TubeTK

Overview

TubeTK is being developed to host algorithms for applications involving images of tubes. By focusing on the geometry of tubes we can accomplish grand challenges in image analysis in a subset of significant cases.

Applications being pursued include:

• Diagnosis of retinopathy of prematurity
• Analysis of vascular differences within and between populations to identify focal (e.g., stroke) and diffuse (e.g., schizophrenia) diseases.
• Vascular atlas formation
• Radiofrequency ablation guidance via intra-operative registration of pre-op CT with intra-op Ultrasound
• Brain tumor resection guidance via intra-operative registration

Imaging modalities involved include:

• MR and CT
• Ultrasound
• Video
• Light Microscopy
• X-ray Microscopy

Features of TubeTK include:

• Centerline vascular segmentation
• Vascular atlas formation
• Vascular network to image registration
• Organ segmentation
• Vascular-ness measures

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 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