ENGG*4040 Medical Imaging Modalities
ENGG*4040 Medical Imaging Modalities01Fall 2021Section(s): C01School of EngineeringCredit Weight: 0.50Version 1.00 - September 09, 20211 Course Details1.1 Calendar DescriptionThe course will cover the basic knowledge of medical imaging systems, how they operate andto what uses they can be applied. Systems covered will include x-ray radiography, computedtomography, magnetic resonance imaging, positron emission tomography, gama cameras,and ultrasound imaging. Emphasis will be on the underlying physics and computation,highlighting factors affecting image quality, patient safety, and clinical use.Pre-Requisites:Restrictions:ENGG*3390 or PHYS*3130PHYS*40701.2 Course DescriptionMATH*1210, PHYS*11301.3 TimetableThe timetable is subject to change. Please see WebAdvisor/CourseLink for the latestinformation.LecturesTuesdayAll SectionsVirtual1:00PM-2:20PMAll SectionsVirtual1:00PM-2:20PMMondaySec 0102THRN, Room23079:30AM-11:20AMMondaySec 0103THRN, Room1:30PM-3:20PMLectures/TutorialsThursdayLabs
ENGG*4040 C01 F21 v1.002307ThursdaySec 0101THRN, Room23079:30AM-11:20AM##Look on CourseLink for updates.1.4 Final ExamExam: December 11, 2021Time: 7 pm to 9 pm (2 hours)Exam time is subject to change. Please see WebAdvisor/CourseLink for the latestinformation.2 Instructional Support2.1 Instructional Support TeamInstructor:Eran Ukwatta PhD, 20 x53404Office:Richards 1507Office Hours:Wednesdays from 10.30 am to 11.30 am.Official hour will be offered virtually through a video conference software. Any changes to theoffice hours in a given week will be communicated in advance.**Communication by email, phone, CourseLink or video-conference software is muchpreferred to in-person communication.Lab Technician:Email:Telephone:Office:Office Hours:Ahmed Mezilamezil@uoguelph.ca 1-519-824-4120 x53729THRN 2308TBA2.2 Teaching AssistantsTeaching Assistant (GTA):Email:Office:Office Hours:Jenita Manokaranjrajaman@uoguelph.caTHRN 2319TBAPage 2 of 13
ENGG*4040 C01 F21 v1.003 Learning Resources3.1 Required ResourcesCourse Website (Website)http://courselink.uoguelph.caCourse material, news, announcements, and grades will be regularly posted to theENGG*4040CourseLink site. You are responsible for checking the site regularly.J. L. Prince & J. M. Links, Medical Imaging Signals and Systems (2nd Edition), PearsonPrentice Hall, 2014. ISBN: 0-13-214518-9. (Textbook)In my opinion, there is no single book which covers all the material for this course in itsentirety.Therefore supplementary material will be suggested to students as the course proceeds.3.2 Reference BookDigital Image Processing for Medical Applications by Geoff Dougherty, Cambridge UniversityPress, ISBN: 97805218608573.2 Lecture InformationAll the lecture notes are posted on the web page usually a day before the lecture(week #1-#13).3.2 Lab InformationLabs will take place every other week for each group of students. Students are expected toacquire the required data to complete the lab during the lab session. The Lab 1 will be solelybased on Matlab and Lab 5 will be based on 3D Slicer. Labs 2-4 will require you to use theDeskCAT system, an optical CT scanner. The handouts and/or supplementary data for all thelab sessions are within the lab section of the website. Lab reports will be due in two weeksafter the completion of the lab and should be submitted using CourseLink.The TA or the lab coordinator will be available during the off weeks to respond to your lab andproject questions.3.2 AssignmentsAssignments are due according to the schedule given in this outline. Any updates ondeadlines will be posted on the course website.3.2 ExamsAll the exams in this course (i.e, midterm and final exam) are open book. You are allowed tohave your course notes, the course textbook (Medical Imaging Signals and Systems) andcalculator. Browsing of any other material on the Internet on cell phones, computers, andother electronic devices are not allowed.Page 3 of 13
