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Classification of cells in microscopes images with both FPGA and Neuronal Networks

implemented with Matlab and Simulink.

Introduction:
Recognition and classifications cells has been an underlying requirement within different
sciences scope such as Medicine or Biology. Although there are a variety of algorithms
and tools for this purpose, the manual method is still being used by means of the use of
microscopes. The main limitation, is due to the high complex algorithms and the response
time of these ones. The speed efficient of these algorithms can generate a new field to
create new applications in real time which enables to enhance the response of recognition
responses and classification. Modern hardware devices such as FPGA (Field-
Programmable gate arrays) contain a huge amount of login resources which let the
efficient algorithms focused in pararell execution.
In this research, algorithms extractions from the feature images cells for the FPGA were
looked into, implemented and sorted by means of neuronal cells, so that it would be
developed by using Matlab and Simulik with their corresponding packages
The cost of the algorithm was studied, as well as the difficulty of the implementation with
the tool. To do this, FPGA Altera DE1-SOC and Matlab R2016b was used to their
implementation.

State of Art:
There are a few approaches as many as there are in the software and hardware in order
to the extraction of features in images, however, before implementing something its
necessary to know which one is most suitable to the formulated problem.
Characteristics of an image can be defined as functions of more than one measures, one
of this describes a property of the objet quantify.
General characteristics are independent as much from the colour, texture, or shape. This
one can be under classified in different features from the level of a pixel. (That contains
unique information from the pixel and the position), features in a local level. (Functions
applied to a segment of image), global level characteristics (Applied functions to the
image as a whole)

Traits from the specific Domain: they are more complex and conceptual features such as
a human face, or fingerprints.
Due to the FPGA limitation developing to the hardware, its decided the implementation
of the algorithmic for the extraction of characteristics both at the level of pixel and local
level. Among the mechanisms at the local level more known to the extraction of features,
it can be mentioned these followings: Invariant moments, gradients traits, densitys
characteristic, among others.
The study made from A.Suyygh and G.Abandah [2] about the recognition of Arabic
writing, the effectiveness of the algorithmic commented before is showed up, shedding
the DCT (Discrete Cosine Transform) as the better effectiveness as it is in time execution
as it is within error prediction.

With the data shredded for these two comparatives, the decision of implementing the DCT
for extracting the image, is taken. This algorithmic is currently used to compress JPG
files, enable to rebuild a 64 pixel image with only 9 pixel with a fair losing of quality, so
that 9 traits per section of an image 8x8 will be taken. Haitim [3] facilitates a efficient
implementation in hardware from the DCT algorithmic in 2 dimensions applied to images.
With regard to the used of neuronal networks, it will be used the default offered by Matlab.
This tool lets generate neuronal networks introducing index data pointing which the
different types will be

Methodology:
In this section, a general idea about the methodology carried out, within the developing
is shown, the kind of indexed used images, implementation in Matlab and Simulik. The
following image shows the steps to the progress.

Images Algorithmic, Implementation Results


Start analysis. analysis and and readjusted. analysis. END
checkings.

The first steps Project was about the analysis of which the possible extracted features
from the example images were, these images consist on cells samples. To improve the
management images with Matlab was decided to normalized the size of this images,
reducing to a images of 640x480 pixels. In these images it is observed that cells are
16x16 pixels so that this size is taken.
A long the research stage a few studies were analysed to identify which were the most
suitable algorithmic to the extraction the characteristics into images. Once the best
algorithmic was obtained, checking the implementation variability was necessary.
This studied consisted on analysis the different operations developed in the algorithmic,
checking its availability within Matlab R2016 and the HDL competitor (Example: Sin
function, tangent, roots
Within the implementation stage all the resources available from Matlab and Simulink for
the developing were used, having the different Tools Box to the images managements,
as well as the corresponding to the FPGAs developing. Its mentioned that, in spite of the
fact that Matlab enables to make the algorithmic design, the compilation and the unfolded
on the plate, is made throughout the owner Altera, Quantus II software.

In the last stage, the analysis of the obtained results from executions is made as well as
the cost implementation by means of the use of Matlab.

Extraction characteristic Technic:


The main reason of the DCT algorithmic choosing to the traits extraction in images is the
simplicity within its implementation in hardware and its high accuracy. Additionally, that
lets a high parallelism grade what it is traduced in better executed time. Their
implementation in Matlab R2016 b was based on the Arai DCT algorithmic made by
Prtiksha R. Kumbhare [4] for an NXM image sized.

