EE 361

EE 361x: Introduction to Biomedical Imaging, Fall 2023

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Important Information About EE 361x: Introduction to Biomedical Imaging

Dear Engineering Students;

I am writing to inform you about the course that I will be offering this semester (EE 361: Introduction to Biomedical Imaging).

The nature of education has been changing greatly in the last decades, and nowadays online learning is quite popular. Inspired by this trend, EE 361 course will be based on edX, a non-profit educational platform founded by MIT and Harvard in 2012. The aim of EE 361 is really to motivate you to learn about biomedical imaging, an emerging interdisciplinary field of great importance for all of us. Biomedical imaging has a vital part in the early detection, diagnosis, and treatment of many diseases including cancer. In some cases, biomedical imaging is the first step in preventing the spread of diseases through early detection, and in many cases, it makes it possible to cure or eliminate the illness altogether.

Due to the part-time nature of my contract with Antalya Bilim University, during the semesters (which is 14 weeks), I am usually at Antalya for 2-3 weeks only (hence, we won't have regular face-to-face classes in this course, except the 2-3 weeks that I am at the campus). Hence, during this course, you will be learning the topics mostly yourselves by studying the following free online courses on biomedical imaging:

Introduction to Biomedical Imaging, by University of Queensland

https://courses.edx.org/courses/course-v1:UQx+BIOIMG101x+2T2017/course/

Fundamentals of Biomedical Imaging: Ultrasounds, X-ray, positron emission tomography (PET), Magnetic Resonance Imaging (MRI) and applications, by EPFL

https://courses.edx.org/courses/course-v1:EPFLx+FndBioImgx+1T2017/course/

https://courses.edx.org/courses/course-v1:EPFLx+FndBioImg2x+1T2017/course/

Hence, EE 361 will mostly be a self-learning course, and my role will be supervision, grading, and motivation tracking. The topics that we will cover include X-ray, computed tomography (CT), ultrasound, and magnetic resonance imaging (MRI). You will have the chance to learn the course content anytime from anywhere (there will be no lectures). There will be (1 or 2) midterm exams and a final exam to test your level of learning. The exams will test your level of effort and will include general simple questions as well as moderate questions that will test your theoretical and physical understanding of the imaging modalities. The course is suitable for interested Sophomore, Junior, and Senior level engineering/science students from all areas (Phys 102 is the only prerequisite for this course).

Best

Umit Demirbas

PS 1: You can take EE 361, even if the course hours conflict with other courses (consent of the instructor of the conflicting course is also required). Some of the exams might be face-to-face (during class time), and you are required to attend the exams.

PS2: All the announcements for the course will be made in the course web page (please check the page weekly): https://sites.google.com/site/antalyalaserlab/ee-361

EE361x: Biomedical Imaging, Week 1

Dear All,

One more time, I welcome you all to EE 361x: Introduction to Biomedical Imaging course.

Please note again that this is a self-learning course based on edX. If you are not sure about the style of the course feel free to e-mail me for further details (some of your friends took EE362x earlier, and they could also provide you information about the course style).

For the first week, please register to the following edX course, and watch at least Sections 1 & 2 (this means watching all the content, taking notes, solving the exercises, etc...):

Introduction to Biomedical Imaging, by University of Queensland

https://www.edx.org/course/introduction-biomedical-imaging-uqx-bioimg101x-4

Note also that auditing of edX courses is free of charge. Section 1 introduces you to biomedical imaging, and section 2 talks about imaging with x-rays. I found these topics very interesting and important for daily life, and I hope you will also like them. I should mention that the midterm exams will be partly based on these suggested materials (so please start taking notes regularly as you study the material).

Best regards

PS: Please check the course web page regularly for updates:

https://sites.google.com/site/antalyalaserlab/ee-361

EE361x: Introduction to Biomedical Imaging, Suggested Book

Dear All,

I would like to suggest "Introduction to Medical Imaging: Physics, Engineering and Clinical Applications" by Smith and Webb as the course book:

https://www.amazon.com/Introduction-Medical-Imaging-Engineering-Applications/dp/0521190657/

A pdf copy of the book is available at the course web page (look towards the end of the page):

https://sites.google.com/site/antalyalaserlab/ee-361

Note that, the book was written by a married couple, and tragically, one of the authors of the book (Ms. Smith) passed away in an accident in 2010:

https://news.psu.edu/story/168503/2010/04/07/college-engineering-mourns-passing-nadine-smith

Best regards

EE361x: Biomedical Imaging, Week 2

Dear All,

How is it going? I hope you are on pace with the biomedical imaging course. Since this is a self-learning course, it is very important for you to follow the course weekly, otherwise, the content can pile up quite fast.

