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Advanced Computer-Integrated Surgery (CIS II)

CIS II (601.456/496/656/356) is a projects course 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 under the supervision of the instructor and clinical end users. Grades are based both on the project and on classroom recitations. The only difference between the undergraduate versions (601.456/496) and the graduate version (601.656) of this course is the level of project undertaken. Typically, 601.656 projects require a greater degree of mathematical, image processing, or modeling background. Students wishing to attend the weekly lectures as a 1-credit seminar should sign up for 601.356.

Instructor: Russell H. Taylor (rht@jhu.edu)
Course number: 601.456/601.496/601.656/601.356 (formerly 600.446/646/346)
- Note: 601.496 is identical to 601.456, except students must be members of a 3 person team. This option is provided for CS undergrads seeking to satisfy the “team” degree requirement.
Meeting times: Tuesdays and Thursdays 1:30-2:45
Meeting room:
- Tuesdays and Thursdays: Hackerman Hall Room B17 (basement auditorium)
Prerequisite: CIS I or permission of instructor.
Piazza page (for communication): https://piazza.com/jhu/spring2022/cs601456496656/home
- Self signup link: https://piazza.com/jhu/spring2022/cs601456496656
Blackboard Link
Zoom link: Zoom Link
- For passcode, see the the course content in the Blackboard Link
Teaching Assistant: Yixuan Wu
- Email: yixuan_wu@jhu.edu
- Office Address: Hackerman 137
- TA office Hours: By appointment

Whiting School of Engineering Responsible Conduct of Research Training Policy

Resources

Personal Well-Being

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”.

