This course introduces the broad concepts of biomedical imaging across a range of modalities. It provides a foundation towards the understanding of how modern biomedical imaging technologies generate multi-dimensional data for analysis and diagnosis. Key technologies covered include: XRay, CT, MRI, FMRI, Ultrasound, light microscopy, and medical imaging processing. Application of the biomedical images used to interpret biological process and diagnostics disease will also be discussed in small groups. Hands-on practical laboratory visits to cutting edge advanced bioimaging systems will be available to reinforce the lecture material, and quantitative imaging processing in the context of basic research and clinical settings will be covered.

Note: Graduate students attend joint classes with undergraduates but are assessed separately

Learning Outcomes

Upon successful completion, students will have the knowledge and skills to:

1. Evaluate the operation and function of different biomedical imaging instruments on molecules, cells and organs.
2. Describe and apply the principles of advanced biomedical imaging concepts and their application in health sciences.
3. Analyse the limitation of each biomedical imaging modalities and also how they complement each other for molecular, cellular and organ-level systems.
4. Apply advanced image processing to quantify biomedical images, critique the factors that contribute to analysis and evaluate their effectiveness.
5. Understand, analyse and evaluate major biomedical imaging modalities used in health sciences and outline its therapeutic aims.
6. Evaluate the research methods and outcomes from selected scientific publications related to the course curriculum.

Research-Led Teaching

Student will be introduced to advanced imaging processing and instruments developed at the John Curtin School of Medical Research. Student will be provided with opportunities to review leading research articles (peer review) in medical imaging and provide critical assessment of each imaging methods.

Recommended Resources

• Biomedical Imaging: Principles and Applications Reiner Salzer (Editor)

Staff Feedback

Students will be given feedback in the following forms in this course:

• Written comments
• Verbal comments
• Feedback to the whole class, to groups, to individuals, focus groups

Student Feedback

ANU is committed to the demonstration of educational excellence and regularly seeks feedback from students. Students are encouraged to offer feedback directly to their Course Convener or through their College and Course representatives (if applicable). The feedback given in these surveys is anonymous and provides the Colleges, University Education Committee and Academic Board with opportunities to recognise excellent teaching, and opportunities for improvement. The Surveys and Evaluation website provides more information on student surveys at ANU and reports on the feedback provided on ANU courses.

Class Schedule

Week/Session	Summary of Activities	Assessment
1	Modern Medical Imaging- Seeing is believing- Human to Mice to Organ-on-chip to Dish
2	Imaging through tissue I : High Energy• X-Ray, CT (Lung)• PET (Tumor)	Tutorial 1, Image Analysis 1 (X-Ray)
3	Imaging through tissue II : Magnet• MRI (Brain)• fMRI (Neuroactivity)	Tutorial 2, Image Analysis 2 (MRI)
4	Imaging through tissue III : Sounds, Light• Ultrasound (Heart)• Optical Coherent Tomography (Artery)	Tutorial 3, Image Analysis 3 (Ultrasounds)
5	Cellular Imaging with light• Pathology (Tissue slices), Fluorescence• TEM, Cryo-EM	Tutorial 4, Image Analysis 4 (Fluorescence)
6	Machine Learning in Medical Imaging• Fundamentals of signal processing• Machine Learning in medical imaging	Tutorial 5, Image Analysis 5 (Endoscopy)
7	Imaging Data Science• Compression, archiving, retrieval, and communication• Big Data analysis in healthcare	Tutorial 6, Image Analysis 6 (Machine learning)
8	• Review of topics (WK 1, 2, 3)• Review of topics (WK 4, 5, 6)
9	• Laboratory visit to Biofluidic Imaging LabIn Person	Quiz based on Lab Tour
10	• Recap on Image Processing Lab• Image Treasure hunt
11	Individual Report &-Presentation	Individual Presentation, Individual Report
12	• Revision I• Revision II
13	Examination period	Final exam

