Methods In (Bio)Medical Image Analysis - Spring 2024

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
None
N/A
By email or appointment

Syllabus

Meeting over Zoom (email for private link)

Classroom (when used):  GHC 4102
(at Carnegie Mellon University, see campus map)

Class begins Tuesday, Jan. 16th!

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, on zoom and/or in GHC 4102, Carnegie Mellon University.

Class-discussion  Piazza Page


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

Shadow Program:   Approximately 5 or 6 radiology sessions and maybe one or two 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

CMU students can get the Snyder Machine Vision textbook for free online through CMU's Library.  

2020's Website was 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 2023 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 2024? Material Older Video and .pptx files
Week 1
T 1/16

Lecture 1: Introductions, purpose, Syllabus

Power Point
Video (from 2012)

R 1/18

 Y

Lecture 2: Programming background:  C++ & Python (slides 1 - 39)

WARNING: Quiz on book reading next class!

Note: If you have a CMU Andrew account, you can get the book for free online through CMU's Library.  (For non-CMU students, the 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 1/23
 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
Short online  QUIZ on Snyder ch. 1-2 due on Canvas before the start of class.

Power Point
Video (from 2012)
R 1/25

Lecture 4: ITK background & basic usage

Power Point
Video (from 2012)
     
Week 3
T 1/30

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

Power Point
Video (from 2012)

R 2/1
 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 2/6

Lecture 7: ITK registration

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

Power Point
Video (from 2012)
R 2/8
 Y

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

Power Point
Video (from 2012)
     
Week 5
T 2/13
 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 2/15
 

Class cancelled (family medical emergency) 

     
Week 6
T 2/20
 Y

Segmentation lecture continued

 
R 2/22
 Y

Lecture 11: Segmentation, part 3 (active contours)

Lecture 12a: Level set segmentations (Snyder 8.5.2 ) [not required, but recommended: Insight into Images ch 8]

 

Power Point
Video (from 2012)

Power Point
Video (from 2012)

 
Week 7
T 2/27
 

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?

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)

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

R 2/29
 

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
3/5 - 3/7
  Spring Break  
         
Week 8
T 3/12
 

No class due to Pitt Spring Break this week: The rest of the schedule will be pushed later and adjusted.

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 8pmhttps://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 3/14
 

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 3/19
 

Lecture 17 Deformable registration (Insight into Images ch 11)

Power Point
Video (from 2012)

R 3/21
 

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 3/26
 

Intro to artificial neural networks.

 
R 3/28
 

Deep neural networks.

 
     
Week 11
T 4/2
 

Lecture: ITK images & iterators

Power Point
Video (from 2012)
R 4/4
 

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

Power Point (ITK Filters)
Video (from 2012)

 



 

Week 12
T 4/9
 

Open Q&A (feel free to suggest questions/topics in advance); Student project working time and professor meetings.

Presentations:  strong  preference among students for pre-recorded zoom

 Any issues with finishing shadow program?

Google Compute Credits were issued for hw and/or project use (for GPU and/or CPU cloud computing).

R 4/11
 

No Lecture:  CMU Spring Carnival

Student project presentation slides and videos will be due 2 pm Tuesday morning!
Presentation order to be assigned over weekend--email (only hard) conflicts today!

 
     
Week 12
T 4/16
 

Student project presentation using pre-recorded videos (see random order email)
(Each presentation must be 7.0-10.0 minutes long.)
Everyone's videos AND powerpoint slides due by 2 PM today! (.mp4 and .pptx formats preferred, or else .mov, .ppt, or .pdf)

Important: Your presentation should use this name format:
presentation_{Your_last_name}_{Your_first_name}.pptx


R 4/18
  Student project presentations (presentation order)  
     
Week 13
T 4/23
 

Student project presentations (presentation order)

 
R 4/25
  Student project presentations & Projects Due;  All 6 shadow reprots due May 3rd at noon.