CSC621-821 Biomedical Imaging and Analysis

CSC 621-821: Biomedical Imaging & Analysis

Spring 2013

Instructor: Dr. Kazunori Okada
Lecture Time	Tue: 3:00 - 5:50 pm	Lecture Location	TH 311
Office Phone	(415) 338-7687	Office Location	TH 911
Office Fax	(415) 338-6826	Office Hours	Wed: 1:30-2:30 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	Jeffrey Hung hung@mail.sfsu.edu	TA Office Hour TA Office	Thr: 10:00-11:00am SCI 254 (CS Undergrad Lab)

Important Dates:

Lecture plan table has been adjusted (3/11)

2/08: Last day to drop and to request Audit grading

3/22: Last day to request CR/NC grading option

3/05: Midterm 1

4/09: No Lecture

4/16: Midterm 2

5/13: Due (5pm via email): Files needed for final presentations (Proj-Leads)

5/17: Due (10pm via email): Final Project Report

5/21: Due (10pm via email): Literature Survey Report (Only 821)

5/21: Final Exam Slot @TH331 from 4:00pm – 5:50pm

Course Web Page: http://cose-stor.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 (3^rd 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 (2^nd 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
01:01/29	Course Overview: Framework, History, Applications	Note01	[t1] Ch1 [t2] Ch1-2	Final Project
02:02/05	No lecture			Literature Survey
03:02/12	Imaging Methods & Physics: Optical, X-ray, CT, MRI	Note02	[t2]Ch2-6 [t3]
04:02/19	Imaging Methods & Physics: PET, US, Fusion, Biology	Note03	[t2] Ch2-6 [t3]	Due: group assignment
05:02/26	Image Data Structure Image Visualization	Note04	[t2] Ch8
06:03/05	Digital Image Processing: Practical Foundation	Note05	[t1] Ch2-3
07:03/12	Digital Image Filtering: Spatial Domain	Note06	[t1] Ch3		Midterm1
08:03/19	Digital Image Filtering: Frequency Domain	Note07	[t1] Ch4
09:03/26	Spring Recess	-----------	-----------	----------------	-----------
10:04/02	Advanced Processing: Edge Detection & Morphology	Note08	[t1] Ch9-10
11:04/09	No Lecture	-----------	-----------	----------------	-----------
12:04/16	Image Segmentation: Thresholding, Region Growing	Note09	[t1] Ch10
13:04/23	Image Segmentation: Watersheds, Level Sets, Graph	Note10	[t1] Ch10		Midterm2
14:04/30	Image Registration: Geometry-based Registration	Note11	[t2] Ch7
15:05/07	Image Registration: Intensity-Based Registration	Note12	[t2] Ch7	Due on 5/13: Presen files
16:05/14	Project Final Presentation	Pres01		Due on 5/17(5/21): Final (LS) Reports

Final Project: Developing a Biomedical Image Analysis System

Students will engage in a hands-on group project for developing a part of biomedical image analysis system. Each group will consist of several students including at least one graduate student who acts as a project lead and mentors undergraduate members. With data provided, each group will identify, implement and evaluate a specific data analysis algorithm. 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 assignments will not be graded. Complete 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 Policy: http://www.sfsu.edu/~bulletin/current/supp-reg.htm#ppg339

· Computer Science Department Policy: http://cs.sfsu.edu/plagarism.html

American with Disabilities Act (ADA) Accommodation:

The Disability Programs and Resource Center (DPRC) provides university academic support services and specialized assistance to students with disabilities (http://www.sfsu.edu/~dprc/). Students with disabilities who need reasonable accommodations are encouraged to contact the instructor. 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/TTY 415-338-2472) or by email (dprc@sfsu.edu).

Learning Assistances:

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

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.