Genetic Programming based Image Segmentation with

Applications to Biomedical Object Detection

Tarundeep Singh Dhot, Nawwaf Kharma
Department of Electrical and Computer Engineering
Concordia University, Montreal, QC H3G 1M8
t_dhot@encs.concordia.ca, kharma@ece.concordia.ca

Mohammad Daoud
Department of Electrical and Computer Engineering
University of Western Ontario
London, ON, N6A 3K7
mohammad.dauod@gmail.com

Rabab Ward
Department of Electrical and Computer Engineering
University of British Columbia
Vancouver, BC, V6T 1Z4
rababw@ece.ubc.ca

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.
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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].
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, 17]. 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 developed for analyzing multispectral satellite
data. It has also been applied for biomedical feature-extraction
problems [9]. We have used it for comparison purposes.
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
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 best 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 itself 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.
chromosome represents a complete MATLAB® segmentation
program. There is a one-to-one mapping between the genome and
the phenome as shown in Figure 2 (c). It also shows the
representation of the knowledge structure used by the genetic
learning system.

2.1 Stage 1: Learning phase of GPIS [Operator Name, Input Plane 1, Input Plane 2, Weights, SE/FP]
GPIS operates in a typical evolutionary cycle in which a
population of potential program solutions (each meant to segment
(a)
images) is subjected to repeated selection and diversification until
at least one of the individual meets the termination criteria. The
[G1] [G2] [G3] [G4] [G5] ......... [Gn]
flowchart of the learning stage is presented in Figure 1.

START (b)

....
Initialization d1 = input;
h1 = fspecial(‘disk’,[6 6]);
.... io1 = imfilter(d1, h1);
SE1 = strel(‘square’, 2);
Fitness .... io2 = imerode(io1, SE1);
Evaluation io3 = imclose(io2, SE1);
next generation

....
Io4 = imadd(io2,io3);
out = im2bw(io4, 0.55);
....
Termination Output
Yes
(Fittest STOP
Criteria met? individual)
GENOME PHENOME

No

Elitism Parent Selection

(c)
Figure 2. (a) Typical layout of a gene (b) Typical layout of
parents

Genetic
(copy)
elite

Diversification a chromosome comprising of n genes (c) One-to-one

offspring

mapping of the genome and phenome

We use a pool of 20 primitive operators. Table 1 provides the
Survivor
Aggregation Injection complete list of all primitive image analysis operators in the gene
(Σ) pool along with the typical number of inputs required for each
operator.

Figure 1. Flowchart of GPIS
2.1.1 Representation and Initialization
In our scheme, the genome of an individual
MATLAB® program that processes an image. The
program is an image file and the execution of the
program is an image of the same size and format.
image file is a segmented version of the input image.
The general layout of a gene is a shown in Figure 1 (a). As seen in
the figure, each gene specifies information about the primitive
operator it encodes, the input images to the operator and
parameter settings for the operator. This corresponds to a few
lines (1-3) of the equivalent MATLAB® program. The gene
consists of five parts. The first part contains name of the primitive
operator and the second and third part contain the possible input
images to the operator. Based on nature of the primitive operator,
a gene may have one or two input images. The fourth part
contains weights or parameter values for the primitive operator
and fifth part encodes the nature of the Structuring Element or SE
(only in case of morphological operations) or a secondary Filter
Parameter or FP (only in case of filter operators).
The phenomic representation (chromosome) is a linear
combination of the genes, as shown in Figure 1 (b). The
Initialization creates a starting population for the GP. The initial
population to the GP is randomly generated i.e. chromosomes are
formed by a random assigned sequence of operators. The genomic
encodes a initialization is also random i.e. parameter values of operators are
input to the also assigned randomly, based on the operator type. For practical
MATLAB® reasons, the size of each chromosome is limited to a maximum
This output length of 15. In addition, at the time of initialization, the size of
the population along with values of crossover rates and mutation
rates 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
 Table 1. Primitive image analysis operators in the gene pool (1)
Operator where FPR represents False Positive Rate and FNR represents
Description Inputs Operator Type False Negative Rate. The above formula for accuracy extends
Name
image segmentation problem to a pixel-classification problem.
ADDP Add Planes 2 Arithmetic Therefore, ideally value of accuracy should be 1 (or 100%) for a
perfectly segmented image. We also see that the formula is mono-
SUBP Subtract Planes 2 Arithmetic modal i.e. if image A is better segmented than image B 
MULTP Multiply Planes 2 Arithmetic Accuracy (A) > Accuracy (B).

