Wavelet Transforms for

Biomedical Signal
Processing
Tutorial

CONTENTS
Chapter 1 Introduction.....................................................................................3
Chapter 2 Biomedical signal processing in time domain............6
2.1

ECG..................................................................................6
2.1.1

Compression
6 2.1.2
Denoising
8
2.1.3

QRS

detection
11
2.2

EEG.................................................................................13

2.3

Spike

detection
...14
Chapter 3 Biomedical imaging processing........................................15
3.1

Biomedical image compression................................................15

3.2

Biomedical

image

enhancement

and

edge

detection..16
3.3

Biomedical

image

registration.17
Chapter 4 Conclusion........................................................19
2

REFERENCE.........................................................................

Chapter 1 Introduction
For biomedical signals, most of the statistical characteristics of
these signals are non-stationary. In particular, the analysis of
biological signals should exhibit good resolution in both time domain
and frequency domain. Several time-frequency analysis methods
such as the short-time Fourier transform (STFT), Wigner-Ville
Distribution function (WDF), Hilbert-Huang transform (HHT), etc,
were proposed to represent the signals in both time and frequency
domains at the same time. The problem with the STFT is that using
a large window size may improve frequency resolution, but the
assumption of stationary within the window may be compromised;
whereas using a small window leads to poor frequency resolution.
WDF offers high clarity in both time and frequency domains, but
suffers from cross-term problem. For most biomedical signals, WDF
is not suitable either because they have multiple components or
because their phase terms are higher than second order. In addition,
time-frequency analysis methods
An alternative way to analyze the non-stationary biomedical
signals is the wavelet transform, which has variable time-frequency
resolution over the time-frequency plane. The analysis phase of the
wavelet transform decomposes a signal into elementary building
blocks or frequency bands that are localized in both space (time)
and frequency (scale). This differentiates a wavelet transform from a
Fourier transform. The window size (scale) used in wavelet
4

transform is chosen to be short at high frequencies and long at low

frequencies (to pick up all the abrupt changes), providing good time
resolution at high frequency and good frequency resolution at low
frequencies. Because of this localization property, wavelets are very
good in isolating singularities and irregular structures in signals. The
main advantage of wavelet transform over other time-frequency
analysis is little storage space. The dimension and size of the output
signal is about the same as the input signal, which gives wavelet
transform very powerful potential in image processing. Because of
the above reasons, the wavelet transform has become a popular
technique in feature detection, noise reduction, signal compression,
and image and video processing.
With the rapid development of computer and improvement of
fast algorithm of wavelet transform, the discrete wavelet transform
(DWT) has been widely applied in biomedical signal processing and
played an important role in clinical diagnosis and therapy of doctor
and teaching and researching, such as magnetic resonance imaging
(MRI),

computerized

tomography

(CT),

radiography,

electrocardiogram (ECG), and electroencephalography (EEG) etc.

This tutorial introduces several applications of the wavelet
transform in biomedical signal processing. Chapter 2 focuses on 1-D
wavelet transform applied in biomedical signal processing. Chapter
3 focuses on 2-D wavelet transform applied in biomedical image
processing. Chapter 4 is the conclusion.
5

Chapter 2 Biomedical

signal

processing

in

time domain
In this chapter, I will present three types of applications of the
DWT which are compression, filtering, and feature detection in
biomedical signals. When measuring biomedical signals, the sensing
device is desired to have information stored or transmitted with high
quality and low redundancy; this scheme involves two blocks
(filtering and compression) to filter out redundant signal and
compress the signal. In practice, feature detection of the biomedical
signals is required for clinical diagnosis such as QRS detection for
ECG signals and spike detection. The following part of this chapter
narrates the DWT applications in ECG in section 2.1, in EEG in
section 2.2, in heart sounds in section 2.3, in ultrasounds in section
2.4, and in spike detection in section 2.5 respectively.

