===============CIS I (601.455/655) Fall 2021 Schedule=============== ~~NOTOC~~ **NOTE: This page is still under construction and is subject to change** =====Week 1===== *August 31 * {{:courses:455-655:lectures:2021_cis_i_organization.pdf|Fall 2021 Organization Lecture}} * [[https://www.cs.jhu.edu/cista/455/Lectures/2020%20Introductory%20Lecture.pdf|Introductory Lecture]] * September 2 * Introductory Lecture (concluded) * **Hand out {{ :courses:455-655:2021:HW:homework_1_-_fall_2021.pdf | Homework Assignment 1}}** * **Supplemental Materials:** * {{ :courses:455-655:2021:HW:factors_contributing_to_mammography_failure.pdf |}} * {{ :courses:455-655:2021:HW:combined_screening_with_ultrasound_and_mammography.pdf |}} =====Week 2===== * September 7 * {{ :courses:455-655:lectures:robotic_joint_replacement_surgery.pdf |Surgical CAD/CAM Case Study - - Joint Reconstruction Surgery}} * Reference material * CIS Book Chapters 27-29 * [[https://www.cs.jhu.edu/cista/455/Movies/Robodoc1.mpg|Early Robodoc marketing video, showing pin process]] * [[https://www.cs.jhu.edu/cista/455/Movies/borner.mpg|Robodoc clinical case video (pins)]] * [[https://www.cs.jhu.edu/cista/455/Movies/Pinless.mpg|Robodoc pinless clinical case video]] * [[https://www.cs.jhu.edu/cista/455/Movies/ISS_knee_unedited.mpg|Robodoc TKA clinical case video]] * [[https://www.cs.jhu.edu/cista/455/Lectures/Robodoc903.pdf|Lecture on Robodoc (Dr. Kazanzides)]] * [[https://www.cs.jhu.edu/cista/455/Lectures/Stindel%20Summer%20School%202007.pdf|Lecture on computer-assisted joint surgery by Dr. Eric Stindel]] * [[https://www.cs.jhu.edu/cista/455/http://www.bluebelttech.com/videos.php|Blue Belt PFS system]] * [[http://www.youtube.com/watch?v=Wun4AJcFZS|Mako Rio System]] * [[https://www.cs.jhu.edu/cista/455/Lectures/Robotic%20Joint%20Replacement%20Surgery.pptx.pdf|2017 Lecture by Prof. Peter Kazanzides on Robotic Total Hip and Knee Replacement Surgery]] * September 9 * {{ :courses:455-655:lectures:localizers.pdf |Localizers}} * Reference Material * CIS Book Chapters 21-23 * [[https://link.springer.com/content/pdf/10.1007/s10527-020-09980-8.pdf|Localizers for Frameless Neuronavigation Systems]] * [[https://web.stanford.edu/class/me328/lectures/lecture7-tracking.pdf|Slides from lecture by Allison Okamura (Stanford University)]] * [[https://www.oto.theclinics.com/article/S0030-6665(17)30012-9/fulltext|Next-Generation Surgical Navigation Systems in Sinus and Skull Base Surgery]] * Also, you can do web searches on "surgical navigation technology" =====Week 3===== * September 14 * **Guest Lecture by Xingtong Liu on quantitative sinus endoscopy** (Prof.Taylor at Center Review Panel) * September 16 * **Homework Assignment 1 due** * Begin {{ :courses:455-655:lectures:frames.pdf|Mathematical Methods for CIS}} * Additional Reference Material * [[https://www.cs.jhu.edu/cista/455/Lectures/BasicMath-Part2.pdf|Introduction to Coordinate Transformations]] - lecture by Gabor Fichtinger * [[http://cs229.stanford.edu/section/cs229-linalg.pdf|Linear algebra review]] * **Hand out {{ :courses:455-655:2021:hw:homework_2_600-455_fall_2021.pdf |Homework Assignment #2}}** * September 16 (Optional Discussion Section at 5:30 P.M. with Benjamin) * In person: