Genetic Programming Based Image Segmentation
with Applications to Biomedical Object Detection
Tarundeep Singh1, Nawwaf Kharma2, Mohmmad Daoud3 and Rabab Ward4
Electrical & Computer Engineering Department, Concordia University, Montreal, Quebec, Canada1,2
Department of Electrical & Computer Engineering, U. of Western Ontario, London, Ontario, Canada3
Department of Electrical & Computer Engineering, U. of British Columbia, Vancouver, B.C., Canada4
t_dhot@encs.concordia.ca1, kharma@ece.concordia.ca2, mdaoud@imaging.robarts.ca3, rababw@icics.ubc.ca4
ABSTRACT
Image segmentation is an essential process in many image
analysis applications and is mainly used for automatic object
recognition purposes. In this paper, we define a new genetic
programming based image segmentation algorithm (GPIS). It uses
a primitive image-operator based approach to produce linear
sequences of MATLAB® code for image segmentation. We
describe the evolutionary architecture of the approach and present
results obtained after testing the algorithm on a biomedical image
database for cell segmentation. We also compare our results with
another EC-based image segmentation tool called GENIE Pro.
We found the results obtained using GPIS were more accurate as
compared to GENIE Pro. In addition, our approach is simpler to
apply and evolved programs are available to anyone with access
to MATLAB®.
Categories and Subject Descriptors
I.4.6 [Image Processing and Computer Vision]: Segmentation –
pixel classification.
General Terms: Algorithms, Experimentation.
Keywords: Image Segmentation, Genetic Programming.
1. INTRODUCTION
Image segmentation is the process of extraction of objects of
interest from a given image. It allows certain regions in the image
to be identified as an object based on some distinguishing criteria,
for example, pixel intensity or texture. It is an important part of
many image analysis techniques as it is a crucial first step of the
imaging process and greatly impacts any subsequent feature
extraction or classification. It plays a critical role in automatic
object recognition systems for a wide variety of applications like
medical image analysis [8, 9, 14, 15], geosciences and remote
sensing [2, 3, 4, 5, 10, 11], and target detection [10, 11, 16].
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However, image segmentation is an ill-defined problem. Even
though numerous approaches have been proposed in the past [7,
12, 13], there is still no general segmentation framework that can
perform adequately across a diverse set of images [1]. In addition,
most image segmentation techniques exhibit a strong domain or
application-type dependency [7, 12]. Automated segmentation
algorithms often include a priori information of its subjects [8],
making use of well-designed segmentation techniques restricted
to a small set of imagery.
In this paper, we propose a new, simple image segmentation
algorithm called Genetic Programming based Image
Segmentation (GPIS) that uses a primitive image-operator based
approach for segmentation and present results. The algorithm
does not require any a priori information about objects to be
segmented other than a set of training images. In addition, the
algorithm is implemented on MATLAB® and uses its standard
image-function library. This allows easy access to anyone with
MATLAB®.
In the following sections, we provide a brief introduction to
relevant work in GP based image segmentation and image
analysis, followed by an overview of our approach in Section 1.3.
Section 2 describes the methodology of our algorithm and the
experimental setup for compiling results. Finally, Section 3
presents the results of the experiments conducted on a biomedical
image database for cell segmentation purposes. We also compare
our results with another EC-based image segmentation algorithm
called GENIE Pro.
1.1 Related Work
One of the initial works in this field was published by Tackett
[16] in 1993. He applied GP to develop a processing tree capable
of classifying features extracted from IR images. These evolved
features were later used to construct a classifier for target
detection. On the same lines, in 1995, Daida et al. [5, 6] used GP
to derive spatial classifiers for remote sensing purposes. This was
the first time GP was used for image processing applications in
geosciences and remote sensing.
In 1996, Poli [14] proposed an interesting approach to image
analysis based on evolving optimal filters. The approach viewed
image segmentation, image enhancement and feature detection
purely as a filtering problem. In addition, he outlined key criteria
while building terminal sets, function sets and fitness functions
for an image analysis application.
In 1999, Howard et al. [10, 11] presented a series of works using
GP for automatic object detection in real world and military
image analysis applications. They proposed a staged evolutionary
approach for evolution of target detectors or discriminators. This
resulted in achieving practical evolution times.
In 1999, another interesting approach was proposed by Brumby et
al. [4]. They used a hybrid evolutionary approach to evolve image
extraction algorithms for remote sensing applications. These
algorithms were evolved using a pool of low level image
processing operators. On the same lines, Bhanu et al. [2, 3] used
GP to evolve composite operators for object detection. These
operators were synthesized from combinations of primitive image
processing operations used in object detection. In order to control
