===============CIS I (601.455/655) Fall 2022 Schedule=============== ~~NOTOC~~ **NOTE: This page is still under construction and is subject to change** =====Week 1===== *August 30 * {{ :courses:455-655:lectures:2022_cis_i_organization.pdf |Fall 2022 Organization Lecture}} * {{ :courses:455-655:lectures:2022_introductory_lecture.pdf |Introductory Lecture}} * September 1 * {{ :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 6 * 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 8 * Conclude {{ :courses:455-655:lectures:frames.pdf|Basic Mathematical Methods for CIS}} * **Hand out {{ :courses:455-655:2022:2022_cis_i_homework_1.pdf |Homework Assignment #1}}** * **Hand out {{ :courses:455-655:2022:2022_cis_i_homework_2.pdf |Homework Assignment #}}2** =====Week 3===== * September 13 * Guest Lecture from Dr. Amit Jain on Spine Surgery (Prof. Taylor in London for a Center Review) * September 15 * {{ :courses:455-655:lectures:2022_0915_technologyneurosurgery_1.1.pdf |Guest Lecture from Drs. Masaru Ishii and Tito Porras on endoscopic sinus and skull base surgery}} (Prof. Taylor in London for a Center Review) =====Week 4===== * September 20 * **Homework Assignment #1 due** * {{ :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]] * {{ :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" * September 22 * Begin {{ :courses:455-655:lectures:calibration.pdf |Calibration}} * {{ :courses:455-655:lectures:leastsquaresreview.pdf |Least Squares Review}} (if time) =====Week 5===== * September 27 * ** Homework Assignment #2 due** * 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:455-655:2022:2022_homework_3.pdf | Homework Assignment #3}}** * **Hand out {{ :courses:455-655:2022:programmingassignments1and2.pdf |Programming Assignments #1 and #2}}** * {{ :courses:455-655:2022:programmingassignments1and2_scenario.pdf |Scenario Slides}} * {{ :courses:455-655:2022:pa1_student_data.zip |Data for Programming Assignment #1}} * {{ :courses:455-655:2022:pa2_student_data.zip |Data for Programming Assignment #2}} * September 29 * Begin {{ :courses:455-655:lectures:segmentation_-_2022.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]] * September 30 (section) * Topic: Programming assignment 1 * Time: 3PM * Place: Hackerman 320 =====Week 6===== * October 4 * {{ :courses:455-655:lectures:jk_cis_i_vp.pdf |Guest lecture on ultrasound imaging by Dr. Jeeun Kang}} * [[http://dx.doi.org/10.1016/j.pacs.2022.100378|[Y. Wu, J. Kang], W. G. Lesniak, H. K. Zhang, R. H. Taylor, M. G. Pomper, E. M. Boctor, “System-level optimization in spectroscopic photoacoustic imaging of prostate cancer,” Photoacoustics 27, 100378, 10 Jun., 2022 [equally contributed]]] * [[https://doi.org/10.1093/jcde/qwac083|H. Song, (J. Kang*, E. M. Boctor*), “A novel design framework of radial synthetic aperture focusing for volumetric transrectal ultrasound imaging,” Journal of Computational Design and Engineering 9, 1774-1787, 24 Aug., 2022 (*co-corresponding authors)]] * [[http://doi.org/10.1038/s41598-020-63588-2|J. Kang, H. N. D. Le, S. Karakus, J. U. Kang, A. L. Burnett, and E. M. Boctor, “Real-time, functional intra-operative localization of rat cavernous nerve network using near-infrared cyanine voltage-sensitive dye imaging,” Scientific Reports 10, 6618, 20 Apr. 2020]] * October 6 * Finish {{ :courses:455-655:lectures:segmentation_-_2022.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 11 * Guest lecture from Prof. Peter Kazanzides (Prof. Taylor in Hong Kong) * October 13 * **Programming Assignment #1 due** * Guest lecture from Dr. Todd McNutt (Prof. Taylor in Hong Kong) =====Week 8===== * October 18 * **Homework Assignment #3 due** * Guest lecture from Dr. Deepa Galaiya (Prof. Taylor in Hong Kong) * October 20 * **Fall Break (No Class)** =====Week 9===== * October 25 * {{ :courses:455-655:2022:pa_announcement_upload.pdf |Discuss Programming Assignment 1}} * 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]] * October 27 * **Programming Assignment #2 due** * 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}} * 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]] =====Week 10===== * November 1 * **Hand out {{ :courses:455-655:2022:2022_homework_4_-_v05.pdf |Homework Assignment #4}}** * **{{ :courses:455-655:2022:programming_3_and_4_600-445-2022.pdf |Hand out Programming Assignments #3 and #4}}** * {{ :courses:455-655:2022:2022_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)}} * November 3 * 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}} =====Week 11===== * November 8 * {{ :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 10 * **Homework Assignment #4 due** * Finish {{ :courses:455-655:lectures:registration_part_3.pdf |Registration (Part 3)}} (if needed) * Begin {{ :courses:455-655:lectures:medical_robots_part_1.pdf |Medical Robotics, Constrained Control and Virtual Fixtures (Part 1)}} =====Week 12===== * November 15 * 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 |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 17 * **Hand out {{ :courses:455-655:2022:2022_homework_5.pdf |Homework Assignment #5}}** * **Hand out {{ :courses:455-655:2022:2022_homework_6.pdf |Homework Assignment #6}}** * Finish {{ :courses:455-655:lectures:medical_robots_part_2.pdf |Medical Robotics, Constrained Control and Virtual Fixtures (Part 2)}} * **Hand {{ :courses:455-655:2022:programming_5_600-445-2022.pdf |Optional Programming Assignment #5}}** * {{ :courses:455-655:2021:hw:pa5_notes.pdf |Notes for PA#5: Deformable Registration to a Statistical Shape Model}} * November 19 (Saturday, 9PM) * **Programming Assignment #3 due** =====Week 13===== * November 22 - **NO Class (Thanksgiving Week)** * November 24 - **NO Class (Thanksgiving Week)** =====Week 14===== * November 29 * {{ :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}} * November 30 (Wednesday, 11:59pm) * **Homework Assignment #5 due** * December 1 * {{ :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. =====Week 15===== * December 6 * **Homework Assignment #6 due** * Guest lecture on Extended Reality from Prof. Mathias Unberath * December 8 **(Last Class)** * **Programming Assignment #4 due** * Guest lecture from Prof. Emad Boctor * December 16 (11:59pm) * **Optional PA#5 due** * **Note:** If you have a final exam on December 16, 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.