Absolute However, we further extend this formula by introducing a term

DIFF 2 Arithmetic that penalizes longer programs. The fitness function for GPIS is as
Difference
follows:
AVER Averaging Filter 1 Filter
(2)
DISK Disk Filter 1 Filter where FPR represents False Positive Rate, FNR represents False
Negative Rate, len represents length of the program, β is a scaling
GAUS Gaussian Filter 1 Filter factor for the length of a program, such that β ϵ [0.004, 0.008].
LAPL Laplacian Filter 1 Filter We found this range sufficient for our purpose.

UNSHARP Unsharp Filter 1 Filter 2.1.3 Termination Criteria

Termination of the GP is purely fitness based and the evolutionary
LP Lowpass Filter 1 Filter cycle continues till the time there is no major change in fitness
HP Highpass Filter 1 Filter over a 10 generations. In order to do this, first we calculate a
minimum acceptable fitness value based on our trial runs. This
DIL Image Dilate 1 Morphological 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.
ERODE Image Erode 1 Morphological Once, these values were reached, a mechanism of calculating
OPEN Image Open 1 Morphological cumulative means of the fitness of successive generations was
implemented. If the absolute difference between the means of 10
CLOSE Image Close 1 Morphological successive generations was less than 5% of the highest fitness
achieved, the GP stops. If however, the GP is used on any other
Image Open-
OPCL 1 Morphological database, a default value of 90% is set. The termination criteria
Close
can be defined as follows:
Image Close- |current fitness – mean fitness(10 gen)| < 0.05  highest fitness
CLOP 1 Morphological
Open
Histogram 2.1.4 Parent Selection
HISTEQ 1 Enhancement Parent selection is done to select chromosomes that undergo
Equalization
diversification operations. In order to do this, we use a
ADJUST Image Adjust 1 Enhancement tournament selection scheme. It is chosen instead of rank
selection as it is computationally more efficient. The size of the
THRES Thresholding 1 Post-processing
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
(False Positives, FPs). population.

