Winter 2019
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.
__________________________________________
ANNOUNCEMENTS
Take Home Exam on Tracked
Ultrasound Navigation and Calibration posted. Deadline April 29 (Monday), 09:00.
HW2 on Robot-assisted biopsy
navigation posted. Deadline March 24, Sunday, 23:59.9999.
HW1 on Marker Registration
posted. Deadline Feb 18, Monday 09:00
__________________________________________
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
No TA for this course
Class
Times & Location
Monday 08:30 – 10:00 Goodwin 247
Thursday 10:00 – 11:30 Goodwin 247
Monday 10:00 – 11:00 after class Goodwin 747 (Perk Lab)
Thursday 11:30 – 12:30 after class 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.
Teaching Approach
I very much enjoy teaching computer-integrated surgery, 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.
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 & Grading
The assessment will be based
on 2 assignments due during the sessional period and 1 take-home exam during
the exam period. You will receive a numerical grade (0-100) for assignments and
the take-home-exam. Each assignment weighs 30% and the take-home-exam weighs
40% of the final grade. You will receive a final numerical grade (0-100).
There will be no tests,
quizzes, midterms or other exams.
Assignments and take-home exam
The assignments and
take-home exam involve problems pertinent to medical image computing and
computer-assisted surgical navigation. The assignments will be posted on this
website, under
Announcements above.
There will be at least
two full weeks for each assignment and three weeks for the take-home exam, from
posting date to submission date.
They will take a fair
bit of time to complete (understatement :-). 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. You will receive an acknowledgment of receipt. If you do
not get one before or shortly after the deadline, please 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 within in the submission, such as file headers.
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 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.
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, posted on the Faculty of Arts and Science website HERE.
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.
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)
Transformations: Target
Registration Error
Transformations:
Point sets (more background in Arun1987)