Lab Course / Praktikum: Project Management and Software Development for Medical Applications
by Prof. Nassir NavabTeam: Beatrice Lentes, Javier Esteban, Mahdi Saleh
Type: Master Practical Course Module IN2106
SWS: 6
Programs: Biomedical Computing (Master), Informatics (Master)
ECTS: 10 Credits
Preliminary Meeting ("Vorbesprechung"): Monday, February 5th - 18:00 to 18:300 in the CAMP Seminar Room 03.13.010
Further Meetings: See the schedule below.
This course in TUMOnline
The course will be conducted in English.
Announcements
- 10.04.2018:
Projects have been assigned. Please contact your supervisors asap.
- 09.04.2018: Project proposals published.
- 23.01.2018: Preliminary meeting date scheduled.
- 17.01.2018: Course website created.
Registration
Please register in the TUM matching system for the course registration. Keep in mind that your chances to be assigned to the course increase if you give it a higher rank in your choices. For further details about how the matching system works and its schedule please check this website.General content
This Lab Course is intended to teach the basic concepts of software project management and development for medical applications. You will be confronted with a brief introduction to software project management concepts such as requirement analysis, software design, coding guidelines and unified modeling language (UML). In addition, topics like software version control, deployment engineering and testing will be explored. You will be assigned a medical software project to apply the mentioned concepts in a real-life scenario with clinical, industrial or research partners.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 8-10 hours per week for a period of 3 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 the class coordinators, 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 Beatrice Lentes (beatrice.lentes@tum.de) as soon as possible.The deadline for proposal submission is Sunday, March 18th, 2018.
Prerequisites
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 CS lecture are assumed.Schedule
The schedule is preliminary and still subject to change. Please check the course website regularly!| Date - Time | Place | Topic | Conducted by | Materials |
|---|---|---|---|---|
| Monday, 05.02.2018 - 18:00-18:30 | 03.13.010 | Preliminary Meeting | All course tutors |  Preliminary Meeting Slides Project Examples |
| 09.02. to 14.02.2018 | TUM Matching platform | Registration |  Students | Matching FAQ |
| Monday, 09.04.2018 - 14:00-17:30 | 03.13.010 | Introduction, Project Announcements (attendance mandatory) | All course tutors | Introduction Slides |
| Monday, 09.04.2018 - until 23:59 | E-mail to Beatrice Lentes | Students required to indicate project preferences | Students | Student Application Template |
| Tuesday, 20.04.2018 | E-mail / course website | Project assignments published | Beatrice Lentes | |
| Monday, 16.04.2018 - 14:00-17:30 | 03.13.010 | Lecture I: Presentation Tips & Project Management, Lecture II: Software Engineering - UML | Beatrice, Javier | Presentation Rules and Tips Project Management UML |
| Monday, 30.04.2018 - 14:00-17:30 | 03.13.010 | Hands-on Presentation Techniques (attendance mandatory) | ||
| Monday, 07.05.2018 - 14:00-17:30 | 03.13.010 | Requirements (Kick Off) Presentations (attendance mandatory) | All course tutors | |
| Monday, 07.05.2018 - 23:59 | Link will be provided | Presentation slides upload (Kick Off) | Students | |
| Monday, 28.05.2018 - 14:00-16:00 | 03.13.010 | Lecture III: Documentation, Testing & Integration Strategy | Mahdi Saleh | |
| Monday, 11.06.2018 - 14:00-17:30 | 03.13.010 | Intermediate Presentations (attendance mandatory) | All course tutors | |
| Monday, 11.06.2018 - 23:59 | Link will be provided | Presentation slides upload (Intermdediate) | Students | |
 Monday, 09.07.2018 - 14:00-17:30 | 03.13.010 | Final Presentations Vol. 1 (attendance mandatory) | All course tutors | |
| Thursday, 12.07.2018 - 16:00-18:30 | 03.13.010 | Final Presentations Vol. 2 (attendance mandatory) | All course tutors | |
| Thursday, 12.07.2018 - 23:59 | Link will be provided | Presentation slides upload (Final) | Students |
Templates
CAMP presentation slides (PowerPoint) camp-tum-jhu-slides.potxCAMP presentation slides (Latex)
LaTeX_presentation_template.zipStudent application template
application.docxProject proposal template
proposal.docx
Presentation Schedules
Project Requirements Presentations
5 minutes slot for each presentation (plus 2 minutes for questions). We encourage students to practice their presentation w.r.t. pace and time. In order to train compliance with speaking times, your presentation will be interrupted after 5 minutes 30 seconds, no exceptions made. Show ScheduleIntermediate Presentations Schedule
7 minutes slot for each presentation (plus 3 minutes for questions). We encourage students to practice their presentation w.r.t. pace and time. In order to train compliance with speaking times, your presentation will be interrupted after 7 minutes 30 seconds, no exceptions made. Show ScheduleFinal Presentations Schedule
