Methods In Medical Image Analysis - Spring 2016

BioE 2630 (Pitt) : 18-791 (CMU ECE) : 42-735 (CMU BME)

Instructor
John Galeotti
galeotti+miia ATcs.cmu.edu
Usually meets with students after class
 
Teaching Assistant

Ying Ying Wu

yingyingwu ATcmu.edu

5-6pm Friday (starting February), Hamerschlag Hall B127
And by email or other appointments if necessary

Syllabus (general)

Syllabus (ECE detailed format)

Meeting in CIC 1201
(at Carnegie Mellon University)

Class begins Tuesday, Jan. 12th!
Class ends Thursday, April 28th.


Lecture Times and Locations

We comply with both the U. Pitt. and CMU calendars. Lectures are Tuesday and Thursday from 10:30-11:45 AM, in CIC 1201, Carnegie Mellon University.

Shadow Program Times, Locations, & Details

Shadow Program:  6 radiology sessions and 0-2 (TBD) pathology sessions, 8:30-9:30 AM weekday mornings (and possibly other times optional for shadowing pathology).

Online schedule (same password), directions, and required UPMC confidentiality agreement. Reports should be emailed to your TA and Galeotti.


Textbooks, Downloads, & Other References

Last Year's Website has been archived.


Assignments (please do not start until assigned in the schedule)

Assignment #1 - Introductory Email

Assignment #2 - Get ITK & SimpleITK installed, etc.

Assignment #3 - Go through the Python Notebook you installed in Assignment #2; Email the entire completed page (as a pdf) to your TA. (Windows users can install the free and open source PDFCreator to print to pdf.) If imshow() gives an error, try using pylab.imshow() instead. If no image is visible, then insert the commands "%matplotlib inline" and "%pylab inline" on two new lines before imshow(). [5 points]

Assignment #4 - Use SimpleITK to do Segmentation and Pre-processing

Assignment #5 - Registration (optional)

Final Project


Schedule--Subject to Change
(Future plans are tentative, based on the old 2015 schedule)

Note about videos: Lecture videos were recorded in 2012, and you can downlaod the lecture videos from the 2012 schedule here. Be sure to download the videos (right-click the video's link then select either "download" or "save-as") rather than try to watch them in your browser. Please let me know if you notice any problems or video content that should be either fixed or trimmed out if it's not relevant to a general audiance (please reference the 2012 lecture number and the playing time into the video at which the problem occurs).

Week # Date Updated for 2014? Material Video and .pptx files
Week 1
Tu 1/12
Y

Lecture 1: Introductions, purpose, Syllabus
Assignment #1 given

Power Point
Video (from 2012)
Th 1/14
Y

Syllabus
Lecture 2: Programming background:  C++ & Python

Power Point
Video (from 2012)
     
Week 2
Tu 1/19
Y

Lecture 3: Math & probability background
Begin class with a short QUIZ on Snyder ch. 1-2
Pitt's add/drop-with-refund period ends today

Power Point
Video (from 2012)
Th 1/21
Y

Lecture 4: ITK background & basic usage
CMU's add/drop-with-refund period ends on 25th (Monday)

Power Point
Video (from 2012)
     
Week 3
Tu 1/26
Y Lecture 5: Image characterization
Quiz #2 on Snyder ch. 4 (skip hexagonal coordinates on pp 57-59)
Assignment #2 given - due 10pm on Feb. 4th.

Power Point
Video (from 2012)

Th 1/28
Y Finish Image characterization (resume at slide 13)
Lecture 6: Linear processing
Quiz #3 on Snyder 5.1-5.6,5.8-5A (through page 101, but skip hexagonal coordinates on pp 71-73 and skip 5.7)
Take-home quiz #4 assigned - due in class on Feb. 9th.

Power Point
Video (from 2012)
     
Week 4
Tu 2/2
Y

Finish Linear processing (resume Edge Detection at slide 11)
Lecture 7: Image relaxation: restoration & feature extraction
Quiz #5 on Snyder ch. 6

Power Point
Video (from 2012)
Th 2/4
Y

Finish Image relaxation (resume Objective Functions at slide 16)
Lecture 8: ITK registration
HW2 due 10pm today.

Power Point
Video (from 2012)
     
Week 5
Tu 2/9
Y Lecture 9: Finish ITK registration (start slide 9)
Take-home quiz #4 due in class.
 
Th 2/11
Y

Go over take-home quiz.

Lecture 10: Segmentation, part 1
Quiz #6 on Snyder ch. 8 (skip 8.3.2 on pp. 189-196 & 8A.1.1 on pp. 208-209)

Power Point
Video (from 2012)

     
Week 6
Tu 2/16
Y

Lecture 11: Segmentation, part 1 continued (using lecture 9 notes, start with slide 8)

 
Th 2/18
Y

Discuss Shadow Program & signup procedure in class
Imaging Modalities

Shadow Program — be sure to sign up for the Shadow Program THIS WEEK, beginning at 1:00 pm Saturday (all previous signups will be removed).

