Computer-Integrated Surgery (CIS I)

Office: Hackerman Hall 127
Lab: Hackerman Hall B08H
LCSR Executive Director (major adminstrative matters): Lorrie Dodd; ldodd@jhu.edu; 410-516-0740
Personal Assistant (appointments and routine matters): Michele Greatti; RussAdmin@jh.edu;410-516-6841
Office Hours: By appointment

• All students are requested to wear high quality masks for any in-person classes or TA sessions. This is both for your protection and for that of the instructor, the TA, and your fellow students. The class is very full, and the classroom density will reflect this.
• If you test positive for covid-19 (or any other communicable disease) please do not come to class. Notify me and the TA, and we can make arrangements for you to make up any necessary material.

• Times: Tuesday and Thursday 1:30pm - 2:45 pm
• Location: Hackerman B17
  • Online - Zoom links and links to recorded lectures will be posted on the CIS I Canvas page

Tatiana Kashtanova

• Email: tkashta1@jhu.edu
• Office Hours (starting September 9)
  • Time: Monday, 10 am - 11 am
  • Location: Zoom
  • https://JHUBlueJays.zoom.us/j/99052831625?pwd=AFMJsShozAjWfMKpYv47JqLqjz3hAN.1
  • Meeting ID: 990 5283 1625
  • Passcode: 096011

Meetings with the TA/CA (subject to change):

• 9-Sep (Monday): Math (the recording is on Canvas, “Meetings with TA” folder)
  • Math
• 16-Sep (Monday): HW1
• 20-Sep (Friday): HW1 (additional office hours)
• 23-Sep (Monday): HW1
• 26-Sep (Thursday, in class): PA general expectations
  • PA general expectations
• 30-Sep (Monday): PA Intro Code by Hisashi Ishida (the recording is on Canvas, “Meetings with TA” folder)
• 7-Oct (Monday): HW1 Review, PA1
• 14-Oct (Monday): HW2, PA2
• 21-Oct (Monday): HW2, PA2
• 28-Oct (Monday): HW2, PA2
• 4-Nov (Monday): PA2, PA3
• 11-Nov (Monday): HW2 Review, PA3, HW3
• 18-Nov (Monday): HW3, PA4, HW4
• 25-Nov (Monday): N/A (Thanksgiving)
• 2-Dec (Monday): HW3 Review, PA5, HW4

• Fall 2024 Schedule
  • Fall 2024 Organization Lecture
  • Links to all lecture and homework materials are on the schedule page

• Previous years
  • Fall 2023 Schedule
  • Fall 2022 Schedule
  • Fall 2021 Schedule

• The Canvas page for the course is at https://jhu.instructure.com/courses/74500.
  • We will make limited use of Canvas, which is much less versatile for routine communication.
  • We plan to record most lectures. These will be available through Panopto. The links will be available on Canvas.
  • You may not share the zoom link for the class or any of the Panopto recordings with anyone who is not registered in the class.
• We will use Piazza for routine communication. Primarily, this will be for announcements and to provide a means for students to ask questions of the instructor and the TA. We will be monitoring it fairly closely, but don't guarantee instantaneous response.
• Students enrolled in the class need to activate their Piazza accounts and check to see that they have access to the page. If you have problems, contact the TA
  • The link for the class is https://piazza.com/jhu/fall2024/601455655
  • Students should go to this page to sign up
• Here are a few of the uses that are legitimate for the Q/A section of the page:
  • Advertising for a lab partner
  • Asking general questions about concepts in the class (though you may be referred to the TA)
  • Asking for clarification on homework (to be answered only by TA or instructor)
  • Pointing out typographical errors or other problems in handouts
• Here are a few uses that are not acceptable
  • Giving or seeking specific help or providing answers to homework assignments, including posting an answer and asking if it is correct or answering another student's question.
  • Electronic collaboration of any kind
  • Uses unrelated to the course

Downloading and retention of materials linked to from this web site is restricted to students who have registered for this course.

Students who have registered for this course are pemitted to download and save a copy of any course materials for their own use. However, they are not authorized to redistribute or transfer any materials (lecture notes, videos, or anything else) to anyone else.

• Students who are struggling with anxiety, stress, depression or other mental health related concerns, please consider connecting with resources through the JHU Counseling Center. The Counseling Center will be providing services remotely to protect the health of students, staff, and communities. Please reach out to get connected and learn about service options based on where you are living this fall at 410-516-8278 and online at http://studentaffairs.jhu.edu/counselingcenter/.
• Student Outreach & Support will be fully operational (virtually) to help support students. Students can self-refer or refer a friend who may need extra support or help getting connected to resources. To connect with SOS, please email deanofstudents@jhu.edu, call 410-516-7857, or students can schedule to meet with a Case Manager by visiting the Student Outreach & Support website and follow “Schedule an Appointment”.