Academic Resources

* Resources for Students from the JHU Office of Academic Support

Projects in 2022

Projects in Prior Years

Schedule for Spring 2022

January 25
- Introduction and organization
- Non-disclosure agreement
- Presentation of project ideas
  - Can Kocabalkanli (idea 18) - Motion Compensation and Evaluation for 3D Head Reconstruction
  - Deepa Galaiya (idea 29 - 32) - Force Sensing Forceps for Cochlear Implant Surgery and Hand Control Interface for Galen Tool Holder; Force Sensing Drill Experimental Testing and Analysis; Evaluation of Various Sensing Modalities for Accurate Measurement of Neck Flexion Angle during Thyroid and Ear Surgery; Automatic Assessment of Surgical Ergonomics
  - Adnan Munawar (idea 15) - Surgical Skill Analysis with Virtual Reality
  - Max Li (idea 14, 16) - Surgical Phase Recognition using Deep Learning; Virtual Reality Guided Skull-base Surgery
January 27
- Presentation of project ideas
  - Seth Billings (idea 21) - Multisensory Navigational Aid for Visual Prosthesis Users
  - Jim Fackler (idea 17) - Controlled-Monitored-Therapeutic VR environment for post-surgical pediatric critical care
  - Balazs Vagvolgyi (idea 26 - 28) - Estimation of Light Exposure in Vitreoretinal Eye Surgery; Vision Guided Mosquito Dissection for the Production of Malaria Vaccine; Vision-Based Automatic Calibration of Mosquito Dissection System for the Production of Malaria Vaccine
  - Emad Boctor (idea 36 - 39) - Patch ultrasound user interface; Wireless active echo; Correlation between MRI, pathology, and ultrasound tomography images of prostate; Co-robotic Ultrasound Imaging of Breast Assisting Mammography
  - David Usevitch (idea 1-4): FEA and Workspace Analysis of Loop Snare; Actuation Design for Loop Snare Operation in Eye Surgery; Miniature Camera and Light Module Design; Low-Cost Intramedullary Hole Estimation
  - Joshua Liu (idea 7-8): Laser Milling CAD/CAM for Enclosure of Neuroplastic Device in Cranial Implant; Development of a Wearable Intracranial Pressure Monitoring Device
  - Ali Ebrahimi (idea 24): Tele-operation Control of a High Dexterity Robot for Vitreoretinal Surgery
February 1
- Presentation of project ideas
  - Laeben Lester (idea 59, 60)
  - Robin Yang (idea 40, 41)
  - Alejandro Martin Gomez & Adam Margalit (idea 5, 6, 19, 20)
  - Peter Kazanzides (idea 22, 23, 58)
  - Jeeun Kang (idea 57)
  - Yihao Liu (idea 33)
  - Kefan Song (idea 34)
  - Yanzhou Wang (idea 35)
February 3
- Presentation of project ideas
  - Galen Robotics Group (idea 11 - 13)
  - Dimitri Lezcano (idea 9, 10)
  - Benjamin Killeen (idea 42)
  - Daniel Rhee and Swaroop Vedula (idea 43 - 47)
  - Ameen Amanian (idea 50)
  - Axel Krieger (idea 51)
  - Jasmine Cho (idea 52)
  - Yuxiang Gao (idea 61)
February 8
- Presentation of project ideas (if needed)
- Plan Presentation (Project 1: Vision Based Calibration of Mosquito Dissection System)
- Plan Presentation (Project 2: Gaze Tracking Enabled Automatic Error Detection)
- Plan Presentation (Project 3: Automated Segmentation and Registration for Eustachian Tube Disfunction)
February 10
- Plan Presentation (Project 4: In Situ Needle Path Adjustment and Trajectory Optimization)
- Plan Presentation (Project 5: Surgical Phase Recognition using Deep Learning)
- Plan Presentation (Project 6: Vision Guided Mosquito Dissection for the Production of Malaria Vaccine)
- Plan Presentation (Project 7: Co-robotic Ultrasound Imaging of Breast Assisting Mammography)
February 15
- Plan Presentation (Project 8: Surgical Skill Analysis with Virtual Reality)
- Plan Presentation (Project 9: Virtual Reality Guided Skull-base Surgery)
- Plan Presentation (Project 10: Multisensory Navigational Aid for Visual Prosthesis Users)
- Plan Presentation (Project 11: 3D Segmentation of Hard and Soft Tissue for Simulating X-ray Image Formation with Deep Learning)
February 17
- Plan Presentation (Project 12: Patch ultrasound user interface)
- Plan Presentation (Project 13: Development of a Wearable Intracranial Pressure Monitoring Device)
- Plan Presentation (Project 14: Motion Compensation and Evaluation for 3D Head Reconstruction)
- Plan Presentation (Project 15: Building a Workflow for Cooperatively Controlled Robotic Mandibular Surgery)
February 22
- Plan Presentation (Project 16: VR Guided Surgery – SDF Based Guidance and Safety)
- Plan Presentation (Project 17: Actuation Design for Loop Snare Operation in Eye Surgery)
- Plan Presentation (Project 18: Automatic Mechanical Ventilation Control (AMVC))
- Plan Presentation (Project 19: Glioma Classification and Biopsy Guidance with Multimodal MRI and Deep Learning)
February 24
- Plan Presentation (Project 20: Mixed Reality Surgical Team Training)
- Plan Presentation (Project 21: Magnetic PillCam for Medical Diagnosis)
- Plan Presentation (Project 22: Tele-operation Control of a High Dexterity Robot for Vitreoretinal Surgery)
- Plan Presentation (Project 23: Photoacoustic image based intro-operative surgical guidance system in a da vinci surgical robot platform)
March 1
- Approved Project Plans Due
  - By this time, Your initial Wiki pages must also be completed
- Plan Presentation (Project 24: Evaluation of Virtual Remote Center of Motion for Minimally Invasive Surgery)
- Plan Presentation (Project 26: Evaluation of Various Sensing Modalities for Accurate Measurement of Neck Flexion Angle during Thyroid and Ear Surgery)
- Plan Presentation (Project 27: VR Guided Surgery - Registration Pipelines)
March 3
- Plan Presentation (Project 25: Annotation Framework for Recurring Appointments in Medical Applications using Augmented Reality)
- Plan presentation (Project 28: Automatic Segmentation of Anatomical Structures for Core Decompression Procedures )
- Plan presentation (Project 29: Improving transparency of Galen Hand over Hand surgical robot)
- Plan presentation (Project 30: Force Sensing Forceps for Cochlear Implant Surgery and Hand Control Interface for Galen Tool Holder)
