CSC 621-821: Biomedical Imaging & Analysis

Spring 2021 (#8738, #8739)

 

 

Instructor: Dr. Kazunori Okada

Lecture Time

Tue: 4:00 - 6:45 pm

Location

Online (see iLearn)

Office Phone

(415) 338-7687

Office Location

Online (see iLearn)

Office Fax

(415) 338-6826

Office Hours

Wed: 1:00 - 2:00 pm

Email Address

kazokada@sfsu.edu

Web Page

http://online.sfsu.edu/kazokada/

Mailing Address

Computer Science Department, San Francisco State University
1600 Holloway Avenue San Francisco, CA 94132-4163

Teaching Assistant

Luis Chumpitaz Diaz

lchumpit@mail.sfsu.edu

TA Office Hour

TA Office

Mon: 11:00am - 12:00pm

Online (see iLearn)

 

 

Course Web Page: https://bidal.sfsu.edu/~kazokada/csc621-821/

 

Course Summary:

This course, an introduction to biomedical imaging and analysis, covers two main components: physical image formation (e.g., imaging physics, 3D imaging, image formats, visualization) and computational data analysis (e.g., digital image processing, filtering, registration, segmentation, quantification). The objectives of this course include developing comprehensive overview of basic topics in biomedical imaging & analysis and deeper knowledge of a specific biomedical imaging and analysis application. This is a paired course. CSC621 is for upper-division undergraduates while CSC821 caters to graduate students with additional assignments.

 

Prerequisites: CSC621: Upper-division standing; CSC510 and MATH 325 with grades of C or better; GPA of 3.0 or higher; or consent of the instructor. CSC821: Graduate standing or consent of the instructor.

 

Textbooks:

[t1]: Digital Image Processing (4th, Ed), R.C. Gonzalez and R.E. Woods. Prentice Hall, 2018 (3rd edition is also fine: optional for 621) https://www.pearson.com/us/higher-education/program/Gonzalez-Digital-Image-Processing-4th-Edition/PGM241219.html

[t2]: Fundamentals of Medical Imaging (3rd Ed), P. Suetens, Cambridge University Press, 2017 (2nd edition is also fine: optional for 621 & 821) https://www.cambridge.org/us/academic/subjects/medicine/medical-imaging/fundamentals-medical-imaging-3rd-edition?format=HB&isbn=9781107159785

[t3]: Introduction to Biomedical Imaging, A. Webb, IEEE Press, 2003 (optional for 621 & 821) http://www.wiley.com/WileyCDA/WileyTitle/productCd-0471237663.html

 

 

Lecture Plan (subject to change)

Week

Topic: Lecture

Notes

Readers

Assignments

Exam

01:01/26

Course Overview: Framework,

History, Applications

Note01

[t1] Ch1

[t2] Ch1-2

Final

Project

 

02:02/02

Imaging Methods & Physics:

Optical, X-ray, CT, MRI

Note02

[t2]Ch2-6

[t3]

Literature

Survey

 

03:02/09

Imaging Methods & Physics:

PET, US, Fusion, Biology

Note03

[t2] Ch2-6

[t3]

 

 

04:02/16

Image Data Structure

Image Visualization

Note04

[t2]

Ch8

 

05:02/23

Digital Image Processing:

Practical Foundation

Note05

[t1]

Ch2-3

Due: project design 

 

06:03/02

Digital Image Filtering:

Spatial Domain

Note06

[t1]

Ch3

 

Midterm1

07:03/09

Digital Image Filtering:

Frequency Domain

Note07

[t1]

Ch4

 

08:03/16

Advanced Processing:

Edge Detection & Morphology

Note08

[t1]

Ch9-10

09:03/23

Spring Recess

----------

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---------------- 

----------- 

10:03/30

Group Project Work Day

----------

-----------

---------------- 

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11:04/06

Image Segmentation:

Thresholding, Region Growing

Note09

[t1]

