CISC-472: Medical Informatics

 

Winter 2018

 

Course Outline

 

This course is designed for 3rd and 4th year biomedical computing students and  it is mandatory in the Biomedical Computing Honor’s Program at the Queen’s School of Computing.  This course is a continuation of CISC-330 Computer Integrated Surgery, a subject in the intersection of computer science, engineering, medical physics, life sciences and medicine. We will study concepts, methods, component technologies and clinical systems that are currently in clinical use or development at various research institutions including Queen’s.  To see the detailed contents of the course is listed in the bottom of this web page.

 

 

Prerequisite

CISC-330* - Please note that this prerequisite cannot be waived.

 

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ANNOUNCEMENTS image001 

 

This is where the assignments will be posted….

 

 

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COURSE DESCRIPTION

 

Instructor

Gabor Fichtinger, PhD

Professor and Cancer Care Ontario Research Chair

School of Computing, Queen’s University

 

Office: Goodwin 725

Homepage: www.cs.queensu.ca/~gabor

Email: gabor@cs.queensu.ca ß PREFERRED WAY OF COMMUNICATION

 

Course Website

http://www.cs.queensu.ca/home/cisc472

 

Teaching Assistant

Zac Baum (zac.baum@queensu.ca) MSc Candidate    

            Please note that Zac will assist in grading and will not hold regular office hours.

 

Class Times & Location

Monday           10:30 – 11:30  Goodwin 247

Tuesday          12:30 – 13:30  Goodwin 247

Thursday         11:30 – 12:30  Goodwin 247

 

 

Office Hours

Monday           09:30 – 10:30  Goodwin 747 (Perk Lab)

Tuesday          11:30 – 12:30  Goodwin 747 (Perk Lab)

Thursday         10:30 – 11:30  Goodwin 747 (Perk Lab)

 

Please always email me the day before you wish to see me in office hour. Office hours are often crowded, I want to make sure that you receive sufficient time and attention.

 

I strongly encourage you to use the office hours for in-person consultation, especially if you have questions or problems with materials in class or with the homework assignments. Please come to see me within the posted office hours. Please always email me the day before. If you miss me in office, look around in the Perk Lab offices on the 7th floor of Goodwin. If you do not find me for some reason, send me an email note so that I know that you came to see me (which shows that you care about your grade.) Generally, never be embarrassed to ask questions. Asking questions and seeking help will always have a positive impact on your grade. I consider this as an important gauge of your overall interest and commitment. I want you to understand and learn the material, so that I can reward you with a good grade.

 

COURSE DESCRIPTION

 

Teaching Approach

I enjoy teaching computer-integrated, a captivating and challenging subject in the intersection of computing, engineering and heath sciences. My teaching and mentoring philosophy coincides with the Queen’s University Academic Plan, as I strive to prepare my students for advanced learning and equip them with knowledge and skills for tackling the real-life problems they will encounter as future creators or competent users of cutting-edge healthcare technologies.

 

My undergraduate courses are challenging, for they usually need considerable effort (and time) to complete them successfully. I do not use tests, midterms or exams to assess my students, as I am not interested in their ability to answer prepared questions. Instead, I use projects to assess their abilities to pose relevant questions and analyze the meaning and ramifications of their results because I am most interested in encouraging their growth in the creative process. During each term, students must perform about four projects. Each concerns a complete computer-integrated surgery problem and typically requires design, implementation, testing and detailed analysis of the results. I always ask my students to test the limits of their solutions; my mantra about healthcare engineering is “we never know what we created until we break it.” These projects sometimes may be somewhat individualized to fit their prior advancement in the subject and specific career goals, i.e., medicine, science or industry. I strive to prepare my students for their chosen career path while coaching them to think outside the box and nurturing their creativity and insights. As I get to know the individual strengths and needs of my undergrads, mentoring becomes an important aspect; I often help them find thesis supervisors, advise them about graduate school and preparing portfolios, refer them to employers, etc.

 

Course Format

The dominant format is classroom presentations, with as much discussion as time permits. There may be occasional guest lecturers, presenting on various topics of interest. Guest lecturers will be scheduled flexibly depending upon their availability. When I must be away for some reason (conference, etc.) I will arrange for guest lectures if possible, instead of cancelling classes or setting makeup classes.

 

Class attendance is highly recommended, because lecture notes are mostly without words and you will have to take notes. We will move fast in the classroom and often cover material outside the course notes. Every assignment will involve some details that are not in the course notes but will be discussed in class. Students who tend to miss classes tend to do poorly in this course.

