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
Special Project-Help TA & Grader
"Bruce" Chengqian Che
By email or appointment

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Last Year's Website has been archived.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 - iPython Notebooks: Segmentation by Thresholding #1

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 2016 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

To prepare for the quiz, I suggest focussing on big-picture concepts and major themes, what algorithms/methods are trying to do, what they are good for, and (if the text goes over it) when/how they typically fail.

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 sometime around now.

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 not yet ready

Power Point
Video (from 2012)

Th 2/2

Finish Image characterization (resume at slide 12)
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)
Assignment #2 will be given on Friday. (It is now ready as of 5pm Friday)

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 #4 on Snyder ch. 6

Power Point
Video (from 2012)
Th 2/9

Lecture 8: ITK registration
HW2 due 5pm Friday the 10th. Extended deadline: now due 10am Monday morning.

Power Point
Video (from 2012)
Week 5
Tu 2/14

Finish Image relaxation (resume Minimization at slide 18)
Finish ITK registration (start slide 29)

Th 2/16

Discuss Shadow Program & signup procedure in class

Shadow Program — be sure to sign up for the Shadow Program THIS WEEK, beginning at 9:00 am Friday (all previous signups will be removed).

Lecture 9: Segmentation, part 1
Quiz #5 (the most in-depth quiz of the class) 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 10: Segmentation, part 1 continued (using previous notes, start with slide 3)

Shadow Program starts THURSDAY--show up at 8 am (with UPMC form!) until you know where you're going

Th 2/23

Lecture 11: Segmentation, part 3 (active contours)

Assignment #3 is now assigned, due 5pm Tuesday

Power Point
Video (from 2012)
Week 7
Tu 2/28

Follow Up: HW3—easy/helpful? MS Edge & PDF? Shadow?
Plan: Spring Break 2 weeks?

Finish Lecture 11.
Lecture 12
: 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)

Th 3/2

Finish Parametric Transforms

Discuss final projects
Be sure to email me your initial project idea / tentative proposal by the night of Thursday the 16th. Updated: now due Thursday night the 23rd.

Imaging Modalities

Final Project Power Point

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

Pitt Spring Break
3/7 - 3/9

No In-Class Lectures: Instead, there are two lectures below for which you should watch the videos.

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.

Homework delayed until after break, because was not available by the 10th.
Revised Project proposals will be readily accepted through Thursday night the 30th.

CMU Spring Break
3/14 - 3/16
S.B. #1

Lecture SpringBreak1: ITK images & iterators

Power Point
Video (from 2012)
    S.B. #2 Lecture SpringBreak2: ITK pipeline, including reading/writing images and connecting to SimpleITK Power Point
Video (from 2012—link fixed March 14th)
Week 8
Tu 3/21

Go over example projects.

Lecture 12 Registration in depth (Insight into Images ch 10 + Viola & Wells)

SVN accounts distributed Monday evening--let instructor know if not emailed.
Segmentation Assignment given, due 10pm Wednesday the 29th. SVN Access fixed 12:40pm today

Power Point
Video (from 2012)
Th 3/23

Lecture 13: Shape
Quiz on Snyder ch. 9 (read 9.1-9.8, 9.12-9.14)

Lecture 14: Summarize Cootes and Taylor ASM (Cootes CVIU 1995)

Power Point
Video (from 2012)

Power Point (public version)

Week 9
Tu 3/28

No In-Class Lecture: Instead, please watch the following lecture video:
Lecture 15: ITK filters: how to write them (neighborhoods, image boundaries, & numeric traits)

Segmentation assignment due 10pm tomorrow!

Power Point
Video (from 2012)
Th 3/30

Lecture 16 Mathematical morphology & image matching
Quiz on Snyder 7.1-7.5 & 13.1-13.5

Revised project proposals due tonight

Power Point
Video (from 2012)
Week 10
Tu 4/4

Lecture 17: ITK filters, part 2 (advanced filter creation & useful ITK filters you should know about)
CMU's drop-without-withdrawl period ends today

Power Point
Video (from 2012)
Th 4/6

Lecture 18 Deformable registration (Insight into Images ch 11)

Special NeuroPath Shadow Monday 8:30: Enter Scaife Hall from the main doors on Terrace street (directly across from the Peterson event center). Take an elevator up to the 7th floor, then go right as you exit the elevator and go through a set of double doors.

Homework deadline extended (numerous student questions during my travel), now due: Friday April 7, 5pm.

Power Point
Video (from 2012)
  Note: CMU's drop-without-withdrawl period ends on March 30th (Monday)  
Week 11
Tu 4/11

Special Help Session for Final Projecrts: after working on your project over the weekend, bring your questions to this special "office hours" help session, same time and place as normal lecture.

Special note about Neuropathology bonus points (max 2 points per person):

  • If you showed up to neuropath 8:30am yesterday, you can turn in a normal shadow report for +2 bonus points on your final grade.
  • If you didn't or weren't able to show up, you can insead write a 2-page short research report (same topics as a showdow report) covering your own research into neuropathology, to get the same 2 bonus points.

Th 4/13

Summarize Final Project Expectations, new TA reminder
Answer student questions
Lecture 19: ITK Paths
Presentation order to be assigned over weekend--email (only hard) conflicts today!

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 (presentation order)

Th 4/27
  Student project presentations & Projects Due