Methods In (Bio)Medical Image Analysis - Spring 2023

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

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

Instructor
John Galeotti
jgaleott+bmia ATandrew.cmu.edu
Meets students after Thursday's class
TA
Emma Erickson
eerickso+bmia ATandrew.cmu.edu
By email or appointment

Syllabus

Course capacity has been increased.  Everyone should now be able to enroll*. 

Meeting over Zoom (email for private link)

Classroom (when used):  PH A20
(at Carnegie Mellon University, see campus map)

Class begins Tuesday, Jan. 17th!

Lecture Times and Locations

We comply with both the U. Pitt. and CMU calendars. Lectures are Tuesday and Thursday from 3:30-4:45 PM, in PH A20 or on zoom, Carnegie Mellon University.

Class-discussion  Piazza Page

Shadow Program Times, Locations, & Details (details will probably change) 

Shadow Program:  5 radiology sessions and 0-2 (TBD) pathology sessions, 8:30-9:30 AM weekday mornings (and possibly other times optional for shadowing pathology).

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Last Year's Website has been archived.

Need extra disk space?  You can use your BOX and Google-Drive storage as if they were local network drives.  Having one or two 1 TB virtual network drives may be helpful when working with large datasets on a small laptop.

Key ITK Documentation:

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

Schedule—Subject to Change
(Future plans are tentative, based on the old 2020 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 2023? Material Older Video and .pptx files
Week 1
T 1/17

Y 

Lecture 1: Introductions, purpose, Syllabus

 Power Point
Video (from 2012)

R 1/19

 Y 

Lecture 2: Programming background:  C++ & Python

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
T 1/24
  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

Power Point
Video (from 2012)
R 1/26
 Y 

Lecture 4: ITK background & basic usage

 Power Point
Video (from 2012)
     
Week 3
T 1/31
  Y  

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

Assignment #1  will be ready later this week (don't start yet)

Power Point
Video (from 2012)
R 2/2
 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)

 Power Point
Video (from 2012)
     
Week 4
T 2/7
  Y

Lecture 7: ITK registration

Assignment #2 is ready now. Please try to do it this week.

Power Point
Video (from 2012)
R 2/9
 Y 

Lecture 8: Image relaxation: restoration & feature extraction
Quiz #4 on Snyder ch. 6
Assignment 2 posted Friday night.

 Power Point
Video (from 2012)
     
Week 5
T 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)
R 2/16
 Y 

Segmentation lecture continued
     
Week 6
T 2/21
  Y

Segmentation lecture continued

Lecture 11: Segmentation, part 3 (active contours)

Power Point
Video (from 2012)
R 2/23
  Y

Resume Segmentation part 3 (start with PDE approach on slide 21)

Lecture 12a: Level set segmentations (Snyder 8.5.2 ) [not required, but recommended: Insight into Images ch 8]
(Parametric Transforms Quiz and Lecture are on Tuesday.)

Shadow program details still being worked out; expect to discuss in class and schedule sometime in the next 2 weeks.  

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

Lecture: Parametric transforms (Snyder 11.1-11.6)
Quiz on Snyder 11.1-11.6

Lecture: Imaging Modalities

Weekend update: Assignment #3 is now assigned, due Friday the 3rd.

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

Power Point
Video (from 2012)

Imaging Modalities Power Point (contains embedded movies)
Video (from 2012, skip to end for imaging modalities)
R 3/2
 Y 

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

Begin discussion of shadow program and final projects

Power Point
Video (from 2012)
         
Spring Break
3/7 - 3/9
   Spring Break  
         
Week 8
T 3/14
 Y 

Shadow program starts Monday March 20! Complete your UPMC form today.
Mini-lecture discussion of the  Shadow Program & signup procedure

Be sure to sign up for the Shadow Program THIS WEEK, starting tonight at 8pm:  https://signup.com/go/mDEqXQa  (I suggest creating an account on signup.com in advance so that you can sign up for stations faster.)

Discuss final projects
Be sure to email me your initial project idea / tentative proposal by the night of Friday the 17th.
Go over example projects.

Shadow Program Power Point

Final Project Power Point
R 3/16
 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)

Shadow Program — UPMC Confidentiality Forms must be ink-signed, scanned (or photo), and uploaded as pdf or jpeg  to Canvas TODAY

Shadow Program starts MONDAY--show up on your days at 8 am (with ink-signed UPMC form!) until you know where you're going

Power Point (shape)
Video (from 2012)

Power Point (public version of ASM)
       Update:  Additional helpful information for Final Projects has been posted.  
Week 9
T 3/21
 Y 

Lecture 17 Deformable registration (Insight into Images ch 11)

Power Point
Video (from 2012)

R 3/23
  Y

Lecture 16 Mathematical morphology & image matching
Quiz on Snyder 7.1-7.5 & 13.1-13.5 will be posted on Canvas.

Project feedback should be given by later night.

Power Point
Video (from 2012)
     
Week 10
T 3/28
 Y 

Intro to artificial neural networks.

  
R 3/30
 Y 

Deep neural networks.

  
     
Week 11
M 4/6
  

Lecture: ITK images & iterators

Assignment #4 was assigned last Friday, due midnight Friday the 6th.

Segmentation Assignment has now been assigned, on Friday the 6th
Assignment #4 is now assigned, due midnight Friday the 6th.

Segmentation assignment due midnight Thursday April 2). Use svn to add and committ your .mha segmentation images.

note: Project feedback should be given by Monday night.

Power Point
Video (from 2012)
W 4/8
  

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

Discuss project timeline. 

Power Point (ITK Filters)
Video (from 2012)
 



 
Week 12
M 4/13
  

Student project working time, professor meetings, and/or possible Shadow options.

AWS Credits will be issued (for GPU and/or CPU cloud computing)   To use, first create an account on the AWS Educate portal using your andrew ID. Will discuss important  details in class.

Lecture 20: ITK Paths

Shadow Program makeup still TBD, hope to announce details by Friday.

Power Point
Video (from 2012)
W 4/15
  

Student project presentation slides and videos will be due 10:30am Monday morning!
Presentation order to be assigned over weekend--email (only hard) conflicts today!

  
     
Week 12
M 4/20
  

Student project presentation using pre-recorded videos (see random order email)
(Each presentation must be 8.0-12.0 minutes long.)
Everyone's videos AND powerpoint slides due by 10:30 AM today! (.mp4 and .pptx formats preferred, or else .mov, .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


W 4/22
   Student project presentations (presentation order)  
     
Week 13
M 4/27
  

Student project presentations (presentation order)

  
W 4/29
   Student project presentations & Projects Due;  All 6 shadow reprots due May 6th at noon.