Lab Course / Praktikum: Project Management and Software Development for Medical Applications
by Prof. NavabTutors: Christoph Hennersperger, Amit Shah, Felix Achilles and Shadi Albarqouni Type: Master Practical Course SWS: 6
Programs: Biomedical Computing (Master), Informatics (Master), Informatics (Diploma)
ECTS: 10 Credits
Weekly Meetings: See schedule below, Wednesdays 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.* Final Presentations Schedule for Wednesday, 04.02.2015, 15:30-18:00 and Thursday, 05.02.2015, 15:30-18:00 is published.
* You will have only 7 minutes for the intermediate presentation scheduled on 17th and 18th Dec. * NO lecture on Wednesday, 12th of November. It was shifted one week to Wednesday, 19th of November.
* Please use the Slide Template for your presentations.
* Proposals are online! Feel free to already have a look below (available projects) before the seminar starts.
* October 1st, 2014: Participants have been added to seminar in TUM online
* The preliminary meeting is rescheduled to 3rd July, 17:00 in MI 03.13.010 considering students' exams
* June 30, 2014: Schedule confirmed
* June 16, 2014: Course website created.
Registration
Please give rank in the matching system for the course registration between 4-8 July (matching rank link). TUMOnline and First come first serve is not valid for practical and seminar courses anymore. Apologies for confusion. This is the first time experiment of registration via rank matching system so please bear with us.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. Attending CAMP and CAMP II will be of high advantage.Schedule
| Date | Topic | Conducted by | Materials |
|---|---|---|---|
| Thur, 03.07.2014 | Preliminary meeting ("Vorbesprechung") | Course Tutors |  Slides |
| Wed, 15.10.2014 | Organizational Issues, Project Announcements | Course Tutors, Project Supervisors | Slides |
| Wed, 22.10.2014 | Lecture: Software Project Management | Course Tutors | Part I Part II |
| Wed, 29.10.2014 | Lecture: Unified Modeling Language (UML) | Course Tutors | Slides |
| Wed, 05.11.2014 15:30-18:00 | Project Requirements Presentations | Course Tutors, Project Supervisors | Slides |
| Wed, 19.11.2014 | Lecture: Documentation, Tests, Design Patterns & Integration Strategy | Course Tutors | Part I Part II |
| Four weeks of no session. | |||
| Wed, 17.12.2014 15:30-18:00 | Intermediate Presentations I | Course Tutors, Project Supervisors | Slides |
| Thur, 18.12.2014 15:30-18:00 | Intermediate Presentations II | Course Tutors, Project Supervisors | Slides |
| Five weeks of no session. | |||
| Wed, 28.01.2014 08:00-10:00 | Q&A Final Presentations | Course Tutors | Slides |
| Wed, 04.02.2014 15:30-18:00 | Final Presentations I | Course Tutors, Project Supervisors | |
| Thur, 05.02.2014 15:30-18:00 | Final Presentations II | Course Tutors, Project Supervisors |
Final Presentations Schedule
Wednesday, 04.02.2015, 15:30-18:00 and Thursday, 05.02.2015, 15:30-18:00, MI 03.13.010. 10 minutes slot for each presenter (plus 2 minutes for questions).| Slot | Name | Project ID & Name | |||
|---|---|---|---|---|---|
| Wednesday, 04.02.2015, 15:30-18:00 | |||||
| 1 | Bing Liu | 6 | Easy RGBD Video Acquisition – a modular video recording framework for patient surveillance | ||
| 2 | Cemre Senese | 19 | X-ray Depthmaps | ||
| 3 | Satish Balakrishnan | 10 | Real-time screen detection for Eye-Tracking based laparoscopic camera holding system | ||
| 4 | Judith Zimmermann | - | Advanced Random Walk Segmentation for Cardiac Ventricular Modeling | ||
| 5 | Toluwalope Gbakinro | 23 | Multi-image based Shading Correction ImageJ? plugin | ||
