===============CIS I (601.455/655) Fall 2024 Schedule===============
~~NOTOC~~

=====Note: This page is subject to change=====

  * I am still working out the detailed schedule for 2024. 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 27
    * {{ :courses:455-655:2024:2024_cis_i_organization.pdf |Fall 2024 Organization Lecture}}
    * {{ :courses:455-655:2024:2024_introductory_lecture.pdf |CIS I Introductory Lecture}}
  * August 29
    * {{ :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 3
    * Guest Lecture from Prof. Axel Krieger
      * {{ :courses:455-655:lectures:cis_guest_lecture_ak_v4.pdf |The Future of Surgical Robotics: Vision, Challenges, and the Science to Meet Them}}
  * 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)]]

=====Week 3=====
  * September 10
    * Conclude {{ :courses:455-655:lectures:frames.pdf|Basic Mathematical Methods for CIS}}
    * **Hand out{{ :courses:455-655:2024:homework_1_600-455-2024.pdf | Homework Assignment #1}}**  
  * 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]]
 
=====Week 4=====
  * September 17
      * {{ :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 19
    * 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]] 

=====Week 5=====
  * September 24
    * Guest Lecture: Computer-Integrated Surgery: ​Applications in Neurosurgery (Dr. Tito Porras)
      * {{ :courses:455-655:2024:20240924_cis_technologyneurosurgery.pdf |Computer-Integrated Surgery: Applications in Neurosurgery}}
    * **Homework #1 Due**
  * September 26
    * 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:455-655:2024:programmingassignments1and2.pdf |Programming Assignments #1 and #2}}**
        * {{ :courses:455-655:2024:programmingassignments1and2_scenario.pdf |Scenario Slides}}
        * {{ :courses:455-655:2024:pa_general_expectations.pdf | PA general expectations}}
        * {{ :courses:455-655:2024:pa_1_student_data.zip |Data for Programming Assignment #1}}
        * {{ :courses:455-655:2024:pa_2_student_data.zip |Data for Programming Assignment #2}}

=====Week 6=====
  * October 1 
    * 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 3 
    * 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)}}
    * **Hand out {{ :courses:455-655:2024:homework_2_600-455-2024.pdf |Homework #2}}** 

=====Week 7=====
  * October 8
    * {{ :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 10
    * **Programming Assignment #1 due**
      * Guest lecture TBD or continue with Registration
=====Week 8=====
  * October 15 
    * 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}}
      * 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 17
    * **WSE Fall Break - No class**
=====Week 9=====
  * October 22
    * {{ :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)]]
  * October 24
    * **Hand out {{ :courses:455-655:2024:programming_3_and_4_600-445-2024.pdf |Programming Assignments #3 and #4}}**
      * {{ :courses:455-655:2024:2024_pa345_student_data.zip |Programming Assignments 3, 4, and 5 Data}}
    * Finish {{ :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)]]
    * Begin  * {{ :courses:455-655:lectures:medical_robots_part_1.pdf |Medical Robotics, Constrained Control and Virtual Fixtures (Part 1)}} (if time)
=====Week 10=====
  * October 29
    * **Homework 2 Due**
    * Guest lecture from Prof. Emad Boctor    

  * October 31
    * 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}}
=====Week 11=====
  * November 5
    * **Programming Assignment #2 due**
    * Hand out **{{ :courses:455-655:2024:homework_3_600-455-2024.pdf |Homework Assignment #3}}**
    * Finish {{ :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}}
    * Begin {{ :courses:455-655:lectures:medical_robots_part_3_-_autonomy.pdf |Human-Machine Partnerships 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 7
     * Finish {{ :courses:455-655:lectures:medical_robots_part_3_-_autonomy.pdf |Human-Machine Partnerships 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 12
    * Guest Lecture from Manish Sahu on robotic assistance for ENT surgery
  * November 14
    * **Programming Assignment #3 due**
    * **Hand Out {{ :courses:455-655:2024:programming_5_600-445-2024.pdf |Optional Programming Assignment 5}}**
      *{{ :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 19 
    * Guest Lecture from Dr. Swaroop Vedula
      * "What Can AI Teach a Surgeon"
  * November 21
     * **Homework Assignment 3 Due**
     * **{{ :courses:455-655:2024:homework_4_600-455-2024.pdf |Hand out Homework Assignment 4}}**
    * Guest Lecture from Prof. Iulian Iordachita
      * {{ :courses:455-655:2024:autonomous_needle_insertions_iordachita_11_21_24_compact.pdf | Autonomous needle insertions}}

=====Week 14=====

  * November 26 - **NO Class (Thanksgiving Week)**
  * November 28 - **NO Class (Thanksgiving Week)**

=====Week 15=====

  * December 3 
    * Guest Lecture from Prof. Todd McNutt (Prof. Taylor at Malone Center Symposium)
  * December 5
    * {{ :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.
  * December 7 (Saturday)
      * **Programming Assignment 4 Due (1:30PM)**
      * **Homework Assignment 4 Due (1:30PM)**

=====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 (subject to change) 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.