(Frequently also crosslisted as 18-791, CMU ECE : 42-735, CMU BME)
Instructor |
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| John Galeotti | galeotti+mimia ATcs.cmu.edu |
Meets students after Tuesday's class |
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TA |
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| TBD | TBD |
By email or appointment |
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We comply with both the U. Pitt. and CMU calendars. Lectures are Monday and Wednesday from 3:00-4:20 PM, in NSH 1305, Carnegie Mellon University.
There is a piazza page for this class, which you can use for discussion with other students. Get the access code in class.
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.
5 different MS-Teams based Shadow oppertunities (secure link will be provided over email just before each; you can submit up to 5 out of your 6 shadow reports from these sessions):
Last Year's Website has been archived.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.
Key ITK Documentation:
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 2020? | Material | Video and .pptx files |
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Week 1 |
M 1/13 |
Y |
Power Point Video (from 2012) |
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W 1/15 |
Y | Lecture 2: Programming background: C++ & Python 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) |
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Week 2 |
M 1/20 |
Martin Luther King Day -- No Classes |
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W 1/22 |
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 |
Power Point Video (from 2012) |
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Week 3 |
M 1/27 |
Y | Lecture 4: ITK background & basic usage Assignment #1 is ready now - due first Friday in February |
Power Point Video (from 2012) |
W 1/29 |
Y | Lecture 5: Image characterization |
Power Point |
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Week 4 |
M 2/3 |
Y | Lecture 6: Linear processing Assignment #2 is ready now. Please try to do it this week. |
Power Point Video (from 2012) |
W 2/5 |
Y |
Lecture 7: Image relaxation: restoration & feature extraction |
Power Point Video (from 2012) |
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Week 5 |
M 2/10 |
Y | Lecture 8: ITK registration |
Power Point Video (from 2012) |
W 2/12 |
Y | Lecture 9: Segmentation, part 1 HW2 deadline extended to noon Friday Feb. 14. |
Power Point |
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Week 6 |
M 2/17 |
Y | 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. |
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W 2/19 |
Y |
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) |
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Week 7 |
M 2/24 |
Y | 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 |
Power Point |
W 2/26 |
Y |
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] Assignment #4 is now assigned, due midnight Friday the 6th. |
Power Point |
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| M 3/2 | Y | Finish Lecture 12: (Level set segmentations &) Parametric Transforms Discuss final projects Assignment #4 was assigned last Friday, due midnight Friday the 6th.
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| W 3/4 | Y | Lecture: ITK images & iterators Segmentation Assignment has now been assigned, on Friday the 6th |
Power Point Video (from 2012) |
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Spring Break |
3/9 - 3/11 |
Y | Spring Break (Segmentation Assignment now assigned, due Thursday night, the 26th) | |
Week 8 |
M 3/16 |
Y | COVID-19: CMU & PITT CLASSES DELAYED, WILL BE ONLINE DISTANCE LEARNING. Shadow Program: SUSPENDED. DO NOT GO TO HOSPITAL Initial project proposals due tonight. |
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W 3/18 |
Y | 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. |
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Week 9 |
M 3/23 |
Y | Note: Zoom link We will (attempt to) do the quiz online on Canvas, after we get class started. Zoom recording. Lecture 14: Shape 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) |
W 3/25 |
Y | 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 |
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Week 10 |
M 3/30 |
Y | Lecture 16 Mathematical morphology & image matching Zoom Recording Project feedback should be given by later night. |
Power Point Video (from 2012) |
W 4/1 |
Y | Lecture 17 Deformable registration (Insight into Images ch 11) ; may start ITK Filters. Zoom Recording |
Power Point |
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Week 11 |
M 4/6 |
Y |
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) |
W 4/8 |
Y | 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. Shadow Program makeup still TBD, hope to announce details by Friday. |
Power Point Video (from 2012) |
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Week 12 |
M 4/13 |
Student project working time, professor meetings, and/or possible Shadow options. |
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W 4/15 |
Student project presentation slides and videos will be due 10:30am Monday morning! |
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Week 12 |
M 4/20 |
Student project presentation using pre-recorded videos (see random order email) Important: Your presentation should use this directory and name format: |
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W 4/22 |
Student project presentations (presentation order) | |||
Week 13 |
M 4/27 |
Student project presentations (presentation order) |
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W 4/29 |
Student project presentations & Projects Due; All 6 shadow reprots due May 6th at noon. |