585.734.81 - Biophotonics

Expanded Course Description

Suggested prerequisite: Undergraduate courses in optics and electromagnetics

Course Structure

The course materials are divided into modules which can be accessed by clicking Course Modules on the course 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.

Course Topics

• Geometric Optics & Radiometry
  
• Photonics
• Tissue Optics
• Spectroscopy & Fluorescence
• Raman Spectroscopy
• Elastic Light Scattering
• Monte Carlo Simulation
• Light Transport in Tissue
• Imaging & Microscopy
• Optical Coherence Tomography
• Smartphone-Based Optical Biosensors
• Clinical Applications & Photodynamic Therapy

Course Goals

Following the completion of this course, students will have a basic understanding of the different optical signatures found in biological systems and the various methods and instruments used to measure them. This will enable them to evaluate modern bio-photonic instrumentation and understand the most recent literature in the field of bio-photonics.

Course Learning Outcomes (CLOs)

• Compare tissue optical signatures based on absorption, fluorescence, and scattering, including their use for diagnostics and patient monitoring
• Analyze light propagation in tissue using the Monte Carlo and diffusion approximation methods to identify the propagation conditions that are optimal for each method
• Perform experimental measurements using RaspberryPi-based experimental kits to compare experimental results with theoretical model predictions
• Evaluate different tissue spectroscopy and imaging sensor methods based on their strengths, weaknesses, principles of operation, and clinical potential
• Outline the challenges in transitioning biophotonic sensor technology to clinical settings, including examples of successful transitions and why they were successful

Textbooks

Bigio, I. J. and Fantini, S. (2016) Quantitative Biomedical Optics: Theory, methods and applications (1st ed.). Cambridge University Press

            ISBN 987-0-521-87656-8

Textbook information for this course is available online through the appropriate bookstore website: For online courses, search the MBS website.

Required Software

MATLAB

You will need access to a recent version of MATLAB. A license is provided at no cost to you, through JHU.

Visit the JHU IT Services Portal. Log in with your JHED ID and type “Matlab” in the search bar. Click on “Matlab for Students” in the search results and follow the instructions provided.

Student Coursework Requirements

It is expected that each module will take approximately 9–12 hours per week to complete. Here is an approximate breakdown: reading the assigned sections of the text and outside reading from journal papers and chapters from other textbooks (approximately 4–5 hours per week), listening to the audio annotated slide presentations (approximately 2–3 hours per week), and homework assignments (approximately 3–4 hours per week).

This course will consist of the following basic student requirements:

Preparation and Participation (10% of Final Grade Calculation)

You are responsible for carefully reading all assigned material and being prepared for discussion. The readings are from the course text and outside reading from journal papers and chapters from other textbooks.  

Post your initial response to the discussion questions by the evening of Day 4 for that module week. Posting a response to the discussion question is part one of your grade for module discussions (i.e., Timeliness).

Part two 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. Be detailed in your postings and in your responses to your classmates' postings. Feel free to agree or disagree with your classmates. Please ensure that your postings are civil and constructive.

I will monitor module discussions and will respond to some of the discussions as discussions are posted. In some instances, I 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].
• <70 = F—Timeliness [rarely participates; some, or all required postings missing]; Critical Thinking [rudimentary and superficial; no analysis or insight is displayed].

Assignments (30% of Final Grade Calculation)

Assignments consist of problem sets from the course text and outside reading. The problems for each assignment should be submitted with the solution clearly indicated for each problem. Please include a cover sheet with your name and assignment identifier. Also include your name and page indicator (i.e., page x of y) on each page of your submission.  If a mathematical software package such as Matlab or Mathematica is used to perform some of the calculations, explicitly write out an example of a calculation, clearly showing each step and intermediate results. Do not just hand in a printout of the software code and results without any clear explanation of how the calculation was performed.

All assignments are due according to the dates in the Calendar.

Late submissions will be reduced by one letter grade for each week late (no exceptions without prior coordination with the instructors).

Quantitative assignments are evaluated by the following grading elements:

1. Each part of question is answered (20%)
2. Assumptions are clearly stated (20%)
3. Intermediate derivations and calculations are provided (25%)
4. Answer is technically correct and is clearly indicated (25%)
5. Answer precision and units are appropriate (10%)

Quantitative assignments are graded as follows:

• 100–90 = A—All parts of question are addressed; All assumptions are clearly stated; All intermediate derivations and calculations are provided; Answer is technically correct and is clearly indicated; Answer precision and units are appropriate.
• 89–80 = B—All parts of question are addressed; All assumptions are clearly stated; Some intermediate derivations and calculations are provided; Answer is technically correct and is indicated; Answer precision and units are appropriate.
• 79–70=C—Most parts of question are addressed; Assumptions are partially stated; Few intermediate derivations and calculations are provided; Answer is not technically correct but is indicated; Answer precision and units are indicated but inappropriate.
• <70=F—Some parts of the question are addressed; Assumptions are not stated; Intermediate derivations and calculations are not provided; The answer is incorrect or missing; The answer precision and units are inappropriate or missing.

Laboratory Exercises (15% of Final Grade Calculation)

Experimental laboratory kits will be sent to the students by Module 7. The experiments will be performed in the second half of the course by student groups. The data will be collected, analyzed and compared with theoretical models where appropriate. The laboratory reports for the first two experiments are due in Module 10 and the reports for the last two experiments are due in Module 13.

