Definitions
Biomedical Signal Processing
Achmad Rizal
BioSPIN
Definitions
• Typical System
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Rationales for biomedical signal
processing
1.Acquisition and processing to extract a priori
desired information
2.Interpreting the nature of a physiological process
based either on
a) observation of a signal (explorative nature), or
b) observation of how the process alters the
characteristics of a signal (monitoring a
change of a predefined characteristic)
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Definition
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(Some) goals for biomedical signal
processing
• Quantification and compensation for the effects
of measuring devices and noise on signal
• Identification and separation of desired and
unwanted components of a signal
• Uncovering the nature of phenomena
responsible for generating the signal on the
basis of the analysis of the signal characteristics
– Related to modelling / inverse modelling but
often more pragmatic
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 Biomedical signal classification Biomedical signal classification

On the basis of
– signal characteristics
technical point of view
– signal source
from where and how the signal is originated and
measured
– biomedical application
cardiology, neurophysiology, monitoring, diagnosis,…

Classification may be helpful in the selection of processing

methods...

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By Signal Characteristics
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Definition Biomedical signal classification

Deterministic: may be accurately described mathematically
Usually predictable (not in case of chaos!)
Periodic: s(t) = s(t+nT)
Almost periodic: patterns repeat with some unregularity
Transient: signal characteristics change with time
Stochastic: defined by their statistical properties
(distribution)
Stationary: statistical properties of the signal do not change over time
Ergodic: statistical properties may be computed along time distributions
All real (bio)signals may be considered stochastic
– almost deterministic signals (e.g. ECG): waveshapes that (almost)
repeat themselves → characterisation (often) by detection of certain
measures or waves
– “truly” stochastic (e.g. EEG) → characterisation by statistical properties
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Classification by source
• Bioelectric signals: generated by nerves cells
and muscle cells. Single cell measurements
(microelectrodes measure action potential) and
‘gross’ measurements (surface electrodes
measure action of many cells in the vicinity)
• Biomagnetic signals: brain, heart, lungs
produce extremely weak magnetic fields, this
contains additional information to that obtained
from bioelectric signals. Can be measured using
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Biomedical signal classification Biomedical signal classification

• Bioacoustic signals: many phenomena create acoustic
noise. For example, flow of blood through the heart, its
valves, or vessels and flow of air through upper and
lower airways and lungs, but also digestive tract, joints
and contraction of muscles. Record using microphones.
• Biomechanical signals: motion and displacement
signals, pressure, tension and flow signals. A variety of
measurements (not always simple, often invasive
measurements are needed).
• Biochemical signals: chemical measurements from
living tissue or samples analyzed in a laboratory. For
examples, ion concentrations or partial pressures (pO2
or pCO2) in blood. (low frequency signals, often actually
DC signals)
• Bioimpedance signals: tissue impedance
reveals info about tissue composition, blood
volume and distribution and more. Usually two
electrodes to inject current and two to measure
voltage drop
• Biooptical signals: blood oxygenation by
measuring transmitted and backscattered light
from a tissue, estimation of heart output by dye
dilution. Fiberoptic technology.

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 Problems in biomedical signal
Biomedical application domains processing
• Accessibility
• Information gathering
– Patient safety, preference for noninvasiveness
– measurement of phenomena to understand the system
• Diagnosis – Indirect measurements (variables of interest
– detection of malfunction, pathology, or abnormality
are not accessible)
• Monitoring • Variance
– to obtain continuous or periodic information about the – Inter-individual, intra-individual
system • Inter-relationships and interactions among
• Therapy and control physiological system
– modify the behaviour of the system and ensure the result – Subsystem of interest may not be isolated
• Evaluation
– objective analysis: proof of performance, quality control,
• Acquisition interference
effect of treatment – Instrumentation and procedures modify the
system or its state
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Problems in biomedical signal Signal acquisition

processing
• Artefacts and interference
– Interference from other physiological systems (e.g. muscle
artifacts in EEG recordings)
– Low-level signals (e.g. microvolts in EEG) require very sensitive
amplifiers; they are easily sensitive to interference, too!
– Limited possibilities for shielding or other protection

• Nonlinearity and obscurity of the system under study

– basically all biological systems exhibit nonlinearities while most of
the methods are based on the assumption of linearity →
approximation
– exact structures and true function of many physiological systems
are often not known

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Quantization error

• Quantization error eq is the difference between the original and the

sampled signal amplitudes at the time instants of sampling

• Quantization error originates as we have only finite number of

quantization levels (discrete amplitudes) available with finite number
N of bits
– Number of quantification levels = 2N
• Minimization of quantization error:
– Sufficiently high number of bits
– Proper signal scaling (so that true amplitudes “fill in” the whole
dynamic range of the A/D-converter)
• Preamplifiers
• Preconditioning (e.g. removal of DC drift from AC signal such as
ECG, EEG, etc.)

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 Aliasing in time domain
Sampling theorem and aliasing
• Sampling (Shannon) theorem: a
continuous signal can be completely
recovered from its samples if, and only if,
the sampling rate is greater than twice the
highest frequency of the signal (Nyqvist
frequency).