the code-bloat problem, they also proposed size limits for the
composite operators.
In 2003, Roberts and Claridge [15] proposed a GP based image
segmentation technique for segmenting skin lesion images. A key
feature of their work was the ability of the GP to generalize based
on a small set of training images.
Our approach is motivated by the works of Tackett [16], Brumby
et al. [4] and Bhanu et al. [2, 3]. They all effectively implemented
a primitive image operator based approach for image analysis.
This is similar to our approach. In addition, we have used the key
criteria outlined by Poli [14] as references while building our
algorithm.
1.2 GENIE Pro
GENIE Pro [4, 9] is a general purpose, interactive and adaptive
GA-based image segmentation and classification tool. GENIE Pro
uses a hybrid GA to assemble image-processing algorithms or
pipelines from a collection of low-level image processing
operators (for example edge detectors, textures measures, spectral
orientations and morphological filters). The role of each evolved
pipeline is to classify each pixel as feature or non-feature.
The GA begins with a population of random pipelines, performs
fitness evaluation for each pipeline in the population and selects
the fitter pipelines to produce offspring pipelines using crossover
and mutation. In order to compute fitness of a pipeline, the
resultant segmentation produced by a pipeline is compared to a
set of training images. These training images are produced by
manual labeling of pixels by user as True (feature) or False (non-
feature) pixels using an in-built mark-up tool called ALLADIN.
Finally, when a run of GENIE Pro is concluded, the fittest
pipeline in the population is selected and combined using a linear
classifier (Fisher Discriminant) to form evolved solution that can
be used to segment new images.
GENIE Pro was originally developed for analyzing multispectral
satellite data but has been later applied for biomedical feature-
extraction problems also [9]. We use GENIE Pro as a comparative
method to check effectiveness of our algorithm.
1.3 Overview of Our Work
In this paper, we describe a new genetic programming based
image segmentation algorithm, GPIS that uses a primitive image-
operator based approach for segmentation. Each segmentation
algorithm can be viewed as a unique combination of image
analysis operators that are successfully able to extract desired
regions from an image. If we are able to describe a sufficient set
of these image analysis operators, it is possible to build multiple
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segmentation algorithms that segment a wide variety of images.
In GPIS, we define a pool of low level image analysis operators.
The GP searches the solution space for the best possible
combination of these operators that are able to perform the most
accurate segmentation. From now on, we refer to these image
analysis operators as primitives. Each individual in a population is
a combination of these primitives and represents an image
segmentation program. Therefore, GPIS typically breeds a
population of segmentation programs in order to evolve one
accurate image segmentation program.
2. METHODOLOGY
The proposed algorithm GPIS is designed as a general tool for
learning based segmentation of images. In this paper, particular
attention is given to the testing it on biomedical images. Our
approach does not require a particular image format or size and
works equally well on both color and grayscale images in any
MATLAB® compatible format.
For the purpose of learning, a directory with both input images
and matching ground truths (GTs) must be provided. From this
point onwards, we call this a training set. Every input image must
have a corresponding GT of the same size and format. The GT
image is a binary image showing the human expert assessment of
the boundaries of the objects of interest; all pixels inside those
boundaries are by definition object pixels and all pixels outside
the boundaries are by definition, non-object pixels. Pixels on the
boundary of an object are by definition also object pixels.
GPIS has two stages of operation. Stage 1 is a learning phase in
which GPIS uses the training set to evolve a MATLAB® program
which meets user-defined threshold of segmentation accuracy
relative to the input images of the training set.
In the second stage, this evolved individual is evaluated for its
ability to segment unseen images of the same type as the training
images. The accuracy results achieved here are from here on
called validation accuracy.
In a real world situation, due to lack of GTs for unseen images,
validation accuracy will take the form of the subjective
assessment of a human user. However, for this paper, the authors
evaluate the quality i.e. the validation accuracy of the individual
evolved by GPIS by comparing their segmentation results to their
matching GT images. We report the results of our evaluation in
the Results section (Section 3) of this paper.
2.1 Stage 1: Learning phase of GPIS
GPIS operates in a typical evolutionary cycle in which a
population of potential program solutions (each meant to segment
images) is subjected to repeated selection and diversification until
at least one of the individual meets the termination criteria. The
flowchart of the learning stage is presented in Figure 1.
 initialization is also random i.e. parameter values of operators are
also assigned randomly, based on the operator type. For practical
reasons, the size of each chromosome is limited to a maximum
length of 15.