Ch10

 

12:04/13

Image Segmentation:

Watersheds, Level Sets, Graph

Note10

[t1]

Ch10

 

Midterm2

13:04/20

 Image Registration:

Geometry-based Registration

Note11

[t2]

Ch7

 

14:04/27

Image Registration:

Intensity-Based Registration

Note12

[t2]

Ch7

 

 

15:05/04

Image Quantification:

Change Analysis, Classification

Note13

 [t1]

Ch11-12

Due on 5/10 5pm:

Presen files

16:05/11

Project

Final Presentation

Pres01

Due on 5/14 10pm:

Final-&-LS Reports

 

             

 Important Dates:

3/02:    Midterm 1

4/13:    Midterm 2

5/10:    Due (5pm via email): Files needed for final presentations (Proj-Leads)

5/14:    Due (10pm via email): Final Project Report

5/14:    Due (10pm via email): Literature Survey Report (Only 821)

5/18:    Final Exam Slot from 5:00pm – 6:45pm

2/12:    Last day to add; Last day to drop without W grade

 

 

Zoom Lectures/Office Hours:

Lectures will be given via Zoom during the class meeting time. Access to the zoom lecture (only to the section you belong) is given to you in the iLearn page of this course. Do not access the zoom lecture session directly from outside ilearn. Attending zoom sessions for a section that you do not belong is also prohibited. You are requested to keep the video on during the lectures so that the instructor can see you. Microphones are muted by default and maybe activated by the instructor when required. You may participate discussion and ask questions via Zoom’s chat. Instructors will address them as soon as possible during the lectures. Please prepare your work environment with a computer with zoom client installed and working video camera and microphone. Zoom lectures will be recorded and made available later for aiding your study. Office hours will be available for in-person online conversations with both the instructor and the TA during the office hour time specified above. Zoom links for them will be shared in iLearn page.

 

iLearn Usage:

Attendance for each zoom lecture will be recorded by using iLearn’s attendance function manually. Password for self-reporting will be issued at the beginning of each lecture. Sharing of the password to other students who are not present in the zoom session is prohibited.

 

Distribution and submission of your assignments (e.g., homework and exams) will be handled through the iLearn course page. After the instructor made it available, click the specified iLearn link to view the assignment. Work on your problems and write down your answers on your own papers (make sure you write your name and SID# for each page). After you complete it, scan your answers by using a PDF-Scan tool (e.g., CamScanner, Scannable, GeniusScan, AdobeScan, Multifunction Printer, Google Drive Scanner etc) and save it to a single PDF file, combining all pages into one file. After checking that all pages are present and readable, submit your PDF file by using the specified iLearn assignment submission link. Always double-check what you submitted for its completeness and readability.

 

Final Project: Developing a Biomedical Image Analysis System

Students will engage in a hands-on group project for developing a biomedical image analysis system using public APIs. This year we will target building and experimenting a system that analyzes chest CT scans of Covid-19 patients. Each group will consist of about 5-6 students including graduate students who may act as team leads who mentor other undergraduate members. With data provided, each group will identify, design, implement and evaluate specific data analysis algorithms. For coding platform, students will use Insight Segmentation and Registration Toolkit (ITK: http://www.itk.org/) with C++ or (SimpleITK: https://simpleitk.org/TUTORIAL) with Python. Students will then present their resulting work, as a group, at the end of semester while each student is required to submit a final report made individually. Student’s work will be graded based on the quality and completeness of these individual report and group presentation. Late policy will apply. Please read the assignment carefully for more details.

 

Literature Survey Report (Only 821):

An independent literature survey study is to be carried out by each student taking CS821 in order to help them learning how to write their own thesis. Students must i) choose a subtopic related to biomedical imaging & analysis research, ii) conduct a survey of the subtopic’s recent literatures consisting of minimum of five representative peer-reviewed published articles, and iii) submit a written report summarizing and critiquing the survey results. The report must follow the SFSU thesis format specified in the university guidelines and should be no shorter than 18 double-spaced pages (two-page introduction, two pages for each paper, four page critique and conclusion, and two page reference list). Late policy will apply. Please read the assignment carefully for more details.