7 minutes slot for each presentation (plus optional an additional 4 min live demo and plus 3 minutes for questions). We encourage students to practice their presentation w.r.t. pace and time. In order to train compliance with speaking times, your presentation will be interrupted after 7 minutes 30 seconds (resp. 11 min 30 sec with demo), no exceptions made.| Day | Slot  | Student | Project Title |
|---|---|---|---|
| Thursday, 12.07.2018 | 15 Min. | Break | |
| Monday, 09.07.2018 | 15 Min. | Break | |
| Thursday, 12.07.2018 | 07 | Alok | Best of both worlds: Using Deep Learning and Variational Methods for Depth super-resolution |
| Thursday, 12.07.2018 | 06 | Izabela | DeepMRF |
| Monday, 09.07.2018 | 05 | Georgios | Facet Joint Segmentation in US 3D volumes |
| Thursday, 12.07.2018 | 05 | Arturo | Live Avatar of 3D Human Pose Tracking |
| Monday, 09.07.2018 | 04 | Henrique | Real-time 3D Human Pose Estimation from monocular RGB Camera |
| Thursday, 12.07.2018 | 04 | Sri | 3d Joint Motion Visualization for Sports or Physical Therapy |
| Monday, 09.07.2018 | 03 | Gloria | Optimization of Photonic Microstructures for Biofluid Analysis with Artificial Intelligence and Machine Learning |
| Thursday, 12.07.2018 | 03 | Rameshwara | Ultrasound Anatomy Classification |
| Monday, 09.07.2018 | 02 | Mohamad | Development of a Brain-Computer Interface for Neurorehabilitation of Stroke Patients |
| Thursday, 12.07.2018 | 02 | Afshar | VirtUS?: Virtual Ultrasound |
| Monday, 09.07.2018 | 01 | Matthieu | Real-time Gaze Estimation |
| Thursday, 12.07.2018 | 01 | Shyam | CASA: Carotid Artery Shear Assessment |
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 by 09.04.2018, 23.59 CEST. Use the Application Template provided under Templates.| Project ID | Student | Project Title | Supervisor | Additional Material |
|---|---|---|---|---|
| 01 | Izabela Horvath | DeepMRF? | Dr. Pedro Gomez | Project Description |
| 02 | Alok Verma | Best of both worlds: Using Deep Learning and Variational Methods for Depth super-resolution | Dr. Yvain Queau | Project Description |
| 03 | Sri Divya Vajapeyajula | 3d Joint Motion Visualization for Sports or Physical Therapy | Mahdi Saleh | Project Description |
| 04 | Arturo Diaz Coca | Live Avatar of 3D Human Pose Tracking | Mahdi Saleh | Project Description |
| 05 | Florian Hinterwimmer | Object Labeling and Segmentation in Clinical Multispectral Optoacoustic Images | Dominik Jüstel, Prof. Vasilis Ntziachristos | Project Description |
| 06 | Mohamad Atayi | Development of a Brain-Computer Interface for Neurorehabilitation of Stroke Patients | Stefan Ehrlich | Project Description |
| 07 | Henrique Rodrigues Orefice | Real-time 3D Human Pose Estimation from monocular RGB Camera | Felix Bork, Dr. Federico Tombari | Project Description |
| 08 | Rameshwara G. N. Prasad | Ultrasound Anatomy Classification | Walter Simson | Project Description |
| 09 | Shyam Srinivasan | CASA: Carotid Artery Shear Assessment | Dr. Guillaume Zahnd | Project Description |
| 12 | Matthieu Hongtao Zhang | Real-time Gaze Estimation | Benjamin Busam | Project Description |
| 14 | Gloria Zörnack | Optimization of Photonic Microstructures for Biofluid Analysis with Artificial Intelligence and Machine Learning | Lorenz Sykora | Project Description |
| 16 | Georgios Tsekas | Facet Joint Segmentation in US 3D volumes | Javier Esteban | Project Description |
| 17 | Afshar Kakaei | VirtUS: Virtual Ultrasound | Dr. Guillaume Zahnd | Project Description |
Passing Requirements
- Attendance and active participation in ALL presentation and hands-on meetings, in particular questions after each presentation.
- Presence during the lectures is not mandatory but highly recommended.
- Submission of all assignments in time.
- Presentation of your final assignment results.
- Upload of the presentation slides on the day of your presentation. Details will be provided in the introduction.
Literature/Resources
C++
- Online C++ API reference
- A good webpage on C++ including tutorials as well
Python
- Getting started with Python
Documenting your code
- Doxygen, a documentation system for C++, C, Java, Objective-C, Python, IDL (Corba and Microsoft flavors), Fortran, VHDL, PHP, C#, and to some extent D.
MS Visual Studio (2015)
- Can be downloaded from the TUM StudiSoft
Github
- Github, a freeware Github client for Mac/Windows
- A nice Github tutorial for beginners
- With your TUM account you can use the LRZ Gitlab!
Qt
Other useful tools and libraries
- OpenCV Documentation
- CMake
- Insight Segmentation and Registration Toolkit (ITK)
- Visualization Toolkit (VTK)
| TeachingForm | |
|---|---|
| Title: | Project Management and Software Development for Medical Applications |
| Professor: | Prof. Nassir Navab |
| Tutors: | Beatrice Lentes, Javier Esteban, Mahdi Saleh |
| Type: | Praktikum |
| Information: | 6 SWS, 10 ECTS Credits (Module IN2106) |
| Term: | 2018SoSe |
| Abstract: | |
