BME359 Copyright © 2016 SIM University Page 1 of 11 ECA – July Semester 2016 BME359 End-of-Course Assessment – July Semester 2016 Visualization & Image Analysis __________________________________________________________________________________________ INSTRUCTIONS TO STUDENTS: 1. This End-of-Course Assessment paper contains FORTY (40) projects and comprises ELEVEN (11) pages (including cover page). You will be assigned ONE project by your lecturer. 2. You are to include the following particulars in your submission: Title, Your PI, Your Name, and Submission Date. 3. If you fail to submit your End-of-Course Assessment, you will be deemed to have withdrawn from the course. IMPORTANT NOTE ECA Submission date: 12th November 2016, 12 noonBME359 Copyright © 2016 SIM University Page 2 of 11 ECA – July Semester 2016 Please Read This Information before You Start Working on your ECA This ECA carries 70% of the course marks and is a compulsory component. It is to be done individually and not collaboratively with other students. Submission You are to submit the ECA assignment in exactly the same manner as your tutor-marked assignments (TMA), i.e. using MyUniSIM. Submission in any other manner like hardcopy or any other means will not be accepted. Electronic transmission is not immediate. It is possible that the network traffic may be particularly heavy on the cut-off date and connections to the system cannot be guaranteed. Hence, you are advised to submit your assignment the day before the cut-off date in order to make sure that the submission is accepted and in good time. Once you have submitted your ECA assignment, the status is displayed on the computer screen. You will only receive a successful assignment submission message if you had applied for the e-mail notification option. ECA Marks Deduction Scheme Please note the following: a) Submission Cut-off Time – Unless otherwise advised, the cut-off time for ECA submission will be at 12:00 noon on the day of the deadline. All submission timings will be based on the time recorded by MyUniSIM. b) Start Time for Deduction – Students are given a grace period of 12hours. Hence calculation of late submissions of ECAs will begin at 00:00 hrs the following day (this applies even if it is a holiday or weekend) after the deadline. c) How the Scheme Works – From 00:00 hrs the following day after the deadline, 10 marks will be deducted for each 24-hour block. Submissions that are subject to more than 50 marks deduction will be assigned zero mark. For examples on how the scheme works, please refer to Section 5.2 Para 1.7.3 of the Student Handbook. Any extra files, missing appendices or corrections received after the cut-off date will also not be considered in the grading of your ECA assignment. Plagiarism and Collusion Plagiarism and collusion are forms of cheating and are not acceptable in any form of a student's work, including this ECA assignment. You can avoid plagiarism by giving appropriate references when you use some other people's ideas, words or pictures (including diagrams). Refer to the American Psychological Association (APA) Manual if you need reminding about quoting and referencing. You can avoid collusion by ensuring that your submission is based on your own individual effort. The electronic submission of your ECA assignment will be screened through a plagiarism detecting software. For more information about plagiarism and cheating, you should refer to the Student Handbook. UniSIM takes a tough stance against plagiarism and collusion. Serious cases will normally result in the student being referred to UniSIM's Student Disciplinary Group. For other cases, significant marking penalties or expulsion from the course will be imposed.BME359 Copyright © 2016 SIM University Page 3 of 11 ECA – July Semester 2016 Project Guidelines The aim of this ECA assignment is:  Use and integrate the knowledge gained and skills developed during your study of BME358 and BME359.  Demonstrate specific skills in the design and implementation of experiments and prepare a clear presentation of your work within a team.  Demonstrate in the project report your understanding of the themes in the course.  Organise and manage own learning and performance to suit own situation and style.  Prepare a clear project report using appropriate technical language. The assignment is to write an academic report, which is to contain comprehensive introduction, discussion of what had been carried out and implications of your findings. The examiner will look for evidence that you have a thorough grasp of the course principles and that you can apply these principles in the project. The topics for projects have been designed so that students should be able to progress towards the project goal. Students are examined on their project report. The report should be readable and intelligible to someone unfamiliar with the topic, and attention should be given to presentation (grammar, spelling, punctuation, and layout), as well as to the content. Overall presentation is improved if the material is organised into sections with headings and sub-headings. In general, a modest project that has clear explanation and presented in detail is likely to obtain a better grade. The report is to be presented within 2000-4000 words, excluding diagrams, appendices and list of references. A well-presented document should fit comfortably onto 20-30 pages of typed A4 paper. Please remember all sources (dataset) are confidential in your project. In order to avoid any complications, please ensure that the source of information is not circulated. The distribution of marks for the Project Report is described in Table 1. 