For the 2nd week, please register to the following edX course from EPFL, and watch Section 1 as the Intro and Section 3 on x-ray imaging:

FndBioImgx : Fundamentals of Biomedical Imaging: Ultrasounds, X-ray, positron emission tomography (PET) and applications

https://courses.edx.org/courses/course-v1:EPFLx+FndBioImgx+1T2017/course/

Note that EPFL is a highly-ranked university (within the top 20), and the course instructor (Prof. Rolf Gruetter) is a well-known expert on MRI:

https://scholar.google.com/citations?user=m-FOcowAAAAJ&hl=en

This course is more mathematically oriented than the earlier course by the University of Queensland, but not beyond your limits. Please try to understand the physics. What are X-rays? How can we generate them? How can we use them in biomedical imaging? Our aim here is to create an environment that could motivate you to understand the concepts.

Best regards

Umit

PS: We have new students registered for the course----if you have just registered for EE361 and did not receive the earlier emails, please see the course web page for earlier announcements and catch up:

https://sites.google.com/site/antalyalaserlab/ee-361

EE361x: Biomedical Imaging, Week 3

Dear All,

I saw that last week, a large number of new students arrived (first of all, welcome to EE 361). We are now more than 80, as the course is probably one of the few electives which offer flexibility. Please go over the course web page. look at the e-mails that were sent earlier, and complete the assignments. Note that, a copy of all course-related e-mails will be regularly put on our course web page:

https://sites.google.com/site/antalyalaserlab/ee-361

For week 3, I am not assigning any new tasks. Please catch up. Don't let the course content pile up. A few hours every week!

Best Regards

EE361x: Biomedical Imaging, Week 4

Dear All,

I hope all is going well. For week 4, please complete the following:

Section 4: Computed tomography - from Fundamentals of Biomedical Imaging: Ultrasounds, X-ray, positron emission tomography (PET) and applications course

https://courses.edx.org/courses/course-v1:EPFLx+FndBioImgx+1T2017/course/

Best Regards

PS: For those of you who just finished registration, note that a copy of all course-related e-mails is on our course web page. Try to catch up on the content. It is your responsibility to go over the web page regularly for emails and announcements:

https://sites.google.com/site/antalyalaserlab/ee-361

EE361x: Biomedical Imaging, Weeks 5-6

Dear All,

Let's continue with x-ray imaging, but now with x-ray emission computed tomography (we have been doing x-ray tranmission/absorption computed tomography so far). X-ray emission computed tomography is also known as "Single-photon emission computed tomography" (SPECT, or less commonly, SPET).

For weeks 5-6, please complete Section 5 (SPECT) and Section 6 (PET) from the Fundamentals of Biomedical Imaging course:

https://courses.edx.org/courses/course-v1:EPFLx+FndBioImgx+1T2017/course/

Best Regards

Umit

EE361x: Biomedical Imaging, Midterm (online exam, Dec 1-3)

Dear All,

Sorry for keeping you in the dark, and writing late on this.

We tried to arrange a face to face midterm this year, but the assigned date and time has conflicts for some of you. We can try to change the date and time, but then this will create conflict for others. Basically the class has now around 100 students from different departments and years, and it looks like we need to make an online exam this year again.

For the exam, to give you the chance to have a relaxed time, I have chosen Dec 1-3. I will send the questions on Dec 1, and the due date will be Dec 3. The aim is to give you 2-3 days to work on the exam, and hopefully this will help you to learn the topic.

I will put sample online midterms from last year on the course web page. Last year we had 2 midterms, but this year we will have only one midterm and one final exam (as reading the exam takes 3-4 days). The rules of the exam will be similar to the earlier years. Please look at them and let me know if you have any questions.

For midterm 1, you are responsible form the content of weeks 1-6. Please see the curse we page for the content this covers:

https://sites.google.com/site/antalyalaserlab/ee-361

Have a nice evening

Umit

Dear All,

One of our EE department assistants helped me to setup our homework/midterm on the LMS online course system. Please visit the LMS for our course. There you can find the details of our homework.

I believe the link for our course LMS page is the following:

https://lms.antalya.edu.tr/course/view.php?id=5866

We now have 93 students in the course, so this year, I will ask you to submit the solutions to the LMS system (in earlier years, I was collecting the solutions via email, but the class size is too large this year). That's the reason why we have only one midterm and one final exam this year as well (I used to hold two midterms and a term paper).