* Resources for Students from the JHU Office of Academic Support

* Recruiting for CIS I - Related Projects with Faculty Mentors

This course focuses on computer-based techniques, systems, and applications exploiting quantitative information from medical images and sensors to assist clinicians in all phases of treatment, from diagnosis to preoperative planning, execution, and follow-up. It emphasizes the relationship between problem definition, computer-based technology, and clinical application and includes a number of guest lectures given by surgeons and other experts on requirements and opportunities in particular clinical areas. An optional term project may be undertaken under supervision of the instructor and clinician end users. Although this course is primarily intended for graduate students and advanced undergraduate students interested in doing research in this area, it may also be of interest to medical or qualified premedical students wanting to obtain a broader background in this emerging field.

• Required: linear algebra or permission of instructor; reasonable skills in programming
• Recommended: 601.226 or equivalent, image processing, probability or statistics.

• Time - TBD
• Room - TBD

The section for this course will present supplementary material related to the main lectures and the homeworks. Attendance is not mandatory, but it is recommended for those unfamiliar with the topic to be covered on a given date. Section will not be held every week, but rather when there are important topics which require extra time to cover. The focus of the section will be on presenting techniques that will help you to understand and complete the homework assignments, both written and programming. Topics will generally be posted on the website at least a week in advance. If students have topics which they would like to have sections taught on, they should contact the TA and he will try to incorporate them.

• 600.145 - Introduction to Computer-Integrated Surgery (not offered recently)
• 601.456/656 - Advanced Computer-Integrated Surgery (CIS II) – Projects course

• Books
  • R.Taylor, S. Lavalee, G, Burdea, R. Moesges, eds., Computer Integrated Surgery,, MIT Press, 1995
    • This book is 25 years old, but it still has some useful information about basics and applications

• Jocelyne Troccaz, ed. Medical Robotics, Wiley 2012, Print ISBN:9781848213340 Online ISBN:9781118562147, DOI:10.1002/9781118562147
• Rueckert, K. Zhou, and G. Fichtinger, eds., Handbook of Medical Image Computing and Computer Assisted Intervention, Elsevier, 2022, DOI https://doi.org/10.1016/C2017-0-04608-6.

• Journal Articles and Book Chapters
  • 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. DOI https://doi.org/10.1109/JPROC.2022.3177693
    • This is the lead article in a July 2022 special issue on surgical robotics. The entire issue consists of excellent survey articles on some key aspects of the field. The issue is available online.
  • W. P. Liu and R. H. Taylor, “Augmented Reality in Image-Guided Robotic Surgery”. in Mixed and Augmented Reality in Medicine, 2018,Chapter 14, T. M. Peters, C. A. Linte, Z. Yaniv, and J. Williams, Eds.: CRC PRess.
  • R. H. Taylor, P. Kazanzides, G. Fischer, and N. Simaan, “Medical Robotics and Computer-Integrated Interventional Medicine”. in Biomedical Information Technology, 2019,Chapter 19, pp. 617-672, D. Feng, Ed.: Elsevier.
  • R. H. Taylor, “Computer-integrated interventional medicine: A 30 year perspective”. in Handbook of Medical Image Computing and Computer Assisted Intervention, 2020,Chapter 25, pp. 599-624, D. Rueckert, K. Zhou, and G. Fichtinger, Eds.: Elsevier.

• Conference Proceedings
  • Information Processing in Computer Assisted Interventions (IPCAI).
    • This is probably the best conference focused on image-guided surgery. It is a spin-off from MICCAI, which is a more general. Both are high-prestige meetings, and the proceedings are available online. Also, authors often put submitted papers into arXiv.
  • Medical Image Computing in Computer Assisted Interventions (MICCAI).
    • This conference is a broader than IPCAI and includes many papers on general medical image analysis as well as image-guided interventions. Both are high-prestige meetings, and the proceedings are available online. Also, authors often put submitted papers into arXiv.
  • IEEE International Conference on Robotics and Automation (ICRA).
    • This is the flagship robotics conference. It generally has multiple sessions on surgical and interventional robotic systems. Proceedings are available online and free to JHU.
  • IEEE International Conference on Intelligent Robots and Systems (IROS).
    • This is a second, very high prestige robotics conference. It generally has multiple sessions on surgical and interventional robotic systems. Proceedings are available online and free to JHU.

• Assignments should be submitted on Gradescope (https://www.gradescope.com/), entry code: XG25X7
• 4 graded homework assignments (done individually or in teams of 2)
• 5 programming assignments (done individually or in teams of 2). PA#5 is optional
• Throw out grades for up to 1 of HW or one of PA#1-3
• Must hand in HW#4 and PA#4
• Grade for optional PA#5 will replace your lowest remaining grade except that you may not throw out both PA#1 and PA#2 or both of HW#4 or HW#5
• Numerical grading formula is Max(0.4P+0.6H,0.6H+0.4P), where H is homework average and P is the programming average
• Letter grade thresholds vary but usually fairly close to 90-80-70
• Optional project with negotiated modification to formula