ENGG*4040 C01 F21 v1.003.2 Miscellaneous InformationAny other relevant information will also be posted on the web page in Courselink.4 Learning OutcomesThis course aims to familiarize students with existing imaging modalities from both anengineering and clinical/practical perspective. Students are exposed to the underlyingphysics and engineering to understand their implications in the clinical settings. Numerousapplications of the various imaging modalities will be explorered.4.1 Course Learning OutcomesBy the end of this course, you should be able to:1. Describe the physics and engineering design of various medical imaging modalities(ultrasound, x-ray, CT, PET, SPECT, MRI & NMR, digital histopathology)2. Apply knowledge of fundamental engineering principles in implementing concepts ofmedical imaging systems and solving problems3. Examine artifacts and defects in imaging systems and challenges in in-vivo imaging ofhumans4. Operate several model hardware to acquire imaging data5. Write programming code in Matlab to process medical imaging data6. Utilize analysis methods and models to extract clinically relevant information frommedical images7. Compare the technical strengths and limitations of imaging modalities for a given clinicalapplication4.2 Engineers Canada - Graduate Attributes (2018)Successfully completing this course will contribute to the following:#OutcomeLearningOutcome1Knowledge Base1, 21.3 Recall, describe and apply fundamental engineering principles and1concepts1.4 Recall, describe and apply program-specific engineering principles and2concepts3Investigation2, 3, 4, 63.2 Design and apply an experimental plan/investigative approach (forPage 4 of 132, 6
ENGG*4040 C01 F21 v1.00#OutcomeLearningOutcomeexample, to characterize, test or troubleshoot a system)3.3 Analyze and interpret experimental data43.4 Assess validity of conclusions within limitations of data and methodologies 3, 65Use of Engineering Tools3, 5, 75.2 Demonstrate proficiency in the application of selected engineering tools5, 75.3 Recognize limitations of selected engineering tools3, 75 Teaching and Learning ActivitiesThe following is a tentative list of topics covered in the class. As the course progress, theorder in which the topics are covered is subject to change.5.1 LectureWeek 1Topics:Introduction of the CourseWeek 2Topics:Overview of Medical Imaging Modalities & SignalProcessingWeek 3Topics:Signals and Systems (specific focus on FourierTransform)Week 4Topics:Image QualityWeek 5Topics:Projection RadiographyWeeks 6 & 7Page 5 of 13
ENGG*4040 C01 F21 v1.00Topics:Computed TomographyWeek 8Topics:Physics of Ultrasound ImagingWeek 9Topics:Ultrasound Imaging Systems and ApplicationsWeeks 10 & 11Topics:Nuclear Medicine: PET and SPECTWeeks 11 & 12Topics:Magnetic Resonance Imaging (MRI)Week 12Topics:Applications of Medical Imaging ModalitiesWeek 13Topics:Postprocessing of Medical Images5.2 LabMon, Sep 20 - Thu, Sep 23Topics:Fourier Transform (Based on Matlab)There will also be a safety training at the beginning ofthe lab.Learning Outcome:5Mon, Sep 27 - Thu, Sep 30Topics:Lab 1 Follow-up Hour(s)Mon, Oct 4 - Thu, Oct 7Page 6 of 13
ENGG*4040 C01 F21 v1.00Topics:Evaluation of Image Quality (Based on DeskCATsystem)Learning Outcome:3, 4Wed, Oct 13 - Thu, Oct 14Topics:Lab 2 Follow-up Hour(s)Mon, Oct 18 - Thu, Oct 21Topics:CT Reconstruction (Based on DeskCAT system)Learning Outcome:1, 2Mon, Oct 25 - Thu, Oct 28Topics:Lab 3 Follow-up Hour(s)Mon, Nov 1 - Thu, Nov 4Topics:SPECT Reconstruction (Based on DeskCAT system)Learning Outcome:4Mon, Nov 8 - Thu, Nov 11Topics:Lab 4 Follow-up Hour(s)Mon, Nov 15 - Thu, Nov 18Topics:Postprocessing of Imaging Data (Based on 3DSlicerand/or Matlab)Learning Outcome:6Mon, Nov 22 - Thu, Nov 25Topics:Lab 5 Follow-up Hour(s)5.3 Other Important DatesMonday, October 11, 2021: Holiday -- No Classes Scheduled -- Classes rescheduled toFriday, December 3Tuesday, October 12 2021: Fall Study Break Day -- No Classes Scheduled -- classesrescheduled to Thursday, December 2Page 7 of 13
