Course Description

This course builds upon the foundations of Engineering in Medical Imaging in the Clinical Service Engineering certificate, to walk through the operation and implementation of medical imaging systems in a clinical environment, particularly focusing on configuring equipment, designing operational workflows, programming and networking systems, managing data through complex interfaces, and analyzing images.  The course begins with an overview of circuits for digital x-ray imaging, including noise reduction strategies, then transitions into networking interfaces and connectivity, including virtual labs and trouble-shooting exercises for iterative problem-solving, then transitions into an introduction to medical image processing techniques.  The Medical Image Processing Section introduces essential concepts to understand medical images as well as practical computational methods that can visualize, enhance, and analyze medical images to assist in disease diagnosis and therapeutic planning.

Throughout the course, emphasis is given to practical applications and real-world case studies of the foundational concepts.

Prerequisites:

Course 1 in the Clinical Service Engineering certificate, or instructor consent.

Textbooks:

While there is no required textbook for this class, you may find it helpful to refer to the following textbooks for different aspects of the course:

• Introduction to Medical Image Analysis, by Paulsen, Rasmus R.; Moeslund, Thomas B.
  • ISBN 13: 9783030393632
• From Signals to Image: A Basic Course on Medical Imaging for Engineers, by Azhari, Haim; Kennedy, John A.; Weiss, Noam; Volokh, Lana.
  • ISBN 13: 9783030353254
• Medical Imaging: Principles, Detectors, and Electronics, by Krzysztof Iniewski (Editor) 
  • ISBN: 9780470391648
• Medical Imaging for Health Professionals, by Raymond M. Reilly (Editor)
  • ISBN: 9781119120285 

  Course Organization

Topics, Modules, and sub-modules include:

• Noise
• Noise Sources & Mechanisms
  • Noise Models
  • Capacitive Coupling
  • Impact Ionization
  • Physical Properties
  • Power Distribution Networks
  • Substrates
• Noise Characterization
• Networking
• Windows Server
  • Introduction to Virtualization
  • Virtual Environment Configuration
  • Problem Step Recorder
  • Task Manager
  • Disk Management
  • Services
  • Roles & Features
  • Backup/Restore
  • User Account Manager
  • Windows Server Commands
  • Network Cards
  • Firewall
  • Cloud Resources with AWS
• Networking Basics
  • Network Topology
  • Ethernet
  • TCP/IP
  • Subnetting
  • Routing and Default Gateway
  • Name Resolution
  • Networking Troubleshooting Commands
• Linux Operating System
  • Virtual Environment Configuration
  • User Interface and Shell
  • Unix Basic Commands
  • Users and Groups
  • File permissions
  • Computer Network Overview
  • Open SSH tools
• Medical Image Processing
• MATLAB for Medical Image Processing
• Introduction to medical images
  • Types
  • Digital format
  • Geometry
  • Resolution
  • Contrast
  • Dynamic range
  • DICOM
  • 2D/3D visualization
• Image enhancement
  • Contrast enhancement
  • Noise removal
  • Filtering
• Image segmentation
  • Thresholding
  • Clustering
  • Active contour
  • Morphological processing
• Image registration
  • Rigid/non-rigid transformation
  • Optimization

This course has considerable breadth, as one might expect from the list of topics.  Each segment of the networking module has an associated laboratory with it.  Students are expected to read approximately 2 – 3 hours of reading, watch approximately 5 – 7 hours of lecture videos, and complete about 6 hours of assessments (homework, laboratories, discussion boards, etc.) each week. 

Goals:

The course aims to fulfill several academic and professional goals, including ABET Student Outcomes:

• Apply knowledge of math, science, and engineering (ABET Outcome 1)
• Cultivate critical thinking (ABET Outcome 1)
• Prepare students to work in a medical imaging field

 Objectives

At the end of the course, students should be able to: 

1. Diagram, and explain using words and theory, the circuit implementation for X-Ray detectors.
2. Describe common noise problems in detector systems and explain the root cause and solutions for each.
3. Demonstrate the appropriate use of noise reduction techniques for a given noise problem.
4. Explain, using words and diagrams, the various networking methods used to connect and transfer medical image data from or between medical imaging systems and workstations.
5. Demonstrate how to correctly network imaging systems using Windows Server and DICOM.
6. Explain, using words and diagrams, the overarching image process and analysis framework through which medical images are acquired and reviewed.
7. Describe, using words, diagrams, and theory, the primary types of image/video processing and analysis methods, how they function, and how they relate to each other.

