PHYSICS 780 : Advanced Imaging Technologies


2022 Semester One (1223) (15 POINTS)

Course Prescription

Covers the physical basis and use of new imaging technologies and data processing in medicine, biomedicine and biotechnology. Makes use of practical examples from techniques such as computer assisted tomgraphy, nonlinear microscopy, optical coherence tomography, fluorescence or microarray analysis. No formal prerequisite, but an understanding of material to at least a B grade standard in PHYSICS 244, 340, and 15 points from PHYSICS 211, MATHS 253, 260, ENGSCI 211 is recommended.

Course Overview

PHYSICS 780 covers the physical basis and use of new imaging technologies and data processing in medicine, biomedicine and biotechnology. Makes use of practical examples from techniques such as computer assisted tomography, nonlinear microscopy, optical coherence tomography, fluorescence or microarray analysis.

Offered: Semester 1

Credit: 15 points

Prerequisite: No formal prerequisite, but an understanding of material to at least a C+ standard in PHYSICS 340, 280 or 244 and 211 or ENGSCI 211 will be assumed

Delivery mode according to COVID alert levels:
Level 1: Delivered normally as specified in delivery mode.
Level 2: You will not be required to attend in person. All teaching and assessment will have a remote option. 
Level 3 / 4: All teaching activities and assessments are delivered remotely.

Course Requirements

No pre-requisites or restrictions

Capabilities Developed in this Course

Capability 1: Disciplinary Knowledge and Practice
Capability 2: Critical Thinking
Capability 3: Solution Seeking
Capability 4: Communication and Engagement
Capability 5: Independence and Integrity

Learning Outcomes

By the end of this course, students will be able to:
  1. Present a research topic in a short presentation. (Capability 4)
  2. Analyse data in a scientific manner (Capability 1, 2, 3 and 5)
  3. Write codes to analyse data (Capability 1, 2, 3, 4 and 5)
  4. Demonstrate an understanding of optical imaging (Capability 1, 2, 3, 4 and 5)
  5. Demonstrate an understanding of the mathematical skills to understand and apply optical imaging (Capability 1, 2, 3 and 4)


Assessment Type Percentage Classification
Assignments 10% Individual Coursework
Presentation 20% Individual Coursework
Final Exam 70% Individual Coursework
Assessment Type Learning Outcome Addressed
1 2 3 4 5
Final Exam

Key Topics

Current research in medical physics and imaging
● Tomography
● Fluorescence imaging
● Nonlinear imaging techniques
● Vibrational spectroscopic imaging
● Data processing: machine learning
Optical Coherence Tomography
● Elements of the coherence theory of light
● Principle of Optical Coherence Tomography (OCT)
● Wiener–Khinchin theorem and the calculation of the point-spread-function
● Time and Fourier Domain OCT
● Some advanced topics, e.g., Dispersion compensation and mapping or polarisation-sensitive OCT

Special Requirements

Must complete the presentation and the assignment.

Workload Expectations

The time commitment required for studying four university courses in a semester is equivalent to working full-time. Thus, the average weekly workload for this course would be approximately 10 hours a week, including 2-3 hours in class. It is realistic to expect that the actual workload will vary somewhat from week to week across the semester. The course calendar will be a handy reference for planning.

Description                                                  Study time

Lectures 16 × 1-hour                                16 hours

Tutorial 8 x 1 hour                                       8 hours

Seminar Presentation X 1                     24 hours

Numerical Assignment X 1                   36 hours 

Private study (1.5 hours per week)  (recommended)

Tutorials are held on request from the students and teaching staff are available by appointment

Delivery Mode

Campus Experience

Attendance is expected at scheduled activities including tutorials and seminars to complete and receive credit for components of the course.
Lectures will be available as recordings. Other learning activities including tutorials and seminars will not be availabl as recordings.
The course will not include live online events.
The activities for the course are scheduled as a standard weekly timetable.

Learning Resources

Course materials are made available in a learning and collaboration tool called Canvas which also includes reading lists and lecture recordings (where available).

Please remember that the recording of any class on a personal device requires the permission of the instructor.

There is no required text books but these references can be useful
 Physics in nuclear medicine
    Book by Simon R. Cherry; James A. Sorenson; Michael E. Phelps c2012 Further resources
 Medical imaging physics
    Book by William R. Hendee; E. Russell Ritenour; John Wiley & Sons c2002 Further resources
 Optics, global edition
   Book by Eugene Hecht 2015 Further resources
 An introduction to biomedical optics
   Book by Robert Splinter; Brett Andrew Hooper; Taylor & Francis ©2007 Further resources
 Principles of computerized tomographic imaging
   Book by Avinash C. Kak; Malcolm Slaney 2001 Further resources

Student Feedback

During the course Class Representatives in each class can take feedback to the staff responsible for the course and staff-student consultative committees.

