Lab Course / Praktikum: Project Management and Software Development for Medical Applications
by Prof. Nassir Navab and Dr. Benjamin FrischTutors: Felix Achilles, Oliver Zettinig, Rüdiger Göbl
Type: Master Practical Course Module IN2106, Module IN8902, Module IN4136
SWS: 6
Programs: Biomedical Computing (Master), Informatics (Master), Informatics (Diploma)
ECTS: 10 Credits
Preliminary Meeting ("Vorbesprechung"):
Further Meetings: See schedule below
This course in TUMOnline: Link
The course will be conducted in English.
News
Please check back here regularly, as important news will be posted here.- 27JUN2016: We cancelled the final presentations on Monday, July 11th and moved all to Wednesday, July 13th.
- 22JAN 2016: Please register for the course at https://matching.in.tum.de/. Highest priority given to BMC students in their last semester, takeing this course for the 1st time and who sent an e-mail to benjamin.frisch@tum.de before 03FEB2016
- 22JAN2016: Course website created.
Registration
Please register in the matching system for the course registration between 29JAN2016 and 09FEB2016 (link). Keep in mind that your chances to be assigned to the course increase if you give it a higher rank in your choices. We will give highest priority for this course for students of the Biomedical Computing Master (BMC) who are in their last semester, take this course for the first time and send an e-mail to benjamin.frisch@tum.de before 03FEB2016. For further details about how the matching system works and its schedule please check this website.General content
The 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.Prerequisites
This course requires basic knowledge of C++. The concepts of OO Programming and other concepts as conducted in the Introduction to CS lecture are assumed.Schedule
| Date | Place | Topic | Conducted by | Materials |
|---|---|---|---|---|
| 29 JAN 2016, 1000-1100 | MI 03.13.010 | Preliminary meeting ("Vorbesprechung") | Dr. Benjamin Frisch |  Slides |
| 12 APR 2016, 0830-1000 | MI 03.13.010 | Introductory Meeting: Organizational Issues, Project Announcements | Dr. Benjamin Frisch | Rules and Regulations and Project Presentation |
| 13 APR 2016, 09000-1200 | MI 03.13.010 | Lecture: Software Project Management (SPM) + Presentation Tips | Shadi Albarqouni and Dr. Benjamin Frisch | SPM Presentation Tips |
| 14 APR 2016, 1700 | Deadline to send project preferences. Assignments published later this evening. | Seminar Participants | ||
| 19 APR 2016, 0830-1000 | MI 03.13.010 | Lecture: Unified Modeling Language (UML) | Rüdiger Göbl | UML |
| 20 APR 2016, 0900-1200 | MI 03.13.010 | Lecture: Documentation, Tests, Design Patterns & Integration Strategy | Oliver Zettinig | Software Engineering |
| 22 APR 2016, 1300-1600 | MI 03.13.010 | Project Requirements Presentations | Seminar Participants | |
| Four weeks of no session. | ||||
| 23 MAY 2016, 1430-1730 | IFL | Intermediate Presentations Part I | Seminar Participants | |
| 24 MAY 2016, 1430-1730 | IFL | Intermediate Presentations Part II | Seminar Participants | |
| Five weeks of no session. | ||||
| 04 JUL 2016, 1400-1500 | MI 03.13.010 | Q&A Final Presentations | Course Tutors | |
| CANCELLED | CANCELLED | Final Presentations Part I | Course Tutors, Seminar Participants | |
| 13 JUL 2016, 0800-1230 | MI 03.13.010 | Final Presentations | Course Tutors, Seminar Participants |
Final Presentations Schedule
13JUL2016. 10 minutes slot for each presenter (plus 3 minutes for questions). Your presentation has to last at least 9 minutes. It should last 10 minutes. You will be interrupted after 10 minutes 20 seconds, no exceptions made.| Slot | Name |
|---|---|
| 1 | El-Gazzar |
| 2 | Kalim |
| 3 | Navarro |
| 4 | Jimenez Sanchez |
| 5 | Luque Gonzalez |
| 6 | Stelzl |
| 7 | Sarasua |
| 8 | Yajnik |
| 9 | Page |
| 10 | Nitkunanantharajah |
| 11 | Nikolaev |
| 12 | Tran |
| 13 | Kewlani |
| 14 | Ahmad |
Intermediate Presentations Schedule
23MAY2016, 1430-1730, at IFL. 7 minutes slot for each presenter (plus 3 minutes for questions). Your presentation has to last at least 6 minutes and 30 seconds. It should last 7 minutes. You will be interrupted after 7 minutes 20 seconds, no exceptions made.| Slot | Name |
|---|---|
| 1 | Luque Gonzalez |
| 2 | Nitkunanantharajah |
| 3 | Kalim |
| 4 | Yajnik |
| 5 | El-Gazzar |
| 6 | Stelzl |
| 7 | Nikolaev |
| 8 | Jimenez Sanchez |
| Slot | Name |
|---|---|
| 1 | Navarro |
| 2 | Ahmad |
| 3 | Page |
| 4 | Kewlani |
| 5 | Abdo |
| 6 | Tran |
| 7 | Sarasua |
Requirements Presentations
22 APR 2016, 1300-1600, in room MI 03.13.010. 5 minutes slot for each presenter (plus 2 minutes for questions). Your presentation will be interrupted after 5 minutes 20 seconds, no exceptions made. You can use the
CAMP PowerPoint template for your slides.