ENGG*4040 C01 F21 v1.00Thursday, December 2, 2021: Make up for Study Day (Tuesday Schedule)Friday, December 3, 2021: Make up for Holiday, Last day to drop F21 one semester courses(Monday Schedule)6 Assessments6.1 Marking Schemes & DistributionsNameScheme A (%)Assignment #15Assignment #25Lab experiments & Reports (3 marks each)15Group Project15Midterm20Final Exam40Total1006.2 Assessment DetailsAssignment #1 (5%)Due: Thu, Oct 7, 11:59 PMLearning Outcome: 1, 2This assignment will be released on September 23nd.Assignment #2 (5%)Due: Thu, Nov 25, 11:59 PMLearning Outcome: 1, 2The Assignment will be released on November 11th.Lab Reports (15%)Learning Outcome: 3, 4, 5, 6Each lab is weighted equally.A report must be submitted for each lab where it is due in two weeks after the scheduledlab date. The lab report should be brief and must contain information on acquired data andrelevant comments along with answers to the corresponding lab questions. Labs are to becompleted in groups of 1-3. You are responsible to ensure that you/or your group submitthe report.Page 8 of 13
ENGG*4040 C01 F21 v1.00Group Project (15%)Due: Thu, Dec 2, 11:59 PMLearning Outcome: 6, 7The group project will consist of some analytical questions and Matlab experiments relatedto the lecture material of the course. The final report and associated files are to besubmitted electronically on CourseLink. Please follow the naming convention for filesprovided in the project question sheet.Midterm Test (20%)Date: Tue, Oct 19, VirtualLearning Outcome: 1, 3, 7Midterm will be held during the regular class.Final Exam (40%)Date: Fri, Dec 11, 7:00 PM, VirtualLearning Outcome: 1, 3, 67 Course Statements7.1 Course Grading PoliciesMissed Assessments: If you are unable to meet an in-course requirement due to medical,psychological, or compassionate reasons, please email the course instructor. See theundergraduate calendar for information on regulations and procedures for tmlAccommodation of Religious Obligations: If you are unable to meet an in-course requirementdue to religious obligations, please email the course instructor within two weeks of the startof the semester to make alternate arrangements. See the undergraduate calendar forinformation on regulations and procedures for Academic Accommodation of lig.shtmlPassing grade: In order to pass the course, you must pass the overall course and examportions (midterm and final exam). Students must obtain a grade of 50% or higher on thecombined exam and midterm portions (with above weights, i.e. [0.4 x Exam Mark (in %) 0.20x Midterm Mark (in %)] 30.0%) of the course in order to pass the course.Missed midterm tests: If you miss a test due to grounds for granting academic considerationor religious accommodation, the weight of the missed test will be added to the final exam.Page 9 of 13
ENGG*4040 C01 F21 v1.00Lab Work: You should participate in all laboratories. If you miss a laboratory, arrangementsmust be made with the instructor.Late Assignments & Projects: Late submissions of assignments will be subject to a penalty(usually 20%/day). Assignments and projects more than 2 days late will not be accepted.8 School of Engineering Statements8.1 Instructor's Role and Responsibility to StudentsThe instructor’s role is to develop and deliver course material in ways that facilitate learningfor a variety of students. Selected lecture notes will be made available to students onCourselink but these are not intended to be stand-alone course notes. Some written lecturenotes will be presented only in class. During lectures, the instructor will expand and explainthe content of notes and provide example problems that supplement posted notes.Scheduled classes will be the principal venue to provide information and feedback for testsand labs.8.2 Students' Learning ResponsibilitiesStudents are expected to take advantage of the learning opportunities provided duringlectures and lab sessions. Students, especially those having difficulty with the course content,should also make use of other resources recommended by the instructor. Students who do(or may) fall behind due to illness, work, or extra-curricular activities are advised to keep theinstructor informed. This will allow the instructor to recommend extra resources in a timelymanner and/or provide consideration if