 

Practicum (may be offered)

There may be optional lab sessions offered, to experiment with image-guided surgery navigation systems. The sessions will not be graded and they will not be counted in your grade numerically, however it will give me a better understanding of your commitment to the course. The lab sessions will be scheduled individually and flexibly to fit your schedule. The lab sessions are expected to be sometime in November or December and they will be coordinated by Perk Lab researchers. Offering and schedule will depend on research schedules in the Perk Lab and are subject to change. Each session will take about 60 minutes to compete. You will perform some task pertaining to image-guided surgery navigation in non-biohazardous lab environment. During the lab sessions, you will be asked to participate in human performance studies that investigate the use and effectiveness of novel surgical guidance techniques developed in the Perk Lab. You will be given an informed consent form to describe the study and its voluntary nature. Your participation in the studies will help research in the Perk Lab (http://perk.cs.queensu.ca).

 

Learning Outcomes

·         Understanding advanced concepts in computer-integrated surgery

·         Advanced knowledge and competence in computer-integrated surgery and systems applications

·         Ability to design, develop and analyze computer-integrated surgery systems

·         Ability to analyze and “reverse engineer” computer-integrated surgery systems

·         Ability to make connections between computing, electrical engineering, mechanical engineering and medical sciences as they apply to  computer-integrated surgery

·         Understanding of graduate research opportunities pertinent to computer-integrated surgery

Assessment

 

Grace assessment is based on three assignments due during the sessional period and one final take-home exam during the exam period. (The take home exam will be similar to the assignments in weight and structure.) The weighs of the four components will be about equal, but the exact weighting may slightly change, depending the actual contents and construction of the assignments.  No tests and no midterms are planned.

 

Assignments and take-home exam

Assignments involve problems pertinent to medical image computing and computer-assisted surgical navigation. The assignments will be posted on this website, under Announcements above. The assignments are roughly of the same weight, depending on our schedule and progress with the material. The assignments include concept, programming, test and discussion elements.

 

Three or four assignments are planned, depending on how we progress in class with the material. By about mid/late October we will see if three or four assignments will be included. There will be at least two full weeks for each assignment, from posting date to submission date.  There will be at least three weeks for the final project. The assignments and project will take a fair bit of time to complete. Do not leave them for the last few days, when you will discover inevitable difficulties. Start on them early, size up the problem and formulate a solid work plan. Come to office hours when you encounter difficulties. Consultation will not only save you from wasting time and from a poor grade, but it will also give me a better understanding of your commitment to the course.

 

I will try to adjust submission deadlines to avoid mass collision with your other midterms and exams. To this end, I urge you to consult with your classmates and bring constructive suggestions to adjust our schedule. Once the cut-off date and time are set, there will be no individual extension, unless you produce written evidence of a medical reason or other extenuating circumstances.

 

Submission Format

·         Submit the assignments in PDF format, by email to the TA with copy to me. You will receive an acknowledgment of receipt. If you do not get one before or shortly after the deadline, resend the submission with noting the original date of submission.

·         When you submit multiple files, order them and zip them together into a single file.

·         Use a file / folder name that includes your full name and identifies the assignment as “Lastname-Firstname-Assgn-1.gz”.

·         Your submission will often include handwritten inserts, figures and math – scan these into PDF and zip it with the rest of the submission; number the pages sensibly.

·         Include your full name and student number in the submission.

 

Software components

o   Work out your programs in MATLAB.

o   Submit your code in MATLAB file format (m files). 

o   Include screen capture or some evidence that the code runs and produces the results you claim.

o   Include some README or instruction for running your code. 

o   Your code must be complete and self-contained.

o   I and the TA must be able to run your assignment in a common MATLAB environment. If you use special libraries, you must include those with your source, with exact reference to the source where they came from.

o   You must include a proper header in each program file and for each routine; you must follow good software practices you learned in your other courses – this does count in your marks.

 

Notes on integrity and originality

o   You may use any publicly available book, website, article, and open-source software – but you must always fully reference the source.

o   You may not use resources that may contain materials submitted by others for CISC 330 or related courses such as CISC 271 or CISC 472, regardless to when and where and when it was posted or how it was obtained.

o   You may reuse your own work done in other courses.

o   Any attempt to submit fake results will be penalized.

o   I encourage you to study and brainstorm in groups, but independent work is required in the submitted material.

o   If you brainstorm with others, you must acknowledge this in your submission.

o   Do not share any part of the written assignment, including figures, software code, with anyone.

o   You will be penalized if you copy someone else's work or allow your work to be copied.

 

Class Notes

I will post on this website PDF copies of the power point presentations shown in class. I sometimes change the presentation in the last minute, in order to adjust to the flow of the course. (Some ad-hoc subjects may not have pre-made course notes – you will need to take your own notes in class and you can read up on the subject in the recommended literature. The slides do not contain many words and sometimes no words at all. I recommend that you download and/or print out the slides and take notes, either electronically or manually. If you miss a class, you still may like to print out the handouts for the following time, because lectures tend to be grouped by themes, rather than by calendar. As there is no concise textbook for the course, your notes will serve as primary reference in the assignments.

