Methods In (Bio)Medical Image Analysis - Spring 2019

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

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

Instructor
John Galeotti
galeotti+mimia ATcs.cmu.edu
Meets students after Tuesday's class
TA
Vibha Nasery
vnasery+mimia ATandrew.cmu.edu
By email or appointment

Syllabus

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

Class begins Tuesday, Jan. 15th!
Class ends Thursday, April 25th.

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Last Year's Website has been archived.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 - Jupyter Notebooks on Registration

Assignment #4 - iPython Notebooks: Segmentation by Thresholding #1

Assignment #5 - Use SimpleITK to do Segmentation and Pre-processing

Assignment #6 - Registration (small, SKIPPED IN 2018)

Final Project

Schedule—Subject to Change
(Future plans are tentative, based on the old 2018 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 2019? Material Video and .pptx files
Week 1
Tu 1/15

Y

Lecture 1: Introductions, purpose, Syllabus

 Power Point
Video (from 2012)

Th 1/17

 Y

Lecture 2: Programming background:  C++ & Python
(Do NOT submit HW1 yet, TA still being finalized.)

WARNING: Quiz on book reading next class!

Note: first chapters (ch 1, ch 2) of the text book may be freely accessible by scrolling down on Google's book page.

 Power Point
Video (from 2012)
     
Week 2
Tu 1/22
 Y

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

Assignment #1 given - due Friday

 Power Point
Video (from 2012)
Th 1/24
 Y

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 1/29
 Y

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

Power Point
Video (from 2012)
Th 1/31
 Y

Class Cancelled! CMU classes cancelled due to frigid weather.

UPDATE: Assignment #2 is ready now. Please try to do it over this weekend.

  
     
Week 4
Tu 2/5
 Y

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 already given last week.

 Power Point
Video (from 2012)
Th 2/7
 Y

Finish Linear processing (resume Scale Space at slide 15)
Lecture 7: Image relaxation: restoration & feature extraction
Quiz #4 on Snyder ch. 6
HW2 due 11:59pm Monday the 11th.

 Power Point
Video (from 2012)
     
Week 5
Tu 2/12
 Y

Lecture 8: ITK registration

Power Point
Video (from 2012)
Th 2/14
 Y

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 2/19
 Y Lecture 10: Segmentation, part 1 continued (using previous notes, start with slide 8)  
Th 2/21
 Y

Lecture 11: Segmentation, part 3 (active contours)

Assignment #3 is now assigned, due 5pm Thursday the 28th.


 Power Point
Video (from 2012)
     
Week 7
Tu 2/26
 Y

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 registration

Shadow Program — be sure to sign up for the Shadow Program THIS WEEK on Wednesday at 9pm. (link is here; you may be able to sign up for stations faster if you create an account on signup.com in advance).

Shadow Program Power Point

Imaging Modalities Power Point (contains embedded movies)
Video (from 2012, skip to end for imaging modalities)
Th 2/28
 Y

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?

Lecture 12: Level set segmentations & 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

Assignment #4 is now assigned, due 5pm Thursday the 7th.

Final Project Power Point

Power Point
Video (from 2012)
       

 
  Tu 3/5 Y

Finish Lecture 12: (Level set segmentations &) Parametric Transforms

Discuss final projects
Be sure to email me your initial project idea / tentative proposal by the night of Tuesday the 19th.
Go over example projects.

 

  
  Th 3/7 Y

Lecture: ITK images & iterators

Segmentation Assignment (ready now) assigned now (svn accounts will be emailed by Monday), due Tuesday the 26th. SVN accounts have now been emailed. If you don't receive your emailed svn account yet, let you instructor know.

 Power Point
Video (from 2012)
         
Spring Break
3/12 - 3/14
   Spring Break  
         
Week 8
Tu 3/19
 Y

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

Initial project proposals due tonight.

Power Point
Video (from 2012)
Th 3/21
 Y

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

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

Power Point (shape)
Video (from 2012)

Power Point (public version of ASM)
         
Week 9
Tu 3/26
 Y

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

Segmentation assignment due midnight Wednesday March 27 (24 extension due to planned power outage!)tonight). Use svn to add and committ your .mha segmentation images.

 Power Point
Video (from 2012)
Th 3/28
 Y

Lecture 17 Deformable registration (Insight into Images ch 11) ; may start ITK Filters part 2.

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

Power Point
Video (from 2012)

Power Point (ITK Filters)
Video (from 2012)
     
Week 10
Tu 4/2
 Y

 

Lecture 18: ITK filters: how to write them (neighborhoods, image boundaries, & numeric traits)

All project proposals were replied ~ 9:40pm Monday night.

CMU's switch to pass/fail option ends today

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

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

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

Note: Our usual neuropathologist has retired; I'm still trying to find a replacement.

 Power Point (ITK Filters 2)
Video (from 2012)
     
Week 11
Tu 4/9
 Y

Discuss deep learning.
Summarize Lecture 20: ITK Paths

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

 Power Point
Video (from 2012)
Th 4/11
   No Lecture - CMU Spring Carnival  
 



 
Week 12
Tu 4/16
 Y

Student project presentations (see random order email)
(Each presentation must be 7.0-9.0 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:
MIMIA\{Your_SVN_User_Name}\proj\presentation_{Your_last_name}_{Your_first_name}.pptx


Th 4/18
   Student project presentations (presentation order)  
     
Week 13
Tu 4/23
  

Student project presentations (presentation order)

  
Th 4/25
   Student project presentations & Projects Due