time - frequency analysis applied to biomedical signals hiew yen ha supervisor: dr. barry cheetham...
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Time - frequency Analysis Applied Time - frequency Analysis Applied To Biomedical SignalsTo Biomedical Signals
Hiew Yen HaHiew Yen Ha
Supervisor: Dr. Barry Cheetham
Advisor: Mr David Tait
ContentsContents
Participants. Motivation. Aims. Types of biomedical signals.
Participants. Motivation. Aims. Types of biomedical signals. Intro
Recording system. Database. Physiology of cough. Cough analysis. De/Compression.
Gold Standard cough counting technique.Software Version-MCA101, 401 & 801.
Recording system. Database. Physiology of cough. Cough analysis. De/Compression.
Gold Standard cough counting technique.Software Version-MCA101, 401 & 801.
Year 1 Work
Results of Gold Standard Vs software.
Conclusion.
Results of Gold Standard Vs software.
Conclusion.
Preliminary Results
Additional goalsAdditional goalsFuture Works
IntroIntro
Participants
North West Lung Centre, Wythenshawe Hospital
Aintree Chest Centre, University Hospital Aintree
Dr. John Earis
Prof. Ashley Woodcock Dr. Jackie Smith
IntroIntro
Types of biomedical
signals
Cough signals
•Asthma
•Cystic Fibrosis (CF)
•Cryptogenic Fibrosing Alveolitis (CFA)
~ Factors: allergy, airborne irritants, infection & weather change.
~ Airways clogged by mucus & swelling, causing difficulty to breath in and especially out.
~ Genetic disorder (usually Caucasian).
~ Affects mucus-secreting glands, interfering with lung function & digestive system.
~ Possible factors: cigarette smoking, exposure to metal, wood & coal dust.
~ Associated with fibrosing pulmonary and alveoli inflammation
IntroIntro
Motivations (I) Study of lung diseases by investigating pathological
vocalisation - cough sound analysis
(II) Application of wavelet analysis
(III) Objective long-term cough monitoring
~Euro. Resp. Jr 1999 13:1447-1450• Used in cough challenge methodology
• Wavelets useful for time-frequency analysis of non-stationary signals. According to R.A.L.E., application of wavelets to coughs is new.
• Although much research in cough challenge methodology, air-flow & volumetric variations of lungs, & lung sounds analysis has been done in the past, little work has been done on the acoustic analysis of cough.
• Objective measurements of cough more reliable than subjective descriptions from doctors or patients. ~ Arch.Dis.Child 2001 84:31-34
IntroIntro
Aims Software package with functions of...
Cough recognition Counting & measurement
• Discrimination from background noise
• Number of coughs per unit time
• Long term distribution with time
• At least 80% accurate
Year 1 WorkYear 1 Work
Recording system
c L
R
A C
L a p e lm ic ro p h o n e
T h ro a tm ic ro p h o n e
S o u n d s o u rc e
A m p lifie r
L L e ft c h a n n e l
R R ig h t c h a n n e l
A C A lte rn a tec u rre n t
D .A .P .J u k e bo x pla y e r
L E G E N D
Fs: 16K Hz
Format: Wav format, stereo type
Recording: Tracks (30 min) -112,512KB
selectselect
Year 1 WorkYear 1 Work
Database
Asthma
8 recordings with mean duration of 8 hr
C.F.
11 recordings with mean duration of 9.5 hr
C.F.A.
9 recordings with mean duration of 10 hr
All-night recordingsAll-night recordings
Year 1 WorkYear 1 Work
De/compression
Compression & Decompression
•Size of each 30-min track is 112MB.
•Compression program eliminates silent periods & compresses the file without affecting the information.
•Decompression program reconstructs the original files.
Year 1 WorkYear 1 Work
Physiology of cough
A respiratory reflex thatrid noxious substances from the lungs.
What’s a cough?
Acute cough = cough < 3 weeks, Chronic cough = cough > 3 weeks.Cough Mechanics
Inspiratory cough phase
Compressive cough phase
Expiratory cough phase
•Take 1 sec.
•Deep inspiration
•Glottis firmly closed.
•Closure of the glottis.
•High intra-thoracic pressure.
•Glottis opens, followed by a high expiratory flow rate. The pressure of the central airway falls rapidly.
•Cough sounds = Excitation phase + mid-noisy phase.
