CIS Spring 2023 Projects

To CIS II Students: Project Ideas

Here is a list of the project ideas and each individual set of slides for 2023. These will be presented in class over the first few sessions of class.

Remember several points, however:

This list is not necessarily complete. More will be added.
You are ultimately responsible for finding and proposing a project.
You must get agreement from your mentors that your proposed project is one for which you are appropriate.
Your project does not have to be one of the ones in this suggested list.
- However, if it is not one of these, you should also get my agreement that it is appropriate for the course.
- Also, feel free to fill out a “potential project” template if you have a project idea but want to recruit additional students

To Potential CIS II Project Mentors: How to Propose a Project Idea

Our Advanced CIS II projects course has a large enrollment this year, and we are actively soliciting possible projects. As you may recall, CIS II is intended for graduate students and upper-level undergrads, in which students work in teams of 1-3 on semester-long projects broadly related to computer-integrated interventions, AI in medicine, medical image analysis, or related topics. In addition to material covered in lectures/seminars by the instructor and other faculty, students are expected to read and provide critical analysis/presentations of selected papers in recitation sessions. Students taking this course are required to undertake and report on a significant term project. Project mentors may include faculty, engineering staff, postdocs, and (with appropriate approvals) advanced graduate students. Students taking the course sign a non-disclosure agreement at the start of the semester, in order to enable free discussion without compromising patentability. We also keep project web pages restricted for at least a year, or until the mentor(s) agree that they can be made public.

Generally, students select projects in the first 2-3 weeks of class, although some come with an idea beforehand. In order to suggest a project, you can fill out this template (typically about 2-3 slides) and send it to me (rht@jhu.edu) and to the TA (jbarrag3@jh.edu), along with an indication if you would like to present the idea yourself or if you would like us to present it for you. If the file is too big to email, then feel free to send a link.

A note to Project Mentors

First, thank you for mentoring a CIS II project this year. This course provides a great educational experience for the students, and also can produce useful research results. Its success depends greatly on the project mentors, and I hope that your experience this year has been productive both for you and for the students.

As part of our grading process, we are encouraging project mentors to provide some input. You all should have been granted access to the course web site and to the individual project(s) that you are mentoring.

We would really appreciate it if you can answer a few questions. Either edit the linked form and email it to me (rht@jhu.edu) and the TA (Juan Barragan, jbarrag3@jh.edu), with a file name like “Project xxx mentors report.docx” or just sent an email with a similar subject line.

Finally, note that the annual final exam / poster session will be on the assigned final exam day on Zoom (https://wse.zoom.us/j/635091574). I very much hope that you can attend. Also, the project reports are due on the day of the poster session, but the students have been told that you need an opportunity to review the reports before then. Also, we will need your comments to us by 9 PM on the day of the poster session, since we will be using them to help us with our evaluation of the projects.

Instructions to 456/496/656 Students

The links below point to the Wiki pages for your projects. You should follow the link. This will bring you to a project home page that you can edit once you log in. The two little gear symbols on the upper right give access to functions like login, logout, edit page, etc. The login/logout is on the leftmost gear. Note that there are many styles of Wiki, with different syntax. This one is “dokuwiki”. There is a link to help pages from the edit page.

The current default access settings are “read” for the CiiS lab, no access to members of the general public, and full power to members of your group. If you want to restrict read access to smaller group (e.g., all 456 students, etc.) contact Prof. Taylor. Prof. Taylor can also implement access control for individual pages if you so desire. If you want the whole world to be able to read your project pages, that can be arranged. Do not post anything to unprotected pages that you want kept private until you have arranged with Prof. Taylor to protect them.

Also, verify that each member of your group can log in. If you have trouble, contact Prof. Taylor via email providing correct name and JHED id.

