Instructor: Prof. Yun-Sheng Chen
Office: Beckman Institute, Room 4255
Email: yunsheng@illinois.edu
Office Phone: 217-300-2801
Lecture: Tuesdays & Thursdays, 12:30 – 13:50
Instructor Office Hours: Available in person or Zoom. Thursdays 14:00-15:00 or by appointment.
Credit: 4 hours
Pre-Requisites: ECE 460 or PHYS 402, or consent of the instructor. A fundamental course in biology and optics is recommended.
Course Objective:
This graduate-level course offers a comprehensive exploration into the cutting-edge field of super-resolution biomedical imaging, covering a wide array of modalities, including optical, acoustic, MRI, CT, and PET imaging. This course is designed for students with a background in electrical and computer engineering, biomedical engineering, medical physics, or a related field, aiming to equip students with a deep understanding of the principles, computational strategies, and practical applications of super-resolution techniques in biomedical sciences.
Through lectures and project-based learning, students will delve into the mathematical foundations and algorithmic approaches underpinning super-resolution technologies. The course will navigate through three modules of optical microscopy enhancements, acoustic resolution improvements, and the advancements enabling higher resolution in clinical imaging, such as optical, MRI, CT, and PET imaging technicques. At the end of each imaging module, emphasis will be placed on the practical applications of these techniques in clinical diagnostics, therapeutic guidance, and biomedical research, highlighting their impact on understanding complex biological systems and enhancing patient care.
Instructor Teaching & Learning Philosophy:
I believe and teach that technology is becoming increasingly interdisciplinary, particularly between engineering, medicine, and biology. Your ability to learn and integrate ideas and concepts from multiple disciplines will enable you to investigate and solve many of the new engineering problems we will face in the future. I value three things in students and colleagues: hard work, productivity, and creativity. To be successful in my course and in life, you must demonstrate that you possess one or more of these three values.
Course materials:
Course materials will be distributed weekly.
Classroom lectures will emphasize the main points in the material and allow for discussion. I expect you to read the assigned reading materials but focus on the concepts presented in the lecture. Homework and exams will be structured with the assumption that you have read all of the assigned text and handout materials.
Recommended Textbooks:
Udo J. Birk, Super-Resolution Microscopy: A Practical Guide. John Wiley & Sons, 2017.
Barry R. Masters, Super-resolution Optical Microscopy: The Quest for Enhanced Resolution and Contrast¸ Springer, 2020.
Vasily Astratov, Label-Free Super-Resolution Microscopy, Springer, 2019
Douglas B. Murphy, Michael W. Davidson, Fundamentals of Light Microscopy and Electronic Imaging, Wiley, 2012
Jerrold T. Bushberg, The Essential Physics of Medical Imaging, Lippincott Williams & Wilkins, 2002
Born and Wolf, Principles of Optics, 7th edition
Other Suggested References:
Papoulis, The Fourier integral and its applications (McGraw-Hill, New York, 1962).
W. Goodman, Introduction to Fourier optics (McGraw-Hill, New York, 1996).
Saleh and Teich, Fundamentals of Photonics (the ECE 460 textbook)
Hecht, Optics, 4th edition
L. Wang, Biomedical Optics: Principles and Imaging
G. Popescu, Quantitative phase imaging of cells and tissues (McGraw-Hill, New York, 2011).
B. R. Masters and P. T. C. So, Handbook of biomedical nonlinear optical microscopy (Oxford University Press, New York, 2008).
Alberts, et al., Molecular Biology of the Cell (Garland Science, 5th edition, 2008)
Homework:
There will be four graded homework sets for this course. Homework assignments will be distributed approximately one week before they are due. Solutions will be posted on the course website. Late homework will be accepted, but 10% will be deducted for each day it is late.
Exams:
Two midterm exams will be given in class. The exams will account for 30% of the final grade (15% each). There will be no final exam. The second exam will be comprehensive. A calculator is allowed. Cell phones, PDAs, digital music players, or other personal electronics are not allowed during the exam. The use of electronic devices during an exam may be construed as a violation of the student code of conduct.
Final Report:
There will be a problem-based learning report due on the last day of class. This report will comprehensively describe and solve a set of biomedical imaging-related questions using at least a super-resolution imaging technique. Students will be expected to integrate their new knowledge to offer technical-based solutions. There will be one class period workshop set aside to discuss and formalize these reports.
Final presentation:
Each student in the class will be required to present to the class one journal article that will cover related course topics throughout the semester and follow the sequence of topics presented in lectures. Journal articles must be pre-approved by Prof. Chen to emphasize the important topic areas. Selected articles will be shared with the class before the presentation, and all students will be expected to read the article and participate in the discussion. The 15 minutes of presentation (followed by up to 10 minutes of discussion) should discuss the important points of the article, as well as show and discuss the figures, data, and images. Students will be graded on their presentation, their understanding of the material, and their ability to lead the class discussion.
Super-resolution Imaging Facilities Tour:
Our university has a large number of facilities and resources dedicated to super-resolution imaging research. One class period will be dedicated to visiting and touring some of these campus resources to see first-hand the technology and instrumentation related to super-resolution optical imaging.