Krieger 306. * Online: [[https://jhubluejays.zoom.us/my/benjamindkilleen]] =====Week 4===== * September 21 * Conclude {{ :courses:455-655:lectures:frames.pdf|Basic Mathematical Methods for CIS}} * **Hand out {{ :courses:455-655:2021:hw:homework_2_600-455_fall_2021.pdf |Homework Assignment #2}}** * Present **{{ :courses:455-655:2021:surgical_simulator_project_teaser.pptx |Possible student project involving surgical simulator}}** * September 23 * {{ :courses:455-655:lectures:rigid3d3dcalculations.pdf |Computing rigid 3D-3D transformations from point and line pairs}} * Begin {{ :courses:455-655:lectures:calibration.pdf |Calibration}} * {{ :courses:455-655:lectures:leastsquaresreview.pdf |Least Squares Review}} (if time) * September 23 (Optional Discussion Section at 5:30 P.M. with Maia) * In person: Krieger 306. * Online: [[https://jhubluejays.zoom.us/my/maiastiber]] * **{{ :courses:455-655:2021:cis_hw_2_sample_qs.pdf | Section HW2 Practice Questions}}** =====Week 5===== * September 28 * **Homework Assignment #2 due** * **Hand out {{ :courses:455-655:2021:hw:homework_3_600-455_fall_2021.pdf |Homework Assignment #3}}** * Continue {{ :courses:455-655:lectures:calibration.pdf |Calibration}} * {{ :courses:455-655:lectures:leastsquaresreview.pdf |Least Squares Review}} * {{ :courses:455-655:lectures:interpolationreview.pdf |Interpolation Review}} * [[https://citeseerx.ist.psu.edu/viewdoc/download?doi=10.1.1.8.6623&rep=rep1&type=pdf|Paper on scattered point set interpolation]] * September 30 * **{{ :courses:455-655:lectures:spine_talk_-_amit_jain_-_cis_i_2021.pdf |Guest Lecture on spine surgery by Dr. Amit Jain}}** * September 30 (Optional Discussion Section at 5:30 P.M. with Benjamin) * In person: Krieger 306. * Online: [[https://jhubluejays.zoom.us/my/benjamindkilleen]] =====Week 6===== * October 5 * **Hand out {{ :courses:455-655:2021:hw:programmingassignments1and2.pdf |Programming Assignments #1 and #2}}** * {{ :courses:455-655:2021:hw:programmingassignments1and2_scenario.pdf |Scenario Slides}} * {{ :courses:455-655:2021:hw:2021_pa_1-2_student_data.zip |Data for Programming Assignments #1 and #2}} * Finish {{ :courses:455-655:lectures:calibration.pdf |Calibration}} * {{ :courses:455-655:lectures:interpolationreview.pdf |Interpolation Review}} * October 7 * **(Homework Assignment #3 due date extended to October 11)** * Begin {{ :courses:455-655:lectures:segmentation_-_2021.pdf |Segmentation and Modeling}} * Supplemental material: [[https://www.cs.jhu.edu/cista/455/Lectures/Segmentation%20-%202020.pdf|2018 Guest lecture by Prof. Jerry Prince #1]] * October 7 (Optional Discussion Section at 5:30 P.M. with Maia) * In person: Krieger 306. * Online: [[https://jhubluejays.zoom.us/my/maiastiber]] =====Week 7===== * October 11 * **Homework Assignment #3 Due at noon** * October 12 * **Hand out {{ :courses:455-655:2021:hw:homework_4_-_600-455_fall_2021-c.pdf |Homework Assignment #4}}** * Finish {{ :courses:455-655:lectures:segmentation_-_2021.pdf |Segmentation and Modeling}} * [[https://www.cs.jhu.edu/cista/455Lectures/Segmentation-2%20%28Rev%20D%29.pdf|2018 Guest lecture by Prof. Jerry Prince #2]] * October 14 * Begin {{ :courses:455-655:lectures:registration_part_1.pdf |Registration (Part 1)}} * {{ :courses:455-655:lectures:finding_point-pairs.pdf |Finding point pairs for Iterated Closest Point algorithms}} * Reference Material * CIS Book Chapters 5 & 7 * CIS Book pp 3-75 * [[https://en.wikipedia.org/wiki/Point_set_registration|Wikipedia article on point set registration]] * {{ :courses:455-655:lectures:laryngealproject_cis_recruitppt_-_read-only.pdf |Possible student project (recruiting now)}} =====Week 8===== * October 19 * Finish {{ :courses:455-655:lectures:registration_part_1.pdf |Registration (Part 1)}} * {{ :courses:455-655:lectures:finding_point-pairs.pdf |Finding point pairs for Iterated Closest Point algorithms}} * {{ :courses:455-655:lectures:coherent_point_drift_registration.pdf |Coherent Point Drift Algorithm}} * Reference and supplemental Material * [[http://www.robots.ox.ac.uk/%7Eavsegal/resources/papers/Generalized_ICP.pdf|Paper on Generalized ICP Method]] * [[https://en.wikipedia.org/wiki/Point_set_registration|Wikipedia article on point set registration]] * October 21 * Begin {{ :courses:455-655:lectures:registration_part_2.pdf |Registration (Part 2)}} * Reference and supplemental Material * [[http://www.robots.ox.ac.uk/%7Eavsegal/resources/papers/Generalized_ICP.pdf|Paper on Generalized ICP Method]] * [[https://en.wikipedia.org/wiki/Point_set_registration|Wikipedia article on point set registration]] * [[https://www.cs.jhu.edu/cista/455/Lectures/Gouthami_StatisticalAtlas_CIS446-converted.pptx.pdf|Statistical Atlases Construction and Application (G. Chintalapani)]] * [[https://www.cs.jhu.edu/cista/455/Lectures/AtlasValidation%20-%20Chintalapani%202010.pptx.pdf|Statistical Atlas Validation (G. Chintalapani)]] * [[https://www.cs.jhu.edu/cista/455/Lectures/Miccai_2011_TALK_Sharmi.pdf|Improving mesh vertices (S. Seshamani)]] =====Week 9===== * October 26 * **Hand out {{ :courses:455-655:2021:hw:homework_5_-_600-455_fall_2021-final.pdf |Homework Assignment #5}}** * Finish {{ :courses:455-655:lectures:registration_part_2.pdf |Registration (Part 2)}} * October 28 * **Programming Assignment #1 due** * Begin {{ :courses:455-655:lectures:registration_part_3.pdf |Registration (Part 3)}} * [[https://www.cs.jhu.edu/cista/455/Lectures/Active%20Appearances.pdf|Active appearances]] =====Week 10===== * November 2 (Election Day in US - Vote if you are eligible) * **Homework Assignment #4 due** * **Hand out {{ :courses:455-655:2021:hw:programming_3_and_4_600-445-2021.pdf |Programming Assignments #3 and #4}}** * {{ :courses:455-655:2021:hw:2021_pa_3-5_student_data.zip |Data for PA 3,4,5}} * Finish {{ :courses:455-655:lectures:registration_part_3.pdf |Registration (Part 3)}} * Begin {{ :courses:455-655:lectures:medical_robots-part_1.pdf |Medical Robotics, Constrained Control and Virtual Fixtures (Part 1)}} * November 4 * Finish {{ :courses:455-655:lectures:medical_robots-part_1.pdf |Medical Robotics, Constrained Control and Virtual Fixtures (Part 1)}} * Begin {{ :courses:455-655:lectures:medical_robots-part_2.pdf |Robotics, Constrained Control and Virtual Fixtures (Part 2)}} * Supplemental Material: [[https://www.cs.jhu.edu/cista/455/Lectures/Max%20Li%20IROS%202020%20Presentation.pdf|Anatomical Mesh-Based Virtual Fixtures for Surgical Robots]] * November 