PMSD: Project Management and Software Development for Medical Applications (winter 2022/23)

About the course

Course offered by Prof. Nassir Navab
Team: Ardit Ramadani, Lennart Bastian, Tianyu Song, and Vanessa Gonzales Duque (Contact the course tutors)
Type: Praktikum (IN2106, IN4136)
SWS: 6
ECTS: 10 Credits

Announcements

Final presentations (as of 01.02.2023): Zoom link has been provided below, as well as instructions on uploading the presentation slides. The order of presentations is based on Student ID as indicated in the schedule table below.

Intermediate presentations (as of 05.12.2022): Zoom link has been provided below, as well as instructions on uploading the presentation slides. The order of presentations is based on Student ID as indicated in the schedule table below.

Requirements presentations (as of 03.11.2022): Zoom link has been provided below, as well as instructions on uploading the presentation's slides. The order of presentations is based on Student ID, so we will start from Student ID 01 until Student ID 20 in order.

Project assignment (as of 29.04.2022): The project assignment has been complete. Please check the projects below to find out which project has been assigned to you. We have tried really hard to fulfill everyone's preferences and include as many supervisors as possible, we hope everyone is happy with the assigned project. You are advised to contact your supervisor as soon as possible to introduce yourself and appoint a meeting to kick-off the project. Good luck!

Choice	Number of students	Percentage
1st choice assigned	13 students	65%
2nd choice assigned	6 students	30%
3rd choice assigned	1 students	5%

Tab. Percentage of assigned projects based on student's preferences

Project Number	Selected by
25	6 students
11 and 14	4 students
7, 12, 13 and 26	3 students

Tab. Top favorite projects (based on student's preferences)

Project announcements (as of 17.10.2022): Projects have been announced. Read through all project proposals and choose three favorite for which you write a short motivation and submit it to TUM Moodle by THURSDAY, 20.10.2022 at 23:59 Munich time. Upload your file as PDF named StudentID-FullName-choices.pdf (e.g. 05-ArditRamadani-choices).The form to apply can be found at "Downloads > Student project application template". We will assign projects once everyone has submitted their preferences, we will try use the combination that maximizes the number of first choices. Until now, only the students that have proposed their own project have been assigned on the table below (those projects are reserved to those students and cannot be chosen from the rest). Good luck!

Canceled class: Please note that the class on Monday, 17.10.2022 has been canceled. We will start the course with a block session on Tuesday (18.10.2022) from 09:00 - 12:00.

De-registration deadline: Friday, 30.09.2022, 23:59 Munich Time zone. All students who want to deregister the course without getting booked with a grade, please make sure to send all the course tutors an email for deregistration before the deadline.

Registration: Please use the form below to register for the course. We will collect all submissions and inform the students regarding their registration status mid-August.

Updates due to CoViD-19: All lectures and student presentations, until any further notice, are scheduled to be held online through Zoom. Make sure to have Zoom installed and ready for the First session. The details for joining the lecture and presentation sessions, students will be informed through email in timely manner at least one day before the session. Please also follow course's web-site and TUMOnline for any further announcements.

Schedule

For lecture sessions, presentation sessions and changes in the schedule, please also refer to TUMOnline.