Instructor

Instructor:

Prof. Changyu Sun

Email: [email protected]

Office Hours:

I will send a whenisgood poll out to find a time for office hours for the term; office hours will be held via Zoom.  The purpose of office hours is to provide help with the homework and to answer any questions regarding general concepts or solving problems.  Office hours are synchronous (live or real-time), in that I will be answering questions as I receive them.  We will also use office hours for exam reviews; if you have questions but can't make the office hours, please post to the Exam Review discussion board, and I will respond within 36 hours.

 Assignments

Homework Policies

1. Homework is due at 11:59 pm central time on Fridays; it will be submitted online via Canvas.
   1. Homework is late if it is turned in after 11:59 pm.
   2. Late homework will be given a zero.
2. Each problem will be graded with partial credit. However, in order to earn partial credit, you must do the following:
   1. Fully comment your work. This means that, instead of pulling an equation out of the air (or your notes or books), tell me what the equation is (i.e., Fick’s Law), so I or the grader know what you are doing.  Also, write out the steps so we can accurately follow your thought process.
   2. Explain your reasoning for using certain equations or doing the steps you did.
   3. If you use a reference (published paper, textbook, website) to find information, including for diagrams, graphs, etc., list the source as a reference at the end of the problem you used it in. Not including a reference when it is obvious you used a reference will cause a 1 point deduction from that problem’s grade. 
3. Homework sets should be written in the following way:
   1. All sets should be turned in as a .pdf file named “Your Last Name – HW # - Collaborators’ Last Names.” They should be written on a blank white background to make grading easier.  Please number your pages.  Collaborators should be clearly indicated on the top of the first page.
   2. List the information that has been given to you in the problem statement.
   3. State the assumptions (in a list at the beginning of each problem) you are working with to do the problem.
   4. Draw a diagram of your system if a diagram is possible, and fully label it, along with definitions of all your variables. This helps me see if you’ve done something wrong from the start so I can give you as much credit as possible. Diagrams are required for:
      1. Problems with stated dimensions (either in numbers or variables) or geometries
      2. Problems with stated forces (either in numbers, variables, or general descriptions)
      3. If you don’t know if a diagram is required: ASK ME!
   5. Define ALL your variables, so I can follow your math.
   6. Comment your work.
   7. Once completed, make a single .pdf file that combines all pages. You may use CamScanner (a free app for smart phones) or another piece of software to do this.  Note that the final file must be legible, so be sure the resolution is high enough!
4. Standard deductions:
   1. Missing figures/graphs                 10%
   2. Variables not defined                 10 %
   3. Wrong final answer                 10 %
   4. Wrong unit/conversion                 10 %
   5. Missing reference                 5%
   6. Assumptions not listed                 5%
5. Lastly, if I or the grader cannot read your handwriting, I will give your sets a zero. Make sure you write neatly so I can give you the grade you deserve. 

Extra Credit

There are two choices for extra credit in this class.  You may do both of them as you wish, but they are all due on the last Thursday of the class at midnight CST.  Keep in mind that you will earn extra credit on the quality of your work, so the maximum you can earn is not necessarily what you will earn. 

1. Sample exam problems (≤ 2.0%)
   1. Write 1 creative exam problem, with step-by-step, detailed solutions. Include all figures, equations, etc. needed for the problem.
   2. Check the extra credit problems given on assignments for types of “creative” or “fun” problems that would be appropriate.
   3. Higher credit will be given to problems that involve protagonists from under-represented groups (women, people of color, etc.), as these groups are typically under-represented on engineering homework and exams.
2. Creativity assignment (≤ 1.0%)
   1. Submit a creative work - made entirely by you - that accurately describes something (engineering related) that you learned from the class.
   2. This could be a video, a children’s book, an at-home activity that K12 students could do, an interpretive dance – whatever you want. But you need to make it – you can’t just buy something from the store and bring it in.  Not acceptable: anything that is illegal or unethical,

Quizzes 

During lecture videos, you may have (un-graded) self-check quizzes. These are for your benefit to make sure you understand the basic concepts. 

 Discussions

Each week, you will be required to do a read/review/respond activity.  This activity is intended to help you identify areas in which I can help you, and for you to practice what you’ve learned. 

1. By Tuesday at midnight, central time, of each week, you will be required to respond to one discussion board prompt for that week. Responses must be 50 words minimum. (Up to five points)
2. Once you have posted your response, you will be able to see other students’ responses to the prompts.
3. Then, by Friday at midnight, central time of the next week, you should post ONE response to another student’s response. Response must be 25 words minimum.  (Up to five points)

Please note that you will be graded on the quality of your responses.  While it is relatively easy to post numerous, non-substantive comments, it takes more thought and effort to post intelligent, meaningful comments that move the discussion forward. For example, meaningful posts tend to:

• Provide concrete examples, perhaps from your own experience
• Identify consequences or implications
• Challenge something that has been posted – perhaps by playing - devil’s advocate
• Pose a related question or issue
• Suggest a different perspective or interpretation
• Pull in related information from other sources – books, articles, websites, courses, etc.