 

Exams:

There will be two midterms. No final exam.

 

Quiz/Homework:

No quiz and homework is currently planned. There may be some quizzes with a short notice for making sure that you are following the covered materials.

 

 

Numerical Grade Weights for 621 (for 821):

·         60% (40%):         Midterms

·         40% (40%):         Final Project

·         0% (20%):           Literature Survey Report

·        In general, students will be evaluated on their ability to devise, organize and present complete solutions to problems. Solutions need to be presented in a neat and organized way; cryptic answers or untidy presentation will not be graded. Completing answers to all problems with sound and in-depth analytical reasoning are required; a correct answer with no reasoning or with wrong reasoning will result in no (partial) credit

·         The grade distribution is as follows: A (100% - 92.5%), A- (92.4%-90%), B+ (89.9% - 87.5%), B (87.4% - 82.5%), B- (82.4% - 80%), C+ (79.9% - 75%), C (74.9% - 65%), C- (64.9% - 60%), D+ (59.9% - 57.5%), D (57.4% - 52.5%), D- (52.4% - 50%), F (49.9% - 0%).

 

Late Policy:

·       No make-up exams and homework late submission will be allowed. If you know that you will be missing an exam or assignment due, you must arrange with the instructor.

·       When allowed, late submission will be penalized by 10% per day up to 50%.

·       After 5 days, late assignments receive zero credit.

 

Grade Appeal:

To appeal your grades on assignments and exams, you must do so within one week after your work was returned or made available to you. There will be no exception even if you miss those classes. You are responsible to find out your own grades.

 

Absence:

Regular attendance is recommended as attending lectures is the best way to learn the material. From the SFSU bulletin: “Students are expected to attend classes regularly because classroom work is one of the necessary and important means of learning and of attaining the educational objectives of the institution.” In the event of an absence, it is the student’s responsibility to learn of any material missed and acquire assignments and announcements given during the class. Lectures and demonstrations will not be repeated during office hours. In case of extraordinary circumstance, it is the student’s responsibility to inform the instructor as soon as s/he can.

 

Syllabus is Subject to Change:

This syllabus and schedule are subject to change. The official syllabus will be maintained at the course website. It is your responsibility to check on the site frequently and when such a change is announced even when such announcements were made while you were absent.

 

 

 

COVID-19 and Our Campus:

Your health and safety is our paramount concern at SF State. During the COVD-19 pandemic, every member of our Gator community is expected to do their part in keeping fellow students, faculty, and staff safe and well. Feeling well and safe will support you in focusing on your academic success. For the limited number of classes meeting face-to-face, In-person class attendance is an option, but not a requirement. Students who do not wish to or are unable to comply with these requirements will be allowed to take the class virtually or provided with other remote options for course completion Please consult the campus plan website (https://news.sfsu.edu/campus-plan) for up-to-date information and explanation of requirements. For all students attending in-person, the following are required:

·       Wear a face covering when around other people outside of those in your household.

·       Stay at least 6 feet physically distant from people outside the members of your household.

·       Stay home if you have one or more symptoms of COVID-19 (Please check in with the SF DPH website for the most up-to-date symptoms & testing: https://www.sfcdcp.org/wp-content/uploads/2020/04/GetTestedSF-Eng-052920.pdf)

·       If you would like to discuss reasonable accommodations based on disability related to COVID-19, please contact the Disability Programs & Resource Center: dprc@sfsu.edu

Information is changing rapidly, as our health professionals, scholars, and researchers are learning more about COVID-19, and as such, we encourage you to frequently check your San Francisco State University email account and https://news.sfsu.edu/campus-plan/students-families for the most current information.