(a)

(b)

Figure 1. Flowchart of GPIS (c)

Figure 2. (a) Typical layout of a gene (b) Typical layout
2.1.1 Representation and Initialization of a chromosome comprising of n genes (c) One-to-one
In our scheme, the genome of an individual encodes a mapping of the genome and phenome
MATLAB® program that processes an image. The input to the
program is an image file and the execution of the MATLAB® Table 1. Primitive image analysis operators in the gene pool
program is an image of the same size and format. This output Operator
Description Inputs Operator Type
image file is a segmented version of the input image. Name
ADDP Add Planes 2 Arithmetic
The general layout of a gene is a shown in Figure 2 (a). As seen in
the figure, each gene specifies information about the primitive SUBP Subtract Planes 2 Arithmetic
operator it encodes, the input images to the operator and MULTP Multiply Planes 2 Arithmetic
parameter settings for the operator. This corresponds to a few Absolute
lines (1-3) of the equivalent MATLAB® program. The gene DIFF 2 Arithmetic
Difference
consists of five parts. The first part contains name of the primitive AVER Averaging Filter 1 Filter
operator and the second and third part contain the possible input
images to the operator. Based on nature of the primitive operator, DISK Disk Filter 1 Filter
a gene may have one or two input images. The fourth part GAUSSIAN Gaussian Filter 1 Filter
contains weights or parameter values for the primitive operator LAPL Laplacian Filter 1 Filter
and fifth part encodes the nature of the Structuring Element or SE
UNSHARP Unsharp Filter 1 Filter
(only in case of morphological operations) or a secondary Filter
Parameter or FP (only in case of filter operators). LP Lowpass Filter 1 Filter
HP Highpass Filter 1 Filter
The phenomic representation (chromosome) is a simple
combination of genes, as shown in Figure 2 (b). The chromosome DIL Image Dilate 1 Morphological
represents a complete MATLAB® segmentation program. There ERODE Image Erode 1 Morphological
is a one-to-one mapping between the genome and the phenome as
OPEN Image Open 1 Morphological
shown in Figure 2 (c). It also shows the representation of the
knowledge structure used by the genetic learning system. CLOSE Image Close 1 Morphological
Image Open-
We use a pool of 20 primitive operators. Table 1 provides the OPCL 1 Morphological
Close
complete list of all primitive image analysis operators in the gene
Image Close-
pool along with the typical number of inputs required for each CLOP 1 Morphological
Open
operator.
Histogram
HISTEQ 1 Enhancement
Initialization creates a starting population for the GP. The initial Equalization
population to the GP is randomly generated i.e. chromosomes are ADJUST Image Adjust 1 Enhancement
formed by a random assigned sequence of operators. The genomic THRESH Thresholding 1 Post-processing