Expectations for Online Etiquette

Your instructor and fellow students wish to foster a safe online learning environment. All opinions and experiences, no matter how different or controversial they may be perceived, must be respected in the tolerant spirit of academic discourse. You are encouraged to comment, question, or critique an idea but you are not to attack an individual.

Our differences, some of which are outlined in the University's nondiscrimination statement at the end of the syllabus, will add richness to this learning experience. Please consider that sarcasm and humor can be misconstrued in online interactions and generate unintended disruptions. Working as a community of learners, we can build a polite and respectful course ambience.

Diversity

We value the voice of every student in this course. We embrace our diversity as a group—in race, gender, age, sexual orientation and gender identity, religion, language, ability, culture, ethnicity, socioeconomic and veteran status, —is an asset, resource and strength that is critical to our learning experience.  As a result, we are committed to designing inclusive lessons and assignments that encourage diverse perspectives to be recognized and respected, while providing you with the opportunity to speak and be heard, explore your own understanding, and engage with one another.

 Assessment and Grading

Examination Policies 

1. The final exam will be cumulative.
2. The exam will be closed book, closed notes, closed friends, and will be available on Canvas. 
3. The exam will be proctored; you may choose from the proctoring options listed on the Exam which works best for you (in-person proctoring, live online proctoring, etc.).
4. You may take the exam at a time convenient for you; however, the exam will be due at midnight on the indicated date.  You must schedule your exam with whichever proctoring method you choose two weeks prior to the due date.
5. All equations required for the exam will be given to you on the exam.

If you wish me to re-grade your exam, I will be happy to do so, but I will re-grade the entire exam, not just the problem about which you have concerns. Frequently, I find areas where I gave too much credit, in comparison to how I graded your peers, and in those cases, I will be required to mark off to correct the discrepancy. Keep this in mind if you ask for a re-grade.

Grading:

Homework:                                           65%

Discussion Boards:                              10%

Examinations:                                      25%

The grades will be based on the following grading scale (there is no curve):

              92.00 – 100.00%                  A 

                                90.00 – 91.99%                    A-

                                89.00 – 89.99%                    B+

                                82.00 – 88.99%                    B

                                80.00 – 81.99%                    B-

                                79.00 – 79.99%                    C+

                                72.00 – 78.99%                    C

                                70.00 – 71.99%                    C-

                                69.00 – 69.99%                    D+

                                62.00 – 68.99%                    D

                                59.00 – 61.99%                    D-

Grade Questions:

Using Canvas, you will be able to keep track of your overall class grade throughout the term via the “Class Grade” column.  This means that you have no reason to be surprised by your final grade going into the last exam.  If you are concerned about your grade, please set up a meeting with me via email, and we can discuss what options you have to improve your situation.

Once final grades are posted, I do not change them.  Since you have access to your class grade, including your final exam, online, it behooves you to affect your grade before the final exam.  It is not appropriate for students to tell faculty that they think they deserve a better grade, to ask for a grade increase outright, or to suggest that you had no idea you weren’t doing well, and therefore should be graded with leniency.  Your TA and I spend a large amount of time very carefully planning and grading your homework sets and exams.  Please respect that by not contacting us after your final grades are posted to fish for a higher grade.   

Policies Regarding Uncontrollable Circumstances / Sickness

Each year, I have students ask for things like extensions, make-up quizzes / exams, etc., for circumstances ranging from a death in the family to hangovers.  My policy is, generally, that we are all adults.   It is your responsibility to ensure that your work is complete and on time.  With that being said, sometimes things happen that are out of your control, and I don’t want you to be penalized for those.

Below, I give lists of uncontrollable circumstances, what the policies are in these cases, and also what are not eligible circumstances.  If in doubt, please ask me.  If in doubt, get a doctor’s note or go to the Disability Center to discuss accommodations for temporary disabilities (like a concussion).  Absences or late submission of coursework caused by unexpected dependent care obligations will be treated as equivalent to those caused by illness of the student themselves. Unexpected dependent care obligations would include, for example, short notice of early closing of Columbia Public Schools, or sickness of a child or other dependent. Basically, I just want notice and some evidence of what is happening so I can work with you to find an appropriate alternative arrangement.

