Lab Course / Praktikum: Project Management and Software Development for Medical Applications
by
Prof. Navab
Tutors:
Christian Schulte zu Berge,
Tobias Benz,
Shadi Nabil Albarqouni and Felix Achilles
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"): 29.01.2014, 15:00,
MI 03.13.010
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.
- July 02, 2014: Preliminary schedule for final presentations is online.
- May 26, 2014: Preliminary schedule for intermediate presentations is online.
- May 2, 2014: Schedule for requirements presentations is online.
- April 14, 2014: Application for projects closed. We were able to accomodate 21 students for this semester.
- April 09, 2014:Please mind the deadlines for applying for projects: April 11th, 23:59 (soft deadline to respect prioritization), April 15th, 23:59 (hard deadline).
Please note: We encourage you to apply for projects even if you only have a waiting position since some people might drop out!
- March 06, 2014: Due to the high number of registrations, we will try to increase the number of places to max. 20 students, subject to having a sufficient number of available projects.
- January 30, 2014: Schedule confirmed, fixed registration date in TUMOnline to 03.03.2014, 17:00.
- January 10, 2014: Course website created.
Registration
Please register on TUMOnline (
link). Registration will be open starting from 03.03.2014, 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 |
29.01.2014 | Preliminary meeting ("Vorbesprechung") | Course Tutors | Slides |
09.04.2014 | Organizational Issues, Project Announcements | Course Tutors, Project Supervisors | Slides |
23.04.2014 | Lecture: Software Project Management | Course Tutors | Slides Canvas01 Canvas02 |
30.04.2014 | Lecture: Unified Modeling Language (UML) | Course Tutors | Slides |
07.05.2014 | Project Requirements Presentations | Course Tutors, Seminar Participants | Guidelines Slide Template (PPTX) Slide Template (ODP) |
14.05.2014 | Lecture: Documentation, Tests, Design Patterns & Integration Strategy | Course Tutors | Slides |
Three weeks of no session. | | | |
04.06.2014 15:30-18:00 | Intermediate Presentations I | Course Tutors, Seminar Participants | Guidelines |
05.06.2014 16:00-18:00 | Intermediate Presentations II | Course Tutors, Seminar Participants | |
Five weeks of no session. | | | |
02.07.2014 | Q&A Final Presentations | Course Tutors | |
09.07.2014 15:30-18:00 | Final Presentations I | Course Tutors, Seminar Participants | Guidelines |
10.07.2014 16:00-18:00 | Final Presentations II | Course Tutors, Seminar Participants | |
Requirements Presentations Schedule
Wednesday, May 7th, 15:30-18:00,
MI 03.13.010. 5 minutes slot for each presenter (plus 2 minutes for questions).
Slot | First Name | Last Name | Project ID & Name |
1 | Felix Bork & Christoph Graumann | 7 | Evaluation of Dictionary Learning Algorithms for Image Segmentation |
2 | Ana | Lopez | 4 | Prediction of Postoperative Ligament Balance in Computer Assisted Total Knee Replacement |
3 | Yuxiang | Gong | 14 | Hybrid Fluorescence / SPECT system for image-guided open surgery |
4 | Poulami | Chakrabarti | 11 | Analysis of phase-amplitude-gating mechanisms in electrical rhythms of the human brain from electroencephalographic (EEG) data acquired in different states of consciousness |
5 | Pedro | Gomez Damian | 1 | Fitting the rotated Diffusional Kurtosis Tensor to MR Diffusion Images |
6 | Cristina | Precup | 15 | Towards Prostate Cancer Fusion Biopsy |
7 | Catalina | Raymond Guzman | 20 | Creation of a Mesh Preparation Tool for Patient Specific Hemodynamic Simulations |
8 | Hossain | Mahmud | 3 | Visualisation and Segmentation GUI for 3D Microscopy Images |
9 | Iro | Laina | 9 | A texture analysis plug-in for a multi-modal, multi parametric analysis package (M3P -Anima) |
10 | Andrii | Kravtsiv | 10 | A flexible toolbox for affine and elastic volume registration in cardiac SPECT and PET |
11 | Salvatore | Virga | 21 | Automatic Inverse Kinematics for Aortic Interventions |
12 | Denis | Declara | 16 | Interactive Exploration of Large Histological Images |
13 | Patmaa | Sridharan | 12 | Depth perception improved Xray mapped on a 3D surface reconstrucion: Application to CAD tools |
14 | Stefano | Trebeschi | 8 | Generation of a normalized template for Arterial Spin Labeling to diagnose dementia |
15 | Shweta | Shitole | 18 | Graphics and GUI development for clinical testing of vertigo |
16 | Faisal | Ibne Mozher | 2 | Tool development for DICOM data anonymization |
17 | Ivan | Olefir | 5 | GUI Development for Performing Spectral Unmixing for Quantitative Multispectral Optoacoustic Tomography and Visualization of Its Results |
18 | Sai Gokul | Hariharan | 13 | OpenIGTLink Interface to Robot Operating System |
19 | Shanmugapriya | Survarachakan | 19 | Stent Graft Detection in X-ray Fluoroscopy |
20 | Beatrice | Lentes | 17 | Automation of Gamma Camera Calibrations |
Intermediate Presentations Schedule
Wednesday, 04.05.2014, 15:30-18:00 and Thursday, 05.05.2014, 16:00-18:00,
MI 03.13.010. 10 minutes slot for each presenter (plus 2 minutes for questions).
