CIS Spring 2022 Projects

To CIS II Students: Project Ideas

Here is a list of the project ideas and each individual set of slides for 2022. 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 (yixuan_wu@jhu.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.

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 (Yixuan Wu, yixuan_wu@jhu.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.

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 https://livejohnshopkins-my.sharepoint.com/:x:/g/personal/ywu115_jh_edu/EWyuHZiRrDlPkGR7YNqyr5kBONyrurGx9wTgWRyun64hqA?e=fOjd9d. 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.

01: Vision-Based Automatic Calibration of Mosquito Dissection System for the Production of Malaria Vaccine

Team Members: Miles Liu
Mentors: Balazs Vagvolgyi, Anna Goodridge
Project Pages: Vision-Based Automatic Calibration of Mosquito Dissection System for the Production of Malaria Vaccine

02: Gaze Tracking Enabled Automatic Error Detection

Team Members: Kaitlynn Pineda
Mentors: Maia Stiber, Chien-Ming Huang
Project Pages: Gaze Tracking Enabled Automatic Error Detection

03: Automated Segmentation and Registration for Eustachian Tube Disfunction

Team Members: Ameen Amanian, Yuliang Xiao, Chanha Kim
Mentors: Francis Creighton, Mathias Unberath, Russell Taylor
Project Pages: Automated Segmentation and Registration for Eustachian Tube Disfunction

04: In Situ Needle Path Adjustment and Trajectory Optimization

Team Members: Yanzhou Wang
Mentors: Iulian Iordachita, Russell Taylor
Project Pages: In Situ Needle Path Adjustment and Trajectory Optimization

05: Surgical Phase Recognition using Deep Learning

Team Members: Xucheng Ma, Xiaorui Zhang, Wenkai Luo
Mentors: Max Li, Danielle Trakimas, Francis Creighton, Mathias Unberath, Russell Taylor
Project Pages: Surgical Phase Recognition using Deep Learning

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

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

07: Co-robotic Ultrasound Imaging of Breast Assisting Mammography

Team Members: Julian Brown, Kevin Wang, Yuxin Chen
Mentors: Yixuan Wu, Web Stayman, Russell Taylor, Emad Boctor
Project Pages: Co-robotic Ultrasound Imaging of Breast Assisting Mammography

08: Surgical Skill Analysis with Virtual Reality

Team Members: Liza Naydanova, Aditya Khandeshi, Alexandra Szewc
Mentors: Max Li, Adnan Munawar, Francis Creighton, Mathias Unberath, Russell Taylor
Project Pages: Surgical Skill Analysis with Virtual Reality

09: Virtual Reality Guided Skull-base Surgery

Team Members: HongYi Fan, Tommy Liang, Jintan Zhang
Mentors: Max Li, Adnan Munawar, Francis Creighton, Mathias Unberath, Russell Taylor
Project Pages: Virtual Reality Guided Skull-base Surgery

10: Multisensory Navigational Aid for Visual Prosthesis Users

Team Members: An Chi Chen
Mentors: Seth Billings, Chi Ewulum
Project Pages: Multisensory Navigational Aid for Visual Prosthesis Users

11: 3D Segmentation of Hard and Soft Tissue for Simulating X-ray Image Formation with Deep Learning

Team Members: Sean Darcy, Qiyuan Wu, Zhiyuan Ding
Mentors: Benjamin Killeen, Mathias Unberath
Project Pages: 3D Segmentation of Hard and Soft Tissue for Simulating X-ray Image Formation with Deep Learning

12: Patch ultrasound user interface

Team Members: Shuran Zhang, Yuanwu He
Mentors: Keshuai Xu, Emad Boctor
Project Pages: Patch ultrasound user interface

13: Development of a Wearable Intracranial Pressure Monitoring Device

Team Members: Ese Bowry, Marissa Hsu
Mentors: Joshua Liu, Chad Gordon, Mehran Armand
Project Pages: Development of a Wearable Intracranial Pressure Monitoring Device

14: Motion Compensation and Evaluation for 3D Head Reconstruction

Team Members: Unnat Antani
Mentors: Can Kocabalkanli
Project Pages: Motion Compensation and Evaluation for 3D Head Reconstruction

