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8iosigna/ processing
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Biosignal processing in the overall “biopicture"
Pattern
Recognition
ClassificatiOn Event Analysis — Events Remove
Feature Extract
Diagnostic Detection Artifacts
information
UNIVERSITY 0f 19 Apr 3
Outline
• Biosignal definition
• Biosignal processi
• Event detection
UNIVERSITY 0f 19 Apr 4
Outline
• Biosignal definition
• Biosignal processi
• Event detection
UNIVERSITY 0f 19 Apr 5
Bios :
Signal: function that "conve s information about
the behavior or attributes o some phenomenon
Biosignal (also biomedical si naI5 bioelectrical
signal or physiological signal
• any biological quantity or magnitude exhibiting
variation in time or variation in space is potentially a
signal that provides information on the status of a
biological system
• In time (1D): e.g., electrocardiOgram (ECG)
measures heart activity by detecting
changes associated with heart muscle
contractiO
• In space (2D): e.g., functiOnal magnetic
resonance imaging (fMRI) measures brain
iaxcv by detecting changes assOciated with
blood flow
• In time-space (3D): e.g., a medical ultrasound
measures nsurface O i teao a s stiuctu lal
UNIVERSITY 0f 19 Apr 6
Bios :
movements by detecting changes in the
reflectiO OI sound waves on the
tissues
UNIVERSITY 0f 19 Apr 7
Biosi : exam
Electroencephalogram Electroretinogram Electrooculogram
(EEG) (ERG) (EOG)
Electroneurogram
(ENG) Electroogastrogram
(EGG)
Phonocardiogram (PCG).
Photopletismogram (PPG).
Vibromyogram (VMG).
Vbroarthrogram (VAG)...
and also Speec ,
Motion, etc.!!
• Videos:
• ooo. ItOe 5 Potential Trains {IdUAPTs)
UNIVERSITY OF TWENTE.
10-Apr-18 10
Outline
• Biosignal definition
• Biosignal processi
• Event detection
• Compression
UNIVERSITY 0f TWENTE. 19 Apr 18 11
Biosi nals: time-domain characterisation
• Signal domain
• Continuous-time4 Signal as a function of time x(IQ
• e g., temperature measured seamlessly
• Discrete-time 4 Signal as a function of samples x(n
• e.g., temperature measured every hour
• Digital 4 Discrete-time signal with values limited to
quantised levels 1(n)
• e g., temperature measured every hour with a resolution oT 1OC
UNIVERSITY 0f 19 Apr 1
Bios nals: time-domain
• Amplitude
• Describes the intensity of the biological phenomenon
(a.k.a, dependent variable, range, or ordinate)
• Not to be confused with range or peak-to-peak amplitude
• Duration
• Signals are considered to exist for all time {e.g., sin(wt))
• We normally take just some samples of the signal
{subpart or realisation of the actual signal)
UNIVERSITY 0f 19 Apr 1
Bios nals: time-domain
• Periodicity
• Periodic: the shape of the signal repeats with an interval
• Aperiodic: the shape of the signal never repeats
• Predictability
• Deterministic: predictable for the time span of interest
• Random: signal values cannot be precisely anticipated
• Stationary: (nearly) constant statistics or frequency spectra over time
• Non-stationary: varying statistics or frequency spectra over time
UNIVERSITY 0f 19 Apr 1
Bios nals: time-domain characterisation
• Time-domain parameters B,C, ?)
A
B
1.0
0.5
E
ECG
UNIVERSITY 0f 19-Apr- 1
Bios nals: time-domain characterisation
• Time-domain parameters
S gnat
Maximum
(local / absolute) Signal Period Signal Frequency = 1 / Signal
Period
1.0
0.5
Amplitude
ECG vo
(peak-to-peak)
0.5 .0 1.5 /
-0.5 (s)
Signat
Signal duration = # samples / Sampling Frequency
Different concepts!
Sampli ng Frequency Signal Frequency n
UNIVERSITY 0f 19-Apr- 1
Bios nals: time-domain characterisation
Period SignaI Period Min mum
(local / absolute)
UNIVERSITY 0f 19-Apr- 1
Biosignals: frequency-domain characterisation
• Continuous Fourier transform (CFT)
• Decomposes a signal into sinusoidal
components invariant over time
UNIVERSITY 0f 19 1 2
Biosignals: frequency-domain characterisation
• DFT is a complex function
• Real + imaginary parts
• X(k) ¥ X(jk) = X (jk) + j X(jk)
• Magnitude -r phase The corr ple6spectrum
magnitude is predominantly
• l> •k (( • ))
used for the characterisation
• zX(jk) = t n2(X(jk),X (jk)) of biosignals
Magnitude response
20 0›
150
10 0
L
50
20 30 40 50— 60 70 80 90 › 100 !
