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The purpose of this study was to design a filter which could isolate the high frequency components in our cell images. These high frequency components are essentially the inclusions present in cells which indicate that the cell is diseased. Thus, if we could design a suitable filter for them, then by observing their corresponding histogram responses, we could derive a means of classification of cells based on the frequency spectrum of the cell image. The approach selected for the filter design was chosen to be Discrete Wavelet Transform using Daubechies and Haar Filters due to their ability to provide time-frequency information of the signal and secondly due to its simplistic yet effective implementation and analysis.

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Tarundeep Singh Dhot

Dept of ECE

Concordia University

Montreal, QC H3G 1M8

t_dhot@encs.concordia.ca

Abstract and translations obeying some defined rules. In other words, this

The purpose of this study was to design a filter which could transform decomposes the signal into mutually orthogonal set of

isolate the high frequency components in our cell images. These wavelets, which is the main difference from the continuous

high frequency components are essentially the inclusions wavelet transform (CWT), or its implementation for the discrete

present in cells which indicate that the cell is diseased. Thus, if

time series sometimes called discrete-time continuous wavelet

we could design a suitable filter for them, then by observing

their corresponding histogram responses, we could derive a transform (DT-CWT). For most signal and image processing

means of classification of cells based on the frequency spectrum applications, DWT-based analysis is best described in terms of

of the cell image. The approach selected for the filter design was filter banks i.e. iteration of filters. The use of group of filters to

chosen to be Discrete Wavelet Transform using Daubechies and divide up a signal into various spectral components is termed

Haar Filters due to their ability to provide time-frequency sub-band coding. Considering the most basic implementation of

information of the signal and secondly due to its simplistic yet DWT using only two filters in the filter bank, the waveform

effective implementation and analysis.

under analysis is divided into two components, ylp(n) and

Categories and Subject Descriptors yhp(n), by digital filters H0(w) and H1(w). The spectral

I.4 [Image Processing and Computer Vision]: Segmentation – characteristics of the two filters must be carefully chosen with

pixel classification H0(w) having a lowpass spectral characteristic and H1(w) a

highpass spectral characteristic. The highpass filter is analogous

General Terms

to the application of the wavelet to the original signal, while the

Algorithms, Experimentation.

lowpass filter is analogous the application of the scaling or

Keywords smoothing function. The scaling function facilitates computation

Image Segmentation, Spectral Analysis of DWT. To implement the DWT efficiently, the finest

resolution is compared first. The computation then proceeds to

coarser resolutions, but rather than start over on the original

1. INTRODUCTION

waveform, the computation uses a smoothed version of the fine

resolution waveform which is obtained using the scaling or

1.1 Wavelet Transform smoothing function. If the filters are invertible filters, then it is

A transform can be thought of as a remapping of a signal that possible to construct complementary filters that will recover the

provides more information than the original without changing

original waveform from either of the sub-band signals, ylp(n) or

the information content present in the signal. The Fourier

Transform fits this definition quite well because the frequency yhp(n).

information it provides leads to new insights about the original

signal. However, the inability of the Fourier Transform to x (n) H0(w) ylp(n)

describe both time and frequency characteristics of the

waveform limits its utility in time-frequency problems. The

wavelet transform provides time-frequency information of the

H1(w) yhp(n)

signal and uses multi-resolution technique by which different

frequencies are analyzed with different resolutions.

Figure 1: Simple filter bank consisting of only two filters

applied to the same waveform. Filters have lowpass and

1.2 Discrete Wavelet Transform highpass spectral characteristics. Filter outputs consist of a

lowpass sub-band, ylp(n) and highpass sub-band, yhp(n)

The discrete wavelet transform (DWT) is an implementation of

the wavelet transform using a discrete set of the wavelet scales

1.3 The Daubechies Wavelet Transform in the fact that it connects the continuous-time multiresolution to

discrete-time filters.

The Daubechies wavelets are a family of orthogonal wavelets

defining a discrete wavelet transform and characterized by a

Given a signal x of length N, the DWT consists of log2N stages

maximal number of vanishing moments for some given support.

at most. Starting from x, the first step produces two sets of

With each wavelet type of this class, there is a scaling function coefficients: approximation coefficients A1, and detail

(also called father wavelet) which generates an orthogonal coefficients D1. These vectors are obtained by convolving s

multi-resolution analysis. Daubechies orthogonal wavelets D2- with the low-pass filter H0 for approximation, and with the

D20 (even index numbers only) are commonly used. The index high-pass filter H1 for detail coefficients. It can represented

number refers to the number N of coefficients. Each wavelet has more precisely as a wavelet decomposition tree as shown in Fig

2.1.

a number of zero moments or vanishing moments equal to half

the number of coefficients. For example D2 (the Haar wavelet) At each level, the high pass filter produces detail information,

has one vanishing moments, D4 has two moments, etc. A Dj, while the low pass filter associated with scaling function

vanishing moment refers to the wavelets ability to represent produces coarse approximations, Aj. The length of each filter is

polynomial behaviour or information in a signal. For example, equal to 2N. If n = length (x), the signals F and G are of length n

D2, with one moment, easily encodes polynomials of one + 2N – 1.

coefficient, i.e. constant signal components. D4 encodes

The next step splits the approximation coefficients A1 in two

polynomials of two coefficients, i.e. constant and linear signal

parts using the same scheme, replacing x by A1 and producing

components, D6 encodes 3-polynomials, i.e. constant, linear and A2 and D2, and so on.

quadratic signal components.