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In addition, at the time of initialization, the size of the population
along with values of crossover rates and mutation rates are
assigned by the user.
2.1.2 Fitness Evaluation
A segmented image consists of positive (object) and negative
(non-object) pixels. Ideally the segmentation of an image would
result in an output image where positive pixels cover object pixels
perfectly and the negative pixels cover non-object pixels
perfectly. Based on this idea, we can view segmentation as a
pixel-classification problem. The task of the segmentation
program now becomes assignment of the right class to every pixel
in the image. As such, we can apply measure of classification
accuracy to the problem of image segmentation. Every
segmentation program can be expected to identify not only pixels
belonging to the objects of interest (True Positives, TPs), but also
some non-object pixels identified as objects (False Negatives,
FNs). Further, in addition to identifying non-object pixels (True
Negatives, TNs), some pixels belonging to non-objects can be
identified as object pixels (False Positives, FPs).
Therefore for an ideal segmentation, the number of FPs and FNs
should be zero while the number of TPs and TNs should be
exactly equal to number of object and non-object pixels. If we
normalize the value of TPs and TNs by the total number of object
and non-object pixels respectively, their individual values in the
best case scenario would be 1 and 0 in the worst case scenario.
However, for the segmentation problem, achieving this is a
challenging task, thus we define two more measures based on
TPs, TNs, FPs and FNs called the False Positive Rate (FPR) and
False Negative rate (FNR). FPR is the proportion of non-object
pixels that were erroneously reported as being object pixels. FNR
is the proportion of object pixels that were erroneously reported
as non-object pixels.
Therefore, for an ideal segmentation, the values of FPR and FNR
should be zero. For finding accuracy of a segmentation program,
we use a pixel-based accuracy formula based on FPR and FNR.
This formula reflects the training and validation accuracy for
GPIS. It is as follows:
(1)
where FPR represents False Positive Rate and FNR represents
False Negative Rate.
The above formula for accuracy extends image segmentation
problem to a pixel-classification problem. Therefore, ideally value
of accuracy should be 1 (or 100%) for a perfectly segmented
image. We also see that the formula is monotonicity, i.e. if image
A is better segmented than image B then Accuracy (A) >
Accuracy (B).
However, we further extend this formula by introducing a term
that penalizes longer programs. The fitness function for GPIS is
as follows:
(2)
where FPR represents False Positive Rate, FNR represents False
Negative Rate, len represents length of the program, β is a scaling
factor for the length of a program, such that β belongs to [0.004,
0.008]. We found this range sufficient for our purpose.
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2.1.3 Termination Criteria
Termination of the GP is purely fitness based and the
evolutionary cycle continues till the time there is no major change
in fitness over a 10 generations. In order to do this, first we
calculate a minimum acceptable fitness value based on our trial
runs. This value was found to be 95% for the database in use. Till
the time, these values of fitness were not achieved, the GP keeps
running. Once, these values were reached, a mechanism of
calculating cumulative means of the fitness of successive
generations was implemented. If the absolute difference between
the means of 10 successive generations was less than 5% of the
highest fitness achieved, the GP stops. If however, the GP is used
on any other database, a default value of 90% is set. The
termination criteria can be defined as follows:
|current fitness – mean fitness(10 gen)| < 0.05 × highest fitness
2.1.4 Parent Selection
Parent selection is done to select chromosomes that undergo
diversification operations. In order to do this, we use a
tournament selection scheme. It is chosen instead of rank
selection as it is computationally more efficient. The size of the
tournament window λ is kept at 10% of the size of the population.
The number of parents selected is 50% of the size of the
population.
2.1.5 Elitism
We use elitism as a means of saving the top 1% chromosomes of
a population. Copies of the best 1% of the chromosomes in the
population are copied without change to the next generation.
2.1.6 Diversification
We employ five genetic operators in total: one crossover and four
mutation operators. These are selected probabilistically based on
their respective rate of crossover and mutation.
Crossover: We use a 1-point crossover for our GP. Two parents
are chosen randomly from the parent pool. A random location is
chosen in each of the parent chromosomes. The subsequences
before and after this location in the parents are exchanged
creating two offspring chromosomes.
Mutation: We use four mutation operators for our GP. There are
three inter-genomic mutation operators, namely, swap, insert and
delete and one intra-genomic mutation operator, alter, which
typically alters the weight element of the selected gene. The gene
to be mutated is randomly chosen from the selected parent
chromosome.
2.1.7 Injection
In order to overcome loss of diversity in a population, we use an
injection mechanism. We inject a fixed percentage of new
randomly initialized programs to the population after every n
generation. In the current configuration, we inject 20% new
programs every 5 generations.
2.1.8 Survivor Aggregation
The aim of this phase is to collect chromosomes that have
qualified to be part of the next generation (parent, offspring, elite,
injected) in order to build the population for the next generation.
This phase works in two modes: non- injection and injection
mode. In the non-injection mode, copies of all parent
chromosomes (50%), offspring chromosomes (49%) and elite
chromosomes (1%) form the population of the next generation. In
the injection mode, since a fixed size population (20%) of new
chromosomes is inserted into the population, the top 79% of
parent-offspring population is selected along with the elite set
(1%) to form the population of the next generation.
2.1.9 Output (Fittest Individual)
Once the termination criterion has been satisfied, the output of the
GP is typically the “fittest” chromosome present in the final
population. This chromosome is then chosen to be tested on a set
of unseen test images and it is explained in Section 2.2. Our aim
