Lab Course / Praktikum: Project Management and Software Development for Medical Applications
by Prof. Nassir NavabTeam: Beatrice Demiray, Javier Esteban, Hendrik Burwinkel
Type: Master Practical Course Module IN2106
SWS: 6
Programs: Biomedical Computing (Master), Informatics (Master)
ECTS: 10 Credits
Preliminary Meeting ("Vorbesprechung"): Monday, 25.06. at 18:30 - 19:00 CEST in the CAMP Seminar Room 03.13.010
Further Meetings: See the schedule below.
The course will be conducted in English.
Announcements
- !NEW! 12.06.2018 Preliminary Meeting scheduled!
- 10.06.2018: Course website created.
Registration
Registration through the TUM matching system is mandatory. Keep in mind that your chances to be assigned to the course increase if you give it 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 in any case you have to register through the matching system. 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 10-14 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 Demiray () as soon as possible.The deadline for proposal submission is Sunday, September 9th, 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 CE(S)T | Place | Topic | Conducted by | Materials |
|---|---|---|---|---|
| Monday, 25.06.2018 - 18:30 - 19:00 | 03.13.010 | Preliminary Meeting | All course tutors | |
| 29.06. to 04.07.18 | TUM Matching platform | Registration |  Students | Matching FAQ |
| Thursday, 18.10.2018 - 15:00-17:30 | 03.13.010 | Introduction, Project Announcements (attendance mandatory) | All course tutors | |
| Thursday, 18.10.2018 - until 23:59 | E-mail to Beatrice Demiray | Students required to indicate project preferences | Students | Student Application Template |
| Monday, 22.10.2018 | E-mail / course website | Project assignments published | Beatrice Demiray | |
| Thursday, 25.10.2018 - 14:00-17:30 | 03.13.010 | Lecture I: Presentation Tips & Project Management, Lecture II: Software Engineering - UML | Hendrik Burwinkel, Beatrice Demiray |  Presentation Rules and Tips Project Management UML |
| Monday, 29.10.2018 - 10:00-12:00 | 03.13.010 | Presentation Training (attendance mandatory) | Marcus Vollrath, Beatrice Demiray | Slides |
| Monday, 05.11.2018 - 09:00-12:00 | 03.13.010 | Requirements (Kick Off) Presentations (attendance mandatory) | All course tutors | |
| Monday, 05.11.2018 - 23:59 | Link will be provided | Presentation slides upload (Kick Off) | Students | |
| Thursday, 08.11.2018 - 13:00-14:30 | 03.13.010 | Lecture III: Documentation, Testing & Integration Strategy | Javier Esteban | Documentation, Testing & Integration Strategy |
 Thursday, 13.12.2018 - 14:00-18:00 | Big Auditorium @ TranslaTUM (ground floor) | Intermediate Presentations Vol. 1 (attendance mandatory) | All course tutors | |
| Friday, 14.12.2018 - 10:00-14:00 | Small Auditorium @ TranslaTUM (ground floor) | Intermediate Presentations Vol. 2 (attendance mandatory) | All course tutors | |
| Friday, 14.12.2018 - 23:59 | Link will be provided | Presentation slides upload (Intermdediate) | Students | |
| Monday, 04.02.2019 - 10:00-12:30 | 03.13.010 | Final Presentations Vol. 1 (attendance mandatory) | All course tutors | |
| Thursday, 07.02.2019 - 14:00-17:30 | 03.13.010 | Final Presentations Vol. 2 (attendance mandatory) | All course tutors | |
| Thursday, 07.02.2019 - 23:59 | Link will be provided | Presentation slides upload (Final) | Students | |
Presentation Schedules
Project Requirements Presentations (Kick-Off)
5 minutes slot for each presentation (plus 2 minutes for questions). The group presentation has an 8 minute slot. 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. Make sure to comply with the TUM Code of Conduct (see Download) and the rules for this course (slides from the first lecture). Show ScheduleIntermediate Presentations
7 minutes slot for each presentation (plus 2 minutes for questions). The group presentation has an 11 minute slot. 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. Make sure to comply with the TUM Code of Conduct (see Download) and the rules for this course (slides from the first lecture). Thursday 13.12.2018: Show ScheduleFriday: 14.12.2018 Show Schedule
Final Presentations
7 minutes slot for each presentation (plus 3 minutes for questions). The group presentation has an 11 minute slot. 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. Make sure to comply with the TUM Code of Conduct (see Download) and the rules for this course (slides from the first lecture). Monday 04.02.2019: Show ScheduleThursday: 07.02.2019 Show Schedule
