courses:455-655:2021:fall-2021-schedule

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===============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]])
courses/455-655/2021/fall-2021-schedule.txt · Last modified: 2021/12/05 16:30 by rtaylor2