At the end of the course students will be invited to give feedback on the course and teaching through a tool called SET or Qualtrics. The lecturers and course co-ordinators will consider all feedback.

Your feedback helps to improve the course and its delivery for all students.

Academic Integrity

The University of Auckland will not tolerate cheating, or assisting others to cheat, and views cheating in coursework as a serious academic offence. The work that a student submits for grading must be the student's own work, reflecting their learning. Where work from other sources is used, it must be properly acknowledged and referenced. This requirement also applies to sources on the internet. A student's assessed work may be reviewed against online source material using computerised detection mechanisms.

The University encourages students to seek ways to improve their writing skills, including through the use of advice on coursework from third parties. When getting help with your university work, you must ensure that this assistance does not endanger the academic integrity and originality of the work. The University views cheating - including “submitting without acknowledgement work to which others have contributed” - as a serious academic offence. When seeking assistance with written work, it is your responsibility to ensure that the third party also understands the limits of providing help.
A student's assessed work may be reviewed against electronic source material using computerised detection mechanisms. Students may be required to provide an electronic version of their work for review.
UoA student policies and regulations:
● Academic integrity and copyright
● Third party assistance in UG and PG coursework guidelines

Class Representatives

Class representatives are students tasked with representing student issues to departments, faculties, and the wider university. If you have a complaint about this course, please contact your class rep who will know how to raise it in the right channels. See your departmental noticeboard for contact details for your class reps.


The content and delivery of content in this course are protected by copyright. Material belonging to others may have been used in this course and copied by and solely for the educational purposes of the University under license.

You may copy the course content for the purposes of private study or research, but you may not upload onto any third party site, make a further copy or sell, alter or further reproduce or distribute any part of the course content to another person.

Inclusive Learning

All students are asked to discuss any impairment related requirements privately, face to face and/or in written form with the course coordinator, lecturer or tutor.

Student Disability Services also provides support for students with a wide range of impairments, both visible and invisible, to succeed and excel at the University. For more information and contact details, please visit the Student Disability Services’ website

The Department of Physics is committed to equity and diversity, aspiring to provide everyone an inclusive environment in which to work and study, regardless of age, disability, gender, ethnicity, religion, or sexual orientation.
If you have any physical impairment or special learning need, please consult Student Disability Services for the support options available, and contact the course coordinator to discuss how we could help realise the recommended learning support as early as possible.
The Department of Physics subscribes to the University of Auckland Code of Conduct (both on campus and online) and hosts an active equity committee to coordinate equity initiatives. Students are encouraged to discuss any equity-related issues with members of the committee. For more details, please see the committee website.

Special Circumstances

If your ability to complete assessed coursework is affected by illness or other personal circumstances outside of your control, contact a member of teaching staff as soon as possible before the assessment is due.

If your personal circumstances significantly affect your performance, or preparation, for an exam or eligible written test, refer to the University’s aegrotat or compassionate consideration page

This should be done as soon as possible and no later than seven days after the affected test or exam date.

Learning Continuity

In the event of an unexpected disruption, we undertake to maintain the continuity and standard of teaching and learning in all your courses throughout the year. If there are unexpected disruptions the University has contingency plans to ensure that access to your course continues and course assessment continues to meet the principles of the University’s assessment policy. Some adjustments may need to be made in emergencies. You will be kept fully informed by your course co-ordinator/director, and if disruption occurs you should refer to the university website for information about how to proceed.

The delivery mode may change depending on COVID restrictions. Any changes will be communicated through Canvas.

Student Charter and Responsibilities

The Student Charter assumes and acknowledges that students are active participants in the learning process and that they have responsibilities to the institution and the international community of scholars. The University expects that students will act at all times in a way that demonstrates respect for the rights of other students and staff so that the learning environment is both safe and productive. For further information visit Student Charter


Elements of this outline may be subject to change. The latest information about the course will be available for enrolled students in Canvas.

In this course students may be asked to submit coursework assessments digitally. The University reserves the right to conduct scheduled tests and examinations for this course online or through the use of computers or other electronic devices. Where tests or examinations are conducted online remote invigilation arrangements may be used. In exceptional circumstances changes to elements of this course may be necessary at short notice. Students enrolled in this course will be informed of any such changes and the reasons for them, as soon as possible, through Canvas.

Published on 10/11/2021 08:57 p.m.