·       You are encouraged to keep your emergency information updated on Campus Solutions in order to receive campus emergency alerts: https://upd.sfsu.edu/ENSFAQ

·       You are also encouraged to provide your contact information to receive city of SF emergency alerts, including COVID-19 updates and instructions for public safety: https://sfdem.org/get-city-alerts

·       If you have any questions regarding COVID-19 or your own health during this time, please reach out to Student Health Services: https://health.sfsu.edu

·       If you are feeling overwhelmed, you are encouraged to connect with our on-campus health professionals in Counseling & Psychological Services: https://caps.sfsu.edu

·       If you are looking for education on how to keep yourself and your loved ones healthy, then reach out to our Health Promotion & Wellness Team: https://wellness.sfsu.edu

 

Academic Integrity & Plagiarism:

Academic Integrity refers to the “integral” quality of the search for knowledge that a student undertakes. Plagiarism is a form of cheating or fraud; it occurs when a student misrepresents the work of another as his or her own. I encourage discussion among students, but I expect each student to hand in original work. You are responsible for doing your own work and for insuring that your work is protected from copying. Violation to the university and departmental rules (found in below links) is a serious offence and can result in severe penalties. It is your responsibility to familiarize yourself with the following rules:

·         SFSU Code of Student Conduct: http://conduct.sfsu.edu/standards

·         Academic Dishonesty: http://conduct.sfsu.edu/academic-dishonesty

·         Plagiarism: http://conduct.sfsu.edu/plagiarism 

·         Computer Science Department Policy: https://cs.sfsu.edu/cheating-plagiarism-policy

 

Honor Code:

Your continued enrollment in this class indicates that you have carefully and entirely read and pledge to aide by the Honor Code published in the iLearn page of this course, and accept the consequences to violations of its terms. You will be asked to acknowledge this Honor Code in iLearn page.

 

Learning Assistances:

The Tutoring and Academic Support Center (TASC) is a new university-wide center that supports the academic success of all San Francisco State students. They are offering services online via Zoom. Please email tutoring@sfsu.edu from your SF State email address with your name, student ID, course for which you are seeking tutoring, and available days/times for an appointment. They will reply with details for your online appointment. More information can be found at https://ueap.sfsu.edu/tutoring.

·          Phone Number: 415-405-5516

·          Location: Tutoring is currently being offered online via Zoom

·          Hours: Mon-Thr, 9:00 a.m. to 7:00 p.m. and Fri, 9:00 a.m. to 2:00 p.m.

·          Email: tutoring@sfsu.edu

 

Religious Holidays:

Reasonable accommodations will be made for you to observe religious holidays when such observances require you to be absent from class activities. It is your responsibility to inform the instructor during the first two weeks of class, in writing, about such holidays.

 

Disability Access:

Students with disabilities who need reasonable accommodations are encouraged to contact the instructor.  The Disability Programs and Resource Center (DPRC: https://access.sfsu.edu/) is available to facilitate the reasonable accommodations process. The DPRC is located in the Student Service Building and can be reached by telephone (voice/415-338-2472, video phone/415-335-7210) or by email (dprc@sfsu.edu).

 

Student Disclosures of Sexual Violence:

SF State fosters a campus free of sexual violence including sexual harassment, domestic violence, dating violence, stalking, and/or any form of sex or gender discrimination.  If you disclose a personal experience as an SF State student, the course instructor is required to notify the Title IX Coordinator by completing the report form available at http://titleix.sfsu.edu, emailing vpsaem@sfsu.edu or calling 338-2032.

To disclose any such violence confidentially, contact:

·       The SAFE Place - (415) 338-2208; http://www.sfsu.edu/~safe_plc/

·       Counseling and Psychological Services Center - (415) 338-2208; http://psyservs.sfsu.edu/

·       For more information on your rights and available resources: http://titleix.sfsu.edu

 

 

Kazunori Okada © 2021, All rights are reserved.