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SYSC 4203 - Biomedical Instrumentation

Description

Bioinstrumentation and biological signals; instrumentation systems, noise, electrical safety, and biocompatibility; bioelectric signals; biopotential electrodes: material properties, selection, and fabrication; measurement of flow and pressure; data acquisition; signal processing; biomedical imaging technologies; performance and characteristics of bioamplifier systems; major physiological systems and associated measurements.

Prerequisites

(SYSC 3600 or SYSC 3500 or SYSC 3610) and (ELEC 2507 or ELEC 3605 or SYSC 3203) and fourth-year status in Biomedical and Electrical Engineering or fourth-year status in Biomedical and Mechanical Engineering. It is assumed that students
  • Understand basic analog electronics components
  • Are proficient at design of biomedical amplifiers
  • Understand frequency-domain analysis of signals
  • Understand the principles of cardio-vascular and pulmonary anatomy and physiology.

Instructor

Andy Adler
Email: adler@sce.carleton.ca
Office: Canal 6204
Phone: +1-613-520-2600 x 8785
Office Hours: Mon 10h00–11h00 & Thurs 13h00—14h00

Teaching Assistant

Symon Stowe
Email:   symonstowe@cmail.carleton.ca

Times and Locations

Section  Activity  Day  Location 
SYSC4203    LEC 1    Tues 11:35−12:55    SA515   
   LEC 2    Thurs 11:35−12:55    SA515   
   LAB 1    Fri 14:35−17:55    MC6070   
   LAB 2    Mon 14:35−17:55    MC6070   

Course Objectives, Learning Outcomes and Graduate Attributes

  • Course Objectives: This course will introduce simple biomedical instrumentation systems used for common biomedical signals, including the relevant issues in the design and use of the systems including instrumentation systems, noise, electrical safety, and biocompatibility. It will describe the major physiological systems and associated measurements, focusing on bioelectric signals and their measurement using biopotential electrodes, as well as systems for measurement of flow and pressure. The issues in data acquisition, signal processing and bioamplifier systems will be discussed.
  • Learning Outomes By the end of this semester, students should be able to:
    • Visualize the anatomy and electrophysiology of humans and animals
    • Describe the origin and characteristics of common biological signals
    • Assess the performance of a biopotential acquisition system in terms of noise and interference
    • Appraise biomedical measurement methods for blood pressure, flow, and oxygenation
    • Choose appropriate signal conditioning and processing methods to analyze biomedical signals
    • Build a biomedical system to measure and correlate common biological signals
    • Describe high-level operation of medical imaging systems
    • Understand biomedical safety and standards
  • Graduate Attributes Biomedical Systems, Biomedical Instrumentation
    Graduate Attribute   Learning Outcome   Measurement

    1.11 (Discipline-specific concept SCE-8) Biomedical systems a,b,c,d,e,f,g,h Final
    2.1 Problem definition c,d Project
    2.2 Approach to the problem d Project
    2.3 Use of assumptions f Final
    2.4 Interpreting the solution - validity of results c,f Final
    4.1 Clear design goals c,d,e,f Project
    4.2 Detailed design specifications and requirements e,f,h Project
    4.4 Design solution(s) e,f Project
    4.5 Design implementation / task(s) definition c,d,e,f Project
    4.6 Alternate Solutions Definition c,d,e,f Project
    4.7 Evaluation Based on Engineering Principles c,d,e,f,h Final
    5.3 Tools for design, experimentation, simulation, visualization, and analysis d,e,f,g,h Labs
    6.1 Personal and group time management d,f Project

Marks

Work  Value
Labs    15%
Project    10%
Quiz #1/#2/#3    15%
Midterm Exam    10%
Final Exam    50%

Text

John G. Webster, Medical Instrumentation: Application and Design, 4rd Edition: ISBN: 0-471-67600-3,

Exams (Quizzes, Midterm and Final)

  • Midterm exam is Oct. 29 (80 minutes, in class).
  • Final exam date will be set by the university
  • For all exams and quizzes, you will be permitted a calculator and one (1) 8.5"×11" paper sheet containing any information you choose (double sided).

Marks Policies

  • If you have a question about a mark you have received, please fill out, sign and submit this form.
  • Academic fraud will be taken very seriously. Cooperation between students for assignments is expected and encouraged, however, copying of another's work is not. You should not be leaving a discussion with copies of another student's work.

