Dissemination:EPFL Workshop 2005

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ITK intensive course

Summary

This course was successfully concluded. This was a developer course in ITK for which new advanced material was created. This was the first course for ITK that was not attached to a conference. 37 attendees were present (enrollment was limited to 30!) from 9 countries: Switzerland (14), Spain (7), Belgium (7), Italy (3), France (3 - the developers of gdcm ITK dicom reader), Germany (1), UK (1), Sweden (1), US (1).


Organization

Swiss Federal Institute of Technology (EPFL), Lausanne, Switzerland

October 5-7, 2005


http://itk.epfl.ch


Context

ITK is an open-source software toolkit for performing registration and segmentation. ITK is implemented in C++. ITK is cross-platform, using the CMake build environment to manage the configuration process. In addition, an automated wrapping process generates interfaces between C++ and interpreted programming languages such as Tcl, Java, and Python. This enables developers to create software using a variety of programming languages. ITK's C++ implementation style is referred to as generic programming (i.e., using templated code). Such C++ templating means that the code is highly efficient, reusable, and that many software problems are discovered at compile-time, rather than at run-time during program execution. Because ITK is an open-source project, developers from around the world can use, debug, maintain, and extend the software. ITK uses a model of software development referred to as extreme programming. Extreme programming collapses the usual software creation methodology into a simultaneous and iterative process of design-implement-test-release

Objectives of the course

This intensive course aims both at giving a brief introduction to ITK for new and potential users, as well as in-depth details on advanced ITK programming for ITK developers. Moreover, a special session will be dedicated to the link between ITK and different medical image viewers. The course will include plenary presentation by specialists from Kitware Inc. (http://www.kitware.com) as well as hands-on exercises on real, practical problems in medical imaging.

Organization

The course is organised by the Signal Processing Institute (ITS) of the Swiss Federal Instittue of Technology (EPFL), Lausanne, Switzerland (http://itswww.epfl.ch), under the direction of Prof. Jean-Philippe Thiran. It is supported by the European Network of Excellence (NoE) SIMILAR (http://www.similar.cc) on multimodal interfaces.

Instructors

  • Luis Ibanez, Kitware Inc,
  • Steve Pieper of Isomics, Inc,

Isomics Inc. is the company in charge of the Dissemination core of the National Alliance for Medical Image Computing (NAMIC).

Kitware Inc. is the company responsible for the maintenance of the ITK toolkit, and dedicated to providing professional consulting services about ITK and other open-source packages, including VTK, CMake and ParaView.

Program

Picture of the group at the EPFL workshop

Wednesday, October 5th 2005

  • 12:00 - 12:30 Hands on exercices (hoe) (Ibanez)
  • 12:30 - 13:30 Lunch
  • 13:30 - 13:50 NAMIC Introduction - NAMIC Kit (Ron Kikinis: NA-MIC Overview)
  • 13:50 - 14:50 Writing an ITK filter (hoe) (Ibanez: Presentation: Insight-Writing-a-New-Filter)
  • 17:20 - 19:00 Poster Session

Thursday, October 6th 2005

  • 10:30 - 11:00 Coffee Break
  • 11:00 - 12:00 Optimization: Inlining, Functors, Metaprogramming (Ibanez)
  • 12:00 - 13:00 Lunch
  • 14:30 - 15:30 New classes, ITK Road Map (Ibanez)
  • 15:30 – 16:00 Coffee Break
  • 16:00 – 17:30 Iterators, Adaptors, Calculators + open discussion (Ibanez)

Friday, October 7th 2005

  • 8:30 - 9:30 Registration Framework (Ibanez: Presentation: ITK Image Registration)
  • 9:30 - 10:30 Writing an Image Metric (hoe) (Ibanez)
  • 10:30 - 11:00 Coffee Break
  • 14:00 - 15:00 Segmentation Methods (Ibanez: Presentation: ITK Segmentation)
  • 15:00 - 16:00 Practical Case : Brain Tumor (Ibanez)
  • 16:00 - 17:00 Practical Case : Abdominal Aortic Aneurysm (Ibanez)

Exercises Source Code

The source code of the hands-on exercises is contained in the following zip file.

File:ITKCourseExercises.zip

Open Discussions and Attendant Projects

Open Discussions and Attendants Projects

Venue and accommodation

Lausanne is a beautiful city in the heart of western Switzerland on the shores of Lake Geneva. It is easy to reach from anywhere – by road (the A1/E25 and A9/E27 motorways), by rail (both the Swiss Federal Railway network and the French TGV Paris-Milan line) and by air (just 40 miles from Geneva-Cointrin International Airport). Lausanne is also close to many popular excursion destinations such as Montreux and Chillon Castle, Zermatt and the Matterhorn, the Jungfrau and Lucerne, the historical hamlet of Gruyères, the Les Diablerets Glacier, the Vaud Alps and the famous French resort of Chamonix.

A list of selected hotels will be provided. Moreover, low cost student accommodation will be proposed.

Registration

Registration and registration fees: will be published later on http://itk.epfl.ch Attendance will be limited. Potential participants are invited to send already an email to JP.Thiran@epfl.ch for declaring their interest and receiving updated information when available.

For more information: Please visit regularly our web page: http://itk.epfl.ch

Course Preparation

Please download the 3D Slicer 2.5 binaries for your platform by following the links here:

http://wiki.na-mic.org/Wiki/index.php/Slicer:Workshops:User_Training_101

Binaries are available for windows, linux, mac and solaris.

Please also get the following data sets that we will use for the hands on exercises:

http://wiki.na-mic.org/Wiki/images/f/f8/Tutorial-with-dicom.zip

http://wiki.na-mic.org/Wiki/images/5/5c/Mrt-images.zip

http://wiki.na-mic.org/Wiki/images/a/aa/Reg-sample.zip

http://wiki.na-mic.org/Wiki/images/2/2d/SlicerSampleDTI.zip


We won't have time to cover much about programming in 3D Slicer, but if you are interested in more detail, please see the information at:

http://www.slicer.org

There is also programming and architecture information here:

http://www.na-mic.org/Wiki/index.php/Dissemination:Workshop_Feb17-18_2005