Assessment Summary

Assessment task	Value	Due Date	Return of assessment	Learning Outcomes
Tutorial (10%)	10 %	*	*	1,2,3
Computer Lab (10%)	10 %	*	*	2,4,5
Individual Presentation and Individual Report (25%)	25 %	20/10/2023	03/11/2023	1,2,3,5
Lab Visit Quiz (15%)	15 %	*	*	1,3,5
Written Exam (40%)	40 %	*	*	1,2,3,4,5

* If the Due Date and Return of Assessment date are blank, see the Assessment Tab for specific Assessment Task details

Policies

ANU has educational policies, procedures and guidelines, which are designed to ensure that staff and students are aware of the University’s academic standards, and implement them. Students are expected to have read the Academic Misconduct Rule before the commencement of their course. Other key policies and guidelines include:

• Student Assessment (Coursework) Policy and Procedure
• Special Assessment Consideration Policy and General Information
• Student Surveys and Evaluations
• Deferred Examinations
• Student Complaint Resolution Policy and Procedure

Assessment Requirements

The ANU is using Turnitin to enhance student citation and referencing techniques, and to assess assignment submissions as a component of the University's approach to managing Academic Integrity. For additional information regarding Turnitin please visit the ANU Online website Students may choose not to submit assessment items through Turnitin. In this instance you will be required to submit, alongside the assessment item itself, hard copies of all references included in the assessment item.

Moderation of Assessment

Marks that are allocated during Semester are to be considered provisional until formalised by the College examiners meeting at the end of each Semester. If appropriate, some moderation of marks might be applied prior to final results being released.

Assessment Task 1

Tutorial (10%)

Responses to Weekly session

Week conducted: Weeks 2-7

Value:10%

Due date: 7 days after the tutorial is posted.

Assessment to be returned:

5 days after tutorial submission ended.

Assessment (Tutorial):

Short qualitative answers on the application of each imaging modality. A sample question will be like

"Recent research is indicating that patients with severe COVID-19 infection appear to be at greater risk of developing blood clots in the blood vessels, which is particularly dangerous

for hospitalized patients. Blood clots are the body’s mechanism to stop bleeding. Describe the sequence of major events/phases that occur as blood clots around an injured site and why a

blood clot can be hazardous, and more importantly, which imaging modality is suitable for rapid diagnosis of COVID-19 blood clots" Hint: ChatGPT

Students are expected to evaluate on the ChatGPT’s answers

KNOWLEDGE:

Provide objective criticism of the answers provided by ChatGPT with clear reasonings based on the knowledge from the course

UNDERSTANDING:

Demonstrate an ability to provide illustration, Discussing the pros and cons of the answers provided by ChatGPT

INSIGHTS:

Suggest improvements to the questions and justify why your answers is better than ChatGPTs.

Assessment Task 2

Computer Lab (10%)

Assessment (Image Analysis)

Students will be given image analysis projects related to "de-noising", "image averaging", "image segmentation", "thresholding", "object counting" using the ImageJ (NIH) software suite. Student will be expected to provide their tutor a Written Reflection for each computer class.

Week conducted: Weeks 2-7

Value: 10%

Due date: 1 day after the computer lab.

Assessment to be returned:

2 days after submission

KNOWLEDGE: Demonstrate and replicate the desired steps to achieve digital image processing.

UNDERSTANDING: Explain to your tutor the use of the digital processing steps in research or clinical setting.

INSIGHTS: Discussing the pros and cons of the digital processing steps.

Assessment Task 3

Individual Presentation and Individual Report (25%)

Due date: Week 12

Assessment to be returned: 7 days after submission

Value: 25%

Individual Project- Essay (5 pages)

Presentation: Illustration (15 mins, recorded presentation)

The goal of the report and presentation is to convey the advantages of a given imaging modality for a disease versus others.

