Methods In Medical Image Analysis - Spring 2008

BioE 2630 (Pitt) : 16-725 (CMU RI) : 42-735 (CMU BME)

Instructor: John Galeotti
(galeotti+miia ATcs.cmu.edu)

Teaching Assistant: Andrew Whitord
(asw35+miia ATpitt.edu)

Syllabus

New Room: Benedum Hall Conference Room 750
(at the University of Pittsburgh, accessable via Benedum Hall 749)

Class begins Tuesday, Jan. 15th!
Class ends Thursday, April 24th.


Lecture and Shadow Program / Times and Locations

We comply with both the U. Pitt. and CMU calendars. Lectures are Tuesday and Thursday from 10:00-11:15 AM, In the conference room at 750 Benedum Hall, University of Pittsburgh.

Shadow Program - 5 sessions 8:30-9:30 AM, weekday mornings, see online schedule (same password) and directions.

Last Year's Website has been archived, and may also be available at the original website.


Textbooks, Downloads, & Other References

myITKgui - Warning: Does not work on Mac (specifically on my intel Mac with VTK5.x)


Assignment #1 - Introductory Email

Assignment #2 - Install and Test: ITK, VTK, & FLTK

Assignment #3 - Fun with Filters


Schedule

   
Week 1
Tu 1/15
Lecture 1: Introductions, Purpose, Syllabus, & Imaging Modalities
Assignment #1 given.
 
Th 1/17
Lecture 2: Programming Background  
   
Week 2
Tu 1/22
Lecture 3: ITK Background & Basic Usage  
Th 1/24
Lecture 4: Math & Probability Background
Begin class with a short QUIZ on Snyder ch. 1-2
Recommend also looking at 16-720's Math Tutorial
 
   
Week 3
Tu 1/29
Lecture 5: ITK Images & Iterators
Assignment #2 given. Due by midnight on 2/5.
 
Th 1/31
Lecture 6: Image Characterization and Linear Processing 1
Quiz on Snyder ch. 4-5.3 (skip hexagonal coordinates on pp 57-60 & 71-3)
 
   
Week 4
Tu 2/5
Lecture 7: ITK Pipeline & working with a GUI.  
Th 2/7
Lecture 8: Linear Processing 2
Quiz on Snyder 5.4-5.6,5.8-5A (through page 101, but skip 5.7)
 
   
Week 5
Tu 2/12
Lecture 9: ITK Filters: How to write them (Neighborhoods & Numeric Traits)
Assignment #3 given.
Be sure to sign up for the Shadow Program THIS WEEK.
 
Th 2/14
Lecture 10: Image relaxation: restoration & feature extraction
Quiz on Snyder ch. 6
 
   
Week 6
Tu 2/19
Lecture 11: ITK Filters (Advanced Filter Creation & Misc. Tools)  
Th 2/21
Lecture 12: Segmentation, part 1 (begin by finishing ch 6: VCD)
Quiz on Snyder ch. 8 (skip 8.3.2 on pp. 189-196 & 8A.1.1 on pp. 208-209)
 
   
Week 7
Tu 2/26

Lecture 13: Segmentation, part 2

 
Th 2/28
Lecture 14: Segmentation, part 3  
   
Week 8
Tu 3/4
Lecture 15: ITK Registration  
Th 3/6
Class Cancelled due to BioE Recruitment Weekend poster session.  
   
Spring Break
3/10 - 3/14
No Lectures  
       
Week 9
Tu 3/18
Lecture 16: Guest Lecture: Using ITK to HELP my research, rather than AS my research--a practical use perspective, by Ken Urish  
Th 3/20

Lecture 17: ITK Misc. & Open Source Techniques
Also, be sure to email me your project proposals!

 
   
Week 10
Tu 3/25

Lecture 18: Guest Lecture: Cootes and Taylor (Cootes CVIU 1995), by Ken Urish

 
Th 3/27
Lecture 19: Shape
Quiz on Snyder ch. 9 (read 9.1-9.8, 9.12-9.14)
 
   
Week 11
Tu 4/1
Lecture 20: Level Set Segmentations & Parametric Transforms (Snyder 8.5.2 + Insight into Images ch 8 & Snyder 11.1-11.6)  
Th 4/3
Lecture 21: Mathematical morphology & Image Matching
Quiz on Snyder 7.1-7.5 & 13.1-13.5
 
   
Week 12
Tu 4/8
Lecture 22: Registration in Depth (Jen Mercer's slides: Insight into Images ch 10 + Viola & Wells)  
Th 4/10
Lecture 23: Deformable Registration  
   
Week 13
Tu 4/15
Lecture 24: Scientfic Paper Review: ITK Paths  
Th 4/17
No Lecture - CMU Spring Carnival  
   
Week 14
Tu 4/22
Student Project Presentations  
Th 4/24
Student Project Presentations & Projects Due