Methods in (Bio)Medical Image Analysis

Methods In (Bio)Medical Image Analysis - Spring 2022

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
Noah Schweitzer	NES93 ATpitt.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. 18th!

Lecture Times and Locations

We comply with both the U. Pitt. and CMU calendars. Lectures are Tuesday and Thursday from 3:05-4:25 PM, in PH A20 or on zoom, Carnegie Mellon University.

Class-discussion Piazza Page

Shadow Program Times, Locations, & Details SUSPENDED FOR REST OF SEMESTER

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).

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Last Year's Website has been archived.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.

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)

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 2022?	Material	Video and .pptx files
Week 1	T 1/18	Y	Lecture 1: Introductions, purpose, Syllabus	Power Point Video (from 2012)
	R 1/20	Y	Lecture 2: Programming background: C++ & Python	Power Point Video (from 2012)

Week 2	M 1/20	Y	Lecture 3: ITK background & basic usage CMU's add/drop-with-refund period ends sometime around now. 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)
	W 1/22		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 4: Math & probability background Begin class with a short QUIZ on Snyder ch. 1-2	Power Point Video (from 2012)

Week 3	M 1/27		Assignment #1 is ready now - due first Friday in February
	W 1/29		Lecture 5: Image characterization Quiz #2 on Snyder ch. 4 (skip hexagonal coordinates on pp 57-59)	Power Point Video (from 2012)

Week 4	M 2/3		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 is ready now. Please try to do it this week.	Power Point Video (from 2012)
	W 2/5		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	M 2/10		Lecture 8: ITK registration	Power Point Video (from 2012)
	W 2/12		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) HW2 deadline extended to noon Friday Feb. 14.	Power Point Video (from 2012)

Week 6	M 2/17		Lecture 10: Segmentation, part 1 continued (using previous notes, start with slide 8) Shadow program starts Monday the 24th! Complete your UPMC form today. Mini-lecture discussion of the Shadow Program & signup procedure Assignment #3 is now assigned, due 5pm Tuesday the 25th.	Shadow Program Power Point
	W 2/19		Imaging Modalities Shadow Program — Signed UPMC Confidentiality Forms DUE IN CLASS TODAY; be sure to sign up for the Shadow Program THIS WEEK, starting tonight at TBD. (link is here; you may be able to sign up for stations faster if you create an account on signup.com in advance).	Imaging Modalities Power Point (contains embedded movies) Video (from 2012, skip to end for imaging modalities)

Week 7	M 2/24		Lecture 11: Segmentation, part 3 (active contours) Follow Up: HW3—easy/helpful? Issues with web browsers, snap, or PDF? 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?	Power Point Video (from 2012)
	W 2/26		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 midnight Friday the 6th.	Final Project Power Point Power Point Video (from 2012)

	M 3/2		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 17th. Go over example projects. Assignment #4 was assigned last Friday, due midnight Friday the 6th.
	W 3/4		Lecture: ITK images & iterators Segmentation Assignment has now been assigned, on Friday the 6th	Power Point Video (from 2012)

Spring Break	3/9 - 3/11		Spring Break (Segmentation Assignment now assigned, due Thursday night, the 26th)

Week 8	M 3/16		COVID-19: CMU & PITT CLASSES DELAYED, WILL BE ONLINE DISTANCE LEARNING. Shadow Program: SUSPENDED. DO NOT GO TO HOSPITAL Initial project proposals due tonight.
	W 3/18		COVID-19: PITT CLASSES DELAYED, MIMIA not having class today. Lectures will resume on Monday 23rd in an online format. More details will be coming.

Week 9	M 3/23		Note: Zoom link We will (attempt to) do the quiz online on Canvas, after we get class started. Zoom recording. 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) Segmentation assignment due midnight Thursday April 2 (1-week extension due to COVID-19). Use svn to add and committ your .mha segmentation images.	Power Point (shape) Video (from 2012) Power Point (public version of ASM)
	W 3/25		Zoom link Lecture 13 Registration in depth (Insight into Images ch 10 + Viola & Wells) Zoom recording note: Project feedback should be given by Monday night.	Power Point Video (from 2012)

Week 10	M 3/30		Lecture 16 Mathematical morphology & image matching Zoom Recording 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)
	W 4/1		Lecture 17 Deformable registration (Insight into Images ch 11) ; may start ITK Filters. Zoom Recording	Power Point Video (from 2012)

Week 11	M 4/6		Lecture 18: ITK filters: how to write them (neighborhoods, image boundaries, & numeric traits) Discuss project timeline. (Zoom apparently stopped working (and then crashed) as we were trying to take the last question in class. Please email any remaining questions.	Power Point (ITK Filters) Video (from 2012)
	W 4/8		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. Discuss deep learning. Only if time (doubtful): Summarize Lecture 20: ITK Paths Shadow Program makeup still TBD, hope to announce details by Friday.	Power Point Video (from 2012)

Week 12	M 4/13		Student project working time, professor meetings, and/or possible Shadow options.
	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.