| 6 | Ahmed El Fiky | - | Image Denoising in High Dimensional Space | ||
| 7 | PS Viswanath | 19 | Hybrid Optoacoustic (OA) and Magnetic resonance (MR) Imaging: Registration | ||
| 8 | Yeshaswini Nagaraj | 19 | Hybrid Optoacoustic (OA) and Magnetic resonance (MR) Imaging: Segmentation | ||
| Thursday, 05.02.2015, 15:30-18:00 | |||||
| 9 | Mhd Hasan Sarhan | 18 | Evaluation of Real-time Tracking of Endovascular Devices | ||
| 10 | Imran Mashood Badshah | 7 | GUI Development for Performing Spectral Unmixing for Quantitative Multispectral Optoacoustic Tomography and Visualization of Its Results | ||
| 11 | Fatemeh Nejatbakhshesfahani | 8 | Development of a multi-parametric analysis tool for PET/MRI to fingerprint the heterogeneity of glioma | ||
| 12 | Anca-Elena Stefanoiu | 11 | Implementation of Exponential and Logarithm Maps for Processing Manifold-valued Data | ||
| 13 | Deepa Gunashekar | 4 | Implementation and Evaluation of Iterative Solvers for Non-Symmetric Equation Systems | ||
| 14 | Sing Lee | - | Surgical Simulator Evaluation | ||
| 15 | Phalgun Chintala | 17 | Evaluation of the radiation free drill guidance after the upgrade of CamC | ||
| 16 | Sasa Cheng | 11 | Visualisation and Segmentation GUI for 3D Microscopy Images | ||
| 17 | Sindhushree Jayasankar | 1 | Fitting the rotated Diffusional Kurtosis Tensor to MR Diffusion Images | ||
Intermediate Presentations Schedule
Wednesday, 17.12.2014, 15:30-18:00 and Thursday, 18.12.2014, 15:30-18:00, MI 03.13.010. 7 minutes slot for each presenter (plus 2 minutes for questions).| Slot | Name | Project ID & Name | |||
|---|---|---|---|---|---|
| Wednesday, 17.12.2014, 15:30-18:00 | |||||
| 1 | Cemre Senese | 19 | X-ray Depthmaps | ||
| 2 | Imran Mashood Badshah | 7 | GUI Development for Performing Spectral Unmixing for Quantitative Multispectral Optoacoustic Tomography and Visualization of Its Results | ||
| 3 | Toluwalope Gbakinro | 23 | Multi-image based Shading Correction ImageJ? plugin | ||
| 4 | Sindhushree Jayasankar | 1 | Fitting the rotated Diffusional Kurtosis Tensor to MR Diffusion Images | ||
| 5 | Ahmed El Fiky | - | Image Denoising in High Dimensional Space | ||
| 6 | Fatemeh Nejatbakhshesfahani | 8 | Development of a multi-parametric analysis tool for PET/MRI to fingerprint the heterogeneity of glioma | ||
| 7 | Phalgun Chintala | 17 | Evaluation of the radiation free drill guidance after the upgrade of CamC | ||
| 8 | Sasa Cheng | 11 | Visualisation and Segmentation GUI for 3D Microscopy Images | ||
| Thursday, 18.12.2014, 15:30-18:00 | |||||
| 9 | PS Viswanath | 19 | Hybrid Optoacoustic (OA) and Magnetic resonance (MR) Imaging: Registration | ||
| 10 | Yeshaswini Nagaraj | 19 | Hybrid Optoacoustic (OA) and Magnetic resonance (MR) Imaging: Segmentation | ||
| 11 | Satish Balakrishnan | 10 | Real-time screen detection for Eye-Tracking based laparoscopic camera holding system | ||
| 12 | Judith Zimmermann | - | Advanced Random Walk Segmentation for Cardiac Ventricular Modeling | ||
| 13 | Anca-Elena Stefanoiu | 11 | Implementation of Exponential and Logarithm Maps for Processing Manifold-valued Data | ||
| 14 | Mhd Hasan Sarhan | 18 | Evaluation of Real-time Tracking of Endovascular Devices | ||
| 15 | Deepa Gunashekar | 4 | Implementation and Evaluation of Iterative Solvers for Non-Symmetric Equation Systems | ||
| 16 | Bing Liu | 6 | Easy RGBD Video Acquisition – a modular video recording framework for patient surveillance | ||
| 17 | Sing Lee | - | Surgical Simulator Evaluation - Done on 5th Nov | ||
Passing requirements
