ISSC 2010, UCC, Cork, June 2324

Ecient EEG Compression using JPEG2000 with

Coecient Thresholding
Garry Higgins, Brian McGinley, Edward Jones and Martin Glavin

Electrical & Electronic Engineering,

National Centre for Biomedical Engineering Science (NCBES)
National University of Ireland, Galway
E-mail: g.higgins1@nuigalway.ie

Abstract This paper outlines a scheme for compressing EEG signals based on the
JPEG2000 image compression algorithm. Such a scheme could be used to compress
signals in an ambulatory system, where low-power operation is important to conserve
battery life; therefore, a high compression ratio is desirable to reduce the amount of data
that needs to be transmitted. The JPEG2000 specication makes use of the wavelet
transform, which can be eciently implemented in embedded systems. In this research,
the JPEG2000 standard was broken down to its core components and adapted for use
on EEG signals with additional compression steps added. Variations on the compres-
sion architecture were tested to maximize compression ratio (CR) while minimizing re-
constructed percentage root-mean- squared dierence (PRD) and power requirements.
Tests indicate that the algorithm performs well in eciently compressing EEG data,
without signicant loss in signal delity.

Keywords EEG compression; Wavelets; JPEG2000; Low power

I Introduction is a method of recording a patients EEG signals

Recent advances in health care have seen an in-
creased focus on ambulatory monitoring of pa-
tients. Portable devices allow patients to be mon-
itored at home on an out-patient basis, thus ad-
vancing the goal of providing ubiquitous and per-
vasive healthcare. This remote observation conse-
quently relieves pressure on over-burdened hospi-
tal systems, and allows the patient remain in an
environment in which they are comfortable. It
also allows more comprehensive monitoring with
patients involved in a variety of activities in their
day-to-day lives. However, for a device to be truly
portable, a reasonable battery is essential. As a
result, a principle factor in designing a portable
health care device is ensuring that power consump-
tion is minimised.
Multichannel electroencephalogram (EEG) is
commonly used for measuring the electrical activ-
ity of the brain. The application of EEG to di-
agnose a variety of neurological conditions such as
Epilepsy and Alzheimers disease [1] has long been
established. Diagnosis of these conditions how-
ever, often requires long-term monitoring of the
patients EEG activity. Ambulatory EEG (AEEG)
using a portable device that can be worn as the
patient goes about their everyday lives. Such a de-
vice allows the patient to remain at home in com-
fort, without the need for frequent visits to a clinic.
Furthermore, wireless transmission of data from an
ambulatory unit to a central server e.g. located in
a clinic, allows for the possibility of near-constant
remote monitoring of the patient by a clinical ex-
pert. Due to the nature of EEG signals however,
even a short period of capture can result in large
amounts of data being recorded. Therefore, di-
culties in data storage and transmission arise, par-
ticularly in a wireless monitoring scenario. This is
because wireless communications are a signicant
contributor to power consumption in a portable
system [2],[3]. Eective compression of data is
therefore important to minimize the amount of in-
formation that needs to be transmitted wirelessly.
A coexisting goal is that the compression itself
needs to be carried out in an ecient manner so
as not to unduly add to the power consumption of
the device.
Compression of EEG signals is the focus of this
paper. In comparison to other measures of biomed-
ical electrical activity, such as
 Original
Image Discrete Wavelet
Pre-Processing
Transform (DWT)
Compressed
Data Adaptive Binary
Quantization
Arithmetic Coder
F igure 1: Core components of JP E G2000 Part 1
electrocardiogram (ECG), there has been relatively
little work done in the field of EEG compression. Of
the work that has been done, most researchers have
focused on lossless compression, with only a few
having tested some form of lossy compression
[4],[5]. Lossless compression maintains complete
signal integrity in the reconstructed signal, but this
limits the compression ratio (CR) that can be
achieved. Lossy compression can achieve much
higher CRs but results in a loss of some signal
fidelity.
This paper proposes a scheme for efficient
lossy EEG compression, based on the JPEG2000
image compression standard, targeted at