2.1

ECG

2.1.1Compression
By converting the signal into its DWT coefficients and then
removing all except those containing the most pertinent signal
information, the resulting transform is much smaller in size, which
provides a good way of compressing a signal. Performing an
inverse transform on the remaining components recreates a signal
that very nearly matches the original. This concept has been widely
adopted for effective signal compression and applied in ECG data.
Data compression seeks to reduce the number of bits of information
7

required to store or transmit digitized signals without significant loss

of signal quality. In practice, ECG signals are collected both over
long periods of time and at high resolution. Thus, effective ECG
compression techniques are required to enlarge storage capacity
and improve methods of ECG data transmission over internet lines.
Crowe et al. in 1992 (Crowe, Gibson et al. 1992) used the ECG and
heart rate variability data to demonstrate that the DWT is well
suited for the compression and reconstruction of ECG data.
To compress data, we have to find the redundancy in the
information and eliminate it. The basic idea of compression model is
showed in Fig. 1. The thresholding block is used to remove the
redundancy in the signal. The encoding block is used to improve the
Compression Relation (CR).

Fig. 1: Compression model for transmission channel and reception

channel
Several encoding algorithms can be used such as Huffman
encoding and run-length encoding (RL). Huffman encoding defines
the codebook according to the repetition of every data. It uses more
bits in the no-frequent data and fewer bits for the data with higher
occurrence. The steps for creating the code are: (1) sorting the data
8

from high to low level of repetition, (2) Grouping in pairs of minor

repetition, (3) repeating the second step until all data have been
combined, and (4) drawing the Huffman tree with branches of two
nodes, where data sets with higher levels of repetition are located to
the left of the tree and the lowest level on the right, and assigning
1 to the data of the left and a 0 to the right. Huffman code is read
from top to bottom of the tree. The Run-Length encoding (RL) is
done by the selection of a value that is repeated many times in a
row to be represented through the number of times of the repetition
RL encoding. The length of the new data decreases when the
quantity of zeros increases. Ballesteros et al. in 2010 (Ballesteros,
Moreno et al. 2010) developed a compression model for ECG based
on DWT and RL encoding. In practice, the real time processing the
DWT in filtering and compression of biomedical signals is conceived
on FPGAs because of lower time of response compared to
implementations on software.

2.1.2Denoising
The morphology of ECG signal has been used for recognizing
much variability's of heart activity, so it is very important to get the
parameters of ECG signal clear without noises and artifacts in order
to support clinical decision making. To address this issue, DWT
allows effective noise reduction. In contrast to continuous wavelet
transform, DWT is a fast algorithm for machine computation. Like
the Fast Fourier Transform (FFT), DWT is linear operation that
9

operates on a data vector, transforming it into a numerically

different vector of the same length. In addition, DWT is invertible
and orthogonal. Instead of using sines and cosines as the basic
functions in FFT, the basic functions in the DWT are hierarchical set
of wavelet functions that satisfy certain mathematical criteria and
are all translations and scaling of each other. The DWT splits the
signal into two components, each of half the original length, with
one containing the low-frequency or smooth information and the
other the high-frequency or difference information. The process is
performed again on the smooth component, breaking it up into lowlow and high-low components and it is repeated several times. A
remarkable feature of many useful wavelet transforms is that they
obey a perfect reconstruction theorem. The block diagram of the
decomposition and reconstruction of DWT is displayed in Fig.2.

Fig. 2: Filter bank tree of a) Decomposition and b)

Reconstruction
M. Alfaouri and K. Daqrouq in 2008 (Alfaouri and Daqrouq 2008)
employed Daubechies wavelet to decompose the signal into five
levels of wavelet transform and determined a threshold through a
loop to find the value where minimum error is achieved between
10

the detailed coefficients of thresholded noisy signal and the original.

Their denoising method proceeds in the following steps, as
illustrated in Fig. 3: (1) decomposing of the noisy and original
signals

using

wavelet

transform,

(2)

choosing

and

applying

threshold value by finding minimum error of denoised and original

wavelet subsignal (coefficients), and (3) reconstructing denoised
signal using inverse DWT.