1. Uncontrollable Circumstances may include, but are not limited to:
   1. Death in the family
   2. Hospitalization
   3. Contagious sickness
   4. Needing medications that alter your mental state
   5. Needing to care for a sick family member
   6. Unexpected dependent care obligations
   7. Accident that impairs you
   8. Interview for a job
   9. Work conflict that you have made a good-faith effort to rearrange
   10. Travel for class, professional society in your field, or research-related reasons, including interviews, conferences, site visits, etc.
   11. Disabilities of any kind that have been accommodated through the Disability Center
   12. Athletics that have been accommodated through the Athletics Program and Provost’s Office. For instance, if you are on the track team and will miss something due to a race.
2. Controllable Circumstances may include, but are not limited to:
   1. Your work schedule. You have all the dates in advance so that you may work around tests, homework, etc.  You also have all the homework in advance.  You need to plan accordingly.  I am happy to contact your supervisor if that would help with rearranging schedules.
   2. The university’s sports schedules. I know they are fun, but you make the decision on whether or not you watch or go to the games.
   3. Your workout schedules, competitions, intramural activities, or other activities that you choose to participate in that are not accommodated by the university.
   4. Your social life.
3. Documentation may include:
   1. Notes from your family
   2. Notes from your doctor
   3. Receipts that you’ve bought medication (although I may ask for more evidence)
   4. Notes from your roommates
   5. Notes from your family member’s school/daycare/care facility
   6. Any appropriate, safe-for-work, evidence that would convince a reasonable person
4. Uncontrollable Circumstances Policies:
   1. If you have documentation, and have emailed me ahead of time, you may:
      1. Turn in homework electronically by the deadline without penalty
      2. Be given an extension on the homework if the situation warrants it
      3. Make-up any in-class quizzes
      4. Make-up any exam scheduled for that day
      5. Be given copies of the lecture notes if you arrange to do so
   2. If you do not have documentation, and have emailed me ahead of time, you may:
      1. Turn in homework electronically by the deadline without penalty
      2. Make-up any quizzes if you arrange with me to do so
      3. Be given copies of the lecture notes if you arrange to do so

Course Completion

Where we fit in the curriculum:

This class is intended to be taken in your junior or senior year after having two terms of undergraduate Calculus and Physics and after having taken Engineering in Medical Imaging in the Clinical Service Engineering certificate.  This course may be followed by any engineering course that focuses on a specific medical imaging technique, either from a physics or engineering perspective, or provides an overview of medical imaging techniques, image analysis, or applications of medical imaging.  Additionally, this course may be followed by design work where the student learns to design/build/test medical imaging equipment for specific use-cases.  While courses in networking or programming are not required for this course, some topics will naturally dovetail with topics you may learn in that course. 

  Accommodations and Academic Dishonesty 

Statement for ADA:

If you anticipate barriers related to the format or requirements of this course or if you have emergency medical information to share with me, please let me know as soon as possible. If disability related accommodations are necessary (for example, a note taker, extended time on exams, captioning), please contact MU Extension ADA Support as soon as possible so we can provide you with appropriate accommodations.  

Statement for Academic Dishonesty:

Academic integrity is fundamental to the activities and principles of a university.  All members of the academic community must be confident that each person's work has been responsibly and honorably acquired, developed, and presented.  Any effort to gain an advantage not given to all students is dishonest whether or not the effort is successful.  The academic community regards breaches of the academic integrity rules as extremely serious matters.  Sanctions for such a breach may include academic sanctions from the instructor, including failing the course for any violation, to disciplinary sanctions ranging from probation to expulsion.  When in doubt about plagiarism, paraphrasing, quoting, collaboration, or any other form of cheating, consult the course instructor.

  Technical Requirements

This course uses the Canvas Learning Management System.  In addition to Canvas, you will use external tools, such as links to research articles on their journal websites, YouTube videos, and document preparation/processing tools, such as the Microsoft Office suite or similar tools.  The minimum technology requirements for this course can be found here. In addition to these, this course also requires access to a working video/web camera and microphone for several of the activities. 

Students will be expected to be familiar with typical document preparation/processing software, such as the Microsoft Office Suite (or similar tools from other companies).  

Students will be expected to be able to use basic internet searches through the search engine of their choice, as well as using resources from the Mizzou Libraries.  

See our Getting Started with Canvas page for short tutorial videos to provide an overview of Canvas.  Download the Canvas Student App to access your Canvas course from your mobile device.

For the best user experience, we recommend using  Google Chrome as your browser (Safari for Macintosh). If you don't have Google Chrome installed on your computer, you can download the latest version.

If you have questions or need additional help, please please email Canvas Support. You can find more information on the technical requirements on the Canvas website.