525.603.81 - Advanced Topics in Optical Medical Imaging

Expanded Course Description

The course  will  review  the recent  advances  in  photonics  technologies  for  medical imaging  and sensing.  The  course  is  designed for  graduate  students  with  some background in optics  and  engineering.  The  main topics  for  the  course  are:   

1. Review  of  basic  imaging  concepts
2. Light  sources  and devices  for  biomedical  imaging
3. Fluorescence Raman, Rayleigh  Scatterings  based  imaging
4. Confocal  and laser  scanning  imaging  systems
5. Novel  imaging  contrast  dyes, nanoparticles, and optical  clearing  reagents
6. Label-free optical  imaging  technologies  in clinical  applications

Course Structure

The course materials are divided into modules which can be accessed by clicking Modules on the course navigation menu. A module will have several sections including the overview, content, readings, discussions, and assignments. You are encouraged to preview all sections of the module before starting. Most modules run for a period of seven (7) days, exceptions are noted in the Course Outline. You should regularly check the Calendar and Announcements for assignment due dates. Of course, any discussion on the topics under study would be welcome, please use the forum on Canvas.

Course Topics

This course will cover the following topics:

1. Visual representation of an object, such as a body part or celestial body, for the purpose of medical diagnosis or data collection, using any of a variety of techniques
2. Study of diseased cells and tissues using a microscope
3. Two-photon excitation, design of the microscope, fluorophores for two-photon microscopy
4. Wave propagation and imaging in structured optical media
5. The properties of light sources and optical detectors, light-emitting diode (LED), charge-coupled device (CCD)
6. Main methods in optical microscopy that allow images to have resolutions higher than those imposed by the diffraction limit
7. Basic principles of optical coherence tomography and the use of this method in biomedical research
8. Adaptive optics as a valuable tool for high resolution microscopy, providing correction for aberrations introduced by the refractive index structure of specimens.
9. Basic principles of photoacoustics and the application of this method in biomedical research
10. Principles of endoscope design, types of endoscopes, their application of this method in biomedical research
11. Optical fibers as a tool for light transmission, properties Optical fibers, their application in biomedical research
12. Examples of the use of endoscopic technology in biomedical research and clinical medicine

Course Goals

The aim of the course is to highlight the following questions:

What is optical imaging?
What are the advantages of optical imaging?
What types of optical imaging are there and what are they used for?
How we can used different types of optical imaging in biomedical research?

Textbooks

The following books may be of interest as an additional source:

Fiber Optic Sensing and Imaging 2013th Edition
by Jin U. Kang (Editor)
Springer; 2013th edition
https://www.amazon.com/Fiber-Optic-Sensing-Imaging-Kang/dp/1461474817
In Vivo Optical Imaging of Brain Function 
Frontiers in Neuroscience 2009
Ron D. Frostig
https://www.amazon.com/Optical-Imaging-Function-Frontiers-Neuroscience/dp/1420076841

Imaging the Brain with Optical Methods
Anna W. RoeNov 2009
Springer Science & Business Media
https://www.amazon.com/Imaging-Brain-Optical-Methods-Anna/dp/1441904530

Functional Brain Mapping: Methods and Aims
Springers, 2020
Editors: Tsytsarev, Vassiliy, Yamamoto, Vicky, Zhong, Ning (Eds.)
https://www.springer.com/us/book/9789811568824

Other Materials & Online Resources

Online Resources: Please log into Canvas for all materials related to this course.

Some additional resources may be helpful for those interested in functional optical imaging, fluorescence probes and optogenetics: https://opt-imaging.com/
https://www.scimedia.com/
http://www.redshirtimaging.com/

Student Coursework Requirements

It is expected that each module will take approximately 2-3 hours per week to complete. Here is an approximate breakdown: reading the assigned sections of the texts, as well as some outside reading and listening and watching to the audio annotated slide presentations.

You are responsible for carefully reading all assigned material and being prepared for discussion. Post your questions to the discussion questions by the evening of day 3 for that module week. Part of your grade for module discussion is your interaction (i.e., responding to classmate postings with thoughtful responses) with at least two classmates (i.e., Critical Thinking). Just posting your response to a discussion question is not sufficient; we want you to interact with your classmates. Please be detailed in your postings and in your responses to your classmates' postings. Feel free to agree or disagree with other participants. Please ensure that your postings are civil and constructive. I/We will monitor module discussions and will respond to some of the discussions as discussions are posted. In some instances, I/we will summarize the overall discussions and post the summary for the module. Evaluation of preparation and participation is based on contribution to discussions

Preparation and participation is evaluated by the following grading elements:
Timeliness (50%)
Critical Thinking (50%)

Preparation and participation is graded as follows:

• 100–90 = A—Timeliness [regularly participates; all required postings; early in discussion; throughout the discussion]; Critical Thinking [rich in content; full of thoughts, insight, and analysis].
• 89–80 = B—Timeliness [frequently participates; all required postings; some not in time for others to read and respond]; Critical Thinking [substantial information; thought, insight, and analysis has taken place].
• 79–70 = C—Timeliness [infrequently participates; all required postings; most at the last minute without allowing for response time]; Critical Thinking [generally competent; information is thin and commonplace].