1 1
2 2 (2 + 1) (2 + 1)
(, ) = () ( ) () ( ) (, )
2 2
=0 =0

1 , =0 1 , =0
() = { 2 () = { 2
1 , 0 1 , 0
Where f(i,j) is the pixel i,j de from the image, and F(u,v) is the DCT u,v coefficient

Figure1. General Formula DCT in to 2D.

In this algorithm a screen shot of 8x8 pixels which moves along the whole image is taken.
It is applied to this screen the indicated function shown in Fig 1. From this 8x8 Pixels 64
DCT Coefficients are obtained which depict features from whom the 3x3 pixel matrix is
only considered from the top of the left window since this one has enough information to
make up the window such the Ashraf Suyyagh indicated [2].

DCT algorithm enables to make a Row-Column disassemble, in other words, to apply


DCT formula to pixels rows and subsequently to the columns, which carries to increase
the paralelism grade.
Procesador Cyclone V SoC 5CSEMA5F31C6

Puertas lgicas Programables 85000

Memoria embebida 4,450 Kbits

SDRAM Para FPGA 64MB (32Mx16)

Para su implementacin y ejecucin se utiliz el modo FPGA in-the-loop. Este modo establece una conexin de ida y vuelta de los
datos desde el Host (El PC conectado a la placa) y la FPGA permitiendo ejecutar en tiempo real el algoritmo programado.

El siguiente diagrama muestra el flujo general de datos del proyecto (Fig2):

Fig 2. Diagrama de flujo de ejecucin

The whole design was implemented directly by using Simulink, by means of blocks of
HDL Coder toolbox and HDL visin toolbox. The tool enables to generate designs and
execute them in the faster way, yet, a negative aspect it is that does not give the user
the mistakes that are made so far to the compilation by the external tool such as
Quantus II.
Once the design was generated, the execution of Fixed Point Toolbox was neccesary to
run, to make the type approval used within the designed, since FPGA can not operate
with different types of data, such as Double o flopping point. Due to this a transformation
to a fixed point was neccesary. This transformation involves a loss of precision, so that it
will be analysed to what extend of precision it is necessary to indicate to the type of the
point of the flotting point without lossing efficience within the pattern recognition. The
analysis results will be shown in the head line of analysis results.

In order to create the neuronal network for its ordering; the system was previously feeded
to obtain the images characteristics, and they are therefore labeled in data which are
features which subsequently are the traits which corresponds to a certain types of cells.
For each 640x480 image of a total of 4661 samples of 36 features to be classified since
a image of 16x16 pixel is taken as a pattern overlapping grups of patterns.
The neural toolbox network is run after obtaining the characteristics samples, which
enables to create the automatic of the neuronal net, however, this tool does not let modify
aditional designed parameters, only the amount of the hidden nodes within the net. The
default parameters were used a long the creation by using the 70% for the samples for
trying, 15% for checking and 15 % for sampling. The generated net has 36 entry
parameters corresponding to the 36 sample per feature and 3 exit parameter within the
exit layer, which indicates 2 types of cells, one of this represents an empty space of the
image.
For subsequent trials, new neuronal nets are generated again modyfing the number of
hidden nodes of the net, to check whats the optimal number of nodes. The results of
this hidden nodes changes would be observed in the analysis result section.
Analysis results.

References. Referencias

[1] R. S. Choras, Image feature extraction techniques and their applications for CBIR and biometrics
systems, Int. J. Biol. Biomed. Eng., vol. 1, no. 1, pp. 616, 2007.
[2] A. Suyyagh and G. Abandah, FPGA Parallel Recognition Engine for Handwritten Arabic Words, J.
Signal Process. Syst., vol. 78, no. 2, pp. 163170, 2013.
[3] A. Hatim, S. Belkouch, T. Sadiki, and M. MRabet Hassani, Efficient hardware architecture for
direct 2D DCT computation and its FPGA implementation, 2013 25th Int. Conf. Microelectron.
ICM 2013, no. December 2013, 2013.
[4] P. R. Kumbhare and U. M. Gokhale, Design and Implementation of 2D-DCT by Using Arai
Algorithm for Image Compression, vol. 16, no. 5, pp. 18, 2015.
[5] T. S. Pawar, R. G. Sawant, P. S. Bothe, and Sh. A. Chopade, FPGA Implementation of Forward 2D-
DCT and Inverse 2D-DCT Based On Row-Column Decomposition Method, Int. J. Innov. Res.
Comput. Commun. Eng., vol. 3, no. 10, pp. 1013110138, 2015.
[6] Altera, DE1-SoC Board. [Online]. Available: http://www.terasic.com.tw/cgi-
bin/page/archive.pl?Language=English&No=836.

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