Date	Time	Place	Topic	Conducted by	Materials
Monday, 25.07.2022	09:00 - 10:00	Zoom	Preliminary meeting ("Vorbesprechung")	Course tutors	L00_PreliminaryMeeting.pdf
Friday, 30.09.2022	23:59 CEST	Email	De-registration Deadline		To: All tutors
~~Monday, 17.10.2022 (canceled)~~	~~11:00 - 12:00~~	~~Zoom~~	~~Lecture 1: Introduction and Project Announcement~~	~~Course tutors~~
Tuesday, 18.10.2022	09:00 - 12:00	Meeting ID: 643 9514 7115 Passcode: PMSDWS22	Lecture 1: Introduction and Project Announcement Lecture 2: Presentation Tips and Project Management	Course tutors	L00_Introduction.pdf L01_PresentationTips.pdf L01_ProjectManagement.pdf
Thursday, 20.10.2022	23:59 CEST	TUM Moodle	Deadline to send project preferences	Seminar Participants
Monday, 07.11.2022	09:00 - 12:00	Meeting ID: 645 9393 1354 Passcode: PMSDWS22	Requirements Presentations	Seminar Participants	Order of presentation from Student ID 01 to 20
Tuesday, 08.11.2022	10:00 - 12:00	Meeting ID: 645 7360 7596 Passcode: PMSDWS22	Lecture 4: Documentation, Tests, Design Patterns & Integration Strategy	Course tutors	L04_SE.pdf
Tuesday, 15.11.2022 (new session)	09:00 - 10:00	Meeting ID: 623 2053 0294 Passcode: PMSDWS22	Lecture 3: UML	Course tutors	L03_UML.pdf
Monday, 12.12.2022	09:00 - 12:00	Meeting ID: 623 5289 2272 Passcode: PMSDWS22	Intermediate Presentations Part I	Seminar Participants	Order of presentation from Student ID 01 to 10
Tuesday, 13.12.2022	09:00 - 12:00	Meeting ID: 622 9044 4123 Passcode: PMSDWS22	Intermediate Presentations Part II	Seminar Participants	Order of presentation from Student ID 11 to 20
Monday, 06.02.2022	09:00 - 12:00	Meeting ID: 615 9170 7497 Passcode: PMSDWS22	Final Presentations Part I	Seminar Participants	Order of presentation from Student ID 11 to 20
Tuesday, 07.02.2022	09:00 - 12:00	Meeting ID: 659 6078 1961 Passcode: PMSDWS22	Final Presentations Part II	Seminar Participants	Order of presentation from Student ID 01 to 10

Available Projects

Projects will be announced in due time and presented during the Introductory meeting. Please communicate a selection of 3 choices, each with an explanation (ca. 5 sentences) for why you want to work on this project and how you meet the requirements specified in the project proposal. Use the Student Application Template provided in the Download section.

ID	Title	Supervisor	Student	PDF
1	Deep Learning-based Tool for Automated Lymph Node Detection in Lymphoma Patients	Simone Bendazzoli and Mehdi Astaraki	Karine	Bendazzoli_Astaraki_DL-Tool-for-Automated-Lymph-Node-Detection-ASSIGNED.pdf
2	Graph-Learning in Resting-state Functional MRI	Stephan Wunderlich	Agata	Wunderlich_Graph-Learning-in-Resting-state-Functional-MRI-ASSIGNED.pdf
3	Indoor Mapping of Devices using QR Code and Geolocation	Dr. Stephan Dörfler	Hussain	Auguris_Indoor-Mapping-Medical-Devices.pdf
4	Object Recognition for Medical Devices	Dr. Stephan Dörfler	Niels	Auguris_Object-Recognition-for-Medical-Devices.pdf
5	Name Entity Recognition of Patients in MDOP	Dr. Stephan Dörfler	Amna	Auguris_Patient-Name-Detection.pdf
6	Robotic Ultrasound Calibration	Yuan Bi and Zhongliang Jiang		Bi_Jiang_Robotic-Ultrasound-Calibration.pdf
7	Real-time movement data acquisition and analysis software for patients with DBS for movement disorders	Mohamad Atayi	Julia	CereGate_Movement-data-acquisition-and-analysis-software-for-movement-disorders.pdf
8	Development of a preoperative plan plugin for fracture and deformity correction treated with the iFixation exapodalic platform	Fernando Garnica	Deniz	Garnica_Preoperative-Plan-Plugin-for-Fracture-and-Deformity.pdf
9	Patientflow: a WebApp-based patient guidance and analysis system	Dr. Joshua Gawlitza	Huong	Gawlitza_Patientflow-InformMe.pdf
10	DAF3D implementation in MONAI	Vanessa Gonzalez Duque		Gonzalez_DAF3D-implementation-in-MONAI.pdf
11	Quicknat implementation in MONAI	Vanessa Gonzalez Duque	Inés del Val	Gonzalez_Quicknat-implementation-in-MONAI.pdf
12	CVAT for Medical Imaging	Mickael Tardy	Bikem	Hera-MI_CVAT-for-Medical-Imaging.pdf
13	Synthetic data for unleashed machine learning	Mickael Tardy	Maitri	Hera-MI_Synthetic-data-for-unleashed-ML.pdf
14	MIMIC-CXR Structured Reporting Dataset	Matthias Keicher	Ömer Alp	Keicher_MIMIC-CXR-Structured-Reporting-Dataset.pdf
15	Reinforcement-Learning based Catheter Trajectory Generation for Bioelectric Navigation	Heiko Maier	Dilara	Maier_Reinforcement-Learning-based-Catheter-Trajectory-Generation-for-Bioelectric-Navigation.pdf
16	Unity-based VR Application for Medical Data Exploration	Sasan Matinfar		Matinfar_Unity-based-VR-Application-for-Medical-data-exploration.pdf
17	Development of a Brain Computer Interface with Virtual Reality Neurofeedback	Dr. Sebastian Herberger	Marta	Mentalab_Development-of-a-Brain-Computer-Interface-with-Virtual-Reality-Neurofeedback.pdf
18	MaLibU: Open-Source Math Utility Library for Medical Augmented Reality Unity Applications	Tianyu Song, Kevin Yu, Michael Sommersperger, Alexander Winkler		NARVIS_MaLibU.pdf
19	Motion Compensation for EM Catheter Tracking in Pre-operative MR/CT Images	Ardit Ramadani	Ha Young	Ramadani_Motion-compensation-for-EM-Tracker.pdf
20	Live Digital Human Generation using Dense Pose	Mahdi Saleh	Ata Jadid	Saleh_Live-Digital-Human-Generation-using-Dense-Pose.pdf
21	Volume Fusion for 4D Intraoperative Optical Coherence Tomography	Michael Sommersperger		Sommersperger_Volume-Fusion-for-4D-IOCT.pdf
22	Breathing Compensation for Autonomous Robotic Ultrasound Abdominal Sweep	Yordanka Velikova	Amr Abu	Velikova_Breathing-Compensation-for-Autonomous-Robotic-Ultrasound.pdf
23	Robotic Ultrasound Catheter Tracking based on Intermediate Ultrasound Representations	Yordanka Velikova		Velikova_Robotic-Ultrasound-Catheter-Tracking.pdf
24	4D Heart model visualization	Ching-En Lin, Sam Wray	Kristina	Virtonomy_4D-Heart-model-visualization.pdf
25	Big data in cardiac medical imaging	Diogo Ferreira de Almeida, Moritz Jung	Yijin	Virtonomy_Big-data-in-cardiac-medical-imaging.pdf
26	Point cloud registration for anatomical measurements	Diogo Ferreira de Almeida, Ching- En Lin	Malek	Virtonomy_Point-cloud-registration-for-anatomical-measurements.pdf
27	AR Visualization and Interaction of Patient data in Intensive Care Unit with Hololens 2	Kai Wu		Wu_AR-Visualization-and-Interaction-of-Patient-Data-in-ICU-with-Hololens2.pdf