is to create a pool of such outputs (segmentation programs) which
allows us to have multiple segmentation algorithms for the same
database. This is created by subsequent runs of the GP.
Note: When we apply percentages, the results are rounded to the
closest integers. In case of elitism, if 1% < 1, 1 individual is
copied.
2.2 Stage 2: Evaluation Methodology
As mentioned in the previous section, the output of Stage 1 gives
us one chromosome, which was the fittest chromosome amongst
the population of final generation. The accuracy of the
segmentations produced by this chromosome on the training
images is known as training accuracy of the run. The actual
challenge for this individual is to produce similar segmentation
accuracies on an unseen set of images known as the validation
images.
In order to do this, we randomly select a fixed number of new
images from outside the training set along with their
corresponding GTs, from the image database. From this point
onwards, we refer to call this the validation set. Once the
validation set is chosen, the “fittest chromosome” is applied on
the entire set of images, one-by-one and segmentation accuracies
for each image is calculated based on the accuracy formula (1)
given is Section 2.1.2. Once this process ends, the average
segmentation accuracy of set or validation accuracy of the run is
calculated.
We repeat the above process for various runs and calculate the
overall training accuracy (average training accuracies of runs) and
validation accuracy (average validation accuracies of runs) for the
algorithm. From here on, we refer to the above as training
accuracy and validation accuracy respectively.
The output of Stage 2 is a chromosome that performs equally well
on both training and validation sets and produces high overall
validation accuracy.
2.3 Experimental Setup
In order to test the effectiveness and efficacy of our algorithm, we
tested the algorithm on a biomedical image database that
consisted of HeLa cell images (in culture) of size 512 pixels ×
384 pixels . The task of the algorithm was to segment the cells
present in the images. The procedure for obtaining results using
our algorithm is given in Section 2.3.1.1.
We also compare the results of our algorithm with those produced
by GENIE Pro. The procedure used for obtaining results using
GENIE Pro is given in Section 2.3.1.2.
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The final set of parameter values used for GPIS is given in Table
2.
2.3.1 Procedure for Training and Validation
In order to plan a run of the algorithm, we first decide size of the
training and validation sets. To do so, we define G as the global
total number of images in a database, T as the training set, V as
the validation set, and R as the number of times optimal
individuals are evolved for the same database. The final values for
the above used in the present configuration are: G = 1026, T = 30,
V = 100 and R = 28.
Table 2. Parameter settings for GPIS
Population size: µ 200  
Crossover Rate: Pc 0.45
Swap Mutation Rate: Pms 0.25
Insert Mutation Rate: Pmi 0.25
Delete Mutation Rate: Pmd 0.2
Alter Mutation Rate: Pma 0.7
Scalability factor for length: β 0.005
2.3.2 Procedure for Training and Validation
In order to plan a run of the algorithm, we first decide size of the
training and validation sets. To do so, we define G as the global
total number of images in a database, T as the training set, V as
the validation set, and R as the number of times optimal
individuals are evolved for the same database. The final values for
the above used in the present configuration are: G = 1026, T = 30,
V = 100 and R = 28.
2.3.1.1 Procedure for Obtaining Results using GPIS
Step 1. Randomly select T images and other V images from the
G images in the database.
Step 2. Perform training on T images to choose fittest
individual for validation.
Step 3. Validate this individual on V images to check the
applicability of this individual on unseen images. If
individual produces high validation accuracy, save it in
the result set, else discard it.
Step 4. Repeat Steps 1 to 3, R times producing a set of optimal
individuals (result set).
Step 5. Calculate values of average training and validation
accuracy of the result set.
2.3.1.2 Procedure for Obtaining Results using GENIE
Pro
Step 1. Select the same T and V images from the G images in
the database, used for the corresponding GPIS run.
Step 2. Load each of the T images as a base image and create a
training overlay for each image by marking Foreground
(object) and Background (non-object) pixels manually.
Step 3. Train on these manually marked training overlays using
the in-built Ifrit Pixel Classifier.
Step 4. Apply learned solution on V images to produce
corresponding segmented images.
Step 5. Calculate validation accuracy for these V images using
formula (1).
Step 6. Repeat Steps 1 to 5, R times, same as like GPIS.
Step 7. Calculate values of average training and validation
accuracy of the result set.
3. RESULTS
We have based our results on two criteria, effectiveness of the
algorithm to accurately segment the given images, and efficiency
of the algorithm in doing so.
Effectiveness is based on two measures, pixel accuracy of the
evolved solution and the cell count rate (percentage of cell
structures correctly identified). In order to calculate the cell count
rate, we have categorized cells into two types: Type1 and 2. Type
1 cells are those which can be identified by eye with relative ease.
Type 2 cells are those which are relatively difficult to be
identified by eye. We also provide comparative results for
effectiveness for GENIE Pro. This is presented in Section 3.1.1.
3.2 Efficiency
Table 5 reflects the efficiency of the process to produce the
required results. We measure efficiency based on number of
generations taken by GPIS to produce one individual of minimum
acceptable fitness. This acceptable fitness is 95% training
accuracy. In our runs, we observed that GPIS never failed to
produce an acceptable individual.
The experiments were performed on an Intel Pentium (R) 4 CPU,
3.06 GHz, 2GB RAM computer. To execute 1 generation, GPIS
took at an average 4.21 minutes. The average time taken for a
complete run was approximately 513 minutes. The maximum
time taken for a complete run was 580 minutes.
Since GPIS is designed to run as an offline tool and the time it
takes to execute an evolved program is between 1-3 seconds, the
period of evolution of an optimal program is within reasonable
real world constraints. Also, the standard deviation for number of
generations is low. This shows that GPIS runs consistently to
produce an optimal program within a tight window.

