2019 XXII Symposium on Image, Signal Processing and Artificial Vision (STSIVA)
Automatic Cell Image Segmentation
Using Genetic Algorithms
Margarita Gamarra Andrés Mitre-Ortiz
Electronic Engineering department Human-Centered Computing Lab
Politécnico de la Costa Atlántica Center for Resarch in Mathematics
Barranquilla, Colombia Zacatecas, México
mgamarraa@pca.edu.co andres.mitre@cimat.mx
Abstract—Cell image segmentation is a fundamental stage for
cell identification process, but it is not an easy task. Several
methods for cell segmentation have been proposed. However, the
selection of parameters for the available algorithms depends on
the cell type and finally they are designated by an expert.
Whereas this approach can result in good performance, it is not
necessarily the optimal and may inherit expert’s biases. We
propose in this paper an autonomous machine learning technique
based on genetic algorithms for the selection of parameters in the
cell image segmentation process. The use of optimized
parameters improved the performance of the cell segmentation
algorithm.
Keywords—cell segmentation, genetic algorithms, auto machine
learning, auto tuning.
I. INTRODUCTION
Recent advances in microscopy and improvements in
image processing algorithms have allowed the development of
computer-assisted analytical approaches in the identification of
cells [1]. Several applications can be mentioned in this field:
identification of cellular phenotypes, detection and treatment of
diseases, identification of virus entry into cells and virus
classification. These applications could help complement the
opinion of medical experts.
Despite the great advances in the areas of cell imaging,
image processing and pattern recognition, each type of cell and
image is a new challenge and requires of its own
configurations, where the performance of techniques can vary.
In addition to this, the analyst performs a manual tuning of the
parameters in each of the algorithms and even the selection of
the same algorithms is a search task made by the human expert.
Finally, a model with its adjusted parameters and with an
acceptable performance is obtained by trial and error and the
expert's criterion.
Nevertheless, if the task of choosing the model and its
parameters is carried out automatically, under the measurement
Hugo Escalante
Instituto Nacional de Astrofísica, Óptica y
Electrónica
Puebla, México
hugojair@inaoep.mx
of exact indicators and in order to obtain a minimum error in
the classification, then better results can be achieved.
Faced with these challenges in cell image segmentation,
this research implements an Autonomous Machine Learning
(AutoML) strategy for the parameters selection process, in
order to obtain an improved performance in the segmentation
of cells from fluorescence microscope images.
II. RELATED WORK
The review of the state of the art in the analysis of cell
images segmentation is quite broad, and it is a topic of growing
research. This is because the biological sciences have found
great support in the tools of computing and digital processing
of information for the development of their research [2].
Although the work is vast, there is no a single-best method
for cell segmentation and the choice of a suitable algorithm
depends on required computational efficiency, performance,
and type of images being segmented [3].
In [4] the authors explain how Machine Learning (ML)
methods work and the considerations for their successful
application in cell biology. It summarizes how microscopy
images can be converted into a suitable data representation for
machine learning, and then present several next-generation ML
algorithms, highlighting recent applications in image-based
detection.
Similarly, a review is carried out in [5] which is focused on
ML applications for the analysis of images in microscopy
experiments with typical segmentation and cell tracking tasks.
This review also offers a brief historical perspective of ML and
presents several example applications in various stages of
image processing, including the use of supervised learning
methods to improve cell segmentation and the application of
active learning for tracking.
Although different approaches for parameter optimization
have been developed and successfully applied in several
application fields [6], there is still a lot to explore regarding its
implementation in cell segmentation. The main contribution of
our research is the adaptation of a method for parameter
optimization based on Genetic algorithms (GA), applied in the
context of cell image segmentation.
III. PROPOSED APPROACH
In this study we are interested in the auto-tuning of the
parameters, more specifically, in a setting where the parameter
space of a cell segmentation algorithm is automatically
explored by a genetic algorithm. The method for cell
segmentation is the reported algorithm marker-controller
watershed [7]. The auto-tuning process compares the results
with ground truth, obtaining four basic cardinalities of the
confusion matrix: true positives (TP), false positives (FP), true
negatives (TN), and false negatives (FN). Based on these
values, the following performance indicators can be obtained
[8]:
a) Sensitivity or recall: TPR=TP/(TP+FN)
b) Specificity: TNR=TN/(TN+FP)
c) Precision: PPV = TP / (TP + FP).
d) Negative predictive value: NPV = TN / (TN + FN).
e) Accuracy: (TP+TN)/(TP+FN+TN+FP)
f) F-Index= 2(PPV*TPR)/(PPV+TPR)
g) Dice: 2TP/(2TP+FP+FN)
h) Jaccard: TP/(TP+FP+FN)
These metrics offer information about the segmentation
process. Precision and Recall are meaningful when considered
jointly. In general, under-segmentation generates high values
of precision and low recall, while over-segmentation is the
opposite [9]. An appropriate behavior between precision and
recall is revealed in higher f-index values.
The auto-tuning process is repeated to find a set of
parameters that produces the most accurate results as measured
by a comparison metric that in our case is the F-index.
We selected a Genetic Algorithms (GA) as our
optimization method, since it has obtained a suitable
performance in similar applications [6] and it allows use
different configurations with the aim to obtain the optimal
output. Besides, this is a derivative free optimization technique
that can be implemented in parallel.
For our experiments, first we selected the parameters of the
segmentation algorithm based on the expert criterion and some
visible results. Second, we separate the samples in training and
test and execute the GA with the fitness function with the aim
to obtain the optimal set of parameters.
A. Cell segmentation algorithm
The used method to distinguish between background and
cell is the marker-controlled watershed (MC-Watershed)
[10][11]. The goal of this block is to recognize as many cells as
