Methods In Medical Image Analysis - Spring 2017

16-725 (CMU RI) : BioE 2630 (Pitt)

(Frequently also crosslisted as 18-791, CMU ECE : 42-735, CMU BME)

John Galeotti
Usually meets with students after class
Teaching Assistant



__pm __ (starting February), building room#
And by email or other appointments if necessary

Syllabus (general)

Meeting in CIC 1201
(at Carnegie Mellon University)

Class begins Tuesday, Jan. 17th!
Class ends Thursday, April 27th.

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Last Year's Website has been archived.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 2017? Material Video and .pptx files
Week 1
Tu 1/17

Lecture 1: Introductions, purpose, Syllabus

Power Point
Video (from 2012)

Th 1/19


Lecture 2: Programming background:  C++ & Python

Power Point
Video (from 2012)
Week 2
Tu 1/24

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
Assignment #1 given

Power Point
Video (from 2012)
Th 1/26

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 1/31
  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 2/2
  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 2/7

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 2/9

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 2/14

Lecture 9: Finish ITK registration (start slide 9)
Take-home quiz #4 due in class.

Shadow Program — be sure to sign up for the Shadow Program THIS WEEK, beginning at 11:00 pm Wednesday (all previous signups will be removed).

Th 2/16

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 2/21

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

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

Th 2/23

Discuss Shadow Program & signup procedure in class
Imaging Modalities

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

Week 7
Tu 2/28

Lecture 12: Segmentation, part 3 (active contours)

Power Point
Video (from 2012)
Th 3/2

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.
Inline Plots
How is the shadow program going?

Power Point
Video (from 2012)

Pitt Spring Break
3/7 - 3/9

No Lectures: Due to non-overlapping spring breaks this year, you should expect some type of online/take-home assignment that you can do during the time of your choosing during this 2 weeks.

CMU Spring Break
3/14 - 3/16
Week 8
Tu 3/21
  Discuss final projects
Be sure to email me your project proposals by the night of Thursday the 23rd.
Power Point
Th 3/23

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)

Week 9
Tu 3/28

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

Power Point
Video (from 2012)
Th 3/30

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 4/4

Tentative project proposals due tonight
Finish ITK images & iterators

Th 4/6
  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 4/11

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

Power Point
Video (from 2012)
Th 4/13

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

Power Point
Video (from 2012)

Week 12
Tu 4/18

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 4/20
  No Lecture - CMU Spring Carnival  
Week 13
Tu 4/25

Student project presentations (see random order email)

Th 4/27
  Student project presentations & Projects Due