Efficiency reflects the time the algorithm takes to produce one Table 3. Segmentation accuracy: GPIS Vs GENIE Pro
individual of acceptable fitness. This is measured in terms of
number of generations. These results are presented in Section Algorithm Training Data Validation Data
3.1.2. GPIS 98.76% 97.01%
We also briefly discuss one evolved program and also provide GENIE Pro 94.12% 93.12%
segmented images produced. This is presented in Section 2.4.3
and Figure 5 and 6.
Table 4. Cell count rate: GPIS Vs GENIE Pro
3.1 Effectiveness Cell GPIS GENIE PRO
Tables 3 & 4 presents results obtained for training and validation Count
accuracies of segmentation achieved for GPIS and GENIE Pro. Training Validation Training Validation
Measure Data Data Data Data
These values represent each algorithm’s ability to correctly
classify each pixel in an image as an object or non-object pixel. Detected
98.24% 97.98% 97.02% 96.56%
We found that our algorithm performed better in segmenting the Cells
cells in the images as compared to GENIE Pro.
Type 1
100% 100% 100% 100%
The second measure for effectiveness that we used was cell count Cells
rate. We extend the concept of TPs, TNs, FPs and FNs to object
detection where a TP denotes an object that is correctly identified Type 2
98.78% 98.22% 97.49% 96.89%
by the algorithm as cell, FN denotes an object incorrectly Cells
identified as a cell, FP denotes non-object incorrectly identified as Undetecte
cell, and TN denotes a non-object correctly identified as the 1.32% 1.55% 2.12% 2.25%
d Cells
background. In order to consider an object as belonging to any of
the above four options, a minimum of 70% of object pixels must
correspond to any of the four options mentioned above. Cells Table 5. Performance of GPIS based on number of
identified were manually counted. generations
Similar to the accuracy formula, based on TPs, TNs, FPs and FNs,
we can define the FPR and FNR for cell count. FPR is the Statistical Measure Number Of Generations
proportion of non-cell structures that were erroneously reported as MEAN 122.07
being cell structures. FNR is the proportion of cell structures that
were erroneously reported as non-cell structures. The cell count MEDIAN 122
rate formula used is as follows: STANDARD DEVIATION 6.85
Cell Count Rate = (1-FPR) × (1-FNR) (3) UPPER BOUND 138
LOWER BOUND 112