1) Disease focused Imaging

2) Brief overview of existing technology

3) Working Principles

4) Examples of successes

5) Cost benefit Analysis? Comparing with other technologies

6) Future technological developments for the diseases diagnosis

Example : Optical Coherence Tomography (OCT) for Cardiovascular Diseases

Guiding Questions

1. Who developed and is currently advancing OCT

2. What are the challenges in introduction to OCT in Cardiovascular Diseases

3. What are the working principles and How are OCT images processed?

4. How OCT enables new findings in Cardiovascular Diseases

5. What Next Generation OCT in intravascular diagnosis

6. How does OCT Compare with other Cardiovascular Diseases

Assessment Task 4

Lab Visit Quiz (15%)

OUTLINE

Due date: Week 10

Assessment to be returned: 7 days after submission

Value: 15%

There will be 10 individual questions

Example questions:

In cellular imaging using light, light source is an essential component to visualize cell activities in real time. There are many different types of light sources used for cellular imaging in the lab tour. Can you

1) Lists the 2 main differences in light sources used in multiphoton microscope and quantitative phase microscope.

2) Quantitative phase microscope is highly suited for long term live cell imaging. Discuss the key limitation between the light source used in multiphoton microscope for long term imaging.

KNOWLEDGE: List out the desired practical steps taken to record a digital image.

UNDERSTANDING: Explain to the practical use of light microscopy processing steps in research or clinical setting.

Example of lab tour:

Multiphoton microscope:

https://www.youtube.com/watch?v=g86xPUt92NQ&list=PLO7Gi3zX5DTjoq1_63yG3tCIY2hYtnACz&index=5

Quantitative phase microscope:

https://www.youtube.com/watch?v=Cc-giYHnvpI&list=PLO7Gi3zX5DTjoq1_63yG3tCIY2hYtnACz&index=8

Assessment Task 5

Written Exam (40%)

Written exam (2.5 hrs) in the university examination period.

Value: 40%

Assessment will take the form of short answer written answers on how to practically apply the imaging technologies.

Example question:

QUESTION 3

Write at least 20 words for each of the following questions.

Use equations and diagrams where necessary (20 points):

(i) X-Rays are produced when high velocity electrons collide and “eject” from a metal target. This phenomenon of “braking radiation” relates to a sudden deceleration of electrons. Increased temperature was applied to the cathode along with decreased voltage in the X-ray tube. Describe the changes to the resulting energy of X-rays produced. (2 points)

(ii) X-Rays are attenuated by either absorption or scattering events in tissue. Angiography is a method using of a liquid dye (gadolinium) injected through a fine tip flexible needle (called a catheter). The dye fills the blood vessel which changes the attenuation factor and in turn alters the final X-ray image. Coronary angioplasty uses a special balloon and a metal mesh tube (stent) to open up a narrowed or blocked coronary artery.

a. Assume that the attenuation coefficient and thickness of the dyed blood vessel is µBlood, tBlood and soft tissue is µSoft, tSoft,.respectively. When the initial number of X-Rays projected on the body is Nin, provide an analytical expression of the remaining photons Nout at positions A, B, C. (Hint: final amount of photon received at the X-ray detector) (4 points)

b. Describe the main physiological reasons and working principle behind the differences in contrast i.e. appearance of the different grayscale levels in A, B, C in the X-ray image. (4 points)

(iii) Magnetic resonance imaging (MRI) and Positron emission tomography (PET) provides a volumetric reconstruction of a full body. a. Describe the differences between how the signals in an MRI (proton spin) and PET (Gamma radiation) are collected and subsequently converted into a 2D cross section for 2 major organs: muscle and brain. (4 points)

(iv)Functional magnetic resonance imaging (fMRI), which measures the oxygenation of red blood cells, is a complementary imaging technique that extract functional information in a living subject.

a. Describe the difference between signals acquired in fMRI and traditional MRI. (3 points)

b. A patient was particularly uncomfortable about the noise produced by the MRI machine and fidgeting nervously. Explain how this in turn, affected the signal to noise ratio in the fMRI reading. (3 points) 

Academic Integrity

Academic integrity is a core part of our culture as a community of scholars. At its heart, academic integrity is about behaving ethically. This means that all members of the community commit to honest and responsible scholarly practice and to upholding these values with respect and fairness. The Australian National University commits to embedding the values of academic integrity in our teaching and learning. We ensure that all members of our community understand how to engage in academic work in ways that are consistent with, and actively support academic integrity. The ANU expects staff and students to uphold high standards of academic integrity and act ethically and honestly, to ensure the quality and value of the qualification that you will graduate with. The University has policies and procedures in place to promote academic integrity and manage academic misconduct. Visit the following Academic honesty & plagiarism website for more information about academic integrity and what the ANU considers academic misconduct. The ANU offers a number of services to assist students with their assignments, examinations, and other learning activities. The Academic Skills and Learning Centre offers a number of workshops and seminars that you may find useful for your studies.

