contain 957 candidate of nucleus namely 122
LRE 31.34 4.419 25.71 21.33 47.04 nuclei and 837 inflammatory cells. The calculation of the value
GLN 46.27 23.58 105.7 11.31 117
RLN 215.64 74.08 320.83 105.61 426.45
of True Positive (TP), True Negative (TN), False Positive (FP),
RP 0.99 0.23 1.21 0.55 1.76 and False Negative (FN) used two statistical calculations for
LGRE 0.2 0.08 0.37 0.03 0.4 performance. Sensitivity which was calculated the proportion
HGRE 291.71 172.03 812.5 61.593 874.09 of nuclei were detected correctly and defined as:
SRLGE 0.031 0.017 0.083 9E-04 0.084
SRHGE 68.78 63.18 425.6 6.978 432.6
LRLGE 2.5 0.94 3.82 0.83 4.65
Sensitivity = TP / (TP + FN) x 100% (2)
LRHGE 10532.77 5523.99 23898.99 1866.51 25765.5
Specificity that calculates the proportion of inflammatory cells
TABLE IV
THE TEXTURE OF INFLAMMATORY CELLS
was detected correctly and defined as:

GLRLM Mean St Dev Range Min Max Specificity = TN / (TN+FP) x 100 % (3)
Features
SRE 0.18 0.05 0.22 0.06 0.28
The specificity of 75.04% indicates that inflammatory cells
LRE 27.55 2.756 14.61 21.59 36.2
GLN 96.32 40.71 239.1 21.84 260.9 detected properly and few inflammatory cells are considered as
RLN 175.15 63.639 371.17 54.216 425.39 the nucleus cell while the value of sensitivity of 49.82%
RP 1.29 0.26 1.17 0.76 1.93 indicates that there is still a nucleus of cells which are
LGRE 0.35 0.08 0.35 0.16 0.5 considered as inflammatory cells. It is in accordance with the
HGRE 173.98 98.14 482.95 27.418 510.37 conditions of the difficulties faced by the pathologist.
SRLGE 0.05 0.02 0.07 0.02 0.09
SRHGE 40.42 30.11 125.6 3.306 128.9
LRLGE 4.45 1.4 5.83 1.66 7.49
LRHGE 8007.21 5573.54 27095.52 795.95 27891.47

There is a significant difference between the cell nuclei and

inflammatory cells in LRHGE features, namely the Long Run
High Gray-Level Emphasis, a feature GLRLM used to measure
the distribution of distribution relationships run and high-value
gray level. The overall distribution of datum values for the
texture GLRLM groups of nuclei and inflammatory cells can (a) (b)
be seen in Table III and IV.
In figure 4, eleventh value GLRM of inflammatory cells and
nuclei have the same size, and the line on the graph of the two
sets of data is almost coincide. To compare the average value
for the eleventh texture of nuclei and inflammatory cells, the
mean or average for the two groups of data are graphed in
Figure 4.

(a) (b)

(a) (b)
Fig. 5. a) Initial image, (b) The resulted image with multiple segmented
inflammatory cell

Figure 5 (a) shows several the initial image in normal Pap

Fig. 4. Mean of Texture Nucleus and Inflammatory Cells
smear and figure 5 (b) shows the nuclei with centroid cell and

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 2015 4th International Conference on Instrumentation, Communications, Information Technology, and Biomedical Engineering (ICICI-BME)
Bandung, November 2-3, 2015

these inflammatory cells will be extracted and eliminated by
changing their color into a color that is similar to the color of
the cytoplasm. The detected cell nucleus is remaining with its
original color. Figure 5(b) shows the result of this procedure in
an original image. In this figure, we can see that the
inflammatory cells in this image are suppressed.
Smear Images,” International Journal of E-Health and Medical
Communications (IJEHMC), ISSN: 1947315x, 19473168, Vol:6, Issue:2,
27-43, April-June 2015.
[14] D. Xu, A.S. Kurani, J.D. Furst, and D.S. Raicu,“Run-length Encoding for
Volumetric Texture,” The 4th IASTED International Conference on
Visualization, Imaging, and Image Processing, 2004.

V. CONCLUSION

The identification of nucleus in the Pap smear images is a

challenging issue mainly these images which present
inflammatory cell and other limitations. In this paper, we
propose the rule classification of texture GLRLM that can be
used to extract the nucleus cells and inflammatory cells in
normal Pap smear images, which results in efficient
discrimination with a Decision Tree (J48) algorithm.
Meanwhile, the percentage of specificity indicates that the
proposed method can be used in future studies to perform the
classification of inflammatory cell because only few
inflammatory cells are not detected. However, further research
will be done by finding a classification rule nucleus and
inflammatory cells obtained from cropping automatically, to
obtain better results.
ACKNOWLEDGMENT
Dwiza Riana would like to thank Laboratorium Khusus
Patologi Veteran, Bandung, Indonesia for the database Pap
smear images.
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