4 (Optional Discussion Section at 5:30 P.M. with Maia) * In person: Krieger 306. * Online: [[https://jhubluejays.zoom.us/my/maiastiber]] =====Week 11===== * November 9 * **Programming Assignment #2 due** * **Hand out {{ :courses:455-655:2021:hw:homework_6_-_600-455_fall_2021.pdf |Homework Assignment #6}}** * {{ :courses:455-655:lectures:medical_robots-part_2.pdf |Medical Robotics, Constrained Control and Virtual Fixtures (Part 2)}} * November 11 * **{{ :courses:455-655:lectures:creighton_guest_lecture_-_jhu_nsg_gr.pdf |Guest Lecture from Dr. Francis Creighton on Lateral Skull Base Surgery}}** =====Week 12===== * November 16 * **Homework Assignment #5 due** * {{ :courses:455-655:lectures:robotic_imaging_lecture_11-16_cis_2021.pdf |Robotically-assisted imaging (Boctor)}} * November 18 * **Programming Assignment #3 due** * Begin {{ :courses:455-655:lectures:medical_robots_part_3_-_autonomy.pdf |Autonomy and Semi-Autonomous Behavior in Surgical Robot Systems}} * Slides from 2018 guest lecture on [[https://www.cs.jhu.edu/cista/455/Lectures/Farshid%20CIS%20I-talk-pdf.pdf|Dexterity and Autonomy in Medical Robotics]] * **Hand out {{ :courses:455-655:2021:hw:programming_5_600-445-2021.pdf |Programming Assignment #5}}** * (5:15PM special session for early people ready to start) * {{ :courses:455-655:2021:hw:pa5_notes.pdf |Notes for PA#5: Deformable Registration to a Statistical Shape Model}} =====Week 13===== * November 23 - **Thanksgiving Break (No Classes)** * November 23 - **Thanksgiving Break (No Classes)** =====Week 14===== * November 30 * **Guest Lecture from Nassir Navab** * Robotic Imaging, Machine Learning and Augmented Reality for Computer Assisted Intervention * December 2 (Last class) * **Programming Assignment #4 due** * Hand out **{{ :courses:455-655:2021:hw:programming_5_600-445-2021.pdf |Programming Assignment #5}}** * {{ :courses:455-655:2021:hw:pa5_notes.pdf |Notes for PA#5: Deformable Registration to a Statistical Shape Model}} * Finish {{ :courses:455-655:lectures:medical_robots_part_3_-_autonomy.pdf |Autonomy and Semi-Autonomous Behavior in Surgical Robot Systems}} * {{ :courses:455-655:lectures:therac.pdf |Safety Case Study: The Therac 25 Accidents}} (time permitting) * Background Material: * [[https://web.stanford.edu/class/cs240/old/sp2014/readings/therac-25.pdf|Nancy Levenson and Clark Turner, "The Investigation of the Therac 25 Accidents", Computer 26(7) pp18-41]] * [[http://sunnyday.mit.edu/papers/therac.pdf|Therac-25 Accidents: An Updated Version of the Original Accident Investigation Paper (by Nancy Leveson)]] from Dr. Leveson's Book, [[http://sunnyday.mit.edu/book.html|Software, System Safety, and Computers]], Addison Wesley, 1995. * Video links to 2019 lecture (split and may not be available): [[https://jh.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=6af7379d-e0d8-4dfb-871b-ab0c0131e1dc|Part 1]], [[https://jh.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=37022003-335c-4521-bf40-ab0c013551bc|Part 2]] * December 4 (Saturday) * **Homework Assignment #6 due (11:39PM) ** =====Final Exams (December 13-21)===== * **Optional Programming Assignment 5 due on final exam day (TBD)** ([[:courses:455-655:2021:HW:Homework Repository]])