Finally, if you want to give other individuals (e.g., your mentors) access to your project pages, provide name and JHED id to Prof. Taylor

NOTE: At the end of the semester, all projects will be made readable to the general public, unless you make arrangements otherwise with Prof. Taylor

Resources

Google Cloud Credits: Some projects (especially those involving machine learning) many require significant computing resources. We have obtained a small Google Cloud Platform Education Grant to help support these projects. See the TA if you need a coupon.
Sample background reading presentation from 2022
Sample background reading report from 2022
Poster template final exam 2023
Best project selection form - poster session 2023: Follow this link to vote for the best project during the poster session.

Nondisclosure agreement for in-class discussion

As we discussed in class, some of the projects may contain potentially patentable material or other material that should not be disclosed publicly until a later time. In order to permit free in-class discussion of this material, we have developed a non-disclosure agreement. When asked, the entire class agreed to sign such an agreement, a copy of which is linked below.

Here is a link to current year's agreement.
If any member of the class has any reservations about this, please inform us immediately.
Also, class members are reminded to identify potentially confidential material on any slides or other presentation material used in class

Project signup sheet

Here is the link to the signup sheet . A couple of things to note:

If you are interested in any projects, the first thing to do is to contact the mentors. Once and only after you get approved by the mentors, sign yourself up in the signup sheet.
A project number will then be assigned to you and your project page will be created.
If your name has been highlighted, it means your project has been created on the wiki page and you can start to edit it.

Projects for 2023

Follow this link for CIS II Spring 2023 class schedule

01: Transparency Optimization of the Galen Surgical System with Frequency Domain Admittance Controller Design

Team Members: Brevin Banks
Mentors: Ugur Tumerdem, Manish Sahu, Adnan Munawar, Mohammad Salehizadeh, Russell Taylor
Project Pages: Transparency Optimization of the Galen Surgical System with Frequency Domain Admittance Controller Design

02: Continuum Microgripper Modelling for Retinal Surgery

Team Members: Shuyuan Wang
Mentors: David Usevitch, Prof. Iulian Iordachita
Project Pages: Continuum Microgripper Modelling for Retinal Surgery

03: Quality assurance of radiotherapy treatment using scattered x-ray

Team Members: Samuel Ydenberg, Tatiana Kashtanova
Mentors: Xun Jia, Lin Su
Project Pages: Quality assurance of radiotherapy treatment using scattered x-ray

04: Vision Guided Mosquito Dissection for the Production of Malaria Vaccine

Team Members: Yutai Wang
Mentors: Balazs Vagvolgyi
Project Pages: Vision Guided Mosquito Dissection for the Production of Malaria Vaccine

05: Recreating Pelvic Trauma Surgery in Virtual Reality for the Development of Novel C-arm Interfaces

Team Members: Han Zhang, Zixuan Liu, Liam Wang
Mentors: Benjamin Killeen, Prof. Mathias Unberath
Project Pages: Recreating Pelvic Trauma Surgery in Virtual Reality for the Development of Novel C-arm Interfaces

06: 3D Reconstruction of Inner Ear from Histopathology

Team Members: Aseem Jain
Mentors: Dr. Creighton, Dr. Lauer, Dr. Ward
Project Pages: 3D Reconstruction of Inner Ear from Histopathology

07: Real-time Integration of 2D-3D Pelvic Registration with Robotic X-ray Acquisition

Team Members: Jiaming Zhang, Zhangcong She
Mentors: Benjamin Killeen, Prof. Mathias Unberath
Project Pages: Real-time Integration of 2D-3D Pelvic Registration with Robotic X-ray Acquisition

08: Automated Spinal Segmentation and Remote Monitor Calibration for Surgical Assessment

Team Members: Jonathan Young, Arijit Nukala, Damiano Marsili
Mentors: Dr. Nicholas Theodore MD,Evan Haas & Antony Fuleihan,Dr. Youseph Yazdi, Drs.John Williams and Siri Khalsa
Project Pages: Automated Spinal Segmentation and Remote Monitor Calibration for Surgical Assessment

09: Electromagnetic Tracking of Endovascular Catheters

Team Members: Fangjie Li, Shanelle Cao, Huilin Xu
Mentors: Dr. Ali Uneri & Dr. Fernando Gonzalez
Project Pages: Electromagnetic Tracking of Endovascular Catheters