Students

ID	Name	ID	Name	ID	Name	ID	Name	ID	Name
1	Hussain S.	6	Julia D.	11	Karine L.	16	Ömer Alp Ş.	21	Cagatay A.^-
2	Huong N.	7	Kristina D.	12	Maitri B.	17	Dilara K.	22	Marta G.^-
3	Ha Young K.	8	Agata L.	13	Amna G.	18	Amr Abu Z.	23	Pascual T.^-
4	Marta H.	9	Ata Jadid A.	14	Yijin J.	19	Inés del Val G.	24	Chengzhi S.^-
5	Malek A.	10	Niels H.	15	Deniz I.	20	Bikem Ç.

Prerequisites and Registration

This course requires basic knowledge of C++ or similar OO programming language. The concepts of OO programming and other concepts as conducted in the Introduction to Computer Science lecture are assumed.Registration through the TUM Matching System is mandatory. Your chances to be assigned to the course increase if you give the course a higher rank in your choices. If you already have a potential project, notify the course tutors via e-mail as soon as possible. This increases your chances to be assigned to the course, but you have to register through the matching system in any case. For further details about how the matching system works and its schedule please check the documentation.

Project Proposals

In this lab course, students work on clinical software projects and find solutions for problems in the field of medical applications. The student's workload should be around 10-14 hours per week for a period of 3 - 4 months on the assigned project (10 ECTS course).

Each project is expected to have one contact person (supervisor) who should be available for regular updates or if the student needs any help. In addition, the supervisors are kindly invited to participate in the student presentations (Requirements, Intermediate, Final) taking place at the CAMP chair. Each project supervisor will decide on 50% of the grade based on the student’s performance in the project. The other 50% will be decided upon by lecturers, based on the quality of project management and presentation skills of the student.The project proposal should give a short introduction into the context and describe the most important aspects and expected outcome of the project. Furthermore it should clearly state the required (and optional) skills (programming language, experience with certain libraries etc.).

If you have a suitable project, preferably with a clinical or industrial partner, you are kindly invited to fill out the project proposal template and send it to the course tutors. The deadline for proposal submission is beginning of the lecture period for the Winter Semester 2022-23.