Online Submission

The ANU uses Turnitin to enhance student citation and referencing techniques, and to assess assignment submissions as a component of the University's approach to managing Academic Integrity. While the use of Turnitin is not mandatory, the ANU highly recommends Turnitin is used by both teaching staff and students. For additional information regarding Turnitin please visit the ANU Online website.

Hardcopy Submission

For some forms of assessment (hand written assignments, art works, laboratory notes, etc.) hard copy submission is appropriate when approved by the Associate Dean (Education). Hard copy submissions must utilise the Assignment Cover Sheet. Please keep a copy of tasks completed for your records.

Late Submission

Late submission of assessment tasks without an extension are penalised at the rate of 5% of the possible marks available per working day or part thereof. Late submission of assessment tasks is not accepted after 10 working days after the due date, or on or after the date specified in the course outline for the return of the assessment item. Late submission is not accepted for take-home examinations.

Referencing Requirements

Accepted academic practice for referencing sources that you use in presentations can be found via the links on the Wattle site, under the file named “ANU and College Policies, Program Information, Student Support Services and Assessment”. Alternatively, you can seek help through the Students Learning Development website.

Returning Assignments

Assignments are returned on wattle to individual students.

Extensions and Penalties

Extensions and late submission of assessment pieces are covered by the Student Assessment (Coursework) Policy and Procedure The Course Convener may grant extensions for assessment pieces that are not examinations or take-home examinations. If you need an extension, you must request an extension in writing on or before the due date. If you have documented and appropriate medical evidence that demonstrates you were not able to request an extension on or before the due date, you may be able to request it after the due date.

Resubmission of Assignments

There are no resubmission of Assignments

Privacy Notice

The ANU has made a number of third party, online, databases available for students to use. Use of each online database is conditional on student end users first agreeing to the database licensor’s terms of service and/or privacy policy. Students should read these carefully. In some cases student end users will be required to register an account with the database licensor and submit personal information, including their: first name; last name; ANU email address; and other information. In cases where student end users are asked to submit ‘content’ to a database, such as an assignment or short answers, the database licensor may only use the student’s ‘content’ in accordance with the terms of service — including any (copyright) licence the student grants to the database licensor. Any personal information or content a student submits may be stored by the licensor, potentially offshore, and will be used to process the database service in accordance with the licensors terms of service and/or privacy policy. If any student chooses not to agree to the database licensor’s terms of service or privacy policy, the student will not be able to access and use the database. In these circumstances students should contact their lecturer to enquire about alternative arrangements that are available.

Distribution of grades policy

Academic Quality Assurance Committee monitors the performance of students, including attrition, further study and employment rates and grade distribution, and College reports on quality assurance processes for assessment activities, including alignment with national and international disciplinary and interdisciplinary standards, as well as qualification type learning outcomes. Since first semester 1994, ANU uses a grading scale for all courses. This grading scale is used by all academic areas of the University.

Support for students

The University offers students support through several different services. You may contact the services listed below directly or seek advice from your Course Convener, Student Administrators, or your College and Course representatives (if applicable).

• ANU Health, safety & wellbeing for medical services, counselling, mental health and spiritual support
• ANU Diversity and inclusion for students with a disability or ongoing or chronic illness
• ANU Dean of Students for confidential, impartial advice and help to resolve problems between students and the academic or administrative areas of the University
• ANU Academic Skills and Learning Centre supports you make your own decisions about how you learn and manage your workload.
• ANU Counselling Centre promotes, supports and enhances mental health and wellbeing within the University student community.
• ANUSA supports and represents undergraduate and ANU College students
• PARSA supports and represents postgraduate and research students