implementation on an ambulatory device. JPEG2000
was chosen as it offers efficient compression
performance in both lossless and lossy
configurations. This algorithmic flexibility allows
exploration of the trade-offs between compression
ratio, signal fidelity, and computational complexity.
Work has already been performed on low-powered
implementations of this algorithm for portable
hardware [6],[7], thus indicating that an efficient
implementation of the %/+25-7,0A6
core elements is
feasible. The compression of EEG will become
increasingly important as AEEG devices become
more prevalent. The work here sets to propose one
potential method of efficiently compressing EEG
while maintaining low power consumption.
Section II of the paper describes some other
proposed methods of EEG compression for
ambulatory devices. In particular those that use lossy
compression. Section III describes the JPEG2000
algorithm, in particular the wavelet transform and
arithmetic coder used in the algorithm. Section IV
describes the implementation of the algorithm and
Section V outlines the methods of performance
evaluation and the dataset used. It also details the
modifications made to the JPEG2000 algorithm and
the results obtained, while Section VI presents
conclusions.
II. EEG COMPRESSION
Recent years have seen an increase in research into
EEG compression for use in AEEG devices. When
wireless communication is employed, the EEG signal
F igure 2: 3-Level D W T of signal x(n)
usually undergoes compression prior to transmission.
Crdenas-Barrera et al. propose a method of EEG
compression based on the Wavelet Packet Transform
[4]. The signals are compressed using lossy
compression, and a maximum PRD of 7% is
suggested as the maximum allowable [4]. The
algorithm is designed to be low-power, and thus, the
authors suggest it could potentially be used on
portable devices. However, the impact of choosing a
7%, or higher PRD on the diagnostically relevant
information is not tested in [4]. Casson et al. propose
a compression method based on discontinuous
recording of EEG, with only diagnostically
significant information being recorded [8]. This
reduces the amount of data to be transmitted as only
the epileptiform data is recorded. This compression
scheme relies on the ambulatory system being able to
correctly identify epileptiform data. This method
suffers from the fact that not all of the data is stored,
and thus is not available for review by clinicians.
III. DESCRIPTION OF THE JPEG2000 ALGORITHM
JPEG2000 is a compression algorithm
designed for both lossless and lossy compression of
image files. JPEG2000 Part 1 was ratified by the
Joint Photographic Experts Group in 2000 [9]. It was
designed to replace the older JPEG file format with
more advanced features such as superior low bit-rate
performance, lossless and lossy compression and
good error resilience [10]. Part 1 contains the
specifications for the core image coding system.
These core components include, Discrete Wavelet
Transform (DWT), quantisation and an Arithmetic
Coder (AC) (Figure 1). Aside from the image
specific modifications in the Pre-Processing and
Quantisation stages, the main areas of divergence
with previous JPEG standards are in the use of the
DWT and AC.
The DWT replaces the Discrete Cosine
Transform (DCT) of the original JPEG format.
While DCT performs well at low compression ratios,
it deteriorates quickly as compression ratios increase
above 30:1. DWT meanwhile, has a much more
gradual degradation [11]. The JPEG2000 Part 1
standard includes two types of DWT. The first is the
Le Gall 5/3 integer-to-integer DWT. This DWT is
used for lossless compression of images due to its
 T able 1: Probabilities and ranges for symbols an
for example in text
Symbol Probability Range
a1 0.5 [0,0.5)
a2 0.25 [0.5,0.75)
a3 0.125 [0.75,0.875)
a4 0.125 [0.875,1)
fixed-point implementation. This allows faster
transforms with a true lossless reconstruction, at the
expense of some loss in CR. A floating-point version
of the CDF 9/7 DWT is used for lossy image
compression to achieve a higher CR. This DWT has
already achieved wide-spread use in a variety of
compression algorithms. The Adaptive Binary
Arithmetic Coder replaces the Huffman coder as the
entropy coder for the JPEG2000 compression
standard. The AC can perform near optimum entropy
coding on a given data set [12] and avoids some
of the limitations of Huffman encoding [13]. The
adaptive arithmetic coder allows the message to be
coded with no prior knowledge of the 0)66%+)A6