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 18.10.2018 - 23:59 CEST. Use the Student Application Template provided under Download.| Project ID | Student  | Project Title | Supervisor | Additional Material |
|---|---|---|---|---|
| 13 | Aashay Tinaikar | Ultrasound Confidence Map | Guillaume Zahnd | Project Description |
| 04 | Adria Font Calvarons | Semi-Automatic Cell Labelling Tool | Mario Emmenlauer | Project Description |
| 15 | Aidana Massalimova | DeepFormer SUPRA Integration | Walter Simson | Project Description |
| 21 | Amir Nourinia | Fully Automatic Fusion of large 3D Microscopy Volumes | Mario Emmenlauer | Project Description |
| 08 | Arian Mehrfad, Yordanka Velikova, Cristina Serrano Gonzalez | Micro-manipulation – From industrial to cell-robots | Javier Esteban | Project Description |
| 18 | Awais Shafique | Adaptation of Weakly-supervised Convolutional Neural Networks Registration for Neurosurgical Setting | Julia Rackerseder | Project Description |
| 17 | Berk Olcay | Mobile test for spatial memory | Virginia Flanagin | Project Description |
| 26 | Christina Bukas | Brachytherapy Planning Software | Thomas Wendler | Project Description |
| 27 | Christopher Watanabe | Monte Carlo simulations for Brachytherapy | Thomas Wendler | Project Description |
| 01 | Courtney Restivo | Quantification of Tissue Oxygenation Saturation with MSOT using Deep Learning | Ivan Olefir | Project Description |
| 30 | Desislava Dimova | Dose Prediction Software for SIRT | Thomas Wendler | Project Description |
| 05 | Eduardo Prado | Diabetes App | Stefan Christoph Kofler | Project Description |
| 25 | Granit Bimbashi | 3D Ultrasound for Thyroid Imaging | Thomas Wendler | Project Description |
| 19 | Hooriya Anam | Utilizing Confidence Maps for Accurate 3D Brain Image Registration | Julia Rackerseder | Project Description |
| 07 | Hyunjun Jung | Spatio-Temporal Depth Estimation in Real-Time | Benjamin Busam | Project Description |
| 11 | Ivan Pavlov | Deep Field: Ultrasound simulation via deep learning | Guillaume Zahnd | Project Description |
| 02 | Javier Danilo Coronel Baracaldo | Deep learning-based tumor detection in 3D scans | Oliver Schoppe | Project Description |
| 20 | Jorge Mario Guerra Gonzalez | Implementation of Landmark free 3D US to MRI Registration Initialization | Julia Rackerseder | Project Description |
| 06 | Julio Alberto Oscanoa Aida | Accelerating water-fat MRI using compressed sensing | Stefan Ruschke, Dimitrios Karampinos | Project Description |
| 24 | Khac Thanh-An Le | Blood Vessel Quantification in MRI | Beatrice Demiray | Project Description |
| 12 | Maria Margarida Regateiro Machado e Costa | Carotid Wall Shear Stress | Guillaume Zahnd | Project Description |
| 16 | Mariya Stankevich | Proteins Colonies Illumination and Behavior Analyzing Software | Andre Stiel | Project Description |
| 23 | Michael Wengler | Arivis Vision4D plugin for automatic vessel segmentation in LSFM stacks | Beatrice Demiray | Project Description |
| 14 | Navdar Karabulut | DeepFormer Data Analysis Tool | Walter Simson | Project Description |
| 09 | Rahman Md Salman | Cloud Service for Human Pose Estimation | Ashkan Khakzar, Raveekiat Singhaphandu, Angelica Crone | Project Description |
| 31 | Rajat Chhabra | Development of a software solution for recognizing motion in various video sources deployed in a clinical environment | Claudia Mattes | Project Description |
| 10 | Stefan Haninger | Ray Tracing with RT Cores for Forward Modeling in Medical X-ray Computed Tomography | Tobias Lasser | Project Description |
| 03 | Tom Nuno Wolf | Computer-aided survival, grading predicton and segmentaton of soft tissue sarcomas in MRI | Fernando Navarro, Jan Peeken | Project Description |
Download
- TUM Informatics Student Code of Conduct
- TUM Citation Guide
- CAMP presentation slides (PowerPoint)
camp-tum-jhu-slides.potx
- CAMP presentation slides (Latex) LaTeX_presentation_template.zip
- Student application template application.docx
- Project proposal template proposal.docx
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 Demiray, Javier Esteban, Hendrik Burwinkel |
| Type: | Praktikum |
| Information: | 6 SWS, 10 ECTS Credits (Module IN2106) |
| Term: | 2018WiSe |
| Abstract: | |