1128

3.3 Evolved Program
Figure 5 shows the chromosomal and genomic structure of an
evolved program. The program evolved is a combination of filters
and morphological operators. The first gene is a 6 × 6 Gaussian
low pass filter with a sigma value of 0.8435 followed by a 4 × 4
averaging filter. The output image from gene 2 is eroded with a
flat, disk-shaped structuring element of radius 2. A 6 × 6 Gaussian
low pass filter with a sigma value of 0.8435 followed by a 4 × 4
averaging filter. The output image from gene 2 is eroded with a
flat, disk-shaped structuring element of radius 2. A 6 × 6
averaging filter is again applied to the output image of the eroded
image. Its output image undergoes a composite morphological
operation of closing and opening with the same structuring
element as above. Finally this image is converted to a binary
output image using a threshold of 0.09022. The validation
accuracy is calculated for this image.
Figure 6 shows implementation of this evolved program on two
validation images along with corresponding results from GENIE
Pro.

GAUSS AVER EROD AVER CLOP THRESH

(a)

[GAUSS, d1, 0, 6, 0.8435] [AVER, io1, 0, 4, 0] [EROD, io2, 0, 0, 1]

[AVER, io3, 0, 6, 0] [CLOP, io4, 0, 0, 1] [THRESH, io5, 0, 0.09022, 0]

(b)

Genomic Structure MATLAB® Implementation

d1 = input;
[GAUSS, d1, 0, 6, 0.8435] h1 = fspecial(‘gaussian’, [6 6], 0.8435) ;
io1 = imfilter(d1, h1);
[AVER, io1, 0, 4, 0] h2 = fspecial(‘average’, [4 4]);
io2 = imfilter(io1,h2);
[EROD, io2, 0, 0, 1] SE1 = strel(‘disk’, 2);
io3 = imerode(io2, SE1);
[AVER, io3, 0, 6, 0] h3 = fspecial(‘average’, [6 6]);
io4 = imfilter(io3,h3);
[CLOP, io4, 0, 0, 1] io5 = imclose(io4, SE1);
[THRESH, io5, 0, 0.09022, 0] output = im2bw(io5, 0.09022);
(c)

Segmentation accuracy on validation set: 99.04 %

Number of operators used = 6
Average execution time = 1.252 seconds
Number of generation needed to converge = 114
Number of fitness evaluation = 10,532

(d)
Figure 5. An evolved program: (a) Chromosome for an evolved program, (b) Genomic structure for the evolved program, (c)
Genomic structure and equivalent MATLAB® implementation of the evolved program, (d) Performance results for the evolved
program

1129
 (a) (b)
Figure 6. (a) Segmentation produced by GPIS using evolved program shown above on validation image 1 (Validation Accuracy =
99.21%, Cell Count Rate = 100%), (b) Segmentation produced by GENIE Pro on validation image 1 (Validation Accuracy =
95.46%, Cell Count Rate = 97.89%), (c) Segmentation produced by GPIS using evolved program shown above on validation image
2 (Validation Accuracy = 98.93%, Cell Count Rate = 100%), (d) Segmentation produced by GENIE Pro on validation image 2
(Validation Accuracy = 94.22%, Cell Count Rate = 96.45
4. CONCLUSIONS
In this paper, we propose a simple approach to the complex
problem of image segmentation. The proposed algorithm, GPIS,
uses genetic programming to evolve image segmentation
programs from a pool of primitive image analysis operators. The
evolved solutions are simple MATLAB® based image
segmentation programs. They are easy to read and implement.
In addition, the algorithm does not require any a priori
information of objects to be segmented from the images. We
have tested our algorithm on a biomedical image database. We
also compare the results to another GA-based image
segmentation algorithm, GENIE Pro. We found that our
algorithm consistently produced better results. Both the
segmentation accuracy and cell count rate were higher than
GENIE Pro. It also produced an optimal solution within a
reasonable time window. In addition, GPIS never failed to
produce an optimal solution.
5. ACKNOWLEDGMENTS
We are grateful to Dr. Aida Abu-Baker and Ms Janet Laganiere
from the CHUM Research Centre, Notre-Dame Hospital,
Montreal for providing us with the images for the cell database.
We would also like to thank Dr. James Lacefield from the
University of Western Ontario, London for his help on this
project.
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