The laboratory exercises evaluated by the following grading elements:

1. Student demonstrated the ability to construct the experimental kits and collect data for each experimental setup (10%)
2. Student’s technical understanding of the purpose of each experimental setup and how it relates to the course lecture material (10%)
3. Team data comparison (10%)
4. Well documented exercise report that includes description of the experimental setups, pictures of the experimental setup, raw data images collected with the setup, and any processed data using the software packages (30%)
5. Analysis of the experimental measurements and comparison with theoretical model where appropriate; discussion of the results and any issue encountered during the measurement or data analysis steps (40%)

Laboratory Exercises are graded as follows:

• 100–90 = A— All laboratory experiments have been performed properly; data was collected and analyzed using the proper software; comparison of experimental data with theoretical models have been completed; clear understanding of the purpose of each experiment; well documented exercise report with all of the proper formatting; proper analysis of the data and well written discussion of the results
• 89–80 = B— — Most laboratory experiments have been performed properly; data was collected and analyzed using the proper software; comparison of experimental data with theoretical models have been partially completed; clear understanding of the purpose of each experiment; reasonable documented exercise report with most of the proper formatting; proper analysis of the partial data that was collected and reasonable written discussion of the partial results
• 79–70 = C—— A small percentage of the laboratory experiments have been performed properly; some data was collected but not properly analyzed; comparison of experimental data with theoretical models was not completed; poor understanding of the purpose of each experiment; poor documented exercise report with all of the improper formatting; partial analysis of the data and poor written discussion of the results
• <70 = F— None of the laboratory experiments have been performed properly; some data was collected but not properly analyzed using the proper software; comparison of experimental data with theoretical models was not completed; no understanding of the purpose of each experiment; poor documented exercise report with all of the improper formatting; data was not analyzed and therefore no discussion of results

Course Project (15% of Final Grade Calculation)

A course project topic and team members will be selected by the end of Module 6. The last week will be devoted to the course project presentations by students.

The course project is evaluated by the following grading elements:

1. Student preparation and participation (as described in Course Project Description) (40%)
2. Student technical understanding of the course project topic (as related to individual role that the student assumes and described in the Course Project Description) (20%)
3. Team preparation and participation (as described in Course Project Description) (20%)
4. Team technical understanding of the course project topic (as related to the Customer Team roles assumed by the students and the Seller Team roles assumed by the students and described in the Course Project Description) (20%)

Course Project is graded as follows:

• 100–90 = A—Student Preparation and Participation/ Team Preparation and Participation [individual/ team roles and responsibilities well defined and understood; individual/ team well versed in use of Adobe Connect; individual/ team work product(s) agreed to, well prepared and available to all team members/ instructors]; Student Understanding/ Team Understanding [rich in content; full of thought, insight, and analysis].
• 89–80 = B—Student Preparation and Participation/ Team Preparation and Participation [individual/ team roles and responsibilities well defined and understood; individual/ team well versed in use of Adobe Connect; individual/ team work product(s) agreed to and prepared]; Student Understanding/ Team Understanding [substantial information; thought, insight, and analysis has taken place].
• 79–70 = C—Student Preparation and Participation/ Team Preparation and Participation [individual/ team roles and responsibilities agreed to; individual/ team well versed in use of Adobe Connect; individual/ team work product(s) prepared]; Student Understanding/ Team Understanding [generally competent; information is thin and commonplace].
• <70 = F—Student Preparation and Participation/ Team Preparation and Participation [individual/ team roles and responsibilities not well understood; individual/ team has difficult with use of Adobe Connect; individual/ team work product(s) partially prepared]; Student Understanding/ Team Understanding [rudimentary and superficial; no analysis or insight displayed].

Midterm Exam (30% of Final Grade Calculation)

The midterm exam will be available in Module 7. You will have one week to complete the exam and it will be due by 5PM EST exactly one week from its release. You may use the course text and supplementary material from the reading assignments to complete the exams. Please include a cover sheet with your name. Also include your name and page indicator (i.e., page x of y) on each page of your submission. If a mathematical software package such as matlab or mathematica is used to perform some of the calculations, explicitly write out an example of a calculation, clearly showing each step and intermediate results. Do not just hand in a printout of the software code and results without any clear explanation of how the calculation was performed.

The exams are evaluated by the following grading elements:

1. Each part of question is answered (30%)
2. Derivations contain all required steps with no gaps; computational problems show all significant intermediate steps and reach the correct answer (60%)
3. Notation is consistent and unambiguous; derivations are written clearly (10%)

Exams are graded as follows:

• 100–90 = A— All parts of question are addressed; all significant intermediate derivations and calculations are provided; answer is correct; logic is sound; notation is clear and consistent
• 89–80 = B— All parts of the question are addressed; most significant intermediate derivations and calculations are provided; most answers are correct; logic is sound with possibly one or two gaps; notation is clear and consistent
• 79–70 = C—Most parts of question are addressed; some significant intermediate derivations and calculations are provided; several answers are correct; logic is sound with several gaps; notation is clear and consistent
• <70 = F—Some parts of the question are addressed; few significant intermediate derivations and calculations are provided; many answers are incorrect; logic is inconsistent; notation is unclear and/or inconsistent

Grading Policy

Assignments are due according to the dates posted in your Canvas course site. You may check these due dates in the Course Calendar or the Assignments in the corresponding modules. I will post grades one week after assignment due dates.

We generally do not directly grade spelling and grammar. However, egregious violations of the rules of the English language will be noted without comment. Consistently poor performance in either spelling or grammar is taken as an indication of poor written communication ability that may detract from your grade.

A grade of A indicates achievement of consistent excellence and distinction throughout the course—that is, conspicuous excellence in all aspects of assignments and discussion in every week.

A grade of B indicates work that meets all course requirements on a level appropriate for graduate academic work. These criteria apply to both undergraduates and graduate students taking the course.

EP uses a +/- grading system (see “Grading System”, Graduate Programs catalog, p. 10).

Final grades will be determined by the following weighting:

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.