Methods In (Bio)Medical Image Analysis - Spring 2018

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
Peiyun Hu
By email or appointment

Syllabus (general)

Meeting in NSH 1305
(at Carnegie Mellon University, see campus map)

Class begins Tuesday, Jan. 16th!
Class ends Thursday, April 26th.

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 NSH 1305, 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, 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Last Year's Website has been archived.

Key ITK Documentation:

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 (small, SKIPPED IN 2018)

Final Project

Schedule—Subject to Change
(Future plans are tentative, based on the old 2017 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 2018? Material Video and .pptx files
Week 1
Tu 1/16

Lecture 1: Introductions, purpose, Syllabus

Power Point
Video (from 2012)

Th 1/18


Lecture 2: Programming background:  C++ & Python
Assignment #1 given

WARNING: Quiz on book reading next class!

Power Point
Video (from 2012)
Week 2
Tu 1/23

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
Finish programming background (starting with typedef)

Power Point
Video (from 2012)
Th 1/25

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 1/30

Lecture 5: Image characterization
Quiz #2 on Snyder ch. 4 (skip hexagonal coordinates on pp 57-59)

Assignment #2 given.

Power Point
Video (from 2012)

Th 2/1

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)

Power Point
Video (from 2012)
Week 4
Tu 2/6

Finish Linear processing (resume Scale Space at slide 15)
Lecture 7: Image relaxation: restoration & feature extraction
Quiz #4 on Snyder ch. 6
HW2 due 5pm Wednesday the 7th.

Power Point
Video (from 2012)
Th 2/8

Lecture 8: ITK registration

Power Point
Video (from 2012)
Week 5
Tu 2/13

Finish Image relaxation (resume Minimization at slide 18)
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)
Th 2/15

Lecture 10: Segmentation, part 1 continued (using previous notes, start with slide 5)

HW3 may be posted later today.


Week 6
Tu 2/20

Lecture 11: Segmentation, part 3 (active contours)

Assignment #3 is now assigned, due 5pm Thursday (2 day extension)

Power Point
Video (from 2012)
Th 2/22

Follow Up: HW3—easy/helpful? Issues with web browsers, snap, or PDF?

Discuss Shadow Program & signup procedure in class (normal time, 10:30am)

Imaging Modalities mini-lecture; finish PDE active contours

Shadow Program — be sure to sign up for the Shadow Program THIS WEEK, beginning at 3:15 pm Sunday (link is here; you may be able to sign up for stations faster if you create an account on in advance).

Shadow Program Power Point

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

Week 7
Tu 2/27

Shadow Program starts TODAY--show up on your days at 8 am (with UPMC form!) until you know where you're going
How is the shadow program going?

Follow Up: HW3—easy/helpful? MS Edge & PDF? Shadow? 2-day extension
Plan: Spring Break & NeuroPath

Discuss final projects
Be sure to email me your initial project idea / tentative proposal by the night of Thursday the 15th.
Go over example projects.

Finish Lecture 11.
Lecture 12
: Level set segmentations & (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

Final Project Power Point

Power Point
Video (from 2012)

Th 3/1

Finish Lecture 12: Level set segmentations & parametric transforms

HW3 revised due date 5pm today

Segmentation Assignment (ready now) assigned Monday March 5th, due 10pm Wednesday the 21st. SVN accounts have been distributed. If you didn't yet receive your svn account by email, let you instructor know.


Pitt Spring Break
3/6 - 3/8

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.

Revised Project proposals will be readily accepted through Thursday night the 30th.

CMU Spring Break
3/13 - 3/15
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 3/20

Special 8:30am group shadow for NeuroPathology: 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.

10:30am Lecture Cancelled due to illness

Segmentation assignment extended until 5pm Wednesday March 28!

Th 3/22

Finish Parametric Transforms
Lecture 13 Registration in depth (Insight into Images ch 10 + Viola & Wells)

Power Point
Video (from 2012)

Week 9
Tu 3/27

Finish Registration (Mutual Information)

Lecture 14: Shape
Quiz on Snyder ch. 9 (read 9.1-9.8, 9.12-9.14)

Segmentation assignment due 5pm tomorrow.

Power Point (shape)
Video (from 2012)

Th 3/29

Finish shape (starting with moments)

Lecture 15: Summarize Cootes and Taylor ASM (Cootes CVIU 1995)

Lecture 16: ITK filters: how to write them (neighborhoods, image boundaries, & numeric traits)

note: Project feedback will be given by weekend (Monday night).

Power Point (public version of ASM)

Power Point (ITK Filters)
Video (from 2012)

Week 10
Tu 4/3

Lecture 17 Mathematical morphology & image matching
Quiz on Snyder 7.1-7.5 & 13.1-13.5

resume ITK filters—boundaries

CMU's drop-without-withdrawl period ends today

Power Point
Video (from 2012)

Th 4/5

Lecture 18 Deformable registration (Insight into Images ch 11) ; may start ITK Filters part 2.

Revised project proposals (if needed) due 10am Friday morning

Power Point
Video (from 2012)
  Note: CMU's drop-without-withdrawl period ends on March 30th (Monday)  
Week 11
Tu 4/10

Lecture 19: ITK filters, part 2 (advanced filter creation & useful ITK filters you should know about)

Reminder: As discussed in class, neuropathology is part of the "required" shadowing for 2018. Students who were not able to attend should instead submit a short report (1 to 2 pages, same topics as a showdow report) covering your own research into neuropathology.

Power Point (ITK Filters 2)
Video (from 2012)
Th 4/12

Summarize Lecture 20: ITK Paths
Review Final Project Expectations
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

Presentation order to be assigned over weekend--email (only hard) conflicts today!

Power Point
Video (from 2012)

Week 12
Tu 4/17

Student project presentations (see random order email)
(Each presentation must be 6-7.5 minutes long.)
Everyone's slides due in svn by 10 AM today! (.pptx format preferred, or else .ppt or .pdf)

Important: Your presentation should use this directory and name format:

Th 4/19
  No Lecture - CMU Spring Carnival  
Week 13
Tu 4/24

Student project presentations (presentation order)

Th 4/26
  Student project presentations & Projects Due