Frequency (Hz)
UNIVERSITY 0f 19 Apr 2
Biosignals: frequency-domain characterisation
• Frequency-domain parameters
Fundamental Frequency =
lowest frequency of
periOdic Harmonics = multiples of the fundamental frequency
wavefOr
Magnitude response
20 0›
150
Maximum
10 0 Frequency
Frequency
50
20 30 40 50— 60 70 80 90 › 100 !
Frequency (Hz)
UNIVERSITY 0f 19 Apr 2
Biosignals: time- characterisation
Temporal information gets lost after transforming
the signal to the frequency domain...
0 ta
• Time-frequency characterisation
• Short-time Fourier transform (STFT)
• Wavelet transform (WT)
Biosignals: time- characterisation
UNIVERSITY Of TWENTE. 19-Apr-18 24
Biosignals: time- characterisation
• STFT:
c
or
n
X bk, m) = x(n + m)w{n)e N“ k, m = 0,1, ... , N — 1 er
s)
w(n) is a finite window function UNIVER
SITY 0f ECG signal
and m is the amount of shil of TWENT
the window function E.
• Shortcomings:
• Fixed window length, thus not able to
. . .
capture events with di0erent durations
{dilemma of tjme frequency resolution}
• Sinusoids used in STFT to model the
signal may not be the best choice
(biosignals may contain sharp
Biosignals: time- characterisation
19 Apr 18 25
Biosignals: time- characterisation
• WT:
• To address the problem of fixed
window widths, the concept oT
“scaling” is used
• A mother wavelet is scaled in time
to create a series of varying-
frequency” components as an STFT
analogy to the harmonics Fourier
UNIVERSITY 0f 19 Apr 2
Outline
• Biosignal definition
• Biosignal processing
• Event detection
• Compression
UNIVERSITY 0f 19 Apr 2
Biosignal processing Biosigna1 processing Bio9igr›al processing
• Visual inspection is not always enough • Visual inspection is not always enough • Visual inspection is not always enough
• B,ios,ignal processing is intended to extract clinically • Biosignal pressing 1s intended to extract clinically • Biosignal processing is intended to extract clinically
significant intormation hidden in the signal significant information hidden in the signal signiñcant information hidden in the signal
• Examqsramefers to her characterize and urderstend tha • gararr/uti:+ s ft twIp ulJar mtce L:c arid +iridcr uluiJd file • rM t gamma to help Cha+afie+ize anrl tin0er stand
the iri*urrriafioiJouiJluiriuw ir' a uigri JI inD+mation rOnl,siñ@ in a siq nil information contained in e s ignal
• Pemcve .a'se to rn Ggate the techn IIaaf ennies of e recording, as • Pi:rrzJ'a .•iw'uc to iiJifigutu II+u Mi with dufic riuic ul a ruooi dirig. au • 5 W m'se to mitiqale the technical rlefcienfiea ci a +erOroing, as
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interfering well as to separate the desired physiological process from interfering
• Biosignal processing methods ’,. • Bio sign al processing me thods : . '.- .. . ' '›. • Bio sign al processing me thods
• Filtering fur removal Of drtif<tcLs .
• Filtering. for removal of . ;... . . .. ' .
• Filtering. for rcmovziI of artifacts
.
• Evem detem@n " • Event detection - - — --- • EvenI deteuJiur
• U'ffJgTUsB'iU'fJ ”
Outline
• Biosignal definition
• Biosignal processing
• Event detection
• Compression
UNIVERSITY OF TWENTE. 1&Apr-18 20
Filterin for Removal of Artifacts
• Noise
• Structured: waveform is known in
advance (power-line 50Hz/60Hz)
• Random: unpredictable waveform
(thermal noise)
• Physiological interference
• e.g., EMG from the intercostal
muscles into the ECG recorded
using chest leads
• e.g., ECG into the EMG recorded
from the back muscles
• Good measurement setu
best way of dealing with
interference and noise
is
avoiding it in the first place! "
UNIVERSITY 0f TWENTE. 19 Apr 18 30
Filterin Removal Artifacts
• Time-domain ital filter
• Offset filter
• Moving average filter
• Median filter
• Detrending
• Frequency-domain digital filter
• Bu#erworth/Chebyshev
• Notch/Comb
• Savitzky Golay
• (Optimal) Adaptive filters
• Wiener
• Kalman
150
sition (e.g. D 1 2
Time (x}
5
UNIVERSITY Of 19-Apr- B
Filterin Removal Artifacts
Example: ECG with
• Moving-average filter high-frequency noise
Noisy ECG
Slwple: y(n) ) x(n)
n+k 2
Shlfted: y(n) ( ) i =n —K f 2 x(n
UNIVERSITY 0f 19-Apr- 3
Filteri for Removal of
• Median filter Example: ECG with
Powerline Interference ( 0Hz)
• Ranks from lowest value to ECG noisy slgnal and Ideal lgnal
highest value and picks
the middle one: —ideal
types of noise in which some ECG noisy signal and median-filtered lgnal
(outliers)
0
M/\SLAB. ii›edfilt I
UNIVERSITY 0f 19-Apr- 3
Filteri for Removal of
• Median filter
• Ranks from lowest value to
highest value and picks the 1000
PSD (ECG Ideal)
middle one:
• e.g., median of [3, 3, 5, 9, 11]
• Good for rejecting certain £' 0 20 3G 70 80 9’ 0 00
M/\SLAB ii›edfilt I
UNIVERSITY 0f 19-Apr- 3
Filteri for Removal of
• Detrending filter b eathidg in E G
• Uses a polynomial
approximation based on
least-squares fit of a straight
line (or composite line for
piecewise linear trends) to
the signal
• Then subtracts the resulting
approximate function from
the original signal
Application: trends/shifis
(low-freouencj/
artifacts) leading
improper e
MATLAB. polylit. cletren
UNIVERSITY Of 19-Apr- 3
Filteri for Removal of
Detrended EN 4IgM I
-1
0 0.5 .5 2 2. 5 â 3.5 4
Time (sl
2x
• Simplicity, monotonically
decreasing magnitude response,
and maximally flat magnitude ECG
response in the pass-band
Tima domaa›
Elec4roca chogram
Program 5 Powerllne interferences in ECG slgnals can
Self-portrait photograph be removed with: '