General Regulations

  • Attendance: Students are expected to attend all lectures and lab periods. The University requires students to have a conflict-free timetable. For more information, see the current Undergraduate Calendar, Academic Regulations of the University, Section 2.1.3, Course Selection and Registration and Section 2.1.7, Deregistration.
  • Health and Safety: Every student should have a copy of our Health and Safety Manual. A PDF copy of this manual is available online.
  • Deferred Term Work: Students who claim illness, injury or other extraordinary circumstances beyond their control as a reason for missed term work are held responsible for immediately informing the instructor concerned and for making alternate arrangements with the instructor and in all cases this must occur no later than three (3.0) working days after the term work was due. The alternate arrangement must be made before the last day of classes in the term as published in the academic schedule. For more information, see the current Undergraduate Calendar, Academic Regulations of the University, Section 4.4, Deferred Term Work.
  • Appeal of Grades: The processes for dealing with questions or concerns regarding grades assigned during the term and final grades is described in the Undergraduate Calendar, Academic Regulations of the University, Section 3.3.4, Informal Appeal of Grade and Section 3.3.5, Formal Appeal of Grade.
  • Academic Integrity: Students should be aware of their obligations with regards to academic integrity. Please review the information about academic integrity online. This site also contains a link to the complete Academic Integrity Policy that was approved by the University's Senate.
  • Plagiarism: Plagiarism (copying and handing in for credit someone else's work) is a serious instructional offense that will not be tolerated.

Academic Accommodation

You may need special arrangements to meet your academic obligations during the term. You can visit the Equity Services website to view the policies and to obtain more detailed information on academic accommodation online. For an accommodation request, the processes are as follows:
  • Pregnancy or Religious obligation: Please contact your instructor with any requests for academic accommodation during the first two weeks of class, or as soon as possible after the need for accommodation is known to exist. For more details see https://carleton.ca/equity/wp-content/uploads/Student-Guide-to-Academic-Accommodation.pdf
  • Academic Accommodations for Students with Disabilities: The Paul Menton Centre for Students with Disabilities (PMC) provides services to students with Learning Disabilities (LD), psychiatric/mental health disabilities, Attention Deficit Hyperactivity Disorder (ADHD), Autism Spectrum Disorders (ASD), chronic medical conditions, and impairments in mobility, hearing, and vision. If you have a disability requiring academic accommodations in this course, please contact PMC at 613-520-6608 or pmc@carleton.ca for a formal evaluation. If you are already registered with the PMC, contact your PMC coordinator to send me your Letter of Accommodation at the beginning of the term, and no later than two weeks before the first in-class scheduled test or exam requiring accommodation (if applicable). Requests made within two weeks will be reviewed on a case-by-case basis. After requesting accommodation from PMC, meet with me to ensure accommodation arrangements are made. Please consult the PMC website (www.carleton.ca/pmc) for the deadline to request accommodations for the formally-scheduled exam (if applicable).
  • Survivors of Sexual Violence: As a community, Carleton University is committed to maintaining a positive learning, working and living environment where sexual violence will not be tolerated, and where survivors are supported through academic accommodations as per Carleton’s Sexual Violence Policy. For more information about the services available at the university and to obtain information about sexual violence and/or support, visit: https://carleton.ca/sexual-violence-support/.
  • Accommodation for Student Activities: Carleton University recognizes the substantial benefits, both to the individual student and for the university, that result from a student participating in activities beyond the classroom experience. Reasonable accommodation must be provided to students who compete or perform at the national or international level. Please contact your instructor with any requests for academic accommodation during the first two weeks of class, or as soon as possible after the need for accommodation is known to exist. For more details, see https://carleton.ca/senate/wp-content/uploads/Accommodation-for-Student-Activities-1.pdf

Labs / Project

  • Completed labs must be submitted to the assignment drop box (4th floor ME) within one week (before the start of the following lab session).
  • A lab write up includes:
    • Answers to Questions (in the indicated boxes)
    • Print-outs of measured waveforms (labelled!!) as requried.
  • The Project will involve design and validation of a medical/fitness device
  • To get your kit, visit the SCE Office (4456, Mackenzie), bringing a signed Sign out form (page 1) and $99 payment (between each group of two) via Credit/Debit card.
  • Kit return instructions
    • Note #1: tech office is closed for kit return until 16 Dec.
    • Note #2: can sign off on kit returns at the final exam
    • Students will perform the last lab test. This process will test all components of the kits
    • Print the Sign out form (page 2), and ask the TA to sign off on the return sheet. (The TA will note that test has been done and all is working with the kit)
    • Students will then come to the technical office ME4224a with the signed sheet for a member of the technical staff to process the inventory of the kit.
    • Once a technical staff member has completed the inventory of the kit the technical staff member will sign off on the second sheet that the deposit can be refunded.
    • Students should note that if there are deficiencies in the kits there may be deductions in the deposited amount.
    • All wires are to be coiled neatly as they were handed out. If wires are not coiled students will have to wait until these wires are processed.
    • All items that were originally in the kit must be returned. Students are to ensure that there is no garbage left in the kit as this will delay the inventorying of the kits.
    • Once a member of the technical staff has inventoried the kit students will be directed to the department office, ME4456, to have their refund processed.
    • ALL kits must be returned by the end of the term. Groups that do not return kits will be reported to the department office.
    • Kits must be returned during tech staff office hours. These are Monday to Friday from 9am to 12pm and 1pm to 4pm. No kits will be taken outside of these hours.
  • In the lab, sign the Student Safety Contract and hand to the TA.
 