- Active participation in the lecture meetings
- Submission of all assignments in time
- Present your final assignment work
Available Projects
| ID | Project Title | Supervisor | Additional Material | |
|---|---|---|---|---|
| 1 | Commissioning of a PET/US imaging system | Benjamin Frisch, Amit Shah | Project Proposal | |
| 2 | Touch CAMPVis – Medical Visualization on Mobile Devices | Christian Schulte zu Berge | Project Proposal | |
| 3 | Integration of Real-time Data Streaming into a 3D Ultrasound Acquisition Framework | Christoph Hennersperger | Project Proposal | |
| 4 | assigned | Implementation and Evaluation of Iterative Solvers for Non-Symmetric Equation Systems | Christoph Hennersperger, Maximilian Baust | Project Proposal |
| 5 | Electrophysiology catheter tracking in fluoroscopic images | Fausto Milletari | Project Proposal | |
| 6 | assigned | Easy RGBD Video Acquisition – a modular video recording framework for patient surveillance | Felix Achilles | Project Proposal |
| 7 | assigned | Development of an intelligent tool for automatic and reproducible pharmacokinetic modeling on dynamic PET | Kuangyu Shi | Project Proposal |
| 8 | assigned | Development of a multi-parametric analysis tool for PET/MRI to fingerprint the heterogeneity of glioma | Kuangyu Shi | Project Proposal |
| 9 | assigned | Visualisation and Segmentation GUI for 3D Microscopy Images | Lichao Wang | Project Proposal |
| 10 | assigned | Real-time screen detection for Eye-Tracking based laparoscopic camera holding system | Mathias Magg | Project Proposal |
| 11 | assigned | Implementation of Exponential and Logarithm Maps for Processing Manifold-valued Data | Maximilian Baust | Project Proposal |
| 12 | assigned | Skin Identification in Digital Breast Tomosynthesis | Michael Kelm | Project Proposal |
| 13 | Deformable Multi-modal Prostate Registration | Oliver Zettinig, Amit Shah, Benjamin Frisch | Project Proposal | |
| 14 | assigned | Multi-modal Prostate Segmentation in MRI and Ultrasound | Oliver Zettinig, Amit Shah, Benjamin Frisch | Project Proposal |
| 15 | 3D Blood Velocity Reconstruction over Time from Doppler Ultrasound for Vascular Imaging | Oliver Zettinig, Christoph Hennersperger | Project Proposal | |
| 16 | Image Processing Toolbox for CamC | Séverine Habert | Project Proposal | |
| 17 | assigned | Evaluation of the radiation free drill guidance after the upgrade of CamC | Séverine Habert | Project Proposal |
| 18 | assigned | Evaluation of Real-time Tracking of Endovascular Devices | Stefanie Demirci | Project Proposal |
| 19 | assigned | X-ray Depthmaps | Stefanie Demirci | Project Proposal |
| 20 | Automated contour definition in cardiac MRI revisited: assessment of regional and global contractility | Stephan Nekolla | Project Proposal | |
| 21 | Toolbox for elastic volume registration in thoracic, multimodal imaging | Stephan Nekolla | Project Proposal | |
| 22 | assigned | Hybrid Optoacoustic (OA) and Magnetic resonance (MR) Imaging | Subhamoy Mandal | Project Proposal |
| 23 | assigned | Multi-image based Shading Correction ImageJ? plugin | Tingying Peng | Project Proposal |
| 24 | A UI for MRI co-registered US-acquisition of the brain | Ahmad Ahmadi | Project Proposal | |
| 25 | A UI for ultrasound-guided needle injection | Ahmad Ahmadi | Project Proposal | |
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. Nassir Navab |
| Tutors: | Christoph Hennersperger, Amit Shah, Felix Achilles and Shadi Albarqouni |
| Type: | Praktikum |
| Information: | 10 ECTS credits |
| Term: | 2014WiSe |
| 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. |
