CSC 621-821: Biomedical Imaging & Analysis

Spring 2018 (5422-5423)

 

 

Instructor: Dr. Kazunori Okada

Lecture Time

Tue: 4:00 - 6:45 pm

Lecture Location

HH 543

Office Phone

(415) 338-7687

Office Location

TH 911

Office Fax

(415) 338-6826

Office Hours

Wed: 4:00-5:00 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

Uengtrakul

xxx@mail.sfsu.edu

TA Office Hour

TA Office

Tue: 10:00-11:00am

CS Undergraduate Lab (SCI254)

 

 

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: A grade of C or better in MATH 325 and CSC 510

 

 

Text Books:

[t1]: Digital Image Processing (3rd Ed), R.C. Gonzalez and R.E. Woods. Prentice Hall, 2008 http://www.pearsonhighered.com/educator/product/Digital-Image-Processing/013168728X.page (optional for 621)

[t2]: Fundamentals of Medical Imaging (2nd Ed), P. Suetens, Cambridge University Press, 2009 (optional for 621 & 821) http://www.cambridge.org/us/catalogue/catalogue.asp?isbn=9780521519151

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

 

 

Lecture Plan (subject to change)

Week

Topic: Lecture

Notes

Readers

Assignments

Exam

01:01/23

Course Overview: Framework,

History, Applications

Note01

[t1] Ch1

[t2] Ch1-2

Final

Project

 

02:01/30

Imaging Methods & Physics:

Optical, X-ray, CT, MRI

Note02

[t2]Ch2-6

[t3]

Literature

Survey

 

03:02/06

Imaging Methods & Physics:

PET, US, Fusion, Biology

Note03

[t2] Ch2-6

[t3]

 

 

04:02/13

Image Data Structure

Image Visualization

Note04

[t2]

Ch8

 

05:02/20

Digital Image fProcessing:

Practical Foundation

Note05

[t1]

Ch2-3

Due: project design 

 

06:02/27

Digital Image Filtering:

Spatial Domain

Note06

[t1]

Ch3

 

Midterm1

07:03/06

Digital Image Filtering:

Frequency Domain

Note07

[t1]

Ch4

 

08:03/13

Advanced Processing:

Edge Detection & Morphology

Note08

[t1]

Ch9-10

09:03/20

Spring Recess

----------

-----------

---------------- 

----------- 

10:03/27

Image Segmentation:

Thresholding, Region Growing

Note09

[t1]

Ch10

 

11:04/03

Image Segmentation:

Watersheds, Level Sets, Graph

Note10

[t1]

Ch10

 

12:04/10

Midterm Exam

 

Midterm2 

13:04/17

 Image Registration:

Geometry-based Registration

Note11

[t2]

Ch7

 

 

14:04/24

Image Registration:

Intensity-Based Registration

Note12

[t2]

Ch7

 

 

15:05/01

No lectures

----------

-----------

---------------- 

-----------  

16:05/08

Image Quantification:

Change Analysis, Classification

Note13

 [t1]

Ch11-12

Due on 5/14 5pm:

Presen files

 

17:05/15

Project

Final Presentation

Pres01

 

Due on 5/18 10pm:

Final-&-LS Reports

 

             

 Important Dates:

2/27:    Midterm 1

4/10:    Midterm 2

5/14:    Due (5pm via email): Files needed for final presentations (Proj-Leads)

5/18:    Due (10pm via email): Final Project Report

5/18:    Due (10pm via email): Literature Survey Report (Only 821)

5/22:    Final Exam Slot @ HH543 from 4:00pm – 6:45pm

2/09:    Last day to add; Last day to drop without W grade

 

 

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. Each group will consist of about 5-6 students including graduate students who may act as project 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++. 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 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 821 (for 621):

·         40% (60%):         Midterms

·         40% (40%):         Final Project

·         20% (0%):           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:

·        Late assignment will be penalized by 10% per day up to 50%.

·        After 5 days, late assignments receive zero credit.

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

 

 

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.

 

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.

 

Grade Appeal:

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

 

Academic Probation:
If you are on academic probation, make an appointment as soon as possible to work out what you need to do to meet the terms of your probation.

 

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: http://cs.sfsu.edu/plagarism.html

 

Learning Assistances:

Learning Assistance Center, located at HSS 348, offers tutoring services for various subjects. More information can be found at http://lac.sfsu.edu and http://lac.sfsu.edu/tutoring

 

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) 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 © 2018, All rights are reserved.