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

by Prof. Nassir Navab and Dr. Benjamin Frisch
Tutors: Felix Achilles, Shadi Albarqouni, Leslie Casas and Kristians Diaz

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"): 10.07.2015 Friday 10:00-11:00, 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.

• January 28, 2016: Room change: Final Presentations II will take place at 15:45 in the seminar room of building 11, in MI 03.11.018.
• November 9, 2015: Reminder: The "Documentation, Tests, Design Patterns & Integration Strategy" lecture will be held on Thursday (12th of November) this week.
• November 4, 2015: The CAMP-template for Power Point presentations can be downloaded here
• October 28, 2015: Today's UML lecture is shifted to Thursday, 05.11., 3:30pm-5:00pm. UML lecture slides are online.
• October 21, 2015: Projects are assigned! Please get in contact with your supervisor and arrange a first meeting. Today: First Lecture! (Software Project Management)
• July 10, 2015: Please register for the course at https://matching.in.tum.de/
• July 7, 2015: Initial meeting is scheduled for July 10, 2015 Friday at 10:00.
• July 7, 2015: Course website created.

Registration

Please give rank in the matching system for the course registration between 10 July - 21 July (link). TUMOnline and first come first serve is not valid for practical and seminar courses anymore. For further details about how 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	Topic	Conducted by	Materials
July 10th, 2015	Preliminary meeting ("Vorbesprechung")	Course Tutors	Slides
Oct 14th, 2015	Organizational Issues, Project Announcements	Course Tutors, Project Supervisors	Slides
Oct 21st, 2015	Lecture: Software Project Management	Course Tutors	Slides
Nov 4th, 2015	Project Requirements Presentations	Course Tutors, Seminar Participants	Guidelines
Nov 5th, 2015 (Thu!)	Lecture: Unified Modeling Language (UML)	Course Tutors	Slides
Nov 12th, 2015 (Thu!)	Lecture: Documentation, Tests, Design Patterns & Integration Strategy	Course Tutors	Slides
Four weeks of no session.
Dec 16th, 2015	Intermediate Presentations Part I	Course Tutors, Seminar Participants	Guidelines
Dec 17th, 2015	Intermediate Presentations Part II	Course Tutors, Seminar Participants
Four weeks of no session.
Jan 20th, 2016	Q&A Final Presentations	Course Tutors
Jan 27th, 2016 15:30-18:00	Final Presentations Part I	Course Tutors, Seminar Participants	Guidelines
Jan 28th, 2016 15:45-18:00	Final Presentations Part II in MI 03.11.018.	Course Tutors, Seminar Participants

Final Presentations Schedule

Wednesday, January 27th 2016, 15:30-18:00, CAMP Seminar room. 10 minutes slot for each presenter (plus 2 minutes for questions). [Projects of 2 people will of course get 20 minutes in total plus 4 minutes for questions.]

Slot	Name	Project ID
1st	Alexander	1
2nd	Yadira	16
3rd+4th	Edengenet+Paula	15
5th	Thomas	2
6th+7th	Noor+Anna	8

Thursday, January 28th 2016, 15:30-18:00, CAMP Seminar room. 10 minutes slot for each presenter (plus 2 minutes for questions). [Projects of 2 people will of course get 20 minutes in total plus 4 minutes for questions.]

Slot	Name	Project ID
1st+2nd	Benedikt+Sara	12
3rd	Mai	10
4th	Javier	14
5th	Stefan	7
6th	Sergey	11
7th	Andrzej	4

Intermediate Presentations Schedule

Wednesday, 16.12.2015, 15:30-17:00, CAMP Seminar room. 7 minutes slot for each presenter (plus 2 minutes for questions).

Slot	Name	Project ID
1st+2nd	Noor+Anna	8
3rd+4th	Edengenet+Paula	15
5th	Francisco	14
6th	Ruchik	13
7th+8th	Benedikt+Sara	12
9th	Sergey	11

Thursday, 17.12.2015, 15:30-17:00, CAMP Seminar room. 7 minutes slot for each presenter (plus 2 minutes for questions).

Slot	Name	Project ID
1st	Mai	10
2nd	Yadira	16
3rd	Stefan	7
4th	Andrzej	4
5th	Thomas	2
6th	Alexander	1

Available Projects

ID	Student	Project Title	Supervisor	Additional Material
16	Yadira	Computer assisted optical biopsy for colorectal polyps	Diana Mateus	Project Proposal
6	Vitaly	Simulation of PET detectors based on continuous crystals using GATE	Jorge Cabello	Project Proposal
2	Thomas	Needle tracking for ultrasound-guided biopsies with inside-out vision	Benjamin Busam	Project Proposal
7	Stefan	Visualizing the volumetric accuracy of medical tracking solutions	Benjamin Busam	Project Proposal
11	Sergey	Tracking using Autoencoders and Manifolds	Federico Tombari	Project Proposal
12	Sara, Benedikt	Parallax-free Xray stitching using depth based pose estimation	Séverine Habert	Project Proposal
13	Ruchik	Image-quality dependent ultrasound gel application	Benjamin Frisch	Project Proposal
15	Paula, Edengenet	Automatic triage of patients using anatomical MR images	Gabriel Castrillón	Project Proposal
8	Noor, Anna	Deep Learning for Biomedicine	Vladimir Golkov	Project Proposal
10	Mai	EP-Catheter Enhancement in Lowest Dose Image Series	Stefanie Demirci	Project Proposal
14	Francisco	Bringing the robotic SPECT-CT prototype into the Operating Room	Marco Esposito	Project Proposal
4	Andrzej	Mobile telephony management in Surgery room	Ahmed Elsherbini	Project Proposal
1	Alexander	Electronic Record Form in Ophthalmology for Documentation of Intravitreal Injections	Chris Lohmann	Project Proposal
3	-	Reducing the orthopaedic risk of cycling with a vision-based anthropometric scanner	Benjamin Busam	Project Proposal
5	-	Simulation and reconstruction of the Siemens Biograph mMR using GATE and STIR	Jorge Cabello	Project Proposal
9	-	3D Interventional Stent Reconstruction	Stefanie Demirci	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).

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

• Qt Reference Documentation

OpenCV

• OpenCV Documentation

Not found what you are looking for?

• SampleCodes.zip: Code and example of OpenGL
• OpenGL_TransformationsViewingLight.pdf: OpenGL presentations