courses:455-655:2022:fall-2022-schedule

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===============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.
courses/455-655/2022/fall-2022-schedule.txt · Last modified: 2022/12/01 13:29 by rtaylor2