TeachingWs18PMSD

Chair for Computer Aided Medical Procedures & Augmented Reality
Lehrstuhl für Informatikanwendungen in der Medizin & Augmented Reality

Lab Course / Praktikum: Project Management and Software Development for Medical Applications

by Prof. Nassir Navab
Team: Beatrice Demiray, Javier Esteban, Hendrik Burwinkel
Type: Master Practical Course Module IN2106
SWS: 6
Programs: Biomedical Computing (Master), Informatics (Master)
ECTS: 10 Credits

Preliminary Meeting ("Vorbesprechung"): Monday, 25.06. at 18:30 - 19:00 CEST in the CAMP Seminar Room 03.13.010
Further Meetings: See the schedule below.

The course will be conducted in English.

Announcements

  • !NEW! 12.06.2018 Preliminary Meeting scheduled!
  • 10.06.2018: 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, September 9th, 2018.

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
Monday, 25.06.2018 - 18:30 - 19:00 03.13.010 Preliminary Meeting All course tutors
29.06. to 04.07.18 TUM Matching platform Registration Students Matching FAQ
Thursday, 18.10.2018 - 15:00-17:30 03.13.010 Introduction, Project Announcements (attendance mandatory) All course tutors
Thursday, 18.10.2018 - until 23:59 E-mail to Beatrice Demiray Students required to indicate project preferences Students Student Application Template
Monday, 22.10.2018 E-mail / course website Project assignments published Beatrice Demiray  
Thursday, 25.10.2018 - 14:00-17:30 03.13.010 Lecture I: Presentation Tips & Project Management, Lecture II: Software Engineering - UML Hendrik Burwinkel, Beatrice Demiray Presentation Rules and Tips

Project Management

UML
Monday, 29.10.2018 - 10:00-12:00 03.13.010 Presentation Training (attendance mandatory1) Marcus Vollrath, Beatrice Demiray Slides
Monday, 05.11.2018 - 09:00-12:00 03.13.010 Requirements (Kick Off) Presentations (attendance mandatory) All course tutors  
Monday, 05.11.2018 - 23:59 Link will be provided Presentation slides upload (Kick Off) Students  
Thursday, 08.11.2018 - 13:00-14:30 03.13.010 Lecture III: Documentation, Testing & Integration Strategy Javier Esteban  
Thursday, 13.12.2018 - 14:00-18:00 Big Auditorium @ TranslaTUM (ground floor) Intermediate Presentations Vol. 1 (attendance mandatory) All course tutors  
Friday, 14.12.2018 - 10:00-14:00 Small Auditorium @ TranslaTUM (ground floor) Intermediate Presentations Vol. 2 (attendance mandatory) All course tutors  
Friday, 14.12.2018 - 23:59 Link will be provided Presentation slides upload (Intermdediate) Students  
Monday, 04.02.2019 - 10:00-12:30 03.13.010 Final Presentations Vol. 1 (attendance mandatory) All course tutors  
Thursday, 07.02.2019 - 14:00-17:30 03.13.010 Final Presentations Vol. 2 (attendance mandatory) All course tutors  
Thursday, 07.02.2019 - 23:59 Link will be provided Presentation slides upload (Final) Students  
1) Students who are attending or have already attended the presentation training as part of either the lab course MedInnovate or the seminar Lost in Translation can be excused from the mandatory presentation training on 29.10.2018. Please write a short e-mail to

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 Schedule



Available 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 18.10.2018 - 23:59 CEST. Use the Student Application Template provided under Download.



Project ID Student Project Title Supervisor Additional Material
01 Courtney Restivo Quantification of Tissue Oxygenation Saturation with MSOT using Deep Learning Ivan Olefir Project Description
02 Javier Danilo Coronel Baracaldo Deep learning-based tumor detection in 3D scans Oliver Schoppe Project Description
03 Tom Nuno Wolf Computer-aided survival, grading predicton and segmentaton of soft tissue sarcomas in MRI Fernando Navarro, Jan Peeken Project Description
04 Adria Font Calvarons Semi-Automatic Cell Labelling Tool Mario Emmenlauer Project Description
05 Eduardo Prado Diabetes App Stefan Christoph Kofler Project Description
06 Julio Alberto Oscanoa Aida Accelerating water-fat MRI using compressed sensing Stefan Ruschke, Dimitrios Karampinos Project Description
07 Hyunjun Jung Spatio-Temporal Depth Estimation in Real-Time Benjamin Busam Project Description
08 Arian Mehrfad, Yordanka Velikova, Cristina Serrano Gonzalez Micro-manipulation – From industrial to cell-robots Javier Esteban Project Description
09 Rahman Md Salman Cloud Service for Human Pose Estimation Ashkan Khakzar, Raveekiat Singhaphandu, Angelica Crone Project Description
10 Stefan Haninger Ray Tracing with RT Cores for Forward Modeling in Medical X-ray Computed Tomography Tobias Lasser Project Description
11 Ivan Pavlov Deep Field: Ultrasound simulation via deep learning Guillaume Zahnd Project Description
12 Maria Margarida Regateiro Machado e Costa Carotid Wall Shear Stress Guillaume Zahnd Project Description
13 Aashay Tinaikar Ultrasound Confidence Map Guillaume Zahnd Project Description
14 Navdar Karabulut DeepFormer Data Analysis Tool Walter Simson Project Description
15 Aidana Massalimova DeepFormer SUPRA Integration Walter Simson Project Description
16 Mariya Stankevich Proteins Colonies Illumination and Behavior Analyzing Software Andre Stiel Project Description
17 Berk Olcay Mobile test for spatial memory Virginia Flanagin Project Description
18 Awais Shafique Adaptation of Weakly-supervised Convolutional Neural Networks Registration for Neurosurgical Setting Julia Rackerseder Project Description
19 Hooriya Anam Utilizing Confidence Maps for Accurate 3D Brain Image Registration Julia Rackerseder Project Description
20 Jorge Mario Guerra Gonzalez Implementation of Landmark free 3D US to MRI Registration Initialization Julia Rackerseder Project Description
21 Amir Nourinia Fully Automatic Fusion of large 3D Microscopy Volumes Mario Emmenlauer Project Description
23 Michael Wengler Arivis Vision4D plugin for automatic vessel segmentation in LSFM stacks Beatrice Demiray Project Description
24 Khac Thanh-An Le Blood Vessel Quantification in MRI Beatrice Demiray Project Description
25 Granit Bimbashi 3D Ultrasound for Thyroid Imaging Thomas Wendler Project Description
26 Christina Bukas Brachytherapy Planning Software Thomas Wendler Project Description
27 Christopher Watanabe Monte Carlo simulations for Brachytherapy Thomas Wendler Project Description
30 Desislava Dimova Dose Prediction Software for SIRT Thomas Wendler Project Description
31 Rajat Chhabra Development of a software solution for recognizing motion in various video sources deployed in a clinical environment Claudia Mattes Project Description



Download



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++

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)

Github

Qt

Other useful tools and libraries


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: 2018WiSe
Abstract:  


Edit | Attach | Refresh | Diffs | More | Revision r1.22 - 31 Oct 2018 - 07:04 - BeatriceLentes

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