Fig. 3: The flow chart of denoising based on DWT and IDWT

The crucial issue of this approach is determination of an
appropriate threshold value. The threshold T was determined as

T =C

Vs(n)

(Vs( n))
n , where n is the number of samples in a subsignal,
( d j (n))

is the standard deviation of the noisy ECG signal,

( d j (n))

is the standard deviation of the j th detailed coefficients, and C is a

constant. The wavelet detailed coefficients of the noisy ECG signal
denoted as d(C(j,k)) is one if the wavelet transform coefficient C(j,k)
is larger than or equal to the threshold value T; otherwise d(C(j,k)) is
zero. The adaptive thresholding allows good quality of noise
reduction. The in vivo ECG signal was used to evaluate their
denoising method, illustrated in Fig. 4.
11

Fig. 4: ECG signal before and after denoising.

2.1.3QRS detection
Fig.5 shows the typical ECG waveform in normal subjects.

Fig. 5: Normal ECG waveform

The QRS complex is the dominant feature of the ECG signal and
accurate detection of QRS is of vital importance in number of clinical
instruments. The problem of automation of this process is quite
challenging because the morphologies of normal as well as
12

abnormal QRS complexes may differ widely and the presence of

noise from many sources make this problem more complicated. In
addition, other sections of ECG (P and T waves) can hinder the
detection

of

QRS

complexes

and

often

result

in

error

in

classification. In general, the commercially used equipment that

detect QRS complex require band-pass filtering and temporal
filtering (time windowing) of the signal. However, the choice of
appropriate bandwidth is a tradeoff between noise and high
frequency details and the duration of the sliding window is a
tradeoff

between

false

and

missed

detections.

Further,

the

bandwidth of the signal and duration of the QRS complex are

dynamic varying and fixed values of either are not suitable for QRS
complex detection. In contrast to conventional techniques, the
wavelet transform provides a new dimension to signal processing
and

event

detection

with

higher

degree

of

flexibility

and

adaptability.
To determine the choice of wavelet, properties of the QRS were
examined. There are three properties of the ECG that are useful for
detection of the QRS complex: the slope, shape, and location of QRS
complex. The shape of the signal is maintained if the phase shift is
linear. Thus one requirement of the wavelet is that it should have a
symmetrical function. Such wavelets are non-orthogonal. Time
localization is important because the ECG events are transient. A
number of wavelet-based techniques have been proposed to detect
13

these features using different mother wavelets. For one, spline

wavelets have properties satisfying the two requirements discussed
above. The order of spline wavelets is a tradeoff factor between
frequency resolution computational time-consumption. Commonly
the cubic spline wavelet is assumed to have a high enough order for
this application. Other mother wavelets such as Daubechies and
first-order derivative of the Gaussian function can also be use for
the characterization of ECG waveform (Sahambi et al., 1997a;b).
The

basic

scheme

of

QRS

detection

combines

DWT

and

thresholding. Li et al. in 1995 proposed a method based on DWT and

thresholded the modulus maxima larger than a threshold obtained
from the pre-processing of preselected initial beats, this threshold
can be updated during the analysis to obtain a better performance
(Li et al., 1995).

2.2

EEG

EEG signals are considered not to be deterministic and they have

no special characteristics like ECG signals. In addition, when the
Fourier transform is applied to successive segments of an EEG
signal, the obtained spectra are observed to be time varying. This
indicates that the EEG signal is also non-stationary. The spectral
analysis based on the Fourier transform classical method assumes
the signal to be stationary, and ignores any time-varying spectral
content of the signal within a window. Both frequency and timedomain characteristics of EEG are very important in clinical
14

diagnosis and studies.

An EEG signal consists of several frequency bands, which are
called and bands, and their corresponding bandwidths are 0
4, 48, 812, and above 12 Hz respectively. Akin in 2002 evaluated
the wavelet transform and FFT methods in the analysis of EEG
signals and concluded that WT is more suitable in EEG analysis then
FFT as the EEG signals are non-stationary (Akin 2002).