 

Grading

All components in this course will receive numerical percentage marks and an overall percentage score will be calculated as the weighted average of the scores from the components.

 

The final numerical grade will be entered on SOLUS, which then automatically computes your letter grade, according to current University/Faculty standards. 

 

Academic Integrity & Dishonesty

Academic Integrity is constituted by the six core fundamental values of honesty, trust, fairness,

Respect, responsibility and courage (see www.academicintegrity.org). These values are central to the building, nurturing and sustaining of an academic community in which all members of the community will thrive. Adherence to the values expressed through academic integrity forms a foundation for the "freedom of inquiry and exchange of ideas" essential to the intellectual life of the University (see the Senate Report on Principles and Priorities http://www.queensu.ca/secretariat/policies/senate/report-principles-and-priorities).

 

Students are responsible for familiarizing themselves with the regulations concerning academic integrity and for ensuring that their assignments conform to the principles of academic integrity. Information on academic integrity is available in the Arts and Science Calendar (see Academic Regulation 1 http://www.queensu.ca/artsci/academic-calendars/regulations/academic-regulations/regulation-1), on the Arts and Science website (see http://www.queensu.ca/artsci/academics/undergraduate/academic-integrity), and from the instructor of this course. Departures from academic integrity include plagiarism, use of unauthorized materials, facilitation, forgery and falsification, and are antithetical to the development of an academic community at Queen's. Given the seriousness of these matters, actions which contravene the regulation on academic integrity carry sanctions that can range from a warning or the loss of grades on an assignment to the failure of a course to a requirement to withdraw from the university.

 

Specifically in this course, the following activities are examples of violations of Academic Integrity:

·        Sharing a partial or complete solution to a marked assignment with another student (not even after the submission deadline).

·        Looking at another student's partial or complete solution to a marked assignment -- with or without their permission

·        Asking another person to write code or pseudo-code for you for a marked assignment

·        Asking for help with a marked assignment from an online site         

 

Copyright for inclusion on all course materials

The material on this website, linked course notes, lectures and assignments is copyrighted and is for the sole use of students registered in this course. The material on this website may be downloaded for a registered student’s personal use, but shall not be distributed or disseminated to anyone other than students registered in this course. Failure to abide by these conditions is a breach of copyright, and may also constitute a breach of academic integrity under the University Senate’s Academic Integrity Policy Statement.

 

Accessibility

The Queen’s University Equity Office has shared the following statement on their webpage for your use in ensuring that all course elements are fully accessible (http://www.queensu.ca/equity/accessibility/policystatements/accessibility-statement). Course materials will be made available in an accessible format or with appropriate communication supports upon request.

 

Accommodations

Queen's University is committed to achieving full accessibility for persons with disabilities. Part of this commitment includes arranging academic accommodations for students with disabilities to ensure they have an equitable opportunity to participate in all of their academic activities. If you are a student with a disability and think you may need accommodations, you are strongly encouraged to contact Student Wellness Services (SWS) and register as early as possible. For more information, including important deadlines, please visit the Student Wellness website at: http://www.queensu.ca/studentwellness/accessibility-services/

 

Considerations for Students in Extenuating Circumstances

The Senate Policy on Academic Consideration for Students in Extenuating Circumstances was approved in April, 2017. Queen’s University is committed to providing academic consideration to students experiencing extenuating circumstances that are beyond their control and which have a direct and substantial impact on their ability to meet essential academic requirements. The Faculty of Arts and Science is developing a protocol to provide a consistent and equitable approach in dealing with requests for academic consideration for students facing extenuating circumstances, which will be posted on the Faculty of Arts and Science website in Fall, 2017.

 

Student Wellness Resources

2017-2018 Student Health and Wellness Slides aim to promote self-care and encourage helping behaviours. They highlight key support services on campus. Queen’s provides these resources and updates the content each fall.

 

Self-Identification

 

Student Wellness Services

 

Queen's Student Accessibility Services

 

 

COURSE CONTENTS

Refresher from CISC-330

 

Marker Registration

 

 

Point Cloud to Surface Registration

 

Iterative Closest Point Registration

 

Medical Images

 

Image Filters

 

Marker Segmentation

 

Curve Segmentation

 

Anatomical Segmentation

 

Model Reconstruction and Display

 

Image Registration

 

Statistical Shape Models and Atlases

 

 

Lecture Notes – CONSTANT WORK IN PROGRESS

The schedule is subject to changes, depending on our progress in the classroom. I WILL KEEP REVISING THE COURSE SCGHESULE NOTES, PLEASE CHECK THE LATEST VERSION SHORTLY BEFORE CLASS.

 

Refresher from CISC-330 – Math 1 (vector geometry)

 

Refresher from CISC-330 – Math 2 (transformations)