No.  Lab / Quesions  Date 
L1   Lab 1: Electrocardiogram (ECG)
Instructions, Report
  Sep. 9, Sep. 13  

P1   Project: Experiment design
Instructions: The lab session will be 3 hours. 1 hour for brainstorming, 1 hour for presentations and 1 hour for questions and discussion.
Presentation: will be 2 minutes with 2-3 minutes for questions.  Each group will prepare a presentation containing:
  • The goal of the project
  • The population that will be studied
  • The exact procedure and what will be recorded
    • number of participants (at least 4)
    • all actions taken by participants (number of repetitions and/or durations must be included)
    • measurements taken (how many recordings taken for how long)
    • time required for a participant to complete the trial
Deliverable: a one-page sheet describing the items in the Presentation, including any changes made because of the groups suggestion.
  Sep. 16, Sep. 20
 

L2   Lab 2: Electromyography (EMG)
Instructions, Report
  Sep. 23, Sep. 27  

P2   Project: Data collection
Instructions: During this lab session, students should acquire data from the participants. If data acquisition outside the lab is required, please coodinate with the TA. Make sure you verify that the data you collected is of good quality, so that the next steps are possible. Deliverable: a one-page sheet describing the data collected, as well as sample plots from one subject in various experimental phases.
  Sep. 30, Oct. 4
 

L3   Lab 3: Blood Pressure (BP)
Instructions, Report
  Oct. 7, Oct. 11  

  No labs, Thanksgiving and fall break   Oct. 14, Oct. 18,
Oct. 21, Oct. 25
 

P3   Project: Circuit design Design and construct a circuit to record ECG using the following components:
  • OP97 × 1
  • ISO124 × 1
  • AD620 × 1
  • LM741 × 4
  • 9 Volt Rechargeable/batteries × 2
  • Electrodes with snap
  • Stereo cable (To output the signal to the audio jack of a computer)
The kits should be collected before the 3rd project session (P3), instructions for pickup are above. More information on these components can be found on their data sheets.
The circuit should meet the following design requirements:
  • Correct isolation between the patient and the computer
  • Filtering of noise in the measured ECG signal
  Oct. 28, Nov. 1
 

L4   Lab 4: Pulse Oximetry (SpO2)
Instructions, Report (only a write-up on one subject required. Due date extended to Tuesday (12 Nov) for all sections.)
  Nov. 4, Nov. 8  

P4   Project: Circuit validation
Instructions: The following must be measured for the report and demonstrated to the TA:
  • Common mode gain
  • Differential mode gain
  • Low frequency cutoff and roll off rate
  • High frequency cutoff and roll off rate
  • Overall gain
  • Output ECG signal
  Nov. 11, Nov. 15
 

P5   Project: Heart-rate variability analysis
Due date: (Dec 6 in drop box ... will be picked up at noon on Dec 9)
Instructions: This project step involves analysing the data acquired in step P3 to answer the research question you identified in P1. During the lab you should:
  • Implement software to detect the QRS R-peaks in your data
  • Visually validate the accuracy of your R-peak detection
  • Choose an HRV parameter and implement software to calculate it
  • Explore the difference between HRV values in your experimental groups
The report combines the results for P4 and P5 and should have the following headings (each section doesn't need to be long … as long as each question is clearly answered):
  • Introduction: Description of the research question, motivation and background
  • Methods (Experimental): Summary of the experimental protocol and data you acquired.
  • Methods (Electronics Design): Description of circuit design and construction.
    • Figures:
      − circuit drawing with chip layouts
      − circuit drawing with 
    • Calculations: For each measure, explain how you measured it (what was the input? what was measured?)
      − Common mode gain 
      − Differential mode gain
      − CMRR
      − Cutoff frequencies 
      − Roll-off rate
  • Methods (HRV analysis): Description of the HRV analysis.
    − Show a sample of raw ECG data
    − Choose/Implement a method to detect QRS R-peaks
    − Validate (visually) the success of your R-peak detection.
    − Choose an HRV parameter and describe it
    − Describe and show the analysis software that you used/wrote
    − A plot of sample HRV results.
    − The HRV parameter values for each subject in the before/after group.
  • Discussion:
    − How did the circuit perform? Did it meet your expectations?
    − What did HRV analysis show? Were there any interesting physiological differences?
    − What is the answer to the scientific question you asked?
    − In light of these experiments, is your initial product idea a good one?
  Nov. 18, Nov. 22
Nov. 25, Nov. 29
Dec. 2, Dec. 6
 

