===============CIS I (601.455/655) Fall 2023 Schedule=============== ~~NOTOC~~ =====Note: This page is subject to change===== * I am still working out the detailed schedule for 2023. In particular, I am still considering the dates for handing out assignments and when they are due. * Also, I have currently left some place-holders for guest lectures. I may need to juggle these a bit, depending on when people are available. =====Week 1===== *August 29 * {{ :courses:455-655:lectures:2023_cis_i_organization.pdf|Fall 2023 Organization Lecture}} * {{ :courses:455-655:lectures:2023_introductory_lecture.pdf|Introductory Lecture}} * August 31 * {{ :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]] =====Week 2===== * September 5 * Begin {{ :courses:455-655:lectures:frames.pdf|Basic Mathematical Methods for CIS}} * Additional Reference Material * [[http://cs229.stanford.edu/section/cs229-linalg.pdf|Linear algebra review]] * [[https://benjamindkilleen.com/files/frame_transformations.pdf|Frame Transformations in Computer Integrated Surgery: A Graphical Introduction (Ben Killeen)]] * September 7 * Conclude {{ :courses:455-655:lectures:frames.pdf|Basic Mathematical Methods for CIS}} =====Week 3===== * September 12 * {{ :courses:455-655:lectures:rigid3d3dcalculations.pdf |Computing rigid 3D-3D transformations from point and line pairs}} * Reference material: [[https://en.wikipedia.org/wiki/Point-set_registration|Excellent Wikipedia article on point set registration]] * **Hand out {{ :courses:455-655:2023:2023 CIS I Homework 1-for students - 0923_HI2.pdf |Homework Assignment #1}}** * September 14 * {{ :courses:455-655:lectures:localizers.pdf |Localizers}} (**Dr. Peter Kazanzides**) * 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 4===== * September 19 * **{{ :courses:455-655:2023:sikder_csp_2023.pdf |Guest Lecture from Dr. Shameema Sikder}}** (Prof. Taylor out of town) * September 21 * **Guest Lecture from Dr. Todd McNutt** (Prof. Taylor out of town) =====Week 5===== * September 26 * **Homework 1 Due** * Begin {{ :courses:455-655:lectures:calibration.pdf |Calibration}} * {{ :courses:455-655:lectures:leastsquaresreview.pdf |Least Squares Review}} (if time) * {{ :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 28 * Finish{{ :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]] * **Hand out {{ :courses:455-655:2023:programmingassignments1and2.pdf |Programming Assignments #1 and #2}}** * {{ :courses:455-655:2023:programmingassignments1and2_scenario.pdf |Scenario Slides}} * {{ :courses:455-655:2023:pa1_student_data.zip |Data for Programming Assignment #1}} * {{ :courses:455-655:2023:pa2_student_data.zip |Data for Programming Assignment #2}} =====Week 6===== * October 3 (Hisashi is at IROS Conference) * Begin {{ :courses:455-655:lectures:segmentation_-_2023.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 5 (Hisashi is at IROS Conference) * Finish {{ :courses:455-655:lectures:segmentation_-_2023.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]] * {{ :courses:455-655:lectures:gueziecsimp.pdf |Surface simplification inside a tolerance volume (Andre Gueziec's method)}} =====Week 7===== * October 10 * {{ :courses:455-655:lectures:2023_1010_cisneurosurgery.pdf |**Guest Lecture: Dr. Tito Porras**}} (Prof. Taylor at MICCAI Conference) * October 12 * **Programming Assignment #1 due** * {{ :courses:455-655:lectures:2023-10-12_cis_i_cochlear_implant_talk_.pdf |**Guest Lecture: Dr. Deepa Galaiya**}} (Prof. Taylor at MICCAI Conference) =====Week 8===== * October 17 * **{{ :courses:455-655:2023:homework_2_-_2023.pdf |Hand out Homework #2}}** * {{ :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]] * October 19 * **Fall break (no class)** =====Week 9===== * October 24 * **{{ :courses:455-655:2023:programming_3_and_4_600-445-2023.pdf |Hand out Programming Assignments #3 and #4}}** * {{ :courses:455-655:2023:2023_pa345_student_data.zip |Data for PA 3,4,5}} * Begin {{ :courses:455-655:lectures:registration_part_2.pdf |Registration (Part 2)}} * {{ :courses:455-655:lectures:coherent_point_drift_registration.pdf |Coherent Point Drift Slides}} * 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]] * {{ :courses:455-655:lectures:defense_presentation_cong_gao_-_handouts.pdf |Fluoroscopic Navigation for Robot-Assisted