Lab Course / Praktikum: Project Management and Software Development for Medical Applications
by Prof. NavabTutors: Tobias Benz, Ralf Stauder and Christian Schulte zu Berge Type: Master Practical Course Module IN2106, Module IN8902, Module IN4136
SWS: 6
Programs: Biomedical Computing (Master), Informatics (Master), Informatics (Diploma)
ECTS: 10 Credits
Weekly Meetings: See schedule below, 15:30-17:00, MI 03.13.010
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.- February 4, 2014: Schedule for final presentations updated.
- January 27, 2014: Schedule and guidelines for final presentations are online.
- December 1, 2013: Uploaded guidelines for intermediate presentations.
- November 15, 2013: Schedule for intermediate presentations has been updated.
- November 7, 2013: Schedule for intermediate presentations is online.
- November 6, 2013: Schedule for requirements presentations is online.
- October 16, 2013: List of all projects is online. The availability of projects will be updated in blocks, as we assign them.
- July 8, 2013: Schedule confirmed.
- July 4, 2013: Information on registration updated, preliminary schedule announced.
- July 2, 2013: Preliminary meeting announced.
- June 28, 2013: Course website created.
Registration
Please register on TUMOnline (link). Registration will be open starting from 10.07.2013, 17:00. Registration is on a first come, first served basis.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 | Topic | Conducted by | Materials |
|---|---|---|---|
| 10.07.2013 | Preliminary meeting ("Vorbesprechung") | Course Tutors |  Slides |
| 16.10.2013 | Organizational Issues, Project Announcements | Course Tutors, Project Supervisors | Slides |
| 23.10.2013 | Lecture: Software Project Management | Course Tutors | Slides |
| 30.10.2013 | Lecture: Unified Modeling Language (UML) | Course Tutors | Slides |
| 06.11.2013 15:30-18:00 | Project Requirements Presentations | Course Tutors, Seminar Participants |  Slide Template (PPTX) Slide Template (ODP) |
| 13.11.2013 | Lecture: Documentation, Tests, Design Patterns & Integration Strategy | Course Tutors | Slides |
| Four weeks of no session. | |||
| 18.12.2013 15:30-18:00 | Intermediate Presentations I | Course Tutors, Seminar Participants | Guidelines |
| 19.12.2013 15:30-18:00 | Intermediate Presentations II | Course Tutors, Seminar Participants | |
| Five weeks of no session. | |||
| 29.01.2014 | Q&A Final Presentations | Course Tutors | |
| 05.02.2014 15:30-18:00 | Final Presentations I | Course Tutors, Seminar Participants | Guidelines |
| 06.02.2014 15:30-18:00 | Final Presentations II | Course Tutors, Seminar Participants |
Requirements Presentations Schedule
Wednesday, November 6, 15:30-18:00, MI 03.13.010. 5 minutes slot for each presenter (plus 1 minute for questions).| Slot | First Name | Last name | Project ID | Project Title |
|---|---|---|---|---|
| 1 | Burcu | Altinkaya | 16 | Mr. Bone's fun and exciting adventure encountering segmentation and alignment |
| 2 | Juan | Castrillon Guzman | 11 | Brain graph classification in multi-site clinical datasets |
| 3 | Eduardo | Coello Uribe | 14 | Color-encoded visualization of bolus arrival time in 4D MR angiography data |
| 4 | Alexandra | Derntl | 20 | Analysis interface for human deep-electrode epilepsy recordings |
| 5 | Radu | Diaconescu | 12 | HCI in the OR: High-precision finger tracking for Signal.Net using the Leap Motion Controller |
| 6 | Ralf | Gutjahr | 3 | A flexible toolbox for affine and elastic volume registration in cardiac SPECT and PET |
| 7 | Xiao | Huang | 28 | A modular experimental virtual reality interface |