March 8
- Background reading presentations
- Project 1: Vision-Based Automatic Calibration of Mosquito Dissection System for the Production of Malaria Vaccine
- Project 2: Gaze Tracking Enabled Automatic Robot Error Detection
- Project 3: Automated Segmentation and Registration Platform for Eustachian Tube Dysfunction
- Project 4: In Situ Needle Path Adjustment and Trajectory Optimization
- Project 5: Surgical Phase Recognition using Deep Learning
March 10
- Background reading presentations
- Project 6: Vision Guided Mosquito Dissection for the Production of Malaria Vaccine
- Project 7: Co-Robotic Ultrasound Imaging of Breast Assisting Mammography
- Project 8: Surgical Skill Analysis with Virtual Reality
- Project 9: Virtual Reality Guided Skull-base Surgery
- Project 10: Multisensory Navigational Aid for Visual Prosthesis Users
March 15
- Checkpoint presentations
- Project 11: 3D Segmentation of Hard and Soft Tissue for Simulating X-ray Image Formation with Deep Learning
- Project 12: Patch ultrasound
- Project 13: Development of a Wearable Intracranial Pressure Monitoring Device
March 17
- Checkpoint presentations
- Project 14: Motion Compensation and Evaluation for 3D Head Reconstruction
- Project 15: Building a Workflow for Cooperatively Controlled Robotic Mandibular Surgery
- Project 16: VR Guided SurgerySDF based guidance and safety
- Project 17: Actuation Design for Loop Snare Operation in Eye Surgery
March 22
- Spring break
March 24
- Spring break
March 29
- Checkpoint presentations
- Project 18: Automatic Mechanical Ventilation Control (AMVC)
- Project 19: Glioma Classification and Biopsy Guidance with Multimodal MRI and Deep Learning
- Project 20: Mixed Reality Surgical Team Training
- Project 21: Magnetic PillCam for Medical Diagnosis
March 31
- Checkpoint presentations
- Project 22: Tele-operation Control of a High Dexterity Robot for Vitreoretinal Surgery
- Project 23: Photoacoustic image based intro-operative surgical guidance system in a da vinci surgical robot platform
- Project 24: Evaluation of Virtual Remote Center of Motion for Minimally Invasive Surgery
- Project 25: Annotation Framework for Recurring Appointments in Medical Applications using Augmented Reality
April 5
All background reading reports due
- Checkpoint presentations
- Project 26: Evaluation of Various Sensing Modalities for Accurate Measurement of Neck Flexion Angle during Thyroid and Ear Surgery
- Project 27: VR Guided Surgery - Registration Pipelines
- Project 29: Improving transparency of Galen Hand over Hand surgical robot
- Project 28: Automatic Segmentation of Anatomical Structures for Core Decompression Procedures
April 7
- Checkpoint presentations
- Project 30: Force Sensing Forceps for Cochlear Implant Surgery and Hand Control Interface for Galen Tool Holder
- Project 1: Vision-Based Automatic Calibration of Mosquito Dissection System for the Production of Malaria Vaccine
- Project 2: Gaze Tracking Enabled Automatic Robot Error Detection
- Project 3: Automated Segmentation and Registration Platform for Eustachian Tube Dysfunction
April 12
- Checkpoint presentations
- Project 4: In Situ Needle Path Adjustment and Trajectory Optimization
- Project 5: Surgical Phase Recognition using Deep Learning
- Project 6: Vision Guided Mosquito Dissection for the Production of Malaria Vaccine
- Project 7: Co-Robotic Ultrasound Imaging of Breast Assisting Mammography
April 14
- Checkpoint presentations
- Project 8: Surgical Skill Analysis with Virtual Reality
- Project 9: Virtual Reality Guided Skull-base Surgery
- Project 10: Multisensory Navigational Aid for Visual Prosthesis Users
April 19
- Background reading presentations
- Project 11: 3D Segmentation of Hard and Soft Tissue for Simulating X-ray Image Formation with Deep Learning
- Project 12: Patch ultrasound
- Project 13: Development of a Wearable Intracranial Pressure Monitoring Device
- Project 14: Motion Compensation and Evaluation for 3D Head Reconstruction
- Project 15: Building a Workflow for Cooperatively Controlled Robotic Mandibular Surgery
April 21
- Background reading presentations
- Project 16: VR Guided Surgery SDF based guidance and safety
- Project 17: Actuation Design for Loop Snare Operation in Eye Surgery
- Project 18: Automatic Mechanical Ventilation Control (AMVC)
- Project 19: Glioma Classification and Biopsy Guidance with Multimodal MRI and Deep Learning
- Project 20: Mixed Reality Surgical Team Training
April 26
- Background reading presentations
- Project 21: Magnetic PillCam for Medical Diagnosis
- Project 22: Tele-operation Control of a High Dexterity Robot for Vitreoretinal Surgery
- Project 23: Photoacoustic image based intro-operative surgical guidance system in a da vinci surgical robot platform
- Project 24: Evaluation of Virtual Remote Center of Motion for Minimally Invasive Surgery
- Project 25: Annotation Framework for Recurring Appointments in Medical Applications using Augmented Reality
April 28 (last class)
- Background reading presentations
- Project 26: Evaluation of Various Sensing Modalities for Accurate Measurement of Neck Flexion Angle during Thyroid and Ear Surgery
- Project 27: VR Guided Surgery - Registration Pipelines
- Project 28: Automatic Segmentation of Anatomical Structures for Core Decompression Procedures
- Project 29: Improving transparency of Galen Hand over Hand surgical robot
- Project 30: Force Sensing Forceps for Cochlear Implant Surgery and Hand Control Interface for Galen Tool Holder
May 01
- Final reports due at 6 PM EDT
- Adjustments are allowed till 11:59 pm May 9th EDT. Notify Prof. Taylor and Yixuan by email and resubmit your report on Blackboard.
May 11
- Project mentors' reports due
May 16
- Posters due at 6 PM EDT
- Email your poster to Yixuan in .png format
May 17 (Final Exam Date)
- Final presentations (2:00 pm - 5:00 pm EDT)
- We are using Gather Town for presentations

courses/456.txt · Last modified: 2022/04/26 18:29 by ywu115