2.3

Spike detection

For a neuroelectric event, there are sometimes small-scale

transient events such as focal epileptogenic spikes occur in the
signal. The flexible resolution in localization property makes the
wavelet transform ideally suited to detect the time of occurrence
and the location of such focal spikes. Several studies have explored
the utility of wavelets for EEG spike identification (Kalayci, Ozdamar,
& Erdol, 1994; Schiff, Heller,Weinstein, & Milton, 1994). Nenadic and
Burdick in 2005 employed the continuous wavelet transforms with
basic detection theory to develop a new unsupervised method for
robustly detecting and localizing spikes in noisy neural recordings
(Nenadic and Burdick 2005). Their methodology proceeds as the
following steps: (1) performing multi-scale decomposition of the
signal using an appropriate wavelet basis, (2) separating the signal
and noise at each scale, (3) based on results from previous 2 steps,
performing Bayesian hypothesis testing at different scales to assess
the presence of spikes, (4) combining the decisions at different
15

scales, and (5) estimating the arrival times of individual spikes. The
fundamental issue of the spike detection is the design of a mother
wavelet that is suitable for the signal of interest, which is the shape
of the spike.

Chapter 3 Biomedical imaging processing

3.1

Biomedical image compression

As medical images have higher resolution, it takes more storage

space. To meet the demand for high-speed transmission of image in
efficient image storage and remote treatment, the efficient image
compression is essential. Recently some new and very promising
method merge in the field of image compression algorithm based on
wavelet transform, such as wavelet packet transform, multi-wavelet
transform, the combination of wavelet transform with fractal, and so
on. Thus, wavelet theory has great potential in medical image
compression. Wavelet transform-based image data compression in
general involves the following successive steps: (1) Selection of the
best wavelet shape according to objective measures such as the
peak signal-to-noise ratio (PSNR), the percent retained energy, the
percent-rate of distortion (PRO), the correlation coefficient between
the original and reconstructed images (), and the normalized
mean-squared error (NMSE), (2) thresholding of the transform
coefficients and forcing small coefficients to a zero value, (3)
efficient vector quantization of the retained transform coefficients,
(4) efficient encoding of transform coefficients.
16

A.S. Tolba in 2002 (Tolba 2002) proposed the good design

parameters for a data compression scheme applied to medical
images of different imaging modalities using wavelet packets (WP).
The proposed technique provides better image representation in the
sense of lower entropy or minimum distortion by selecting the
optimal filter bank and reconstruction basis for best compression
rate.

3.2

Biomedical image enhancement and edge

detection
Medical images generally have poor contrast of object with
surrounding and vague edge. For breast images, the contrast among
soft tissue of breast is little and the position and form of lump are
difficult to distinguish. Thus, in order to convenient doctor to
diagnosis, we need to enhance those image properties that are
useful for clinical and difficult enhance to distinguish under ordinary
conditions.
According to the properties of its multi-scale, direction and local
characteristic, the image edge features can be obtained by
determining the local maxima of wavelet coefficients.

3.3

Biomedical image registration

Medical image registration is a pre-processing step in object

identification and object classification. Traditional image registration
methods identify points on one image and match these points on
the other image, obtaining translation and rotation parameters. Raj
17

Sharman et al. (Sharman, Tyler et al. 2000) proposed a fast and

accurate and automatic method to register medical image using
Wavelet Modulus Maxima. The purpose of using Wavelet Modulus
Maxima is obtain fewer points in an image corresponding to sharp
varying edges and effectively denoised an image by thresholding
the Wavelet Modulus Maxima coefficients.
The registration method proceeds as follow:
1. Find Wavelet Modulus Maxima Image
2. Find convex hull
3. Find principal axis using principal component
4. Find rotation parameters and rotate the image
A wavelet transform provides information that essentially allows
us to isolate sharp variations in the gray level, which are essentially
edges or object boundaries. The Wavelet Modulus Maxima needs a
wavelet that is a derivative of its scaling function. Therefore the
wavelet used in their method is a quadratic spline wavelet and the
cubic spline function is its scaling function. Fewer vanishing
moments were chosen because of computational efficiency. A
Modulus Maxima occurs at a point (a0, x0), if (a0, x0) is a local
maximum of the modulus and the position of Modulus Maxima
points yields the location of edges or corners in the signal. In most
cases Modulus Maxima points corresponding to noise in the signal
usually have a smaller absolute value. Therefore, they can
accurately and effectively detect sharp varying edges and corners
18

from the Modulus Maxima image after thresholding.

