Skip to Main Content

Content

Course Tabs

Overview

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 tomography, nonlinear microscopy, optical coherence tomography, fluorescence or microarray analysis.

Course Overview

For most parts, the course will be research-oriented, i.e., will deal with subjects closely related to current research topics in biophotonics and biomedical imaging with a focus on research taking place at the University of Auckland. Students will also actively contribute to the course content through the preparation of oral presentations on cutting-edge imaging techniques, biosensors and data processing (see below). By the end of this course, you should have a good idea of biomedical imaging and biophotonics as well as some of the most advanced imaging technologies and data processing techniques that are currently under development worldwide. The course assignments will also develop your presentation and numerical modelling skills.

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
  • How to build a system
  • Photoacoustic and Ultrasound imaging
  • Introduction and lab tour

Workload Expectations

This course is a standard 15 point course and students are expected to spend 10 hours per week involved in each 15 point course that they are enrolled in. 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.

In this course, you can expect 2 hours of lectures per week (sixteen 1-hour lectures across the semester), eight 1-hour tutorials across the semester, a seminar presentation with a workload of approximately 24 hours, a numerical assignment with an expected workload of 36 hours, and recommended private study of course material for 1-2 hours per week.

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

Additional Advice on Prerequisites

No formal prerequisite, but an understanding of material to at least a B grade standard in PHYSICS 244, 340, and 15 points from MATHS 221, 231, 253, 260, ENGSCI 211 is recommended.

Locations and Semesters Offered

LocationSemester
City

Teaching and Learning

Campus Experience

Attendance is required at scheduled activities including presentation and tutorials to receive credit for components of the course.
Lectures will be available as recordings on request. Other learning activities including tutorials will not be available as recordings.
The course will not include live online events.
Attendance on campus is required for the exam.
The activities for the course are scheduled as a standard weekly timetable.

Learning Resources

Taught courses use a learning and collaboration tool called Canvas to provide students with learning materials including 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.

Additional Information on 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. Recommended Readings:

  •  Physics in nuclear medicine by Simon R. Cherry; James A. Sorenson; Michael E. Phelps (2012)
  •  Medical imaging physics by William R. Hendee; E. Russell Ritenour; John Wiley; Sons (2002)
  •  Optics (global edition) by Eugene Hecht (2015)
  •  An introduction to biomedical optics by Robert Splinter; Brett Andrew Hooper; Taylor; Francis (2007)
  •  Principles of computerized tomographic imaging by Avinash C. Kak; Malcolm Slaney (2001)

Copyright

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.

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.

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 for potential plagiarism or other forms of academic misconduct, using computerised detection mechanisms.

Similarly, research students must meet the University’s expectations of good research practice. This requires:

  • Honesty - in all aspects of research work
  • Accountability - in the conduct of research
  • Professional courtesy and fairness – in working with others
  • Good stewardship – on behalf of others
  • Transparency – of research process and presentation of results
  • Clarity - communication to be understandable, explainable and accessible

For more information on the University’s expectations of academic integrity, please see the Academic Conduct section of the University policy hub.

Disclaimer

Elements of this outline may be subject to change. The latest information about taught courses is made available to enrolled students in Canvas.

Students may be asked to submit assessments digitally. The University reserves the right to conduct scheduled tests and examinations 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.


Additional Information on Academic integrity

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

Assessment and Learning Outcomes

Special Requirements

To pass this course, students must complete the presentation and the assignment.

Course Learning Outcomes

CLO #Outcome
1
2
3
4
5

Assessments

Assessment TypeAssessment PercentageAssessment Classification

Assessment to CLO Mapping

Assessment Type12345

Student Feedback, Support and Charter

Student Feedback

Feedback on taught courses is gathered from students at the end of each semester through a tool called SET or Qualtrics. The lecturers and course co-ordinators will consider all feedback and respond with summaries and actions. Your feedback helps teachers to improve the course and its delivery for future students. In addition, class Representatives in each class can take feedback to the department and faculty staff-student consultative committees.

Additional Information on Student Feedback

Feedback from students has helped us improve the delivery mode and assessments.

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.

Tuākana

Tuākana is a multi-faceted programme for Māori and Pacific students providing topic specific tutorials, one-on-one sessions, test and exam preparation and more. Explore your options at Tuakana Learning Communities.

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.

Additional Information on Inclusive Learning

The Department of Physics is committed to equity and diversity, aspiring to provide everyone with 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.

Wellbeing

We all go through tough times during the semester, or see our friends struggling. There is lots of help out there - please see the Support Services page for information on support services in the University and the wider community.

Special Circumstances

If your ability to complete assessed work 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.

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.

Student Academic Complaints and Disputes

Students with concerns about teaching including how a course is delivered, the resources provided, or supervision arrangements, have the right to express their concerns and seek resolution. The university encourages informal resolution where possible, as this is quicker and less stressful. For information on the informal and formal complaints processes, please refer to the Student Academic Complaints Statute in the Student Policies and Guidelines section of the Policy Hub.