Available Projects
Projects will be announced in due time and presented during the introductory meeting. Please communicate your selection (first, second and third choice) by 14APR2016, 1700.| ID | Student | Project Title | Supervisor  | Additional Material |
|---|---|---|---|---|
| 1 | El-Gazzar | A vision based anthropometric Scanner | Benjamin Busam | Project Description |
| 2 | Kalim | A hybrid opto-inertial Tracking System Prototype | Benjamin Busam | Project Description |
| 3 | A virtual multi-view Optical Tracking System | Benjamin Busam | Project Description | |
| 10 | Navarro | Computer assisted optical biopsy for colorectal polyps | Diana Mateus | Project Description |
| 6 | Stelzl | Advanced Visualization for Magnetic Resonance Spectroscopic Imaging | Eduardo Coello | Project Description |
| 11 | Jimenez Sanchez | Fully convolutional model for brain tumor segmentation | Fausto Milletari | Project Description |
| 17 | Sarasua | Surgical Instrument Tracking in Minimally Invasive Robotic Surgery | Florian Steidle | Project Description |
| 4 | Nikolaev | Simulation of PET detectors based on continuous crystals using GATE | Jorge Cabello | Project Description |
| 5 | Nitkunanantharajah | Anisotropic PET filtering with MRI | Jorge Cabello | Project Description |
| 13 | Luque Gonzalez | Prostate Cancer Metastases Atlas | Julia Rackerseder | Project Description |
| 14 | Ahmad | 3D PSMA-PET/MR Histology Registration | Julia Rackerseder | Project Description |
| 21 | Page | Intraoperative robotic SPECT reconstruction | Marco Esposito | TBD |
| 15 | Frequency Analysis of Intra-Abdominal Pressure in Laparoscopic Surgeries | Ralf Stauder | Project Description | |
| 16 | Yajnik | Medical Workflow Software Infrastructure Based on Business Workflow Modeling Standards | Ralf Stauder | Project Description |
| 18 | Advanced UI for Autonomous Robotic Ultrasound | Salvatore Virga | Project Description | |
| 19 | Automated contour definition in cardiac MRI revisited: assessment of regional contrast media uptake | Stephan Nekolla | Project Description | |
| 20 | Kewlani | A texture analysis plug‐in for a multi-modal, multi parametric analysis package (M3P‐Anima) | Stephan Nekolla | Project Description |
| 12 | Abdo | Color normalization Fiji/ImageJ Plugin for Histological images | Tingying Peng | Project Description |
| 7 | Tran | Deep Learning for Biomedicine | Vladimir Golkov | Project Description |
| 8 | Statistical Methods and Machine Learning for Diffusion MRI | Vladimir Golkov | Project Description | |
| 9 | Super-Resolution of Cryo-EM using Convolutional Neural Networks | Vladimir Golkov | Project Description | |
| 22 | Deep Learning for QSAR | Vladimir Golkov | Project Description | |
Passing requirements
- Active participation in the lecture meetings
- Submission of all assignments in time
- Present your final assignment work
Literature/Resources
C++
- Online C++ API reference
- A good webpage on C++ including tutorials as well
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 (2010)
- Can be downloaded on the TUM Maniac Server
- Short tutorial on how to create a Win32 Console Project, and to run it
- Tutorial with some debugging tips and tricks in MS Visual Studio (this tutorial features some C# code, but the tips and tricks shown should work similarly on C++ code).
Github
- Github, a freeware Github client for Mac/Windows
- A nice Github tutorial for beginners
- You can ask your Tutors how to create an account on our CAMPgit.
OpenGL
- Online OpenGL Documentation
- Another good page! Overall view of the concepts and basics of OpenGL
- Compiled GLUT library Don't want to spend time over compilation, just get the ready to use pack here
Qt
OpenCV
Not found what you are looking for?
- SampleCodes.zip: Code and example of OpenGL
- OpenGL_TransformationsViewingLight.pdf: OpenGL presentations
| TeachingForm | |
|---|---|
| Title: | Project Management and Software Development for Medical Applications |
| Professor: | Prof. Nassir Navab and Dr. Benjamin Frisch |
| Tutors: | Felix Achilles, Oliver Zettinig, Rüdiger Göbl |
| Type: | Praktikum |
| Information: | 6 SWS, 10 ECTS Credits |
| Term: | 2016SoSe |
| Abstract: | |