Please show the details of your work to get full credit. Do not write anything that you don't understand as a solution. Do not just copy-paste from your friend or from a web page. Understand first, and write later.

Best regards

Umit

PS: Please email me back if you face any difficulties with the system

EE361x: Biomedical Imaging, Week 10

Dear All,

We gave some break due to midterm season, but now let's continue with ultrasound imaging:

For weeks 8, please complete Section 2 from the Fundamentals of Biomedical Imaging course:

https://courses.edx.org/courses/course-v1:EPFLx+FndBioImgx+1T2017/course/

and Episode 3 (ultrasound) from Introduction to Biomedical Imaging, by University of Queensland

https://courses.edx.org/courses/course-v1:UQx+BIOIMG101x+2T2017/course/

Please also read trhough Canan Dagdevirens recent work with ultrasound imaging:

https://news.mit.edu/2023/wearable-ultrasound-scanner-breast-cancer-0728

Best Regards

Umit

EE361x: Biomedical Imaging, Weeks 11-14

Dear All,

Lets continue with the last topic of the term, Magnetic Resonance Imaging (MRI). Note that, the next topic (MRI), is the most challenging topic of the course due to the physics it involves. I hope you will find it interesting as well.

For weeks 11-14, please complete:

Episode 4: Magnetic Resonance Imaging (MRI) from the Introduction to Biomedical Imaging course:

https://www.edx.org/course/introduction-biomedical-imaging-uqx-bioimg101x-4

and

also go through Chapter 8 to Chapter 11, from the Fundamentals of Biomedical Imaging : Magnetic Resonance Imaging (MRI)

https://learning.edx.org/course/course-v1:EPFLx+FndBioImg2x+1T2017/home

I know this is too much of a content for 4 weeks, and I expect you to go through the most important parts of it, and focus on the basics.

Best regards

EE361 Final Exam (Jan 19, 2024, 10-11:30)

Dear All,

On Jan 19 2024 (Friday), we will have our final exam on A1-76 (1.5-hour written exam starting at 10 am).

To motivate understanding of the topic rather than memorizing equations and definitions, we have a cheating sheet policy in this course. For the exam, you can take notes on an A4 sized white paper (you can use both sides of the paper for your notes). The notes should be hand-written by you. The cheating sheet could contain summaries of topics, equations, drawings, derivations, etc... However, the cheating sheet should not contain solutions to specific examples. Note that your cheating sheets will be collected with your exam paper at the end of the exam.

The final exam will be mostly on Magnetic Resonance Imaging (MRI) and Ultrasound Imaging. However, it might also contain some questions/knowledge from earlier topics.

I want to motivate you to enjoy the content rather than getting stressed with the exam.

Best Regards

PS: Lastly, if you want, as a challenge, you can suggest a question for the final exam. In this case, please send the question and the answer to me before Jan 10 (no sharing with others). I may then use some of the suggested questions (or modified versions) in the final exam. The questions should be original (nothing from books or the web) and should be educational.

EE361 Final Exam (Jan 19, 2024, 10-11:30)

Dear All,

I received several e-mails from you related to the exam. I won't be able to reply to your personal emails due to time constraints (sorry about that).

The final will be a regular exam, as announced earlier, due to several ethical issues we have faced and due to the appearance of OpenAI models such as ChatGPT. I know it is a gray region with pros and cons, but I want to keep at least one exam as a regular exam for my courses. Several points:

* Of course, the regular exams are easier than take-home exams

*I use the bell curve system in my grading.

* You might need a calculator in the exam; cell phones will not be allowed.

*Please see midterm 1 and 2 questions from last year as an example. These were both online exams, the regular exam will be easier, but some questions are basic and could be repeated again this year. Focus on the basics first. Don't be stressed; we don't expect you to learn all the details of MRI in this course.

*Some questions we might ask>---What is MRI, how it works? What is ultrasound imaging, and how it works? How do they compare with earlier x-tar-based imaging methods you have learned?

*Lastly, as announced earlier, "To motivate understanding of the topic rather than memorizing equations and definitions, we have a cheating sheet policy in this course. For the exam, you can take notes on an A4 sized white paper (you can use both sides of the paper for your notes). The notes should be hand-written by you. The cheating sheet could contain summaries of topics, equations, drawings, derivations, etc... However, the cheating sheet should not contain solutions to specific examples. Note that your cheating sheets will be collected with your exam paper at the end of the exam. "

In short, don't worry guys; prepare a full A4 page of notes focusing on basics, and you will see that this will allow you to answer more than half of the questions already.

Best regards

Umit

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