If sampling theorem is violated, aliasing • Original signal: thin line

occurs. • Sampling (dashed lines) at 1.3*frequency of signal
• Reconstructed signal: thick line
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Aliasing in frequency domain Mapping of frequencies in DFT &

aliasing
• DFT is periodic with a period of sampling rate
• One period is symmetric with fs/2
– frequencies from fs/2 to fs map into fs/2 to 0

• NOTE: aliasing occurs in sampling and hence

may not be corrected or prevented in discrete
domain anymore
– use high enough sampling rate and anti-alias
analog filters
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Importance of sampling theorem Short-term HRV and BPV

• Incorrect sampling causes unrecoverable errors in the
acquired signal
• Incorrect sampling is surprisingly common with
biomedical signals
– Reasons:
Poor methods / hardware etc. i.e. engineering problem
Impossible to sample more frequently due to physical /
methodological / physiological / psychological / safety
or other practical issues
– Essential to recognise and understand possible
consequences (and manage them)

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 The four stages of biosignal
processing
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Principal signal processing
levels
• Acquisition
– Signal detection: linearity, amplitude and phase distortions correction
– Signal conditioning: prefiltering, normalization
– Analog-to-digital conversion
– Data storage
• Processing
– Filtering: noise reduction, restoration
– Transformation: DFT, WT, STFT, SVD, PCA
– Matching filter: extraction of characteristic waves from signal
– Parameters (features) extraction
– Data compression
– Classification
– Modeling: mathematical, physiopathological
• Interpretation
– Association of classes of parameters with physiopathologic state of patient
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Parameters for digital Digital Signal

acquisition
• Analog signal:
– Amplitude: from 0.5 μV to 10 mV
– Frequency: from 0.5 Hz to 10 KHz
• Digital Acquisition
– Number of bits: 12 to 16
– Sampling: > 40 KHz

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Basic Process Convolution

• Equation
• Convolution ∞
y[n] = ∑ x[k ]h[n − k ]
• Cross-correlation k = −∞

• Z-transform y[n] = x[n] * h[n]

• Filtering
disebut sebagai konvolusi jumlah (convolution sum) atau
superposition sum,

• Visually convolution mean as :

– Cerminkan h[k]
– Geser h[k] untuk seluruh nilai n yang mungkin,
sampai melewati x[n].
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 Cross-Correlation
• Cross correlation

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Z-transform
• Z-Transform plays the same role as the Laplace
Transform for CT signals.
∞
jω
X(z ) = ∑ x[n]z −n
x[n ]←⎯→ X(z )
Z
z = re
n=−∞

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 Z transform Z transform
Z transform expample Application of z transform
• x(-3) = 2, x(-2) = -5, x(-1) = 3, x(0) = 0, x(1) = 4, x(2) = 2, x(3) = -4,
x(n)
x(4) = -2 4
3
2 2

q(t ) = p (t ) * h(t )
-2 3 4
-3 -1 0 1 2

-2

-5
-4
Q( z ) = P( z ).H ( z )
Q( z )
X ( z) = 2z 3 − 5z 2 + 3z1 + 4z −1 + 2z −2 − 4z −3 − 2z −4 H ( z) = transfer function
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P( z )
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Filtering Filtering
Filtering = removing unwanted frequency Filtering equation
component (noise) from the signal • Let x(n) denote current input value
• Linear Filter : LPF, HPF, BPF, BSF (ECG+noise)
• FFT Filter : use FFT to remove signal Æ - x(n-1) is previous input value, x(n-k)
IFFT kthprevoius input
• Non Linear Filter • Let y(n) be the current filtered output value
• Adaptive filter - y(n-1) is previous output value, y(n-k)
kthprevoius output
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Filtering Filtering
Filtering operation carried out by this If we arrange the equation, we’ll get
example : Y(z)(1 - 2z-1+z-2)=X(z)(0.6 – 2z-1 + 3z-2)
y[n] = 2y[n-1]-y[n-2]+ 0.6x[n]-2x[n-1]
+3x[n-2] Y ( z ) 0.6 − 2 z −1 + 3 z −2
H ( z) = =
If we applied Z tranform, we get : X ( z) 1 − 2 z −1 + z −2
Y(z)=2Y(z)z-1-Y(z)z-2+0.6X(z)-2X(z)z-1
+3X(z)z-2

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 Filtering Filtering
• General Equation : • FIR Æ finite impulse response

b0 + b1 z -1 + b 2 z -2 + L + b M z -M b0 + b1 z -1 + b 2 z -2 + L + b M z -M
H(z) = H(z) =
a 0 + a1 z -1 + a 2 z -2 + L + a N z -N a 0 + a1 z -1 + a 2 z -2 + L + a N z -N
M
For FIR a0 = 1, a1...an = 0 .....

Y(z)
∑b r z -r • The transfer function become
r= 0
H(z) = =
X(z) N
H(z) = b0 + b1 z -1 + b 2 z -2 + L + b M z -M
∑a k z -k

k = 0
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• IIR Æ infinite impulse response

b0 + b1 z -1 + b 2 z -2 + L + b M z -M
H(z) =
a 0 + a1 z -1 + a 2 z -2 + L + a N z -N
• For IIR b0, a0, a1...an ≠ 0 .....

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