Probability Distribution Function (PDF) by either the
encoder or the decoder.
a) Wavelets
The Wavelet Transform (WT) decomposes a
signal into a set of basis functions known as wavelets
[14-16]. The initial wavelet, also known as the
mother wavelet, is used to construct the other
wavelets by means of dilation and shifting, according
to the following equation:

 
  (1) boundaries. It can also easily be expanded to use

  integer-to-integer WT for lossless compression.
where  is the scaling parameter, b is the shifting
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can be stretched or compressed to obtain low and
high-frequency basis functions to analyse a signal at
different resolutions.
The DWT is used to perform a fast
computation of the WT of a discrete signal. It is
normally computed quite efficiently with a set of low
and high pass filters being recursively applied. After
the signals are filtered, they are down-sampled by a
factor of 2. The transformation is applied recursively
on the low-pass series until the desired number of
iterations is reached (Figure 2). The high pass filter,
G0, produces detail coefficients, denoted by d[n],
while the low pass filter, H0, produces approximation
coefficients, a [n].
For the inverse DWT, the transform operates
in the opposite way. Each subband is interpolated by
F igure 3: E xample of arithmetic coder for
encoding a four symbol long message
a factor of 2 by inserting zeros between samples and
filtering each resulting sequence by the
corresponding low or high-pass synthesis filter bank.
Finally the filtered sequences are added together to
form an approximation of the original sequence. The
complexity of the DWT depends on a number of
factors such as the filter size, the use of floating point
or fixed-point arithmetic, and the method used to
compute the wavelet coefficients. The use of fixed-
point instead of floating-point filters reduces
complexity of the operation and allows for truly
lossless integer to integer based compression,
because there are no approximations in the forward
or inverse transform operation. However, integer
implementations also reduce the CR achievable by
the transform.
The lifting scheme is an alternative method of
computing wavelet coefficients. Proposed by
Sweldens et al. [17], it has a number of advantages
over traditional methods. Its implementation requires
fewer computations and memory and is better suited
for ambulatory applications where low
computational complexity is important. The inverse
transform has the same complexity as the forward
transform and no signal extension is required at the
b) Arithmetic Coder
Arithmetic coding is an entropy encoding
algorithm used for lossless data compression. It
encodes the required data stream into a single
fractional value between 0 and 1. Similar in
operation to Huffman coding, the coder converts the
symbols to be encoded into a form where the most
frequently used symbols are encoded using the least
number of bits and the most infrequently used
symbols using the most. The basic ideas of
arithmetic coding can be traced back to the 1960's
with more efficient implementations of it appearing
later [18].
Arithmetic coding reduces the symbols to be
encoded to a single, unique binary fraction based on
the PDF of the symbols. In order to understand its
operation, consider the example of a source A that
generates symbols ai from an alphabet of size 4,
A = { a 1, a 2, a 3, a 4}
Let these symbols have the following probabilities of
occurrence:
P(a1) = 0.5 , P(a2) = 0.25 , P(a3) = 0.125 ,
P(a4) = 0.125
which all lie on the interval [0,1)
The encoder begins with the interval [0,1)
which is divided up into ranges for each symbol
based on the probability of them appearing, as seen
in Table 1. When the first symbol is passed to the
encoder, the encoder updates the total range to
correspond to the range of the symbol being
encoded. This range is again divided based on the
probability of the symbolAs occurrence. The next
symbol is passed to the encoder, which again updates
the range depending on the symbol passed. This
continues until all the symbols in the sequence are
encoded (Figure 3). Any number within the final
range can be selected to represent the encoded
sequence.
To decode the message, the decoder accepts
the fractional value as input and again compares it to
the range values from the table. In this case it sees
that the value falls between the lower and upper
bound of a1 and so a symbol with value a1 is
outputted. The decoder must then update the encoded
value to remove the effects of the first symbol. A
new range is calculated by taking the lower bound of
the decoded symbol from the upper bound. The
encoded value is then calculated by taking the lower
ranges, as symbols are encountered and encoded.
This introduces some slight inefficiencies in the
encoding, but does not require the PDF to be
transmitted for use by the decoder.
An additional thresholding step was added to
the algorithm to increase the achievable CR with
minimal impact on PRD. All coefficients below the
selected threshold are deemed to be insignificant and
set to zero. The greater the number of coefficients
with the same value, the more efficiently the AC can
encode them. By varying the threshold level, and
therefore the number of coefficients being discarded,
we can increase or decrease the achieved CR, and in
conjunction, the PRD. The optimum placement of
the thresholding step in the overall system was
determined through experimentation; this is
discussed in more detail in Section V.
V. EXPERIMENTAL EVALUATION AND RESULTS
a) Performance Measures
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performance measures were employed. Firstly, the
quality of the reconstructed signal is tested by
comparing its similarity to the original input signal,
and expressing the difference relative to the original
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Percentage Root-mean squared Distortion (PRD)
measure, defined as follows:
bound of the first symbol from the initial encoded   
   (2)
value and dividing by the upper bound. This process 
continues until all symbols are decoded. It should be
noted that the decoder will continue to decode unless
the length of the original signal is passed as an
argument or a predetermined escape character is
received.
IV. SYSTEM IMPLEMENTATION
For this research, a number of modifications
were made to the JPEG2000 algorithm for
implementing an EEG compression algorithm. The
EEG signal was processed in non-overlapping
frames of size 1024. This window size was selected
based on (a) preliminary tests of compressing
varying sized signals and (b) previous findings in
similar research [4].
While the JPEG2000 Part 1 specification
allows use of a lossy and lossless WT, this research
focuses on the lossy CDF 9/7 WT. This choice
allows us to maximise the attainable CR for the EEG
signal with only a slight increase in computational
requirements.
The Arithmetic Coder implemented was
bas)(
21
%<22(A6
:25.
[19]. This allowed for the
PDF to either be calculated before encoding for the
whole window, or to be updated adaptively as each
new symbol is encoded. In the case of the PDF being
pre-determined, it had to be transmitted as part of the
message for use by the decoder. The adaptive coding
requires the encoder to continually update symbol
where  and  are the original and reconstructed
signals, respectively, and || || represents the
Euclidean or l2 norm.
The second performance measure used
describes the efficiency of the compression process.
The Compression Ratio (CR) for each EEG frame is
calculated as