Grading:
Your final grade in this course will be based on your total score on all the components of the course. The total score is broken down into the following components:
| Exam #1 | 15% |
| Exam #1 | 20% |
| Homework | 20% |
| Final Report | 15% |
| Final Presentation | 20% |
| Participation | 10% |
| Total | 100% |
Absences and Excused Grades:
There is no way to make up a missed exam. An unexcused absence from a semester exam will be assigned a zero grade. An excused absence requires a letter from the Dean’s office. An excused absence from a semester exam will receive an EX grade. At the end of the semester, the EX grade will be replaced with the average of your grades on the other exam and the final presentation.
Grade disputes on homework will be settled at the discretion of the TA. Grade disputes on the semester exams will be settled at the discretion of Prof. Chen. In both cases, the problem in question will be RE-GRADED, making it possible for you to receive a lower score. To dispute an exam grade, you must explain your dispute IN WRITING and staple this to the front of your exam. Prof. Chen will then re-grade your exam.
Participation:
Participation in class will account for 10% of the final grade. The participation include class attending and discussion participation. Note: In the case of an online lecture, and if you are located in a different time zone and cannot log in for the lecture at the designated time, you are required to watch the recording within 24 hours, which will count for your ‘in-class’ participation. In that situation, a question will be asked in the Zoom lecture, and you will email the instructor with the answer to count for your participation within 24 hours. Students are encouraged to contact the instructor directly to discuss their absence due to medical or emergency conditions.
Tentative Topics and Lecture Schedule:
| I. Overview of Super-resolution Imaging Technologies | |
| Lecture 01 (08/27) | IA. History, Types, Applications, & Impact |
| Lecture 02 (08/29) | 1B. Principle of Imaging Resolution |
| Lecture 03 (09/03) | 1B. Principle of Imaging Resolution |
| Lecture 04 (09/05) | 1B. Principle of Imaging Resolution |
| II. Optical Super-resolution Microscopy Technologies | |
| IIA. Fluorescence super-resolution microscopy technologies | |
| IIA-1. Point Spread Function Engineering Microscopy | |
| Lecture 05 (09/10) | Introduction of Point Spread Function Engineering Microscopy |
| Lecture 06 (09/12) | Ground State Depletion (GSD) Microscopy |
| Lecture 07 (09/17) | Reversible Saturable Optical Fluorescence Transition (RESOLFT) Microscopy |
| IIA-2. Single-molecule Localization Microscopy (SMLM) | |
| Lecture 08 (09/19) | Introduction of Single-molecule Localization Microscopy |
| Lecture 09 (09/24) | Point Accumulation for Imaging in Nanoscale Topography (PAINT) |
| IIA-3. Fluorescence Fluctuation-Based Super-Resolution Imaging | |
| Lecture 10 (09/26) | Stochastic Optical Fluctuation Imaging (SOFI) |
| IIA-4. Structured Illumination Microscopy (SIM) | |
| Lecture 11 (10/01) | Introduction of Structured Illumination Microscopy; Point-scanning SIM |
| Lecture 12 (10/03) | Total internal reflection fluorescence SIM (TIRF-SIM); Light-sheet microscopy and lattice light-sheet microscopy |
| IIA-5. Others | |
| Lecture 13 (10/08) | Expansion microscopy |
| Lecture 14 (10/10) | Exam I |
| IIB. Label-Free Super-Resolution Microscopy Technologies | |
| Lecture 15 (10/15) | Interferometric Scattering (iSCAT) microscopy |
| Lecture 16 (10/17) | Super-resolution coherent brightfield microscopy |
| Lecture 17 (10/22) | Super-resolution microscopy with far-field Super-lenses and hyperlenses |
| Lecture 18 (10/24) | Deep-Learning Aided Optical Super-Resolution Microscopy Technologies |
| Lecture 19 (10/29) | Optical super-resolution facility tour |
| III. Acoustic Super-resolution Microscopy Technologies | |
| Lecture 20 (10/31) | IIIA. Ultrasound localization imaging |
| Lecture 21 (11/05) | IIIB. Introduction of photoacoustic imaging and super-resolution photoacoustic tomography |
| Lecture 22 (11/07) | IIIC. Deep-Learning Aided Acoustic Super-resolution Imaging Technologies |
| IV. Super-resolution Imaging Technologies for Medical Imaging | |
| Lecture 23 (11/12) | IVA. Introduction of MRI, PET, and CT |
| Lecture 24 (11/14) | IVB. Deep-learning Super-resolution MRI |
| Lecture 25 (11/19) | IVC. Deep-learning Super-resolution CT&PET |
| Lecture 26 (11/21) | Exam II |
| Fall break | |
| Fall break | |
| V. Student Project Presentations | |
| Lecture 27 (12/03) | Day 1 |
| Lecture 28 (12/05) | Day 2 |
| Lecture 29 (12/10) | Day 3 |
The lecture schedule may be adjusted based on classroom progress.