Ef ukigram Qlfset fihers
Tru
e
UNIVERSITY OF 18-Apr- 4
answers
1 How many legs does a centipede have?
2
4 Powerline interferences in ECG signals can
100 be better detected in the: '
Tima domaa›
Elec1rocerchogram
Phd ogram 5 Powerllne interferences in ECG slgnals can
Self-portrait photograph
be removed with: '
Elect uIc›gram Qlfset fihers
Tru
e
UNIVERSITY OF 18-Apr- 4
Outline
• Biosignal definition
• Biosignal processing
• Event detection
• Compression
UNIVERSITY 0f 19 1 4
Event detection
• Envelope estimation
• Wave delineation
• Peak detection
• Cross-correlation
• Auto correlation
UNIVERSITY 0f 19 1 4
Event detection
• Envelope estimation Raw
• The signal's envelope is
equivalent to its outline, and
an envelope detector Filtration
connects all the peaks in
this signal
• LP filtering + rectification (+ Rectification
smoothing + RMS)
• Other approaches:
Hilberttransform Smoothing
Application: detection of
the burst moments and
RMs RootMe n s u
estimation of the amount of ( a a’ e
UNIVERSITY 0f 19 1 4
Event detection
• Wave delineation
• Direct thresholding
• Boundariesare defined as the instants a wave ’ "
crossesa certain amplitude threshold level
• Seldom applied in practice since signals are ’ ’
usually affected by baseline drips or o0sets ” ’”
• Derivative methods
• Exploits the change of slope that occurs at a
boundary to avoid low-frequency noise
• 1st derivative approximation and analysis with
respectto zero crossings and extreme values
• Application: detection ol the
complex (largest slope/rate of change
in a cardiac cycle)
UNIVERSITY 0f 19 1 5
Event detection
• Peak detection
• Envelope estimation and
wave delineation are
frequently used in
combination
• Thresholding is used to
determine candidate peaks
• A local maxima search is
normally needed to select
outstanding peaks
A ppIi' cati'on: estimation of
the R-R distance
ECG
UNIVERSITY 0f 19 Apr 5
Event detection
• Peak detection
• Pan-Tomkins algorithm:
removing noise,
smoothing the signal,
amplifying the QRS slope
and width, and
thresholding for detecting
peaks of interest
App ica ion:
es ti’ma t•ion the ECG
-R distance
MATLAB: /i/ter, diffe rms, lindpeaks
UNIVERSITY OF TWENTE. 18-Apr-18 51
Event detection
• Cross-correlation
• Measures the similarity of
two series as a function
of the lag of one relative
to the other
UNIVERSITY 0f TWENTE. 19 A 18 53
Outline
• Biosignal definition
• Biosignal processi
• Event detection
• Compression
UNIVERSITY 0f 19 Apr 5
Compression
Process reducing the amount of data in a given
signal to order to lower resource usage, such
as data storage space or transmission capacity
Sampling and quantisation are typical simple
compression techniques used to reduce the size
of the digitised signal
• Advantages:
• Less storage
• Less bandwidth
• Faster processing
• Disadvantages
• Information loss
UNIVERSITY 0f 19 1 5
Compression
• Downsampling/Decimation
• Process of reducing
the sampling rate of a signal
• Utilises LP filtering to
mitigate aliasing distortion, which
can occur when
simply downsampling a signal
• Upsampling/interpolation y) n _ | | /i — kL|. j 0. I , . , L — 1.
L
• Produces an approximation of
the sequence that would
have been obtained by
sampling the signal at a higher
rate
• Extends the bandwidth of the
signal
UNIVERSITY 0f TWENTE. 19-Apr-18 56
References References
• Biomedical IZ@naI Processing and And @: • Bion edict SigWl ProcesSing and A aIysis:
• PriricipaI r 8larur aB: • Pn@pal efererc›e.