Course Outline

Date   Activity   Questions  
Sep. 5   Introduction. Thorax Anatomy and Physiology.   AD620 (p.14)

Sep. 10   Medical Instrumentation.
01-Medical-Instrumentation,

Sep. 12, Sep. 17   Basic sensors and principles, Biopotential Amplifiers
02-Sensors, 03-biopotential-amplifiers
  09Q5,6,7,

Sep. 19   Review and Quiz #1
−Topics: Medical Devices, instruments and wearables; Accuracy, Sensitivity, Resolution, Precision; Medical Device Classifications in Canada; Resistive sensors; Wheatstone bridge circuit; Capacitive, inductive and piezoelectric sensors; Thermal sensors. Instrumentation amplifiers; CMRR.
−Some example Problems (from text): 2.2, 2.3, 2.4, 2.7, 3.5
  Quiz #1

Sep. 24 Sep. 26   Biopotentials: Muscles & EMG; EEG
04-biopotentials, 04a-electrical-safety

Oct. 1, Oct. 3   Filters, signal enhancement and noise reduction, QRS-peak detection, Ensemble averaging
05a-sampling+quantization, 05b-QRS-detection and HRV, The Loudness War [Youtube], Heart-rate detection in Matlab/Octave [Youtube]

Oct. 8   Review and Quiz #2
−Input and output impedances. Instrumentation amplifiers, and amplifier limitations: CMRR, IB, fT, SR (03-biopotential-amplifiers)
− Biopotentials: ECG, EMG, EEG. (04-biopotentials, not including electrical safety)
−Sampling and Quantization (05a-sampling+quantization) (not including QRS detection and Ensemble averaging)
  Quiz #2

Oct. 10 Oct. 15   Measurement of blood pressure and sound.
06a-blood-pressure, 06b-blood-pressure-measurement (updated),

Oct. 17   Measurement of blood flow and volume
06c-blood-flow,
Review

Oct 22, Oct 24   Fall Break (No Classes)

Oct 27   Midterm Review, 1−1:40pm: (zoom.us/f/3667616755)

Oct. 29   Midterm Exam (Class layout) Topics:   Midterm

Nov. 1   Pulse oxymeters, photoplethysmography.
Guest Lecture: S. Rajan
06d-photoplethysmography,

Nov. 5, Nov. 7   Flow measurement and Plethysmography
06e-flowmeters+plethysmography, 06f-doppler-ultrasound
08d-ultrasound.pdf

Nov. 12 Nov. 14 Nov. 19   Measurement of the Respiratory system
07a-lungs-intro, 07b-O2-transport, 07c-lung-mechanics

Nov. 19   Heart-rate variability
In-class code, Function freq_filt.m, data (zipped)

Nov. 21   Review and Quiz #3
−Topics: Blood Flow Measurement (06c-blood-flow), Photoplethysmography (06d-photoplethysmography), Flowmeters (06e-flowmeters+plethysmography), Ultrasound (08d-ultrasound.pdf) and Doppler Ultrasound (06f-doppler-ultrasound), Measurement of the Respiratory system (07a-lungs-intro, 07b-O2-transport, 07c-lung-mechanics)
  Quiz #3

Nov. 26 Nov. 28   Medical Imaging overview: X-rays, nuclear medical imaging, MRI
08a-Xray-CT, 08c-MRI

Dec. 3   Review and "Improvement" Quiz #4
(will replace worst quiz mark)
−Topics: Blood Flow Measurement (06c-blood-flow), Flowmeters (06e-flowmeters+plethysmography), and Doppler Ultrasound (06f-doppler-ultrasound), Measurement of the Respiratory system (07a-lungs-intro, 07c-lung-mechanics)
  Quiz #4

Dec. 5   Review

Dec. 16   Exam Office hours: 13h00−15h00

Dec. 18   Final Exam, 14:00−17:00
− Previous exams: 2009 MT#1, 2009 MT#2, 2009 Final.
Topics:
01-Medical-Instrumentation,
02-Sensors,
03-biopotential-amplifiers (Input and output impedances. Instrumentation amplifiers, and amplifier limitations: CMRR, IB, fT, SR )
04-biopotentials, 04a-electrical-safety
05a-sampling+quantization, 05b-QRS-detection and HRV,
06a-blood-pressure, 06b-blood-pressure-measurement, 06d-photoplethysmography, 06e-flowmeters+plethysmography, 06f-doppler-ultrasound
07a-lungs-intro, 07b-O2-transport, 07c-lung-mechanics
  Intro

Last Updated: $Date: 2019-12-21 10:09:03 -0500 (Sat, 21 Dec 2019) $