• Each part of question is answered (25 - 50%)
• Rationale for answer is provided (25 -50%)
• Examples (if needed) are included to illustrate rationale (22%)
• Outside references (if needed) are included (25%)

Grading Policy

EXAMINATION: There will no examinations, but there will be a final essay on December .

GRADES: The assignments and final presentation account for 60 and 40% of the total grade, respectably. Grades will be assigned according to the standard curve (A>90%, B>80%, C>70%, D>60%, F<60%).

Academic Policies

Deadlines for Adding, Dropping and Withdrawing from Courses

Students may add a course up to one week after the start of the term for that particular course. Students may drop courses according to the drop deadlines outlined in the EP academic calendar (https://ep.jhu.edu/student-services/academic-calendar/). Between the 6th week of the class and prior to the final withdrawal deadline, a student may withdraw from a course with a W on their academic record. A record of the course will remain on the academic record with a W appearing in the grade column to indicate that the student registered and withdrew from the course.

Academic Misconduct Policy

All students are required to read, know, and comply with the Johns Hopkins University Krieger School of Arts and Sciences (KSAS) / Whiting School of Engineering (WSE) Procedures for Handling Allegations of Misconduct by Full-Time and Part-Time Graduate Students.

This policy prohibits academic misconduct, including but not limited to the following: cheating or facilitating cheating; plagiarism; reuse of assignments; unauthorized collaboration; alteration of graded assignments; and unfair competition. Course materials (old assignments, texts, or examinations, etc.) should not be shared unless authorized by the course instructor. Any questions related to this policy should be directed to EP’s academic integrity officer at ep-academic-integrity@jhu.edu.

Students with Disabilities - Accommodations and Accessibility

Johns Hopkins University values diversity and inclusion. We are committed to providing welcoming, equitable, and accessible educational experiences for all students. Students with disabilities (including those with psychological conditions, medical conditions and temporary disabilities) can request accommodations for this course by providing an Accommodation Letter issued by Student Disability Services (SDS). Please request accommodations for this course as early as possible to provide time for effective communication and arrangements.

For further information or to start the process of requesting accommodations, please contact Student Disability Services at Engineering for Professionals, ep-disability-svcs@jhu.edu.

Student Conduct Code

The fundamental purpose of the JHU regulation of student conduct is to promote and to protect the health, safety, welfare, property, and rights of all members of the University community as well as to promote the orderly operation of the University and to safeguard its property and facilities. As members of the University community, students accept certain responsibilities which support the educational mission and create an environment in which all students are afforded the same opportunity to succeed academically. 

For a full description of the code please visit the following website: https://studentaffairs.jhu.edu/policies-guidelines/student-code/

Classroom Climate

JHU is committed to creating a classroom environment that values the diversity of experiences and perspectives that all students bring. Everyone has the right to be treated with dignity and respect. Fostering an inclusive climate is important. Research and experience show that students who interact with peers who are different from themselves learn new things and experience tangible educational outcomes. At no time in this learning process should someone be singled out or treated unequally on the basis of any seen or unseen part of their identity. 
 
If you have concerns in this course about harassment, discrimination, or any unequal treatment, or if you seek accommodations or resources, please reach out to the course instructor directly. Reporting will never impact your course grade. You may also share concerns with your program chair, the Assistant Dean for Diversity and Inclusion, or the Office of Institutional Equity. In handling reports, people will protect your privacy as much as possible, but faculty and staff are required to officially report information for some cases (e.g. sexual harassment).

Course Auditing

When a student enrolls in an EP course with “audit” status, the student must reach an understanding with the instructor as to what is required to earn the “audit.” If the student does not meet those expectations, the instructor must notify the EP Registration Team [EP-Registration@exchange.johnshopkins.edu] in order for the student to be retroactively dropped or withdrawn from the course (depending on when the "audit" was requested and in accordance with EP registration deadlines). All lecture content will remain accessible to auditing students, but access to all other course material is left to the discretion of the instructor.