appropriate.8.3 Lab SafetySafety is critically important to the School and is the responsibility of all members of theSchool: faculty, staff and students. As a student in a lab course you are responsible for takingall reasonable safety precautions and following the lab safety rules specific to the lab you areworking in. In addition, you are responsible for reporting all safety issues to the laboratorysupervisor, GTA or faculty responsible.9 University Statements9.1 Email CommunicationAs per university regulations, all students are required to check their e-mail account regularly:e-mail is the official route of communication between the University and its students.9.2 When You Cannot Meet a Course RequirementWhen you find yourself unable to meet an in-course requirement because of illness orcompassionate reasons please advise the course instructor (or designated person, such as aPage 10 of 13
ENGG*4040 C01 F21 v1.00teaching assistant) in writing, with your name, id#, and e-mail contact. The grounds forAcademic Consideration are detailed in the Undergraduate and Graduate Calendars.Undergraduate Calendar - Academic Consideration and /undergraduate/current/c08/c08-ac.shtmlGraduate Calendar - Grounds for Academic e Diploma Calendar - Academic Consideration, Appeals and rs/diploma/current/index.shtml9.3 Drop DateStudents will have until the last day of classes to drop courses without academic penalty. Thedeadline to drop two-semester courses will be the last day of classes in the second semester.This applies to all students (undergraduate, graduate and diploma) except for Doctor ofVeterinary Medicine and Associate Diploma in Veterinary Technology (conventional andalternative delivery) students. The regulations and procedures for course registration areavailable in their respective Academic Calendars.Undergraduate Calendar - Dropping /undergraduate/current/c08/c08-drop.shtmlGraduate Calendar - Registration ociate Diploma Calendar - Dropping /diploma/current/c08/c08-drop.shtml9.4 Copies of Out-of-class AssignmentsKeep paper and/or other reliable back-up copies of all out-of-class assignments: you may beasked to resubmit work at any time.9.5 AccessibilityThe University promotes the full participation of students who experience disabilities in theiracademic programs. To that end, the provision of academic accommodation is a sharedresponsibility between the University and the student.When accommodations are needed, the student is required to first register with StudentAccessibility Services (SAS). Documentation to substantiate the existence of a disability isrequired; however, interim accommodations may be possible while that process is underway.Accommodations are available for both permanent and temporary disabilities. It should benoted that common illnesses such as a cold or the flu do not constitute a disability.Page 11 of 13
ENGG*4040 C01 F21 v1.00Use of the SAS Exam Centre requires students to book their exams at least 7 days in advanceand not later than the 40th Class Day.For Guelph students, information can be found on the SAS websitehttps://www.uoguelph.ca/sasFor Ridgetown students, information can be found on the Ridgetown SAS bilityservices.cfm9.6 Academic IntegrityThe University of Guelph is committed to upholding the highest standards of academicintegrity, and it is the responsibility of all members of the University community-faculty, staff,and students-to be aware of what constitutes academic misconduct and to do as much aspossible to prevent academic offences from occurring. University of Guelph students havethe responsibility of abiding by the University's policy on academic misconduct regardless oftheir location of study; faculty, staff, and students have the responsibility of supporting anenvironment that encourages academic integrity. Students need to remain aware thatinstructors have access to and the right to use electronic and other means of detection.Please note: Whether or not a student intended to commit academic misconduct is notrelevant for a finding of guilt. Hurried or careless submission of assignments does not