Initialization A0 = x

1.4 The Haar Wavelet Transform So the wavelet decomposition of the signal s analyzed at level j

Each step in the Haar transform calculates a set of wavelet has the following structure: [Aj, Dj, ..., D1]. This structure

coefficients and a set of averages. If a data set s0, s1, ... sN-1 contains for J = 3 the terminal nodes of the following tree.

contains N elements, there will be N/2 averages and N/2

coefficient values. The averages are stored in the lower half of 2.1 Method: Filter Implementation on Cell

the N element array and the coefficients are stored in the upper

half. The averages become the input for the next step in the Images

wavelet calculation, where for iteration i+1, Ni+1 = Ni/2. The

recursive iterations continue until a single average and a single Two filters were used for spectral analysis of the cell images,

coefficient are calculated. This replaces the original data set of namely Daubechies filter (dbN) and Haar Filter. But before we

N elements with an average, followed by a set of coefficients can implement the filter on the images, the images need to be

whose size is an increasing power of two (e.g., 20, 21, 22 ... pre-processed. Pre-processing of the image is done in the

N/2). following manner:

The Haar equations to calculate an average (ai) and a wavelet (i) Grayscale the image

coefficient (ci) from an odd and even element in the data set are (ii) Contrast improvement of the grayscaled image

shown below: (iii) Convert image to double precision

ai = ( si + si+1 )/2

ci = ( si - si+1 )/2 Since we are interested in the frequency response only the cell,

we need to convert the background of the cell from white to

In wavelet terminology the Haar average is calculated by the black. In order to do this, we set a threshold, above which, all

scaling function which is represented by gi. The coefficient is pixels should be converted to black. On the grayscale (0-255),

calculated by the wavelet function represented by hi. the optimum value for this threshold was found to be 241. So we

Algebraically speaking, in Haar transform, the first average is need to run a loop on the image setting the value of all pixel

calculated by the inner product of the signal [s0, s1, ... sN-1] and present above 241 to zero so that we neutralize the background

the vector, of the same size, [0.5, 0.5, 0, 0, ..., 0]. This is the of the cell, as otherwise the histogram results would be way

scaling vector.The first coefficient is calculated by the inner different due to the effect of presence of white background.

product of the signal and the vector [0.5, -0.5, 0, 0, ..., 0]. This is Thus, we can see that all the vacant area outside the border of

the wavelet vector. The next average and coefficient are the cell is set to value 0 on the grayscale.

calculated by shifting the scaling and wavelet vectors by two

and calculating the inner products. Once this is done, we can apply the filters on the image. Three

wavelets of the Daubechies filter (db1, db2, db3) are applied as

well as the Haar filter in similar fashion. Once this is done, the

1.5 DWT: Algorithm corresponding histograms are plotted.

As mentioned above, the DWT is computed by successive

lowpass and highpass filtering of the discrete time-domain

signal. This is called as Mallet algorithm and its significance lies

low-pass filter downsample

H0 ↓2 A1: Approximation

F coefficients

x

H1 ↓2 D1 : Detail coefficient

G

high-pass filter downsample

H0 ↓2 Aj+1

Aj Level j+1

Level j

H1 ↓2 Dj+1

Figure 2 (b): One-Dimensional DWT

A1 D1

A2 D2

A3 D3

2.2 Pseudo-Code for Neutralization of mean, variance and standard deviation can help decide a suitable

threshold above which we could safely classify cells as sick.

Background

Apart from that, conventional filters can also be applied on the

[m,n]= size(ImgGS); image just as an exercise to compare results. Even though it

for i = 1:m would be a slightly more complicated exercise requiring

for j = 1:n calculation of cut-off frequencies (range) which would be

temp = ImgGS(i,j); different for all images and best suited order, by it should offer a

if temp < 0.9 healthy comparison to the method used above.

ImgGS1(i,j) = temp;

else 5 References

ImgGS1(i,j) = 0; [1] P. Sarkar, M. Salazar-Palma and M. Wicks, “Wavelet

end Applications in Engineering Electromagnetics, 2002

end [2] A. Jensen, A. La Cour-Harbo, “Ripples in Mathematics: The

end Discrete Wavelet Transform”, Springer, pp. ix – 246

[3] P. Wojtaszczyk, “A Mathematical Introduction to

Wavelets”, Cambridge Univ Press, 1997

[4] I. Daubechies, “The wavelet transform, time-frequency

3 Results: Filtered Images and Histograms localization and signal analysis”, IEEE Transactions on

The figures shown above are of a sick 2a Hela cell (40X). Fig 3a Information Theory Society, Sept 1990