10: Design and Evaluation of Surgical Guidance Strategies for Continuum Manipulators

Team Members: Nick Zhang
Mentors: Alejandro Martin-Gomez, Mehran Armand, Andreas Keller
Project Pages: Design and Evaluation of Surgical Guidance Strategies for Continuum Manipulators

11: Autonomous Suture Managing for Robotic Suturing

Team Members: Jiawei Liu , Nyeli Kratz, Nathan Van Damme
Mentors: Michael Kam
Project Pages: Autonomous Suture Managing for Robotic Suturing

12: Evaluation of CT Registration for Image-Based Sinus Reconstruction

Team Members: Jan Mangulabnan
Mentors: Roger Soberanis, Mathias Unberath
Project Pages: Evaluation of CT Registration for Image-Based Sinus Reconstruction

13: Simulation Assisted Navigation for Head and Neck Surgery

Team Members: Xinhao Chen, Zhaomeng Zhang
Mentors: Dr. Adnan Munawar, Dr. Manish Sahu, Max Li, Mohammad Salehizadeh, Dr. Peter Kazanzides, Dr. Pete Creighton, Dr. Danielle Trakimas, Dr. Deepa Galaiya, Dr. Russ Taylor
Project Pages: Simulation Assisted Navigation for Head and Neck Surgery

14: Improve Content Validity of Virtual Drilling Simulator

Team Members: Anushruti Singh
Mentors: Hisashi Ishida, Adnan Munawar, Prof. Peter Kazanzides
Project Pages: Improve Content Validity of Virtual Drilling Simulator

15: DaVinci-Assisted Continuum Robot Navigation and Manipulation

Team Members: Jaspor Jiang, Chenhan Zhang, Heyun Wang
Mentors: Mohammad Salehizadeh, Anton Deguet, Russell Taylor
Project Pages: DaVinci-Assisted Continuum Robot Navigation and Manipulation

16: Deep learning continuum wire

Team Members: Zheyu Zhou, Wenxuan Li, Zheyuan Zhang
Mentors: David Usevitch, Iulian Iordachita
Project Pages: Deep learning continuum wire

17: Automatic Calibration of force-sensing Instrument with FBG Sensors

Team Members: Nili Abtahi
Mentors: Dr. Iulian Iordachita, Mojtaba Esfandiari
Project Pages: Automatic Calibration of force-sensing Instrument with FBG Sensors

18: Dual-robotic arm prostate ultrasound tomography

Team Members: Zhenghao Li, Ziyi Wang, Yunpu Zhang
Mentors: Yixuan Wu, Dr. Mohammad Salehizadeh, Dr. Russ Taylor, Dr. Emad Boctor
Project Pages: Dual-robotic arm prostate ultrasound tomography

19: VR Drilling Simulator for Mastoidectomy

Team Members: Jonathan Wang, Kesavan Venkatesh, Yi Wang
Mentors: David Usevitch, Hisashi Ishida
Project Pages: VR Drilling Simulator for Mastoidectomy

20: A reinforcement learning approach to robotic suturing

Team Members: Jocelyn Hsu, Jihoon Kim, Walee Attia
Mentors: Anqi Liu, Adnan Munawar, Manish Sahu, Peter Kazanzides
Project Pages: A reinforcement learning approach to robotic suturing

21: Tele-operation Control of a High Dexterity Robot for Vitreoretinal Surgery

Team Members: Xiao Wei
Mentors: Mojtaba Esfandiari, Dr. Adnan Munawar, Prof. Ugur Tumerdem, Prof. Iulian Iordachita
Project Pages: Tele-operation Control of a High Dexterity Robot for Vitreoretinal Surgery

22: Ultrasound-Guided Robotic Central Line Placement

Team Members: Xuanning Liu, Kesi Liang, Pranathi Golla
Mentors: Dr. Axel Krieger, Lidia Al-Zogbi, Dr. Vinciya Pandian, Dr. Mathias Unberath
Project Pages: Ultrasound-Guided Robotic Central Line Placement