0 2000 4000 6000 8000 10000 12000-3
-2
-1
0
1
2
3x 10
4
Amplitude
sample
Excitation phase
mid-noisy phase
Year 1 WorkYear 1 Work
Cough Analysis
0 0.2 0.4 0.6 0.8 1 1.2 1.4 1.6 1.8 2
x 104
-3
-2
-1
0
1
2
3x 10
4
Amplitude
sample
1st cough sound 2nd cough sound
1 breath
Cough Effort
Excitation phase & Mid-noisy phase
Year 1 WorkYear 1 Work
Cough Analysis
0 0.5 1 1.5 2 2.5 3 3.5
x 104
-4
-3
-2
-1
0
1
2
3
4x 10
4
AsthmaAsthma
0 100 200 300 400 500 600 700-4
-3
-2
-1
0
1
2
3
4x 10
4
Year 1 WorkYear 1 Work
Cough Analysis
0 0.2 0.4 0.6 0.8 1 1.2 1.4 1.6 1.8 2
x 104
-4
-3
-2
-1
0
1
2
3
4x 10
4
C.F.A.C.F.A.
Year 1 WorkYear 1 Work
Gold Standard
•Identify & count coughs.
•Eliminate background noise.
•Count cough sounds instead of cough effort.
MCA101, 401MCA101, 401
MCA801MCA801• Identify “positive cough moments” (PCM).
• PCM = 1 sec frame that contains coughs.
• Count PCMs in each file.
Manual assessment by qualified clinician.
Year 1 WorkYear 1 Work
Software
MCA101MCA101
~ Automatically identify & count cough sounds.
~ Early version.
~ Not suitable for overnight recordings.
MCA401MCA401
~ Automatically identify & count cough sounds.
~ Not suitable for C.F. and C.F.A.
~ Developed for overnight recordings.
MCA801MCA801
~ Automatically Identifies & counts PCMs.
~ Designed to work for asthma,C.F., & C.F.A.
~ Suitable for overnight recordings.
Jan-Aug 2001Jan-Aug 2001
01020304050
12:0
0 A
M
1:0
0 A
M
2:0
0 A
M
3:0
0 A
M
4:0
0 A
M
5:0
0 A
M
6:0
0 A
M
7:0
0 A
M
8:0
0 A
M
9:0
0 A
M
Program
Program
Gold Standard
Cough measurement of program Vs Gold Standard
No. of cough sound
Time
JE RecordingJE Recording Date : 7 June 2001
(JM020 Track007) Gold Standard count VS Program count (PCM)
36
10
20
29
23
19
4
1720
17
41
12
16
26
21
17
4
34
28
20
0
5
10
15
20
25
30
35
40
45
3 min block
Nu
mb
er
of
po
sit
ive
co
ug
h s
ec
program count Jacky's count
program count 36 10 20 29 23 19 4 17 20 17
Jacky's count 41 12 16 26 21 17 4 34 28 20
3 6 9 12 15 18 21 24 27 30
Validation of MCA801
Year 1 WorkYear 1 Work
Conclusion
• Cough recognition & counting software tested on 3 types of disease.
• Version 401 meets spec. for asthma, but not for C.F. & C.F.A. coughs.
• Version 801 still to be validated against “gold standard”.
• Recognition algorithm needs to be refined.
• “Gold standard” is questionable reference & needs further consideration.
Research IssuesResearch Issues
•Identifying characteristics of coughs & relating these to physiology.
(e.g. why does asthmatic coughs have a periodic onset?)
•Cough identification & elimination of background noise.
•Advantages of wavelets for cough analysis (coughlets!)
•Devising objective measures for frequency & time distribution of events.
•Presentation of measurements.
•Mobile technology for remote monitoring.
ApplicationsApplications
(1) Portable 24 hr cough monitoring.
(4) Assessment of effectiveness of anti-tussive drugs.
(5) Medical research into nature of cough.
(2) Recognition of types of pathological cough sounds.
(3) Detect difference between healthy & pathological cough.
~DSP techniques applied to study of characteristic of coughs & related lung diseases.
~ The long term measurements can be used to compare the effectiveness of drugs.
~ Diagnostic tool.
~This type of software (enhanced) is capable of recognising types of pathological cough.
~ So far only over-night recordings made. Higher cough frequency during day.
More background noise to contend with and technology problems to address.