CIS Spring 2024 Projects

To CIS II Students: Project Ideas

Here is a list of the project ideas and each individual set of slides for 2024. 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

Follow this link for CIS II Spring 2024 class schedule

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 (scho72@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.

Project signup Process

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, send email to the TA with the following information
- Project name and project proposal number;
- Team members (with JHED ID); and
- Project mentors (with JHED ID if you know).
A project number will then be assigned to you and your project page will be created.

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 (Sue Min Cho, scho72@jhu.edu@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 2024
Best project selection form - poster session 2024: 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

01: Performance Metrics and Skills Analysis for Skull-Base Surgery

Team Members: Nimesh Nagururu, Hannah Puhov
Mentors: Adnan Munawar, Manish Sahu, Hisashi Ishida, Francis Creighton, Deepa Galaiya
Project Pages: Performance Metrics and Skills Analysis for Skull-Base Surgery

02: Non-invasive photoacoustic circulating tumor cell detection and therapy

Team Members: Gabby Kang
Mentors: Jeeun Kang, Emad M. Boctor, Martin G. Pomper, Stephen B. Solomon
Project Pages: Non-invasive photoacoustic circulating tumor cell detection and therapy

03: Measuring Variability of Pelvic Standard Views in Virtual Reality

Team Members: Danny Chang, Austin Huang
Mentors: Han Zhang, Benjamin Killeen, Mathias Unberath
Project Pages: Measuring Variability of Pelvic Standard Views in Virtual Reality

04: Robotic Assistant for MRI-Guided Low Back Pain Injections

Team Members: Saardhak Bhrugubanda, Vivek Chari, Aabhas Jain
Mentors: Iulian Iordachita, Yanzhou Wang
Project Pages: Robotic Assistant for MRI-Guided Low Back Pain Injections

05: A cannula marker body for tracker-free surgical navigation during Kirschner wire placement

Team Members: Yuxuan Zhao
Mentors: Benjamin Killeen, Han Zhang, Mathias Unberath; Alejandro Martin-Gomez
Project Pages: A cannula marker body for tracker-free surgical navigation during Kirschner wire placement

06: Augmented reality-enhanced surgical microscopes for orthopedic spinal procedures

Team Members: Esther Wang, Zechen Xu, Yu-Chun Ku
Mentors:Alejandro Martin Gomez, Amit Jain
Project Pages: Augmented reality-enhanced surgical microscopes for orthopedic spinal procedures

07: Design of a Closed-Loop Bevel-Tip Needle Steering System Using Electromagnetic Tracking for Prostate Biopsies

Team Members: Chang Chang, Junling Mei
Mentors: Iulian Iordachita, Yanzhou Wang
Project Pages: Design of a Closed-Loop Bevel-Tip Needle Steering System Using Electromagnetic Tracking for Prostate Biopsies

08: Surgical Robotics Environment for NVIDIA Isaac Sim

Team Members: Tae Wan Kim
Mentors: Hisashi Ishida, Juan Barragan, Adnan Munawar, Peter Kazanzides, Jintan Zhang
Project Pages: Surgical Robotics Environment for NVIDIA Isaac Sim

09: Deep learning-based optimization of novel transformable transrectal ultrasound and photoacoustic imaging

Team Members: Boxun Hu, Joe Yan
Mentors: Jeeun Kang, Emad M. Boctor, Hyunwoo Song
Project Pages: Deep learning-based optimization of novel transformable transrectal ultrasound and photoacoustic imaging

10: Withdrawn

Team Members:
Mentors:
Project Pages:

11: Bringing View-invariant X-ray Image Analysis into the Operating Room

Team Members: Janya Budaraju
Mentors: Benjamin Killeen, Mathias Unberath
Project Pages: Bringing View-invariant X-ray Image Analysis into the Operating Room

12: Digital playground for developing medical robotics environments

Team Members: Shiyue Vanessa Wang
Mentors: Adnan Munawar, Peter Kazanzides, Jintan Zhang, Hisashi Ishida, Juan Barragan
Project Pages: Digital playground for developing medical robotics environments

13: Admittance Switching for Virtual Fixtures in Microsurgery

Team Members: Kiana Bronder, Keerthana Thammana
Mentors: Ugur Tumerdem, Deepa Galaiya, Hisashi Ishida, Manish Sahu, Russ Taylor
Project Pages: Admittance Switching for Virtual Fixtures in Microsurgery

14: Learning Based Sensorless Force Estimation for Haptic Feedback on the dVRK

Team Members: Rohan Mukundhan, Kent Shibata
Mentors: Peter Kazanzides, Ugur Tumerdem, Brendan Burkhart, Anton Deguet
Project Pages: Learning Based Sensorless Force Estimation for Haptic Feedback on the dVRK

15: Design of an Automated Robotic Patient Tracheostomy Suctioning System

Team Members: Nidhi Batra, Rena Bi, Lavinia Kong
Mentors: Vinciya Pandian, Michael Brenner, Axel Kreiger
Project Pages: Design of an Automated Robotic Patient Tracheostomy Suctioning System

16: A reinforcement learning approach to robotic suturing

Team Members: Jin Wu
Mentors: Anqi Liu, Adnan Munawar, Peter Kazanzides, Juan Barragan
Project Pages: A reinforcement learning approach to robotic suturing

17: Enabling High Precision Post-Operative Radiation Therapy (PORT) Delivery for Skull Based Cancers

Team Members: Zhiyuan Zhu
Mentors: Carmen Kut, Francis (Pete) Creighton, Xingde Li
Project Pages: Enabling High Precision Post-Operative Radiation Therapy (PORT) Delivery for Skull Based Cancers

18: Design and Control of Miniature Magnetic Surgical Tools

Team Members: Daniel Wang
Mentors: Anuruddha Bhattacharjee, Axel Krieger
Project Pages: Design and Control of Miniature Magnetic Surgical Tools

19: An open source laparoscopic simulator

Team Members: Yihui Yao
Mentors: Peter Kazanzides
Project Pages: An open source laparoscopic simulator

20: Deep Learning for the Auto-Labelling of Prostate Multiparametric Magnetic Resonance Imaging (mpMRI) Scans

Team Members: Jakub Piwowarczyk
Mentors: Dan Stoianovici
Project Pages: Deep Learning for the Auto-Labelling of Prostate Multiparametric Magnetic Resonance Imaging (mpMRI) Scans

21: Exploration of Update Methods for Signed Distance Field

Team Members: Xingyu Chen, Yichen Xie
Mentors: Hisashi Ishida, Juan Antonio Barragan, Laura Connolly, Manish Sahu, Adnan Munawar
Project Pages: Exploration of Update Methods for Signed Distance Field