Slot | First Name | Last Name | Project ID & Name |
Wednesday, 04.05.2014, 15:30-18:00 |
1 | Salvatore | Virga | 21 | Automatic Inverse Kinematics for Aortic Interventions |
2 | Ivan | Olefir | 5 | GUI Development for Performing Spectral Unmixing for Quantitative Multispectral Optoacoustic Tomography and Visualization of Its Results |
3 | Felix Bork | Christoph Graumann | 7 | Evaluation of Dictionary Learning Algorithms for Image Segmentation |
4 | Pedro | Gomez Damian | 1 | Fitting the rotated Diffusional Kurtosis Tensor to MR Diffusion Images |
5 | Catalina | Raymond Guzman | 20 | Creation of a Mesh Preparation Tool for Patient Specific Hemodynamic Simulations |
6 | Stefano | Trebeschi | 8 | Generation of a normalized template for Arterial Spin Labeling to diagnose dementia |
7 | Denis | Declara | 16 | Interactive Exploration of Large Histological Images |
8 | Patmaa | Sridharan | 12 | Depth perception improved Xray mapped on a 3D surface reconstrucion: Application to CAD tools |
9 | Shweta | Shitole | 18 | Graphics and GUI development for clinical testing of vertigo |
Thursday, 05.05.2014, 16:00-18:00 |
11 | Shanmugapriya | Survarachakan | 19 | Stent Graft Detection in X-ray Fluoroscopy |
12 | Faisal | Ibne Mozher | 2 | Tool development for DICOM data anonymization |
13 | Yuxiang | Gong | 14 | Hybrid Fluorescence / SPECT system for image-guided open surgery |
14 | Poulami | Chakrabarti | 11 | Analysis of phase-amplitude-gating mechanisms in electrical rhythms of the human brain from electroencephalographic (EEG) data acquired in different states of consciousness |
15 | Iro | Laina | 9 | A texture analysis plug-in for a multi-modal, multi parametric analysis package (M3P -Anima) |
16 | Hossain | Mahmud | 3 | Visualisation and Segmentation GUI for 3D Microscopy Images |
17 | Ana | Lopez | 4 | Prediction of Postoperative Ligament Balance in Computer Assisted Total Knee Replacement |
18 | Sai Gokul | Hariharan | 13 | OpenIGTLink Interface to Robot Operating System |
19 | Cristina | Precup | 15 | Towards Prostate Cancer Fusion Biopsy |
20 | Andrii | Kravtsiv | 10 | A flexible toolbox for affine and elastic volume registration in cardiac SPECT and PET |
Final Presentations Schedule
Wednesday, 09.07.2014, 15:30-18:00 and Thursday, 10.07.2014, 16:00-18:00,
MI 03.13.010. 10 minutes slot for each presenter (plus 2 minutes for questions).
Slot | First Name | Last Name | Project ID | Project Name |
Wednesday, 09.07.2014, 15:30-18:00 |
1 | Felix Bork | Christoph Graumann | 7 | Evaluation of Dictionary Learning Algorithms for Image Segmentation |
2 | Yuxiang | Gong | 14 | Hybrid Fluorescence / SPECT system for image-guided open surgery |
3 | Shweta | Shitole | 18 | Graphics and GUI development for clinical testing of vertigo |
4 | Ana | Lopez | 4 | Prediction of Postoperative Ligament Balance in Computer Assisted Total Knee Replacement |
5 | Cristina | Precup | 15 | Towards Prostate Cancer Fusion Biopsy |
6 | Ivan | Olefir | 5 | GUI Development for Performing Spectral Unmixing for Quantitative Multispectral Optoacoustic Tomography and Visualization of Its Results |
7 | Stefano | Trebeschi | 8 | Generation of a normalized template for Arterial Spin Labeling to diagnose dementia |
8 | Denis | Declara | 16 | Interactive Exploration of Large Histological Images |
9 | Beatrice | Lentes | 17 | Automation of Gamma Camera Calibrations |
10 | Hossain | Mahmud | 3 | Visualisation and Segmentation GUI for 3D Microscopy Images |
Thursday, 10.07.2014, 16:00-18:00 |
11 | Poulami | Chakrabarti | 11 | Analysis of phase-amplitude-gating mechanisms in electrical rhythms of the human brain from electroencephalographic (EEG) data acquired in different states of consciousness |
12 | Iro | Laina | 9 | A texture analysis plug-in for a multi-modal, multi parametric analysis package (M3P -Anima) |
13 | Andrii | Kravtsiv | 10 | A flexible toolbox for affine and elastic volume registration in cardiac SPECT and PET |
14 | Shanmugapriya | Survarachakan | 19 | Stent Graft Detection in X-ray Fluoroscopy |
15 | Pedro | Gomez Damian | 1 | Fitting the rotated Diffusional Kurtosis Tensor to MR Diffusion Images |
16 | Sai Gokul | Hariharan | 13 | OpenIGTLink Interface to Robot Operating System |
17 | Catalina | Raymond Guzman | 20 | Creation of a Mesh Preparation Tool for Patient Specific Hemodynamic Simulations |
18 | Salvatore | Virga | 21 | Automatic Inverse Kinematics for Aortic Interventions |
19 | Patmaa | Sridharan | 12 | Depth perception improved Xray mapped on a 3D surface reconstrucion: Application to CAD tools |
20 | Faisal | Ibne Mozher | 2 | Tool development for DICOM data anonymization |
Available Projects
Registration closed.