| 8 | Jihye | Jang | 10 | Sliding-window analysis of functional connectivity between brain areas based on functional MRI data in psychiatric patients |
| 9 | Ekaterina | Mikaeva | 1 | Tracking and visualization in intraoperative image-guided radiation therapy (i2gRT) |
| 10 | Nikoleta | Mouriki | 21 | A user-extendable (plug-in) infrastructure for a multi-modal, multi parametric analysis package (M3P -Anima) |
| 11 | Juan | Osorio Valencia | 25 | GUI development for visualization and processing of high-resolution imaging data |
| 12 | Cemre | Senesen | 27 | Evaluation of white matter tracts in the brain |
| 13 | Jun | Shen | 9 | Automatic segmentation of adipose tissue compartments from water-fat MRI data |
| 14 | Shanmugapriya | Survarachakan | 5 | Reactivating depth in X-Ray (ReDeX) |
| 15 | Richeek | Swami | 18 | Analysis of medical data and visualization of quantitative data in CAMPVis |
| 16 | Stavroula | Timioteraki | 26 | Detection of catheter electrodes in C-arm fluoroscopy images |
| 17 | Piotr | Wojewnik | 22 | The neverending story of software for vessel segmentation and processing |
| 18 | Oliver | Zettinig | 7 | 3D Doppler reconstruction for vascular imaging |
Intermediate Presentations Schedule
Wednesday, 18.12.2013 and Thursday, 19.12.2013, 15:30-18:00, MI 03.13.010. 10 minutes slot for each presenter (plus 2 minutes for questions).| Slot | First Name | Last name | Supervisor | Project ID | Project Title |
|---|---|---|---|---|---|
| Wednesday, 18.12.2013, 15:30-18:00 | |||||
| 1 | Stavroula | Timioteraki | Pascal Fallavollita | 26 | Detection of catheter electrodes in C-arm fluoroscopy images |
| 2 | Burcu | Altinkaya | Amit Shah | 16 | Mr. Bone's fun and exciting adventure encountering segmentation and alignment |
| 3 | Piotr | Wojewnik | Amit Shah, Bernhard Fürst | 22 | The neverending story of software for vessel segmentation and processing |
| 4 | Ekaterina | Mikaeva | Philipp Matthies | 1 | Tracking and visualization in intraoperative image-guided radiation therapy (i2gRT) |
| 5 | Shanmugapriya | Survarachakan | Stefanie Demirci | 5 | Reactivating depth in X-Ray (ReDeX) |
| 6 | Jihye | Jang | Afra Wohlschläger | 10 | Sliding-window analysis of functional connectivity between brain areas based on functional MRI data in psychiatric patients |
| 7 | Cemre | Senesen | Verena Rozanski, Ahmad Amadi | 27 | Evaluation of white matter tracts in the brain |
| 8 | Ralf | Gutjahr | Stephan Nekolla | 3 | A flexible toolbox for affine and elastic volume registration in cardiac SPECT and PET |
| 9 | Nikoleta | Mouriki | Stephan Nekolla | 21 | A user-extendable (plug-in) infrastructure for a multi-modal, multi parametric analysis package (M3P -Anima) |
| Thursday, 19.12.2013, 15:30-18:00 | |||||
| 10 | Jun | Shen | Dimitrios Karampinos, Peter Noel | 9 | Automatic segmentation of adipose tissue compartments from water-fat MRI data |
| 11 | Juan | Castrillon Guzman | Richiardi Jonas | 11 | Brain graph classification in multi-site clinical datasets |
| 12 | Oliver | Zettinig | Christoph Hennersperger | 7 | 3D Doppler reconstruction for vascular imaging |
| 13 | Juan | Osorio Valencia | Dominik Soliman | 25 | GUI development for visualization and processing of high-resolution imaging data |
| 14 | Richeek | Swami | Christian Schulte zu Berge | 18 | Analysis of medical data and visualization of quantitative data in CAMPVis |
| 15 | Radu | Diaconescu | Tobias Benz | 12 | HCI in the OR: High-precision finger tracking for Signal.Net using the Leap Motion Controller |
| 16 | Xiao | Huang | Virginia Flanagin | 28 | A modular experimental virtual reality interface |
