Methods in (Bio)Medical Image Analysis

Methods In (Bio)Medical Image Analysis - Spring 2025

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 Monday's class By email or appointment
TA
Malini Shivaram	malinish+bmia ATandrew.cmu.edu
	Thursday 2:00-3:00pm (tentative) By email or appointment

Syllabus

Meeting over Zoom (email for private link)

Classroom (when used): WEH 5310
(at Carnegie Mellon University, see campus map)

Class begins Monday, Jan. 13th!
Last day of (normal) class is Monday, April 21st.

Lecture Times and Locations

We comply with both the U. Pitt. and CMU calendars. Lectures are Monday and Wednesday from 12:30-1:50 PM, on zoom and/or in WEH 5310, Carnegie Mellon University.

Class-discussion Piazza Page

Shadow Program Times, Locations, & Details (currently 2024 details; 2025 will probably have changes)

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.

2024'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.

BOX Drive lets you use your BOX account like a network drive, without forcing you to sync all your files to your computer.
Google Drive File Stream lets you do the same thing with your Google Drive account. Because it only works with University/Enterprise accounts, be sure you are signed into Google with your university-email-address Google account before trying to install Drive File Stream.

Key ITK Documentation:

SimpleITK's Show() and ImageViewer(): Show() has a new bug and hangs on Windows, so Windows users should use ImageViewer() instead.
ITK 4.1.3 Doxygen
ITK Software Guide
SimpleITK 1.2.0 Doxygen
SimpleITK "Sphinx" Consolidated 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 2024 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	Location	Material	Older Video and .pptx files
Week 1	M 1/13	Zoom	Lecture 1: Introductions, purpose, Syllabus	Power Point Video (from 2012)
	W 1/15	Zoom	Lecture 2: Programming background: C++ & Python (slides 1 - 23) You should accept the invitation for Canvas and Piazza 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	M 1/20	None	No class today: MLK Day	Power Point Video (from 2012)
	W 1/22	Weh 5310	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. Assignment 1 (on Canvas) is due midnight Friday night.	Power Point Video (from 2012)

Week 3	M 1/27	Zoom	Lecture 4: Image characterization (through dynamic range; will resume later with the Correspondence Problem) Quiz #2 on Snyder ch. 4 (skip hexagonal coordinates on pp 57-59)	Power Point Video (from 2012)
	W 1/29	Zoom	Lecture 5: ITK background & basic usage; also finished image characterization Assignment #2 should be assigned this week, probably today. Please wait until we announce it is ready; then try to finish it by the end of this weekend.	Power Point Video (from 2012)

Week 4	M 2/3	Zoom	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)
	W 2/5	Zoom	Lecture 7: Image relaxation: restoration & feature extraction Quiz #4 on Snyder ch. 6 Assignment 2 due next week.	Power Point Video (from 2012)

Week 5	M 2/10	Zoom	Lecture 8: ITK registration; finish feature extraction	Power Point Video (from 2012)
	W 2/12	Zoom	Lecture 9: Segmentation, part 1; finish registraiton starting on slide 28 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	M 2/17	Weh 5310	Segmentation lecture continued
	W 2/19	Weh 5310	Lecture 11: Segmentation, part 3 (active contours)	Power Point Video (from 2012)

Week 7	M 2/24	Zoom	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)
	W 2/26	Zoom	Finish discussing Imaging Modalities. Be sure to submit your UPMC confidentiality agreements using the assignment on Canvas by this Friday February 28th. Shadow Program starts Monday March 10--show up on your days at 8 am (with ink-signed UPMC form!) until you know where you're going. Mini-lecture discussion of the Shadow Program & signup procedure Be sure to sign up for the Shadow Program THIS WEEK, starting ~~8pm tonight~~ 8pm Thursday night the 27th. The link will automatically be announced on Canvas at 8pm on the 27th. I suggest creating an account on signup.com in advance so that you can sign up for stations faster. Reminders: Assignment #3 is also due soon, at date posted on Canvas. Start looking through example final projects and thinking about topics. You can also look at the slides and links below.	Shadow Program Power Point Final Project Power Point

Spring Break	3/3 - 3/7	N/A	Spring Break 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.

DARPA Triage Week	3/10	Zoom	Instructor in all-week DARPA Triage Event Shadow Program started. Discuss final projects and go over example projects. Be sure to submit your initial project idea / tentative proposal on Canvas by the due date listed on Canvas.
DARPA Triage Week	3/12	Zoom	Instructor in all-week DARPA Triage Event Lecture 13 Registration in depth (Insight into Images ch 10 + Viola & Wells) Simple Registration homework should be assigned sometime this week.	Power Point Video (from 2012)

Week 8	M 3/17	Zoom	Lecture 14: Shape Quiz on Snyder ch. 9 (read 9.1-9.8, 9.12-9.14)	Power Point (shape) Video (from 2012)
	W 3/19	Weh 5310	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)

Week 9	M 3/24	Weh 5310	Lecture 16 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)
	W 3/26	Weh 5310	Intro to artificial neural networks. (password required)

Week 10	M 3/31	Zoom	Resume prior lecture on slide 71, then Deep neural networks. (password required).
	W 4/2	Zoom	Lecture 19 Deformable registration (Insight into Images ch 11).	Power Point Video (from 2012)

Week 11	M 4/7		The rest of the schedule below is from last year. Only lines above this are current for 2025.
	W 4/9		...

Week 12	M 4/14		Lecture: ITK images & iterators Discuss final projects	Power Point Video (from 2012)
	W 4/16		Lecture: ITK filters: how to write them (neighborhoods, image boundaries, & numeric traits) Student project presentation slides will be due Wednesday the 23rd! Presentation order to be assigned over weekend--email (only hard) conflicts today!	Power Point (ITK Filters) Video (from 2012)

Week 13	M 4/21	N/A	No Class Today: We will be meeting during Pitt's reading day on the 23rd, so to make up for it today is a free day to prepare for your presentations. Student project presentation slides and videos will be due Wednesday morning!
	W 4/23	Weh 5310	Student project presentations in class (Each presentation must be 7.0-9.0 minutes long.) Everyone's powerpoint slides due by 9 AM today! (.pptx format preferred, or else .ppt or .pdf) Important: Your presentation should use this name format: presentation_{Your_last_name}_{Your_first_name}.pptx

Week 14	M 4/28	Weh 5310	Student project presentations
	W 4/30	Weh 5310	Student project presentations Project code and all 6 shadow reprots due at date(s) posted on Canvas (probably 11:59pm tonight)

Week N/A	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).
	N/A		...