15: Building a Workflow for Cooperatively Controlled Robotic Mandibular Surgery

Team Members: Jesse Haworth
Mentors: Robin Yang, Pete Creighton, Russell Taylor, Andy Ding
Project Pages: Building a Workflow for Cooperatively Controlled Robotic Mandibular Surgery

16: VR Guided Surgery – SDF Based Guidance and Safety

Team Members: Hisashi Ishida, Juan Barragan Noguera
Mentors: Max Li, Adnan Munawar, Russell Taylor
Project Pages: VR Guided Surgery – SDF Based Guidance and Safety

17: Actuation Design for Loop Snare Operation in Eye Surgery

Team Members: Wenpeng Wang
Mentors: David Usevitch, Mehran Armand
Project Pages: Actuation Design for Loop Snare Operation in Eye Surgery

18: Automatic Mechanical Ventilation Control (AMVC)

Team Members: Haoyu Shi, Jiahe Xu
Mentors: Antwan D. Clark
Project Pages: Automatic Mechanical Ventilation Control (AMVC)

19: Glioma Classification and Biopsy Guidance with Multimodal MRI and Deep Learning

Team Members: Nhat Le
Mentors: Shanshan Jiang, Mathias Unberath
Project Pages: Glioma Classification and Biopsy Guidance with Multimodal MRI and Deep Learning

20: Mixed Reality Surgical Team Training

Team Members: Haochen Wei
Mentors: Peter Kazanzides, Dayeon Kim
Project Pages: Mixed Reality Surgical Team Training

21: Magnetic PillCam for Medical Diagnosis

Team Members: Jack Yue, Bharath Heggadahalli, Mark Gonzales
Mentors: Axel Krieger, Onder Erin
Project Pages: Magnetic PillCam for Medical Diagnosis

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

Team Members: Muhammad Hadi, Mojtaba Esfendiari
Mentors: Ali Ebrahimi, Alireza Alamdar, Adnan Munawar, Iulian Iordachita
Project Pages: Tele-operation Control of a High Dexterity Robot for Vitreoretinal Surgery

23: Photoacoustic image based intro-operative surgical guidance system in a da vinci surgical robot platform

Team Members: Zijian Wu, Shuojue Yang
Mentors: Hyunwoo Song, Hamid Moradi, Emad Boctor
Project Pages: Photoacoustic image based intro-operative surgical guidance system in a da vinci surgical robot platform

24: Evaluation of Virtual Remote Center of Motion for Minimally Invasive Surgery

Team Members: Yernar Zhetpissov
Mentors: Peter Kazanzides, Adnan Munawar
Project Pages: Evaluation of Virtual Remote Center of Motion for Minimally Invasive Surgery

25: Annotation Framework for Recurring Appointments in Medical Applications using Augmented Reality

Team Members: Guanyu Song
Mentors: Alejandro Martin Gomez
Project Pages: Annotation Framework for Recurring Appointments in Medical Applications using Augmented Reality

26: Evaluation of Various Sensing Modalities for Accurate Measurement of Neck Flexion Angle during Thyroid and Ear Surgery

Team Members: Millan Patel, Zihao Lin
Mentors: Deepa Galaiya, Eric Formeister; Zihao (Danny) Lin; Russell Taylor
Project Pages: Evaluation of Various Sensing Modalities for Accurate Measurement of Neck Flexion Angle during Thyroid and Ear Surgery

27: VR Guided Surgery - Registration Pipelines

Team Members: Ruixing Liang, Hongchao Shu
Mentors: Max Li, Mathias Unberath, Russell Taylor
Project Pages: VR Guided Surgery - Registration Pipelines

28: Automatic Segmentation of Anatomical Structures for Core Decompression Procedures

Team Members: Mingxu Liu
Mentors: Ping-cheng Ku, Alejandro Martin-Gomez
Project Pages: Automatic Segmentation of Anatomical Structures for Core Decompression Procedures

29: Improving transparency of Galen Hand over Hand surgical robot

Team Members: Vishnu Kolal
Mentors: Adnan Munawar, Russell Taylor
Project Pages: Improving transparency of Galen Hand over Hand surgical robot