Orthopedic Surgery (Cong Gao)}} * October 26 * Finish {{ :courses:455-655:lectures:registration_part_2.pdf |Registration (Part 2)}} * {{ :courses:455-655:lectures:coherent_point_drift_registration.pdf |Coherent Point Drift Slides}} * Discuss Programming Assignment 1 =====Week 10===== * October 31 * **Homework 2 Due** * **Hand out {{ :courses:455-655:2023:2023_hw3.pdf |Homework Assignment #3}}** * {{ :courses:455-655:lectures:registration_part_3.pdf |Registration (Part 3)}} * Supplemental material * [[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)]] * November 2 * **Programming Assignment #2 due** * {{ :courses:455-655:lectures:medical_robots_part_1.pdf |Medical Robotics, Constrained Control and Virtual Fixtures (Part 1)}} =====Week 11===== * November 7 * {{ :courses:455-655:lectures:medical_robots_part_2.pdf |Medical Robotics, Constrained Control and Virtual Fixtures (Part 2)}} * Supplemental Material: {{ :courses:455-655:lectures:max_li_iros_2020_presentation.pdf |Anatomical Mesh-Based Virtual Fixtures for Surgical Robots}} * November 9 * {{ :courses:455-655:lectures:medical_robots_part_3_-_autonomy.pdf |Autonomy and Semi-Autonomous Behavior in Surgical Robot Systems}} * [[ https://ieeexplore.ieee.org/stamp/stamp.jsp?tp=&arnumber=9805578 | R. H. Taylor, N. Simaan, A. Menciassi, and G. Z. Yang, "Surgical Robotics and Computer-Integrated Interventional Medicine", Proceedings of the IEEE, vol. 110- 7, pp. 823-834, 2022.]] * [[ https://ieeexplore.ieee.org/stamp/stamp.jsp?tp=&arnumber=9805576| P. Fiorini, K. Y. Goldberg, Y. Liu, and R. H. Taylor, "Concepts and Trends in Autonomy for Robot-Assisted Surgery", Proceedings of the IEEE, vol. 110- 7, pp. 993-1011, 2022.]] * [[ https://doi.org/10.1117/12.2550198 10.1117/12.2550198 | T. Xie, M. Shahbazi, Y. Wu, R. H. Taylor, and E. M. Boctor, "Stabilized ultrasound imaging of a moving object using 2D B-mode images and convolutional neural network", in Proc.SPIE, 2020.]] * {{ :courses:455-655:lectures:tx-stable-us-spie.pdf |Slides from SPIE talk on stabilized ultrasound imaging}} =====Week 12===== * November 14 * **Homework Assignment 3 due** * However we will accept late assignments up to Nov. 20 without penalty * **Hand out {{ :courses:455-655:2023:2023_homework_4.pdf |Homework Assignment #}}4** * In-class discussion of Homework #2 * November 16 * **Programming Assignment #3 due** * **Hand Out {{ :courses:455-655:2023:programming_5_600-445-2023.pdf |Optional Programming Assignment 5}}** * {{ :courses:455-655:2023:2023_pa5_student_data_-_new.zip |New PA5 Data (see also Piazza announcement)}} * {{ :courses:455-655:2023:pa5_-_highres_-_student_data.zip |New high resolution data for PA5 }} (See also Piazza announcement and followup to Question 239) *{{ :courses:455-655:2023:pa5_notes.pdf | Notes for PA#5: Deformable Registration to a Statistical Shape Model}} * Case study: {{ :courses:455-655:lectures:craniofacial_surgery.pdf |Craniofacial osteotomies}} =====Week 13===== * November 21 - **NO Class (Thanksgiving Week)** * November 23 - **NO Class (Thanksgiving Week)** =====Week 14===== * November 28 * {{ :courses:455-655:lectures:therac.pdf |Safety Case Study: The Therac 25 Accidents}} * 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. * November 30 * ** Homework Assignment 4 due** * **Guest Lectures:** * Dr. Suxi Gu - Endoscopic Spine Surgery * Prof. Iulian Iordachita - Robot-Assisted Eye Surgery =====Week 15===== * December 5 * **{{ :courses:455-655:2023:20231205_cis_class_saunders_talk.pdf |Guest Lecture on Medical Device Development - Dave Saunders (Galen Robotics}})** * December 7 **(Last Class)** * **Programming Assignment #4 due** * **Guest Lecture on Augmented Reality and Robotic Surgery - Dr. Alejandro Martin-Gomez** =====Optional Programming Assignment #5 ===== * There will be no written final exam for CIS I. Instead, there is an optional programming assignment that can be used to improve a student's grade. * The due date is **December 14 at 1:30PM**. * If this due date conflicts with another final exam on the same date, then contact the TA. We will give an extension until the first day on which you do **not** have an exam, but no further. We have very limited flexibility for this, since the assignments can require considerable time to grade.