2-0 Structure of Report You are strongly advised to follow the commonly accepted practice of organising your report into several sections (i.e. title page, abstract, introduction, method and design, results, discussion and conclusion, suggestions for future work, acknowledgement, references and appendices). The title page should contain the project title, your name, student PI number, your course name, your supervisor's name, and the date of submission.BME359 Copyright © 2016 SIM University Page 4 of 11 ECA – July Semester 2016 2-1 Abstract This should include the following points (keep it short and should not exceed 300 words): (i) Project objectives (ii) Background information (iii) Main technique used (iv) Summary of results (v) Information for reader to understand what the report is about 2-2 Introduction This section should contain a survey of pertinent background literature (refer to 20-30 references), together with a statement of the aims and methodology of the project. You should endeavour to demonstrate in this section that you have mastered the theoretical background to your topic. The section should end with a statement of what you had originally intended to do at the start of project. It is important that your introduction section is clear and concise. Only quote papers that are directly relevant to your work. 2-3 Method and design This should follow the appropriate journal format for the particular field of science under research. The preparation/composition of all samples must be described in detail. All experimental procedures, including calculations, should be given in detail. When a calculation or procedure is repeated, it only needs to be described once in detail. All procedures used in processing raw experimental data must be described. 2-4 Results All results obtained must be presented, either in tabular or graphical form, and explained briefly to the reader. Obvious features/trends of the data have to be highlighted. In cases where your work generates large amounts of raw data, which is then subsequently processed/refined, you may include the raw data in one or more Appendices at the end of your report. Present only the processed/refined data in your Results section. 2-5 Discussion This is the most important section of your report. You should discuss your findings, their limitations and errors. Discuss how your results agree or disagree with theory and other studies. Discuss the results one aspect at a time and use different sub-sections to break up the discussion. Avoid simply repeating statements made elsewhere in the report. You should make an effort to assess/analyse your results in an in-depth and original way, rather than simply pointing out the obvious trends in your experimental data.BME359 Copyright © 2016 SIM University Page 5 of 11 ECA – July Semester 2016 2-6 Conclusion and suggestions for future work Here, you should summarize your main findings, highlight areas where more work is needed, and suggest avenues for future development of this work. 2-7 References and appendices All references quoted in your report should be listed in a uniform format in this section. In appendices, if any, include all raw data, spectra, ventricular animation, 3D modeling of the heart and any other data not shown in the Results section, but needed to be consulted. Refer to the section below for detailed instructions on appropriate reference format. Books Bird, R. B., Stewart, W. F., and Lightfoot, E. N., 1960. Transport Phenomena, New York: Wiley. Edited books Margoliouth, H. M. (ed.), 1952. The Poems and Letters of Andrew Marvell, 2 vols., 2nd ed., Oxford University Press. Theses Kartheuser B., 1993. An Investigation of the Partial Oxidation of Methane. Ph.D. Thesis, University of Limerick. Chapter in edited book Louis, C., and Che, M., 1985. "The structure of CeO2", in: Reactivity of Solids, P. Barret, Ed, 1057-1059, Amsterdam: Elsevier. Journal articles Kim, K., and Johnston, K.P., 1987. "Molecular Interactions in Dilute Supercritical Fluid Solutions." Ind. Eng. Chem. Res., 26, 1206-1213. Magazine or newspaper articles Divine, D., 1965. "Will Bomber Command last?", Sunday Times, January 31st, p.19. Conference proceedings Bouras, Ch., 1975. "Particular difficulties in the conservation and study of Greek historical monuments." In: Photogrammetric Surveys of Monuments and Sites. Photogrammetria, J. Badekas (Editor), 30: 99-105.BME359 Copyright © 2016 SIM University Page 6 of 11 ECA – July Semester 2016 3-0 Marking Scheme The Marking Scheme for the ECA Final Report is shown in Table 1. Analysis of Marks for ECA final report Marks Awarded Remarks on the Student's Performance Abstract: - Project objectives - Background information - Main techniques used - Results - Major conclusion 20 Introduction: - Comprehensive literature review - Aims - Methodology 20 Methods & Design: - Overall design of project - Summary of image processing - Statistical analysis 10 Results: Clear presentation of results with subject characteristics 15 Discussion: - Interpretation of results with discussion on present and previous research work - Limitations and errors - Questions raised in the project 20 Conclusion and suggestion for future work 5 Report presentation - Written language - Good use of illustrations - Clear structure - Correct references 10 Table 1BME359 Copyright © 2016 SIM University Page 7 of 11 ECA – July Semester 2016 4-0 List of Projects You will be assigned one of the following projects by your lecturer. The description and type of data provided for each project are described below. Projects 1-10 Image processing and analysis are used to extract and interpret the information from biomedical images, and put this information into practical use. In this ECA, we focus on cardiovascular imaging and to detect cardiovascular disease. Projects 1-10 Cardiovascular Image processing Cardiovascular image processing plays an important role in diagnosis and treatment of patients. These projects