| 17 | Alexandra | Derntl | Virginia Flanagin | 20 | Analysis interface for human deep-electrode epilepsy recordings |
Final Presentations Schedule
Wednesday, 05.02.2014 and Thursday, 06.02.2014, 15:30-18:00, MI 03.13.010. 10 minutes slot for each presenter (plus 2 minutes for questions).| Slot | First Name | Last name | Supervisor | Project ID  | Project Title |
|---|---|---|---|---|---|
| 9 | Ekaterina | Mikaeva | Philipp Matthies | 1 | Tracking and visualization in intraoperative image-guided radiation therapy (i2gRT) |
| 7 | Jihye | Jang | Afra Wohlschläger | 10 | Sliding-window analysis of functional connectivity between brain areas based on functional MRI data in psychiatric patients |
| 4 | Juan | Castrillon Guzman | Richiardi Jonas | 11 | Brain graph classification in multi-site clinical datasets |
| 10 | Eduardo | Coello Uribe | Jan Bauer, Tobias Benz | 14 | Color-encoded visualization of bolus arrival time in 4D MR angiography data |
| 3 | Burcu | Altinkaya | Amit Shah | 16 | Mr. Bone's fun and exciting adventure encountering segmentation and alignment |
| 6 | Richeek | Swami | Christian Schulte zu Berge | 18 | Analysis of medical data and visualization of quantitative data in CAMPVis |
| 15 | Alexandra | Derntl | Virginia Flanagin | 20 | Analysis interface for human deep-electrode epilepsy recordings |
| 2 | Nikoleta | Mouriki | Stephan Nekolla | 21 | A user-extendable (plug-in) infrastructure for a multi-modal, multi parametric analysis package (M3P -Anima) |
| 13 | Piotr | Wojewnik | Amit Shah, Bernhard Fürst | 22 | The neverending story of software for vessel segmentation and processing |
| 11 | Juan | Osorio Valencia | Dominik Soliman | 25 | GUI development for visualization and processing of high-resolution imaging data |
| 5 | Stavroula | Timioteraki | Pascal Fallavollita | 26 | Detection of catheter electrodes in C-arm fluoroscopy images |
| 14 | Xiao | Huang | Virginia Flanagin | 28 | A modular experimental virtual reality interface |
| 1 | Ralf | Gutjahr | Stephan Nekolla | 3 | A flexible toolbox for affine and elastic volume registration in cardiac SPECT and PET |
| 8 | Oliver | Zettinig | Christoph Hennersperger | 7 | 3D Doppler reconstruction for vascular imaging |
| 12 | Jun | Shen | Dimitrios Karampinos, Peter Noel | 9 | Automatic segmentation of adipose tissue compartments from water-fat MRI data |
| Thursday, 06.02.2014, 15:30-18:00 | |||||
| Wednesday, 05.02.2014, 15:30-18:00 | |||||
Available Projects
Registration only via email to Ralf Stauder:| ID | Project Title | Supervisor | Additional Material |
|---|---|---|---|
| 1 | ASSIGNED! Tracking and Visualization in intraoperative image-guided Radiation Therapy (i2gRT) | Philipp Matthies | Project Proposal |
| 2 | Lumen segmentation in 3D optical coherence tomography images | Sebastian Pölsterl | Project Proposal |
| 3 | ASSIGNED! A flexible toolbox for affine and elastic volume registration in cardiac SPECT and PET | Dr. Stephan Nekolla | Project Proposal |
| 4 | Ray-shot Selection in Augmented Reality Medical Education Application | Ma Meng | Project Proposal |
| 5 | ASSIGNED! Reactivating depth in X-Ray (ReDeX) | Stefanie Demirci | Project Proposal |
| 6 | ASSIGNED! Stent graft tracking in angiographic sequences | Stefanie Demirci | Project Proposal |
| 7 | ASSIGNED! 3D Doppler reconstruction for vascular imaging | Christoph Hennersperger | Project Proposal |
| 8 | RGBD Fusion for Dermatology | Alexandru Duliu | Project Proposal |
| 9 | ASSIGNED! Automatic segmentation of adipose tissue compartments from water-fat MRI data | Dimitrios Karampinos, Peter Noel | Project Proposal |