(i) shows the preprocessed cell without the background removed

labeled as Original. Fig 3a (ii) shows the filtered image using a

Daubechies filter of order 1 (db1). Its corresponding histogram

is shown in Fig 3b (ii). After applying this filter on a number of

images, we see that nothing conclusive can be inferred from

their corresponding histograms such that we can use some sort

of complexity measure and classify them. Thus we decompose

the filtered image once again using another db1 filter, thus,

effectively it becomes a db2 filter. After observing a number of

images of various cells, the distribution on the histogram is

spread out between 0 and 1 with considerable amount of values

above 0.5. If a corresponding histogram for a healthy cell is

compared to this, it shows that it has considerable amount of

values around and below 0.5. Thus, we can identify this as a

distinguishing feature at db2 filtering. Again this filtered image

was filtered using a db1 filter with resulting effect of a db3

filter. But we observe blurring of the original image as shown in

Fig 3a (iv). The corresponding histogram shows a much spread

out spectrum of values between 0.5 and 1. Similar results are

seen with the spectral analysis using a Haar filter. Thus, we

observe distinguishing features using filters of order 2 shown by

their corresponding histograms.

4 DISCUSSION

The goal of the study was to identify and design which filters

would be useful to cell classification. Spectral analysis using

Discrete Wavelet Transform was done it can be used to solve

time-frequency problems which is not possible using Fourier

Transforms. Using DWT filters for spectral analysis is more

convenient as we don’t need to specifically point out cut-off

frequencies instead they use wavelet analysis for filtering. From

the filters used in our problem, it is seen that both second order

Haar filter and Daubechies filter show differences in the

corresponding histograms of healthy and sick cells. Thus using

statistical methods, we can develop distinct features which could

be used for classifying cells. Simple statistical measures like

(i) (ii)

(iii) (iv)

Figure 3 (a): Filtered Images

(i) (ii)

(iii) (iv)

Figure 3 (b): Histograms of Filtered Images

Figure 3: Spectral Analysis of a Sick Cell Showing Inclusions Using dbN Filter

3 (a): (i) Original pre-possessed image of cell (ii) Filtered Image: db1 Filter

(iii) db2 Filter applied on Image (iv) db3 Filter applied on Image

Figure 3 (b): (i) Histogram of original pre-possessed image (ii) Histogram of db1 Filtered Image

(iii) Histogram of db2 Filtered Image (iv) Histogram of db3 Filtered Image

(i)

(ii)

(iii) (iv)

Figure 4 (a): Filtered Images

(i) (ii)

(iii) (iv)

Figure 4 (b): Histograms of Filtered Images

4 (a): (i) Original pre-possessed image of cell (ii) Filtered Image: db1 Filter

(iii) db2 Filter applied on Image (iv) db3 Filter applied on Image

4 (b): (i) Histogram of original pre-possessed image (ii) Histogram of db1 Filtered Image

(iii) Histogram of db2 Filtered Image (iv) Histogram of db3 Filtered Image

(i)

(ii)

(iii) (iv)

Figure 5 (a): Filtered Images

(i) (ii)

(iii) (iv)

Figure 5 (b): Histograms of Filtered Images

Figure 5: Spectral Analysis of a Sick Cell Showing Inclusions Using Haar Filter

5 (a): (i) Original pre-possessed image of cell (ii) Filtered Image: Haar1 Filter

(iii) Haar2 Filter applied on Image (iv) Haar 3 Filter applied on Image

5 (b): (i) Histogram of original pre-possessed image (ii) Histogram of Haar 1 Filter Image

(iii) Histogram of Haar 2 Filter Image (iv) Histogram of Haar 3 Filter Image

(i) (ii)

(i) (ii)

Figure 6: Spectral Analysis of a Sick Cell Showing Inclusions Using dbN Filter

6 (a): (i) Original pre-possessed image of cell (ii) Filtered Image: db1 Filter

(iii) db2 Filter applied on Image (iv) db3 Filter applied on Image

6 (b): (i) Histogram of original pre-possessed image (ii) Histogram of db1 Filtered Image

(iii) Histogram of db2 Filtered Image (iv) Histogram of db3 Filtered Image

(i) (ii)

(i) (ii)

Figure 7: Spectral Analysis of a Healthy Cell Showing Inclusions Using Haar Filter

7 (a): (i) Original pre-possessed image of cell (ii) Filtered Image: Haar1 Filter

(iii) Haar2 Filter applied on Image (iv) Haar 3 Filter applied on Image

7 (b): (i) Histogram of original pre-possessed image (ii) Histogram of Haar 1 Filter Image

(iii) Histogram of Haar 2 Filter Image (iv) Histogram of Haar 3 Filter Image

(i) (ii)

(i) (ii)

Figure 8: Spectral Analysis of a Healthy Cell Showing Inclusions Using dbN Filter

8 (a): (i) Original pre-possessed image of cell (ii) Filtered Image: db1 Filter

(iii) db2 Filter applied on Image (iv) db3 Filter applied on Image

8 (b): (i) Histogram of original pre-possessed image (ii) Histogram of db1 Filtered Image

(iii) Histogram of db2 Filtered Image (iv) Histogram of db3 Filtered Image

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