ID | Project Title | Supervisor | Additional Material |
1 | ASSIGNED! | Fitting the rotated Diffusional Kurtosis Tensor to MR Diffusion Images | Dr. Marion Menzel (GE) | Project Proposal |
2 | ASSIGNED! | Tool development for DICOM data anonymization | Georg Schummers (Tomtec) | Project Proposal |
3 | ASSIGNED! | Visualisation and Segmentation GUI for 3D Microscopy Images | Lichao Wang (CAMP) | Project Proposal |
4 | ASSIGNED! | Prediction of Postoperative Ligament Balance in Computer Assisted Total Knee Replacement | Dr. Martin Bauer (Brainlab) | Project Proposal |
5 | ASSIGNED! | GUI Development for Performing Spectral Unmixing for Quantitative Multispectral Optoacoustic Tomography and Visualization of Its Results | Stratis Tzoumas (Helmholtz) | Project Proposal |
6 | - | Simulations for Intraoperative Patientspecific Emission Tomography | Benjamin Frisch (CAMP) | Project Proposal |
7 | ASSIGNED! | Evaluation of Dictionary Learning Algorithms for Image Segmentation | Sebastian Poelsterl (CAMP) | Project Proposal |
8 | ASSIGNED | Generation of a normalized template for Arterial Spin Labeling to diagnose dementia | Dr. Jan Bauer (Rechts der Isar) | Project Proposal |
9 | ASSIGNED | A texture analysis plug-in for a multi-modal, multi parametric analysis package (M3P -Anima) | Dr. Stephan Nekolla (Rechts der Isar) | Project Proposal |
10 | ASSIGNED! | A flexible toolbox for affine and elastic volume registration in cardiac SPECT and PET | Dr. Stephan Nekolla (Rechts der Isar) | Project Proposal |
11 | ASSIGNED | Analysis of phase-amplitude-gating mechanisms in electrical rhythms of the human brain from electroencephalographic (EEG) data acquired in different states of consciousness | Dr. Afra Wohlschläger (Rechts der Isar) | Project Proposal |
12 | ASSIGNED! | Depth perception improved Xray mapped on a 3D surface reconstrucion: Application to CAD tools | Séverine Habert (CAMP) | Project Proposal |
13 | ASSIGNED | OpenIGTLink Interface to Robot Operating System | Oliver Zettinig (CAMP) | Project Proposal |
14 | ASSIGNED | Hybrid Fluorescence / SPECT system for image-guided open surgery | Thomas Wendler (SurgicEye) | Project Proposal |
15 | ASSIGNED! | Towards Prostate Cancer Fusion Biopsy | Amit Shah (CAMP) | Project Proposal |
16 | ASSIGNED | Interactive Exploration of Large Histological Images | Loic Peter (CAMP) | Project Proposal |
17 | ASSIGNED | Automation of Gamma Camera Calibrations | Philipp Matthies (CAMP) | Project Proposal |
18 | ASSIGNED | Graphics and GUI development for clinical testing of vertigo | Paul MacNeilage (Klinkum Großhadern) | Project Proposal |
19 | ASSIGNED! | Stent Graft Detection in X-ray Fluoroscopy | Stefanie Demirci (CAMP) | Project Proposal |
20 | ASSIGNED | Creation of a Mesh Preparation Tool for Patient Specific Hemodynamic Simulations | Peter Maday (CAMP) | Project Proposal |
21 | ASSIGNED | Automatic Inverse Kinematics for Aortic Interventions | Stefanie Demirci (CAMP) | Project Proposal |
22 | - | Overlaying Patient-Specific Anatomical Information on the Doctor’s View by Combining Google Glass and Microsoft Kinect | Christoph Hennersperger (CAMP) | Project Proposal |
Passing requirements
- Active participation in the lecture meetings
- Submission of all assignments in time
- Present your final assignment work
Literature/Resources
C++
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
OpenGL
Qt
OpenCV
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