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
TUMOnline: Link
Preliminary Meeting ("Vorbesprechung"): Monday, 04.12.2019 18:00 in 03.13.010. Slides
Further Meetings: See the schedule below.
The course will be conducted in English.
Announcements
- 14.01.2019: Preliminary Meeting scheduled: Monday, 04/Feb/2019 18:00 in 03.13.010.
- 14.01.2019: 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, March 24th, 2019.
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 |
|---|---|---|---|---|
 Tue, 23.04.2019 11:30 - 14:00 | 03.13.010 | Introduction, Project Announcements |  Introduction and Project Announcements | |
| Thu, 25.04.2019 12:00 - 14:30 | 03.13.010 | Lecture I, Lecture II | Presentation Rules and Tips Project Management UML | |
| Thu, 25.04.2019 until 23:59 | E-mail to | Students required to indicate project preferences | ||
| Mon, 29.04.2019 | E-mail / course website | Project assignments published | ||
| Tue, 30.04.2019 11:30 - 14:00 | 03.13.010 | Presentation Training | Workshop Slides | |
| Tue, 07.05.2019 10:00 - 14:00 | 03.13.010 | Requirements Presentations | ||
| Tue, 14.05.2019 12:00 - 14:00 | 03.13.010 | Lecture III | ||
| Tue, 04.06.2019 10:00 - 14:00 | Right Forum @ TranslaTUM (ground floor) | Intermediate Presentations Vol. 1 | ||
| Fri, 07.06.2019 10:00 - 14:00 | Right Forum @ TranslaTUM (ground floor) | Intermediate Presentations Vol. 2 | ||
| Tue, 23.07.2019 10:00 - 14:00 | Left Forum @ TranslaTUM (ground floor) | FSMPI Evaluation (15 min); Final Presentations Vol. 1 | ||
| Thu, 25.07.2019 10:00 - 14:00 | Seminar Room 522.0.44 @ TranslaTUM (ground floor) | Final Presentations Vol. 2 | ||
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). Show ScheduleFinal Presentations
7 minutes slot for each presentation (plus 3 minutes for questions). Additionally, you can use 4 extra minutes to show a live demo of your project. 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). Show ScheduleAvailable 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 Thursday, 25.04.2019 - 23:59 CEST. Use the Student Application Template provided under Download. Project ID  | Student | Project Title | Supervisor | Additional Material |
|---|---|---|---|---|
| 01 | Nikola Budjakoski | Ultrasound-Guided Kyphoplasty Planning Via Optical-See Through Head-Mounted Displays. | Alejandro Martin | Project Description |
| 02 | Francesca De Benetti | Kernel-based Dosimetry for Brachytherapy | Thomas Wendler | Project Description |
| 03 | Asli Ergin | Pose Dependent Human Image Generation | Manuel Nickel | Project Description |
| 04 | Andrea Escartin & Hossam Abdelhamid | Micro-Manipulation | Javier Esteban | Project Description |
| 05 | Ayse Evren | Sinogram-based Interpolation Strategies for Incomplete Trajectories in X-ray Computed Tomography | Fabien Bauer, Tolga Birdal | Project Description |
| 06 | Mert Asim | Ultrasound Simulation Framework | Walter Simson | Project Description |
| 07 | Muhammad Naeem | DeepMicroscope Interpretation Framework | Magda Paschali | Project Description |
| 08 | Miguel Trasobares | Sensor Fusion Framework for precise US-probe Pose Tracking in 3D US-Compounding | Walter Simson, Patrick Ruhkamp | Project Description |
| 09 | Anna Zapaishchykova | 3D Freehand Ultrasound Spatial Calibration | Beatrice Demiray | Project Description |
| 10 | Miguel Hoyos | Smart Augmentation of Laparoscopic Images | Javier Esteban | Project Description |
| 11 | Fabian Gröger | Implementation of a Robotic-Framework for Reinforcement Learning on Ultrasound. | Javier Esteban | Project Description |
| 12 | Patricia Garoz | Compact Neural Networks with Weight/Structural Pruning | Magda Paschali | Project Description |
| 13 | Wai Yan Fok | Peripheral Nerve Examination Tool | Oliver Zettinig | Project Description |
| 14 | Available | Collimator Design Platform | Thomas Wendler | Project Description |
| 15 | Christina Weber | Dose Probe Design Platform | Thomas Wendler | Project Description |
| 16 | Available | Monte Carlo simulations for Brachytherapy | Thomas Wendler | Project Description |
| 17 | Yan Chi Chan | Automatic Segmentation of Spine Lesions in Cancer Patients | Thomas Wendler, Magda Paschali | Project Description |
| 18 | Available | Clinical User Interface for Software Based Ultrasound Machine | Walter Simson | Project Description |
| 19 | Amir Nourinia | Optimization of a DeepLearning Framework | Walter Simson | Project Description |
| 20 | Rebecca Richter | Block-based acceleration strategies for Anisotropic X-ray Dark-field Tomography | PD Dr. Tobias Lasser | 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: | 2019SoSe |
| Abstract: | |