excusestudents from responsibility for verifying the academic integrity of their work beforesubmitting it. Students who are in any doubt as to whether an action on their part could beconstrued as an academic offence should consult with a faculty member or faculty advisor.Undergraduate Calendar - Academic Graduate Calendar - Academic ars/graduate/current/genreg/index.shtml9.7 Recording of MaterialsPresentations that are made in relation to course work - including lectures - cannot berecorded or copied without the permission of the presenter, whether the instructor, a student,or guest lecturer. Material recorded with permission is restricted to use for that course unlessfurther permission is granted.9.8 ResourcesThe Academic Calendars are the source of information about the University of Guelph’sprocedures, policies, and regulations that apply to undergraduate, graduate, and diplomaprograms.Academic rsPage 12 of 13
ENGG*4040 C01 F21 v1.009.9 DisclaimerPlease note that the ongoing COVID-19 pandemic may necessitate a revision of the format ofcourse offerings, changes in classroom protocols, and academic schedules. Any suchchanges will be announced via CourseLink and/or class email.This includes on-campus scheduling during the semester, mid-terms and final examinationschedules. All University-wide decisions will be posted on the COVID-19 virus-information/) and circulated by email.9.10 IllnessMedical notes will not normally be required for singular instances of academic consideration,although students may be required to provide supporting documentation for multiple missedassessments or when involving a large part of a course (e.g. final exam or majorassignment).9.11 Covid-19 Safety ProtocolsFor information on current safety protocols, follow these links: of-g-is-preparing-for-yoursafe-return/ /#ClassroomSpacesPlease note, these guidelines may be updated as required in response to evolving University,Public Health or government directives.Page 13 of 13
The course will cover the basic knowledge of medical imaging systems, how they operate and to what uses they can be applied. Systems covered will include x-ray radiography, computed tomography, magnetic resonance imaging, positron emission tomography, gama cameras, and ultrasound imaging. Emphasis will be on the underlying physics and computation,
1. Medical imaging coordinate naming 2. X-ray medical imaging Projected X-ray imaging Computed tomography (CT) with X-rays 3. Nuclear medical imaging 4. Magnetic resonance imaging (MRI) 5. (Ultrasound imaging covered in previous lecture) Slide 3: Medical imaging coordinates The anatomical terms of location Superior / inferior, left .
Medical X-Ray Medical Imaging N/A N/A 5-100 Tc-99m Medical Imaging (SPECT) 6.02 hours J 140.5 Tl-201 Medical Imaging (SPECT) 73 hours H 135, 167 In-111 Medical Imaging (SPECT) 2.83 days H 171, 245 F-18 Medical Imaging (PET) 1.83 hours E 511 Ga-68 Medical Imaging (PET) 68 minutes E 511 Cs-137 Fission Product 30.17 years E- 662
Physical Therapy Modalities This protocol is intended as a quick reference for the application of a variety of physical therapy modalities, including cryotherapy, thermotherapy, ultrasound and electrotherapy. The modalities are presented in alphabetical order. Many physical therapy modalities
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Medical Imaging Non-invasive visualization of internal . Image - a two-dimensional signal, I(x,y) - I typically include non-imaging sensing (e.g. 1D techniques) as an imaging modality. 2 Major Modalities Projection X-ray X-ray Computed Tomography Nuclear Medicine Ultrasound Magnetic Resonance Imaging Projection .
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This study investigated microRNA and mRNA expression and protein function associated with DNA repair in human oocytes and embryos. MicroRNAs have been shown to down-regulate and in some cases to stabilise the expression of several genes including repair genes. The first aim of this study was to analyse the differences in the expression of microRNAs and their target mRNAs involved in repair .
