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Lecture 1: Introductions, purpose, Syllabus

Lecture 2: Programming background:  C++ & Python
(Do NOT submit HW1 yet, TA still being finalized.)

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.

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

Assignment #1 given
Finish programming background (starting with typedef)

Lecture 4: ITK background & basic usage
CMU's add/drop-with-refund period ends sometime around now.

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

Assignment #2 given.

Power Point
Video (from 2012)

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)

Finish Linear processing (resume Scale Space at slide 15)
Lecture 7: Image relaxation: restoration & feature extraction
Quiz #4 on Snyder ch. 6
HW2 due 5pm Wednesday the 7th.

Lecture 8: ITK registration

Finish Image relaxation (resume Minimization at slide 18)
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)

Lecture 10: Segmentation, part 1 continued (using previous notes, start with slide 5)

HW3 may be posted later today.

Lecture 11: Segmentation, part 3 (active contours)

Assignment #3 is now assigned, due 5pm Thursday (2 day extension)

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

Discuss Shadow Program & signup procedure in class (normal time, 10:30am)

Imaging Modalities mini-lecture; finish PDE active contours

Shadow Program — be sure to sign up for the Shadow Program THIS WEEK, beginning at 3:15 pm Sunday (link is here; you may be able to sign up for stations faster if you create an account on signup.com in advance).

Shadow Program Power Point

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

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? 2-day extension
Plan: Spring Break & NeuroPath

Discuss final projects
Be sure to email me your initial project idea / tentative proposal by the night of Thursday the 15th.
Go over example projects.

Finish Lecture 11.
Lecture 12: Level set segmentations & (briefly begin) 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

Final Project Power Point

Power Point
Video (from 2012)

Finish Lecture 12: Level set segmentations & parametric transforms

HW3 revised due date 5pm today

Segmentation Assignment (ready now) assigned Monday March 5th, due 10pm Wednesday the 21st. SVN accounts have been distributed. If you didn't yet receive your svn account by email, let you instructor know.

Lecture: ITK images & iterators

Special 8:30am group shadow for NeuroPathology: Enter Scaife Hall from the main doors on Terrace street (directly across from the Peterson event center). Take an elevator up to the 7th floor, then go right as you exit the elevator and go through a set of double doors.

10:30am Lecture Cancelled due to illness

Segmentation assignment extended until 5pm Wednesday March 28!

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

Power Point
Video (from 2012)

Finish Registration (Mutual Information)

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

Segmentation assignment due 5pm tomorrow.

Power Point (shape)
Video (from 2012)

Finish shape (starting with moments)

Lecture 15: Summarize Cootes and Taylor ASM (Cootes CVIU 1995)

Lecture 16: ITK filters: how to write them (neighborhoods, image boundaries, & numeric traits)

note: Project feedback will be given by weekend (Monday night).

Power Point (public version of ASM)

Power Point (ITK Filters)
Video (from 2012)

Lecture 17 Mathematical morphology & image matching
Quiz on Snyder 7.1-7.5 & 13.1-13.5

resume ITK filters—boundaries

CMU's drop-without-withdrawl period ends today

Power Point
Video (from 2012)

Lecture 18 Deformable registration (Insight into Images ch 11) ; may start ITK Filters part 2.

Revised project proposals (if needed) due 10am Friday morning

Lecture 19: ITK filters, part 2 (advanced filter creation & useful ITK filters you should know about)

Reminder: As discussed in class, neuropathology is part of the "required" shadowing for 2018. Students who were not able to attend should instead submit a short report (1 to 2 pages, same topics as a showdow report) covering your own research into neuropathology.

Summarize Lecture 20: ITK Paths
Review Final Project Expectations
Special Help Session for Final Projecrts: after working on your project over the weekend, bring your questions to this special "office hours" help session, same time and place as normal lecture

Presentation order to be assigned over weekend--email (only hard) conflicts today!

Power Point
Video (from 2012)

Student project presentations (see random order email)
(Each presentation must be 6-7.5 minutes long.)
Everyone's slides due in svn by 10 AM today! (.pptx format preferred, or else .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

Student project presentations (presentation order)