| 10 | ASSIGNED! Sliding-window analysis of functional connectivity between brain areas based on functional MRI data in psychiatric patients | Dr. Afra Wohlschläger | Project Proposal |
| 11 | ASSIGNED! Brain graph classification in multi-site clinical datasets | Richiardi Jonas | Project Proposal |
| 12 | ASSIGNED! HCI in the OR: High-precision finger tracking for Signal.Net using the Leap Motion Controller | Tobias Benz | Project Proposal |
| 13 | HCI in the OR: advancing Kinect feet tracking for Signal.Net | Tobias Benz, Ralf Stauder | Project Proposal |
| 14 | ASSIGNED! Color-encoded visualization of bolus arrival time in 4D MR angiography data | Dr. Jan Bauer, Tobias Benz, Peter Noel | Project Proposal |
| 15 | Brain artery tree segmentation in CTA Data | Dr. Jan Bauer, Tobias Benz, Peter Noel | Project Proposal |
| 16 | ASSIGNED! Mr. Bone's fun and exciting adventure encountering segmentation and alignment | Amit Shah | Project Proposal |
| 17 | Acceleration Techniques for Volume Rendering | Christian Schulte zu Berge | Project Proposal |
| 18 | ASSIGNED! Analysis of Medical Data and Visualization of Quantitative Data in CAMPVis | Christian Schulte zu Berge | Project Proposal |
| 19 | Interaction Metaphors for Medical Data in CAMPVis | Christian Schulte zu Berge | Project Proposal |
| 20 | ASSIGNED! Analysis interface for human deep-electrode epilepsy recordings | Virginia Flanagin | Project Proposal |
| 21 | ASSIGNED! A user-extendable (plug-in) infrastructure for a multi-modal, multi parametric analysis package (M3P -Anima) | Dr. Stephan Nekolla | Project Proposal |
| 22 | The Neverending Story of Software for Vessel Segmentation and Processing | Amit Shah, Bernhard Fürst | Project Proposal |
| 23 | SuperTrack: To Hybrid Tracking and Beyond! | Bernhard Fürst, Felix Achilles, Amit Shah | Project Proposal |
| 24 | CAMPCommunication at the tip of your fingers | Bernhard Fürst | Project Proposal |
| 25 | ASSIGNED! GUI Development for Visualization and Processing of high-resolution Imaging Data | Dominik Soliman | Project Proposal |
| 26 | ASSIGNED! Detection of catheter electrodes in C-arm fluoroscopy images | Pascal Fallavollita | Project Proposal |
| 27 | ASSIGNED! Evaluation of white matter tracts in the brain | Dr. med. Verena Rozanski, Ahmad Ahmadi | Project Proposal |
| 28 | ASSIGNED! A modular experimental virtual reality interface | Virginia Flanagin | Project Proposal |
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).
SVN
- TortoiseSVN, a freeware SVN client for Windows
- A nice TortoiseSVN tutorial for beginners
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
- SampleCodes.zip: OpenGL samples with code
- OpenGL_TransformationsViewingLight.pdf: OpenGL presentations
| TeachingForm | |
|---|---|
| Title: | Project Management and Software Development for Medical Applications |
| Professor: | Prof. Dr. Nassir Navab |
| Tutors: | Tobias Benz, Ralf Stauder and Christian Schulte zu Berge |
| Type: | Praktikum |
| Information: | 10 ECTS credits |
| Term: | 2013WiSe |
| Abstract: | The Lab Course is intended to teach basic concepts of the software project management and development for medical and intra-operative applications. You will be confronted with a brief introduction to the software project management concepts such as requirement analysis, software design, coding guidelines and unified modeling language (UML). Furthermore, you will be exposed to basic concepts of the C++ programming language, graphical user interface programming using Qt and OpenGL. Last but not least topics like version control, deployment and test will be explored. You will be assigned a medical software project to apply the mentioned concepts in a real-life scenario. |