For image registration, it is essential to use features that are
invariant between the images. For biomedical images such as CT
and MRI, the shape of the head stays the same over reasonable
periods of time. Therefore, they calculated the convex hull from the
Modulus Maxima image derived in previous step to get the shape of
the skull and make the registration insensitive to internal changes in
the brain. Once the convex hull was computed, the principal
component analysis was employed to center each of the images in
the image frame and determine the translation and rotation
parameters.
Validation
Fig. 10 showed the performance of registering MRI images. They
first generated a misaligned image illustrated in Fig. 10(b) from the
original image in Fig. 10(a) by rotation of 30and translation of a few
pixels. Fig. 10(c) is the difference between the Figs. 10(a) and (b).
Fig. 10(d) is obtained from Fig. 10(a) and Fig. 10(e) is obtained from
Fig. 10(b) after our image registration procedure on the images in
Figs. 10(a) and (b). Fig. 10(f) is obtained by taking the pixel by pixel
difference of the images in Figs. 10(d) and (e). The correlation
coefficient between the registered images in Figs. 10(d) and (e) is
0.98487, reflecting accurate registration for gray level MRI images.

19

Fig. 10 The performance of registering MRI images.

Chapter 4 Conclusion
Wavelet analysis in principle offers the researcher or clinician a
superior alternative to standard Fourier analysis techniques. Fourier
techniques are certainly adequate for some applications. However,
wavelet analysis offers increased power to resolve transient and
scale-specific events in neuroelectric data sets, to precisely filter
neuroelectric waveforms for noise reduction, to efficiently store and
transmit neuroelectric waveforms and images, and to observe and
quantify their small-scale structure in time and space. For wavelet
analysis to become an accepted analysis protocol for neuroscientists
and clinicians, it will be necessary to demonstrate that it reveals
important information about brain mechanisms or disease processes
that is not readily obtained with other decomposition techniques.
20

Although the growing experimental literature and theoretical

considerations suggest that this is the case, rigorous comparative
studies of wavelet techniques against alternative analysis protocols
using comprehensive neuroelectric data sets have yet to be
undertaken.

Reference
Akin, M. (2002). "Comparison of Wavelet Transform and FFT Methods for EEG."
Journal of Medical Systems 26(3).
Alfaouri, M. and K. Daqrouq (2008). "ECG Signal Denoising By Wavelet Transform
Thresholding " American Journal of Applied Sciences 5(3): 276-281
Ballesteros, D. M., D. M. Moreno, et al. (2010). Compression of Biomedical Signals
on FPGA by DWT and Run-Length. Proceedings IEEE ANDESCON. Bogota,
Colombia.
Crowe, J. A., N. M. Gibson, et al. (1992). "Wavelet transform as a potential tool
for ECG analysis and compression " J Biomed Eng 14(3): 268-272.
Nenadic, Z. and J. W. Burdick (2005). "Spike Detection Using the Continuous
Wavelet Transform." IEEE TRANSACTIONS ON BIOMEDICAL
ENGINEERING 52(1).
Kalayci, T., Ozdamar, O., and Erdol, N. 1994. The use of wavelet transform as a
preprocessor for the neural network detection of EEG spikes. Proceedings of
the IEEE Southeastcon 94 (pp. 13).
Sahambi, J., Tandon, S. & Bhatt, R. (1997a). Quantitative analysis of errors due to
power-line interference and base-line drift in detection of onsets and offsets in
ecg using wavelets, Medical and Biological Engineering and Computing
35(6): 747751.
Sahambi, J., Tandon, S. & Bhatt, R. (1997b). Using wavelet transforms for ecg
characterization an on-line digital signal processing system, IEEE Engineering
in Medicine and Biology Magazine 16(1): 7783.
Schiff, S. J., Heller, J.,Weinstein, S. L., and Milton, J. 1994.Wavelet transforms and
surrogate data for electroencephalographic spike and seizure detection. Optical
Engineering, 33, 21622169.
Sharman, R., J. M. Tyler, et al. (2000). "A fast and accurate method to register
medical images using wavelet modulus maxima." Pattern Recognition Letters
21: 447-462.
Tolba, A. S. (2002). "Wavelet Packet Compression of Medical Images." Digital Signal
Processing 12(4): 441-470.

21