TubeTK

Overview

TubeTK is being developed to host algorithms for applications involving vascular images. It is intended to provide modules that can be integrated into Slicer.

Driving problems

• TubeTK/Vascular_Pattern_Analysis
• TubeTK/Sliding_Organ_Registration
• TubeTK/Intra-operative_Ultrasound_Registration

Funding

The development of TubeTK is being funded, in part, by the following grants

1. the NIH/NIBIB sponsored "National Alliance of Medical Image Computing" (NA-MIC, PI: Kikinis) project
   • 1U54EB005149-01
   • http://www.na-mic.org
2. the DARPA sponsored "Trust in Integrated Circuits" (EXPOSE, PI: Bajura) program
   • USC/ISI Team
   • http://www.darpa.mil/MTO/Programs/trust/index.html
3. the NIH/NCI sponsored "Image Registration for Ultrasound-Based Neurosurgical Navigation" (NeuralNav, PI: Aylward, Wells)
   • 1R01CA138419-01
   • http://public.kitware.com/Wiki/NeuralNav

License

TubeTK is distributed under the [http://www.apache.org/licenses/LICENSE-2.0 Apache 2.0 license]. You are free to use, modify, and redistribute TubeTK for non-commercial and commercial uses. Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. You may obtain a copy of the License at

Project Development

Collaborative Software Development Tools

• Dashboard
  • https://www.kitware.com/CDash/index.php?project=TubeTK
  • Analytics on dashboard: https://www.google.com/analytics/settings/home#scid=15664873
• Git
  • Website: http://gitorious.org/tubetk/
  • Main Repository:
    • git clone git://gitorious.org/tubetk/tubetk.git
    • git push git@gitorious.org:tubetk/tubetk.git master
  • Playpen
    • git clone git://gitorious.org/tubetk/tubetk-playpen.git
    • git push git@gitorious.org:tubetk/tubetk-playpen.git
• Mantis
  • TBD
• Doxygen
  • TBD

Required third-party tools

• ITK
  • cvs -d :pserver:<YOURNAME>@itk.org:/cvsroot/Insight login ...
  • ITK recommends uuid-dev package on Linux

Optional third-party tools

• Slicer (our preferred method delivery tool)
  • svn co http://svn.slicer.org/Slicer3/trunk Slicer4
  • Requires Qt>=4.6.1 (note: 4.6.2 included with Ubuntu 10.04)
• InsightApplications (Utility apps)
  • cvs -d :pserver:<YOURNAME>@itk.org:/cvsroot/Insight co InsightApplications
  • ImageViewer requires FLTK 1.1.X and VTK
  • ImageColorViewer is a great way to view image registration results.
    • svn co http://svn.easysw.com/public/fltk/fltk/branches/branch-1.1/ fltk-1.1.10
    • http://qt.nokia.com/downloads
  • Requires:
    • VTK
      • git clone git://vtk.org/VTK.git VTK
    • FLTK
      • apt-get install fluid
• IPython (Batch Processing)
  • http://ipython.scipy.org/
  • Using IPython for scientific and parallel computing
    • https://www.osc.edu/cms/sip/

Project Administration

• Events and Meetings

Documentation

• Design discussions
• Build instructions
• Developers guide
• Developers FAQ
• GIT Tips and Tricks
• Applications
  1. GUI Applications
  2. Command-line (CLI) Applications
     • Hessian Vesselness 2D
     • Extract Curves 2D
• Modules
  1. Pre-processing
     • TubeTK/Anisotropic Hybrid Diffusion with Continuous Switch
  2. Object segmentation
  3. Tube extraction
  4. Data structures
  5. Topology analysis
  6. Editing
  7. Export
  8. OpenIGTLink
• References and related works
• Miscellaneous
  • Math formula editing in Wiki
  • General Wiki Editing FAQ

Contacts

• Stephen Aylward
  • stephen.aylward@kitware.com
• Andinet Enquobaharie
• Casey Goodlett
• Patrick Reynolds
• Hua Yang