possible. A flowchart of this process is shown in Fig. 1. Four
stages integrate the MC-Watershed: preprocessing, marking the
foreground objects, computing background markers and
computing Watershed transform [7].
Fig. 1. Flowchart of the MC-Watershed algortithm.
The preprocessing stage adapts the input image Iinput and
adjusts the intensity by trying to contrast the cell and
background; the algorithm cleans the borders in the image as
the cells in these places are not completely visible and it would
result in wrong information for following processes, such as
characterization. The resulting image is Iadj.
Morphological operations like "opening-by-reconstruction"
and "closing-by-reconstruction" are performed to “clean up”
the image. The output of the preprocessing block is Io, which is
the input to obtain foreground and background markers. In this
stage is necessary to define a morphological structuring
element. The “disk” structure is suitable since it fits to the cell
shape. The radio r of the disk is a parameter that affects the
performance of the segmentation. Then it is an input for the
optimization algorithm.
The next block calculates the regional maxima of Io to
obtain foreground markers. The regional maxima are
connected components of pixels with a constant intensity
value, whose all external boundary pixels have a lower value.
It is necessary to clean the edges and remove the elements that
have fewer than P pixels. This is the second input for the
optimization algorithm. The resulting image of this block is IF.
A threshold based on Otsu's method is used to obtain the
background markers. It is not suitable that the background
markers are too close to the edges of the cells. Then, the
background is thinned by using the Watershed transform of the
Distance Transform of the internal marker and by looking for
the watershed ridge-lines. The DT has four options:
“cityblock”, “chessboard”, “Euclidean” and “Quasi-Euclidean”
which influence the performance. Then DT is another
parameter. The resulting image is IB.
 The last stage computes the Watershed transform. This
block needs the inputs IF, IB and Iadj. The gradient magnitude
image is adjusted so that its only regional minima occur at
foreground and background marker pixels. Then the
Watershed transform is computed on this modified gradient.
The output of this first step is a segmented image with cells
identified in the background. The resulting image is a label
matrix Ilabel.
B. Fitness function
The fitness function is based on the cell segmentation
algorithm. The input vector contains the three parameters r, p
and DT, which correspond to radio of the disk, number limit of
the pixels to remove elements and option for the Distance
Transform, respectively. The operations described in the
flowchart in Fig.1 are executed. The output image Ilabel is
compared with the ground truth and the F-index is obtained.
This process is completed for each of the training images (10
images). Then, the average F-index is calculated: it is the
output of the fitness function and the value to optimize by the
GA.
C. Genetic algorithm
The GA maps each parameter of our cell segmentation
algorithm to a gene of an individual [12]. This is the input
vector to the fitness function, which perform the segmentation
algorithm and obtain the F-index for each individual. The
initial population is created randomly and evolved using
crossover and mutation. The crossover uses a one-point
crossover between pairs of individuals with a probability of C.
The mutation in each gene of occurs with an independent
probability of M.
Fig. 2. Auto-tuning process of the Genetic Algorithm.
The new population is evaluated based on the F-index
indicator and the results are input back to the GA to build
another generation. The process continues until a
predetermined number of generations (10 iterations) are
reached. In our experiments, the probabilities C and M were
empirically selected as 0.5 and 0.3, respectively, to maximize
performance. The GA was performed with the Optimization
Toolbox from @Matlab 2018a, where the following constraints
were chosen according to several tests:
• Limits for parameters (r,p,DT): lower bound: (4, 30, 1),
upper bound: (7, 50, 3).
• Population size: 10.
• Creation function: uniform.
• Selection function: roulette.
In Fig. 2 the auto-tuning process of the GA is showed. The
process takes initial parameters (r, p and DT) as a constraint.
The parameters are then introduced into the MC-Watershed
algorithm for the cell segmentation process. Afterwards, the
Ilabel (segmented image) and Ibinarized (ground truth) are used for
the binary classification (foreground or background class).
In the block Binary classification, we calculate the
specificity, accuracy, sensitivity, precision, Jaccard index, Dice
as well of the F-index. The metric to optimize is F-index.
Based on the result of the objective function value and the
configuration, the GA looks for other individuals in the
population, using mutation, crossover, and other operations.
This process is repeated until the GA finds the parameters that
produces the most accurate results for the F-index.
 IV. RESULTS of the True Positive (TP), True Negative (TN), False Positive
This section evaluates the auto-tuning algorithm using GA (FP) and False Negative (FN) values.
with the goal of maximizing the F-index metric. These The average values of the metrics for the complete set of
experiments were executed with the SNP HEp-2 cell dataset. images are presented in Table II. The results show that the
The dataset (SNPHEp-2) [13] was obtained between January auto-tuning algorithms improved the quality of the results
and February 2012 at Sullivan Nicolaides Pathology compared with the results generated by the default input
laboratory, Australia. This dataset contains images of five cell parameters selected by the human expert, regard to F-Index
classes: centromere, coarse speckled, fine speckled, and Jaccard indicator.
homogeneous, and nucleolar; and consists of 1,884 cell images
extracted from 40 specimen images. DAPI image channel was TABLE II. PERFORMANCE INDICATORS.
used to obtain the cell image masks automatically. With the Method
aim of validating this proposal, 40 cell images from the Indicator
homogeneous class were randomly chosen. Default 1 Default 2 GA
Precision 0,86804 0,8975 0,87921
The execution time of the optimization algorithm with GA
was 3 hours in an Intel Core i7-6500U, CPU @2.5 GHz, 8 GB Sensitivity 0,85691 0,83771 0,85372
of RAM, 64 bits OS. The algorithms were run in MATLAB Specificity 0,97384 0,98078 0,97624
@R2018a.
NPV 0,97027 0,96672 0,96970
The values of the parameters obtained with the GA are
showed in Table I and compared with the selected by human Accuracy 0,95338 0,95594 0,95492
expert: F-Index 0,85863 0,86303 0,86309