where  is the length of the input signal in samples,
is the quantisation/bit resolution of each sample and
 is the number of bits representing the compressed
signal. The goal of this research is to achieve the best
trade-off between PRD and CR.
b) Dataset
There is currently no freely available dataset
of AEEG recordings. For this reason an EEG
database provided by the University of Freiburg in
Germany was used. This database provides
recordings of adult EEG from patients suffering from
epilepsy. The database includes 24 hours of seizure
(ictal), and non-seizure (inter-ictal) data for 21
patients. The ictal data are composed of signals
recorded during times when patients were
experiencing seizures. Due to the transient nature of
the seizures the majority of the data in this ictal set is
non-seizure, interspersed with seizure waveforms.
The inter-ictal subset is composed of the data that
was recorded when no seizures were occurring. For
this research, the ictal data was examined as it
contains enough seizure and non-seizure data to be
representative of both epileptic and regular
waveforms.
c) Thresholding
Initial experimentation involved performing
the thresholding step directly after the DWT and
before Quantisation was performed. This
methodology of thresholding is similar to the
algorithm proposed in [4]. Because of the amplitude
variation of the EEG signal, initial tests indicated
that it was difficult to control the level of distortion
introduced across an entire EEG record from the
selection of a static threshold. For certain frames, the
recordings were of such low amplitude relative to the
entire EEG signal that the entire set of wavelet
coefficients for that frame fell below the selected
threshold. This resulted in the whole frame being
reconstructed as a stream of zeros. This varying
amplitude across frames and channels made it
unfeasible to employ fixed thresholds values for all
signals. A potential solution would require the
computation of an appropriate adaptive threshold
value for each EEG frame. However, performing
such a computation would add a computational
overhead to the algorithm, which would be
unsuitable for an ambulatory implementation.
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(<1%0-'
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second architecture was explored whereby the
thresholding was performed after quantisation. In
this case, quantised values below the threshold were
deemed insignificant and consequently zeroed. As
the coefficients are normalised and uniformly
quantised to within a predictable range, the impact of
thresholding (using a static value) on the signalA6