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:
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. The final parameter values used for GPIS is given
in Table 2.
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
2.3.1 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.
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 Table 3. Segmentation accuracy: GPIS Vs GENIE Pro
training overlay for each image by marking Foreground
(object) and Background (non-object) pixels manually. Algorithm Training Data Validation Data
Step 3. Train on these manually marked training overlays using GPIS 98.76% 97.01%
the in-built Ifrit Pixel Classifier.
GENIE Pro 94.12% 93.12%
Step 4. Apply learned solution on V images to produce
corresponding segmented images.
Table 4. Cell count rate: GPIS Vs GENIE Pro
Step 5. Calculate validation accuracy for these V images using
formula (1). GPIS GENIE PRO
Cell
Step 6. Repeat Steps 1 to 5, R times, same as like GPIS. Count Training Validation Training Validation
Step 7. Calculate values of average training and validation Measure Data Data Data Data
accuracy of the result set.
Detected
98.24% 97.98% 97.02% 96.56%
3. RESULTS Cells
We have based our results on two criteria, effectiveness of the
Type 1
algorithm to accurately segment the given images, and efficiency 100% 100% 100% 100%
Cells
of the algorithm in doing so.
Effectiveness is based on two measures, pixel accuracy of the Type 2
98.78% 98.22% 97.49% 96.89%
evolved solution and the cell count rate (percentage of cell Cells
structures correctly identified). In order to calculate the cell count Undetected
rate, we have categorized cells into two types: Type1 and 2. Type 1.32% 1.55% 2.12% 2.25%
Cells
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 Table 5. Performance of GPIS based on number of generations
GENIE Pro. This is presented in Section 3.1.1.
Efficiency reflects the time the algorithm takes to produce one Statistical Measure Number Of Generations
individual of acceptable fitness. This is measured in terms of MEAN 122.07
number of generations. These results are presented in Section
3.1.2. We also briefly discuss one evolved program and also MEDIAN 122
provide segmented images produced. This is presented in Section STANDARD DEVIATION 6.85
2.4.3 and Figure 5 and 6. UPPER BOUND 138
LOWER BOUND 112
3.1 Effectiveness
Table 3 presents results obtained for training and validation
accuracies of segmentation achieved for GPIS and GENIE Pro. 3.2 Efficiency
These values represent each algorithm’s ability to correctly Table 5 reflects the efficiency of the process to produce the
classify each pixel in an image as an object or non-object pixel. required results. We measure efficiency based on number of
We found that our algorithm performed better in segmenting the generations taken by GPIS to produce one individual of minimum
cells in the images as compared to GENIE Pro. acceptable fitness. This acceptable fitness is 95% training
accuracy. In our runs, we observed that GPIS never failed to
The second measure for effectiveness that we used was cell count produce an acceptable individual.
rate. We extend the concept of TPs, TNs, FPs and FNs to object
detection where a TP denotes an object that is correctly identified The experiments were performed on an Intel Pentium (R) 4 CPU,
by the algorithm as cell, FN denotes an object incorrectly 3.06 GHz, 2GB RAM computer. To execute 1 generation, GPIS
identified as a cell, FP denotes non-object incorrectly identified as took at an average 4.21 minutes. The average time taken for a
cell, and TN denotes a non-object correctly identified as the complete run was approximately 513 minutes. The maximum time
background. In order to consider an object as belonging to any of taken for a complete run was 580 minutes.
the above four options, a minimum of 70% of object pixels must Since GPIS is designed to run as an offline tool and the time it
correspond to any of the four options mentioned above. Cells takes to execute an evolved program is between 1-3 seconds, the
identified were manually counted. period of evolution of an optimal program is within reasonable
real world constraints. Also, the standard deviation for number of
Similar to the accuracy formula, based on TPs, TNs, FPs and FNs,
generations is low. This shows that GPIS runs consistently to
we can define the FPR and FNR for cell count. FPR is the
produce an optimal program within a tight window.
proportion of non-cell structures that were erroneously reported as
being cell structures. FNR is the proportion of cell structures that
were erroneously reported as non-cell structures. The cell count 3.3 Evolved Program
rate formula used is as follows: Figure 5 shows the chromosomal and genomic structure of an
evolved program. The program evolved is a combination of filters
Cell Count Rate = (1-FPR)  (1-FNR) (3)
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.
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 Ms Aida Abu-Baker and Ms Janet Laganiere
from 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 University of Western
Ontario, London for his help on this project.
6. REFERENCES
[1] Bhanu, B.; Sungkee Lee; Das, S., ―Adaptive image
segmentation using genetic and hybrid search methods”,
IEEE Transactions on Aerospace and Electronic Systems,
Vol. 31, Issue 4, Oct 1995 Page(s):1268 – 1291.
[2] B. Bhanu and Y. Lin, ―Object Detection in Multi-modal
Images using Genetic Programming‖, Applied Soft
Computing, Vol. 4, Issue 2, 2004, pp. 175-201.
[3] B. Bhanu, Y. Lin, ―Learning Composite Operators for Object
Detection‖, Proceedings of the Conference on Genetic and
Evolutionary Computation, July 2002, pp. 1003–1010.
[4] S. P. Brumby, J. P. Theiler, S. J. Perkins, N. R. Harvey, J. J.
Szymanski, and J. J. Bloch, ―Investigation of Image Feature
Extraction by a Genetic Algorithm‖, Proceedings of SPIE,
Vol. 3812, 1999, pp. 24-31.
[5] J. M. Daida, J. D. Hommes, T. F. Bersano-Begey,S. J. Ross,
and J. F. Vesecky, ―Algorithm Discovery using the Genetic
Programming Paradigm: Extracting Low-contrast Curvilinear
Features from SAR Images of Arctic Ice‖, Advances in
Genetic Programming II, P. J. Angeline, K. E. Kinnear,
(Eds.), Chapter 21, The MIT Press, 1996, pp. 417-442.
[6] B. Bhanu, Y. Lin, ―Learning Composite Operators for Object
Detection‖, Proceedings of the Conference on Genetic and
Evolutionary Computation, July 2002, pp. 1003–1010.
[7] S. P. Brumby, J. P. Theiler, S. J. Perkins, N. R. Harvey, J. J.
Szymanski, and J. J. Bloch, ―Investigation of Image Feature
Extraction by a Genetic Algorithm‖, Proceedings of SPIE,
Vol. 3812, 1999, pp. 24-31.
[8] Bhanu, B.; Sungkee Lee; Das, S., ―Adaptive image
segmentation using genetic and hybrid search methods”,
IEEE Transactions on Aerospace and Electronic Systems,
Vol. 31, Issue 4, Oct 1995 Page(s):1268 – 1291.
[9] B. Bhanu and Y. Lin, ―Object Detection in Multi-modal
Images using Genetic Programming‖, Applied Soft
Computing, Vol. 4, Issue 2, 2004, pp. 175-201.
[10] Bhanu, B.; Sungkee Lee; Das, S., ―Adaptive image
segmentation using genetic and hybrid search methods”,
IEEE Transactions on Aerospace and Electronic Systems,
Vol. 31, Issue 4, Oct 1995 Page(s):1268 – 1291.
[11] B. Bhanu and Y. Lin, ―Object Detection in Multi-modal
Images using Genetic Programming‖, Applied Soft
Computing, Vol. 4, Issue 2, 2004, pp. 175-201.
[12] B. Bhanu, Y. Lin, ―Learning Composite Operators for Object
Detection‖, Proceedings of the Conference on Genetic and
Evolutionary Computation, July 2002, pp. 1003–1010.
[13] S. P. Brumby, J. P. Theiler, S. J. Perkins, N. R. Harvey, J. J.
Szymanski, and J. J. Bloch, ―Investigation of Image Feature
Extraction by a Genetic Algorithm‖, Proceedings of SPIE,
Vol. 3812, 1999, pp. 24-31.
[14] J. M. Daida, J. D. Hommes, T. F. Bersano-Begey,S. J. Ross,
and J. F. Vesecky, ―Algorithm Discovery using the Genetic
Programming Paradigm: Extracting Low-contrast Curvilinear
Features from SAR Images of Arctic Ice‖, Advances in
Genetic Programming II, P. J. Angeline, K. E. Kinnear,
(Eds.), Chapter 21, The MIT Press, 1996, pp. 417-442.
[15] J. M. Daida, J. D. Hommes, S. J. Ross, A. D. Marshall, and J.
F. Vesecky, ―Extracting Curvilinear Features from SAR
Images of Arctic Ice: Algorithm Discovery Using the Genetic
Programming Paradigm,‖ Proceedings of the IEEE
International Geoscience and Remote Sensing Symposium,
Italy, IEEE Press, 1995, pp. 673–75.
[16] K. S. Fu, and J. K. Mui, ―A Survey on Image Segmentation‖,
Pattern Recognition, 13, 1981, pp. 3-16.
P. Ghosh and M. Mitchell, ―Segmentation of Medical Images
using a Genetic Algorithm‖, Proceedings of the 8th Annual
Conference on Genetic and Evolutionary Computation,
2006, pp. 1171—1178.
[17] Harvery, N. Levenson, R. M., Rimm, D. L. Investigation of
automated feature extraction techniques for applications in
cancer derection from multi-spectral histopathology images.
Proceedings of SPIE, Vol. 5032, 2003, 557-556.
[18] D. Howard and S. C. Roberts, ―A Staged Genetic
Programming Strategy for Image Analysis‖, Proceedings of
the Genetic and Evolutionary Computation Conference,
1999, pp. 1047—1052.
[19] D. Howard, S. C. Roberts, and R. Brankin, ―Evolution of
Ship Detectors for Satellite SAR Imagery‖, Proceedings of
EuroGP'99, Vol. 1598, 1999, pp. 135- 148.
[20] N. R. Pal, and S. K. Pal, ―A Review on Image Segmentation
Techniques‖, Pattern Recognition, 26, 1993, pp. 1277-1294.
[23] M. E. Roberts and E. Claridge, ―An Artificially Evolved
Vision System for Segmenting Skin Lesion Images‖,
Proceedings of the 6th International Conference on Medical
Image Computing and Computer-Assisted Intervention, Vol.
2878, 2003, pp. 655- 662.
[24] W. Tackett, ―Genetic Programming for Feature Discovery
and Image Discrimination‖, In S. Forrest, editor,
Proceedings of 5th International Conference on Genetic
Algorithm, 1993, pp. 303–311.

