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)

John Galeotti
Meets students after Thursday's class
By email or appointment


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)

Final Project

Additional hints and details for final project

If you have no idea what to do, consider one of the common topics in this short list of suggestions.

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


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

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

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

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

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

Segmentation lecture continued

R 2/22

Lecture 11: Segmentation, part 3 (active contours)


Power Point
Video (from 2012)

Week 7
T 2/27

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

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

Lecture: Imaging Modalities

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)

Power Point
Video (from 2012)

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

R 2/29

Shadow program starts Monday March 18! 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 (as discussed in lecture):  (I suggest creating an account on 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 15th.
Go over example projects.

Assignment #3 is now assigned; due date posted on Canvas .

Anyone start HW3 yet?  Easy/helpful? Deadline?  Issues with web browsers, snap, or PDF?

Shadow Program — UPMC Confidentiality Forms must be ink-signed, scanned (or photo), and uploaded as pdf or jpeg  to Canvas by the deadline listed on Canvas.

Shadow Program starts Monday March 18--show up on your days at 8 am (with ink-signed UPMC form!) until you know where you're going

Shadow Program Power Point

Final Project Power Point

Spring Break
3/5 - 3/14

Spring Break
Be sure to submit your UPMC confidentiality agreements on Canvas by Monday the 18th.
Additional hints and details for final project
If you have no idea what to do, consider one of the common topics in this short list of suggestions.

Week 8
T 3/19

Lecture 13 Registration in depth (Insight into Images ch 10 + Viola & Wells)
Simple Registration homework is assigned now.

Power Point
Video (from 2012)

R 3/21

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

Power Point (shape)
Video (from 2012)

Week 9
T 3/26

Lecture 15: Summarize Cootes and Taylor ASM (Cootes CVIU 1995). (password protected extra slides)

Project feedback should be given by tonight.

Power Point (public version of ASM)

R 3/28


Note: Currently (still) in the ER with my dad. I expect to be online in time for class, but that could change.  I will post of Piazza if class is delayed or cancelled.

Lecture 16 Deformable registration (Insight into Images ch 11).

Power Point
Video (from 2012)

Week 10
T 4/2

Lecture 17 Mathematical morphology & image matching
Quiz on Snyder 7.1-7.5 & 13.1-13.5 will be posted on Canvas.

Power Point
Video (from 2012)

R 4/4

Intro to artificial neural networks. (password required)

Week 11
T 4/9

WARNING: There is a chance class may be delayed starting. If so, I will announce the delay on piazza as soon as possible.

Resume prior lecture on slide 71, then
Deep neural networks. (password required).

R 4/11

No class today: CMU Spring Carnival
The rest of the schedule below is from last year. Only lines above this are current for 2024.

Week 12
T 4/16

Lecture: ITK images & iterators

Discuss final projects 

Power Point
Video (from 2012)
R 4/18

ZOOM ERROR: Please use this new zoom link:

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

Student project presentation slides and videoswill be due 1pm Tuesday morning! Presentation order to be assigned over weekend--email (only hard) conflicts today!

Power Point (ITK Filters)
Video (from 2012)



Week 13
T 4/23

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 1 PM today! (.mp4 and .pptx formats preferred, or else .mov, .ppt, or .pdf)

Important: Your presentation should use this name format:

R 4/25

Student project presentations (presentation order) & Projects Due;  All 6 shadow reprots due May 3rd at noon. 

Week N/A

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).


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 N/A