energy is more predictable and controllable. It is for
this reason that thresholding after quantisation was
used for the results in this paper.
d) Test Para meters and Results
The EEG records were compressed using a
fixed wavelet decomposition and quantisation level.
These values were based on the results found in [20]
as they provided the best trade-off between CR and
maintaining signal integrity. Each signal was divided
into windows of size 1024. These windows were
compressed and reconstructed using 5 different
threshold values. These threshold values were chosen
to give a range of PRD values from very low (~2%)
to high (>15%). The CR and PRD values were
averaged for each patient, and an overall average was
calculated for all patients in the database, at each
threshold level. The overall results for average CR
versus PRD are plotted in Figure 5.
Using the 7% PRD as the maximum
acceptable PRD we can see from the graph in Figure
5 that an average CR of over 5:1 is achievable.. For
even a low PRD of 3%, a CR of between 3.5:1 and
4:1 is still achieved.
VI. CONCLUSIONS AND FUTURE WORK
This paper has presented a method of
compressing EEG signals using a JPEG2000-based
compression algorithm. A high compression ratio
was achieved
F igure 5: A verage PR D vs C R for all Patients
While other proposed AEEG algorithms from the
literature report achieving higher CRs [8],[21],[5], in
many cases, this is possible only on seizure data, and
as such are only suitable for a single EEG
application. The algorithm proposed here has been
tested with both seizure and non-seizure data, and
can be adapted for a variety of applications, with the
amount of distortion increased or decreased as
needed.
The method of performing thresholding after
normalisation and quantisation provides more
predictable CR and PRD results for a given
threshold. The same threshold values can be used for
all recordings without having to take into the account
the amplitude of the signal. This is useful if the
algorithm is to be implemented on a portable device,
where it could be impractical to adjust the threshold
on a frame-by-frame, or channel-by-channel basis.
In terms of future work, analysis of the power
usage of the algorithm should be completed. It has
already been established by other researchers
[6],[7],[22] that the main elements of JPEG-2000 can
be efficiently implemented, while the addition of
thresholding proposed here will not add significantly
to the computational complexity.
Expert clinical analysis of the decompressed
EEG signal in relation to the original signal, at a
variety of PRD levels, is desirable to ensure that
signal integrity is maintained. Similarly, it is
proposed to test the algorithm in conjunction with
established automated diagnosis algorithms to ensure
detection rates are maintained.
 VII. ACKNOWLEDGEMENTS Algorithms, Springer, 2002.
[19] K. Sayood, Introduction to Data Compression, Third
The authors would like to acknowledge the Edition, Morgan Kaufmann, 2005.
Albert-Ludwigs-Universitt, Freiburg, Germany, for [20] 
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allowing access to their adult EEG database. Power 2035)66-21
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4th International IC S T Conference on Pervasive
This research was supported by Science Computing Technologies for Healthcare 2010.
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