are designed to test your understanding of medical imaging as well as your ability to apply your knowledge in real clinical situations. Objectives: Demonstrate specific skills required for reading and labelling magnetic resonance imaging (MRI) of the heart and quantification of the heart (i.e., atrium and ventricle) size and function, in patients with diverse heart diseases. Figure 1: Example of MRI images of the heart at end-diastole and endsystole phases Project 1: Left ventricular size and volume quantification Project 2: Left atrium size and volume quantification Project 3: Right atrium size and volume quantification Project4: Right ventricular size and volume quantificationBME359 Copyright © 2016 SIM University Page 8 of 11 ECA – July Semester 2016 Project 11-20 Project 5: Mitral annulus size and deformation quantification Project 6: Tricuspid annulus size and deformation quantification Project 7: Aortic annulus size and deformation quantification Project 8: Pulmonary annulus size and deformation quantification Project 9: Left ventricular wall thickness mapping at end-diastole and endsystole phases Project 10: Left ventricular wall curvature mapping Data acquisition: Each student will be provided with a full magnetic resonance imaging dataset (n=3-10) Project 11-20 Image processing using Matlab In Projects 11-20, Matlab provides comprehensive algorithms, functions and apps for image processing, analysis and visualization. Students are to perform image analysis, image segmentation, image enhancement, noise reduction and image restoration using Matlab. Objectives: Examine image processing issues with Matlab & Meshlab for the following projects 11-20. Example of auto-tracking of mitral annulus is shown in Figure 2. Figure 2: Example of auto-tracking of mitral annulus motion.BME359 Copyright © 2016 SIM University Page 9 of 11 ECA – July Semester 2016 Project 21-30 Project 11: Auto-segmentation of left atrium Project 12: Auto-segmentation of left ventricle Project 13: Auto-segmentation of right atrium Project 14: Auto-segmentation of right ventricle Project 15: Auto-segmentation of aorta Project 16: Auto-segmentation of pulmonary artery Project 17: Auto-tracking of mitral annulus motion during cardiac Project 18: Auto-tracking of tricuspid annulus motion during cardiac cycle Project 19: Matlab-based algorithm development to add noise to heart imaging Project 20: Matlab-based algorithm development for the histogram display of heart imaging Data acquisition: Each student will be provided a full Cardiac Magnetic Resonance imaging dataset (n=1 or 2) Project 21-30 Signal processing using Matlab Projects 21-30 use the Matlab software package to develop algorithms which can automatically or semi-automatically read hemodynamic signals from invasive catheterization (i.e. ventricular pressure, aortic artery pressure, and arterial pressure waveform), display the digital signal and analyse the data. Matlab is a high-level programming environment, which is commonly used by researchers and engineers because of its powerful toolboxes and easy to use scripting language. Objectives: Recommend and develop algorithms using Matlab to automatically read hemodynamic signals. Example of ventricular pressure waveform from invasive catheterization is shown in Figure 3.BME359 Copyright © 2016 SIM University Page 10 of 11 ECA – July Semester 2016 Figure 3: Example of ventricular pressure waveform from invasive catheterization Project 21: Digitization and analysis of left atrium pressure waveforms Project 22: Digitization and analysis of left ventricular pressure waveform Project 23: Digitization and analysis of right atrium pressure waveform Project 24: Digitization and analysis of right ventricle pressure waveform Project 25: Digitization and analysis of aortic pressure waveform Project 26: Digitization and analysis of pulmonary artery pressure waveform Project 27: Dynamic pressure gradient analysis from ventricular to aorta Project 28: Analysis of pressure-volume loops for end-systolic ventricular elastance Project 29: Analysis of pressure-volume loops for end-diastolic ventricular elastance Project 30: Analysis of left ventricular pressure-volume loop by coregister MRI and invasive catheterization Data acquisition: Each student will be provided a full pressure waveform dataset (n=1)BME359 Copyright © 2016 SIM University Page 11 of 11 ECA – July Semester 2016 Project 30-40 Projects 31-40 Image Visualization The practice of medicine and study of biology have always relied on visualizations to study the relationship of anatomical structure to biologic function and to detect and treat disease and trauma that disturb life processes. Image visualization includes 2-D (multiplanar reformatting, oblique sectioning and curved sectioning) and 3D display (surface rendering, volume rendering, and volume modelling). Objective: Solve 3D visualization problems by demonstrating skills in MIMICS, Meshlab or Paraview. Example of visualization of a patient with aorta aneurysm is shown in Figure 4. Figure 4: Example of visualization of a patient with aorta aneurysm Project 31: 3D visualization of the heart using Meshlab Project 32: 3D visualization of the coronary artery tree using Meshlab Project 33: 3D visualization of Jaw and prosthesis structure using MIMICS Project 34: 3D visualization of skull using MIMICS Project 35: 3D visualization of hip structure using MIMICS Project 36: 3D visualization of the abdominal aorta from CTA Project 37: 3D visualization of mitral valve using Meshlab Project 38: 3D visualization of heart using Paraview Project 39: 3D visualization of brain from Paraview Project 40: 3D visualization of hands using Paraview Data acquisition: Each student will be provided a full CMR imaging dataset and/or DICOM dataset (n=1 or 2) -----END OF ECA PAPER -----