Imaging Modalities Power Point (contains embedded movies)
Video (from 2012, skip to end for imaging modalities)

     
Week 7
Tu 2/23
Y

No Class

Shadow Program starts WEDNESDAY--show up at 8 am until you know where you're going

 

Th 2/25
Y

Lecture 12: Segmentation, part 3 (active contours)

Power Point
Video (from 2012)
     
Week 8
Tu 3/1
Y

Lecture 13: Level set segmentations, dynamic programming, & (briefly begin) parametric transforms (Snyder 8.5.2 & Snyder 11.1-11.6) [not required, but recommended: Insight into Images ch 8]
Quiz on Snyder 11.1-11.6

Python NoteBook (from assignment #2) Assigned--due 10pm Thursday.
How is the shadow program going?

Power Point
Video (from 2012)

Th 3/3
Y

Inline Plots
Discuss final projects
Be sure to email me your final project proposals by the night of Tuesday the 15th.

Level Set segmentations (start with ITK framework), parametric transforms
Lecture 14: Shape
Quiz on Snyder ch. 9 (read 9.1-9.8, 9.12-9.14)

SVN accounts distributed later today
Segmentation Assignment given Friday (now ready): Segmentation and pre-processing , due 10pm Friday the 18th.

Power Point
Video (from 2012)

Power Point 2

         
Spring Break
3/8 - 3/10
  No Lectures  
         
Week 9
Tu 3/15
Y

Finish shape
Lecture 15 Registration in depth (Insight into Images ch 10 + Viola & Wells)

Power Point
Video (from 2012)
Th 3/17
Y

Finish registration
Lecture 16: ITK images & iterators
Pitt's deadline to submit Monitored Withdrawal forms is 16th (tomorrow)
Segmentation Assignment due tomorrow night (18th)

Power Point
Video (from 2012)
     
Week 10
Tu 3/22
Y

Tentative project proposals due tonight
Finish ITK images & iterators


 
Th 3/24
Y Lecture 17: ITK pipeline, including reading/writing images and connecting to SimpleITK Power Point
Video (from 2012)
  Note: CMU's drop-without-withdrawl period ends on March 30th (Monday)  
Week 11
Tu 3/29
Y

Lecture 18 Mathematical morphology & image matching
Quiz on Snyder 7.1-7.5 & 13.1-13.5

Power Point
Video (from 2012)
Th 3/31
Y

Finish EigenImages, etc.
Lecture 19: ITK filters: how to write them (neighborhoods, image boundaries, & numeric traits)

Power Point
Video (from 2012)

     
Week 12
Tu 4/5
Y

Finish Numeric Traits
Lecture 20 Deformable registration (Insight into Images ch 11)
Registration homework given, due 10am next Thursday morning

Power Point
Video (from 2012)

Th 4/7
Y Lecture 21: ITK filters, part 2 (advanced filter creation & misc. tools)
CMU's drop-without-withdrawl period ends today
Power Point
Video (from 2012)
     
Week 13
Tu 4/12
Y

NeuroPathology -- Normal class time, meet at UPMC:

Please try to arrive before 10:30am; this will be mostly standing room only.

  1. Enter Scaife Hall from the main doors on Terrace street (directly across from the Peterson event center).
  2. Immediately inside are a bank of elevators: Take one up to the 7th floor.
  3. Go right as you exit the elevator and go through a set of double doors.
  4. Ron Hamilton's office and the microscope room are right there

 
Th 4/14
  No Lecture - CMU Spring Carnival  
         
Week 14
Tu 4/19
Y Student project presentations (see random order email)
(Each presentation must be ~8 minutes long.)
Everyone's power-point slides due in svn by 10 AM today!
 
Th 4/21
  Student project presentations (see random order email)
 
         
     
Week 15
Tu 4/26
  Student project presentations (see random order email)
 
Th 4/28
  Student project presentations & Projects Due  
         
Remaining Lecture Fragments:

Lecture 22a: ITK Paths

Lecture 22b: Summarize Cootes and Taylor ASM (Cootes CVIU 1995)

Power Point
Video (from 2012)

Power Point (public version)

Potential Lectures:
  Lecture 23: Open source software development philosophy, and Visualization Power Point
      Later today: TA Help Session for Take-home quiz, 3:15 - 4:15 pm, NSH 4113  
      Class Cancelled:  Extreme cold + windchill, which are especially problemeatic for students having to travel back and forth between universities, and I might not be able to drive in.  
         
      Guest Lecture: MRI/DTI (see also brain anatomy and the fiber track image gallery)  
      Itk Video (w/ OpenCV?)  
      Lecture 24: Advanced Shape Analysis, Shape Comparisons, and Segmentation Validation (includes spherical harmonics, medial, DICE, etc.)  
      NeuroPathology at 10:30 today! Meet at UPMC, not at CMU. Follow emailed directions.