TABLE I. PARAMETERS OBTAINED BY GA. Jaccard 0,75598 0,76276 0,76289

Method Dice 0,85863 0,86541 0,86550
Parameter
Default 1 Default 2 GA
R 4 5 5 An appropriate behavior between precision and sensitivity
P 35 30 33 generates high f-index values. This is the case of our proposal
with GA, where some over-segmentation causes high
DT cityblock cityblock cityblock sensitivity and low precision, compared with default values.
Due to these metrics are based on the comparison of the
A panel with two images (000002_p2.tif and segmented image with the ground truth, the results are very
00005_p1.tif) is presented in Fig. 3 to show the improvement similar (comparing values of default 2 with GA). Nevertheless,
in segmentation output generated by the tuned versus default the visual inspection demonstrates that the automatic GA
input parameters. This image shows that the segmented image tuning achieves an improved performance in the separation of
with GA reach superior results regard to identification and clustered cells, as the Fig.3 shows.
correct separation of clustered cells. However, some objects
were over-segmented. V. CONCLUSIONS
Segmentation with Segmentation with Cell image segmentation algorithms are sensitive to input
Ground Truth
default 2 parameters GA parameters parameters and the selection done by human experts not always
is the optimal option. The proposed auto-tuning algorithm
using GA improved the indicators for cell segmentation and it
produced accurate visual results. Although it may take
computational time, this search method makes it easier for the
programmer to select the multiple parameters of the algorithm.
As a future work, we intend to apply AutoML for the full
selection model problem, which not only include the tuning
parameters, but the selection of the method too.

REFERENCES

Fig. 3. Segmented images using tuned parameters versus default parameters.

The performance of the GA was measured with an
evaluation of binary class according to the final parameters.
The images from the dataset were used for the evaluation. The
following metrics were measured: specificity, accuracy,
sensitivity, precision, dice and Jaccard index; these, in function
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