[21] D. L. Pham, C. Xu, J. L. Prince, ―Survey of Current Methods
in Medical Image Segmentation‖, Annual Review of
Biomedical Engineering, 2, 2000, pp. 315—337.
[22] R. Poli, ―Genetic Programming for Feature Detection and
Image Segmentation‖, T.C. Forgarty (Ed.), Evolutionary
Computation, Springer- Verlag, Berlin, Germany, 1996, pp.
110–125.
[25] W. Tackett, ―Genetic Programming for Feature Discovery
and Image Discrimination‖, In S. Forrest, editor,
Proceedings of 5th International Conference on Genetic
Algorithm, 1993, pp. 303–311.
[26] Y. J. Zhang, ―Influence of Segmentation over Feature
Measurement‖, Pattern Recognition Letters, 16(2), 1992,
201-206.

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

GAUS AVER EROD AVER CLOP THRES 0, 0, 1] [AVER, io3, 0, 6, 0] [CLOP, io4, 0, 0, 1] [THRESH,
io5, 0, 0.09022, 0]
(a)

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);
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
(b)
Figure 5. An evolved program: (a) Chromosomal and genomic structure for the evolved program, (b) Genomic structure and
equivalent MATLAB® implementation of the evolved program with corresponding performance results

(a) (b) (c) (d)

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%)