Difference between revisions of "TubeTK/Documentation"

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= Documentation =
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{| border="1" cellpadding="10" cellspacing="0"
|+ [[image:TubeTK_Header.jpg|1000px]]
|-
| style="background:#efefef;" align="left" valign="top" width="150px" |


* [[TubeTK/MeetingNotes | Events and Meetings]]
'''[[TubeTK|Home]]'''
*[[TubeTK/About|About]]
*[[TubeTK/Images|Image Gallery]]
*[[TubeTK/Data|Data and Publications]]
<br>
----
<br>
'''For Users'''
* [[TubeTK/Installation|Installation]]
* [[TubeTK/Documentation|Methods & Apps]]
* [[TubeTK/Slicer|TubeTK with 3D Slicer]]
* [[TubeTK/OsiriX|TubeTK with OsiriX]]
<br>
----
<br>
'''For Developers'''
* [[TubeTK/Development|Development Docs]]
<br>
----
<br>
'''[https://github.com/TubeTK/TubeTK/issues Report Bugs<br>Request Features]'''
<br>
<br>
----
<br>
'''[[TubeTK/Contact|Contact Us]]'''


| width="800px" align="left" |
= Applications =
# '''GUI Applications'''
# '''Command-line (CLI) Applications'''
#* Command-line applications can be run directly from the command line, or graphically using 3D Slicer
#* [[TubeTK/Documentation/AtlasBuilderUsingIntensity | AtlasBuilderUsingIntensity]]
#* [[TubeTK/Documentation/ComputeBinaryImageSimilarityMetrics | ComputeBinaryImageSimilarityMetrics]]
#* [[TubeTK/Documentation/ComputeImageSimilarityMetrics | ComputeImageSimilarityMetrics]]
#* [[TubeTK/Documentation/ComputeImageStatisticsUsingMask | ComputeImageStatisticsUsingMask]]
#* [[TubeTK/Documentation/ComputeSegmentTubesParameters | ComputeSegmentTubesParameters]]
#* [[TubeTK/Documentation/ComputeTubeGraphProbability | ComputeTubeGraphProbability]]
#* [[TubeTK/Documentation/ComputeTubeMeasures | ComputeTubeMeasures]]
#* [[TubeTK/Documentation/ComputeTubeProbability | ComputeTubeProbability]]
#* [[TubeTK/Documentation/ConvertInnerOpticToPlus | ConvertInnerOpticToPlus]]
#* [[TubeTK/Documentation/ConvertShrunkenSeedImageToList | ConvertShrunkenSeedImageToList]]
#* [[TubeTK/Documentation/ConvertTRE | ConvertTRE]]
#* [[TubeTK/Documentation/ConvertTubeGraphToImage | ConvertTubeGraphToImage]]
#* [[TubeTK/Documentation/ConvertTubesToDensityImage | ConvertTubesToDensityImage]]
#* [[TubeTK/Documentation/ConvertTubesToImage | ConvertTubesToImage]]
#* [[TubeTK/Documentation/ConvertTubesToSurface | ConvertTubesToSurface]]
#* [[TubeTK/Documentation/ConvertTubeToTubeGraph | ConvertTubeToTubeGraph]]
#* [[TubeTK/Documentation/CropImage | CropImage]]
#* [[TubeTK/Documentation/DeblendTomosynthesisSlicesUsingPrior | DeblendTomosynthesisSlicesUsingPrior]]
#* [[TubeTK/Documentation/EnhanceCoherenceAndEdgesUsingDiffusion | EnhanceCoherenceAndEdgesUsingDiffusion]]
#* [[TubeTK/Documentation/EnhanceCoherenceUsingDiffusion | EnhanceCoherenceUsingDiffusion]]
#* [[TubeTK/Documentation/EnhanceContrastUsingPrior | EnhanceContrastUsingPrior]]
#* [[TubeTK/Documentation/EnhanceEdgesUsingDiffusion | EnhanceEdgesUsingDiffusion]]
#* [[TubeTK/Documentation/EnhanceTubesUsingDiffusion | EnhanceTubesUsingDiffusion]]
#* [[TubeTK/Documentation/EnhanceTubesUsingDiscriminantAnalysis | EnhanceTubesUsingDiscriminantAnalysis]]
#* [[TubeTK/Documentation/EnhanceUsingDiscriminantAnalysis | EnhanceUsingDiscriminantAnalysis]]
#* [[TubeTK/Documentation/EnhanceUsingNJetDiscriminantAnalysis | EnhanceUsingNJetDiscriminantAnalysis]]
#* [[TubeTK/Documentation/ImageCompareCommand | ImageCompareCommand]]
#* [[TubeTK/Documentation/JsonCompareCommand | JsonCompareCommand]]
#* [[TubeTK/Documentation/MergeAdjacentImages | MergeAdjacentImages]]
#* [[TubeTK/Documentation/MergeTubeGraphs | MergeTubeGraphs]]
#* [[TubeTK/Documentation/RegisterImages | RegisterImages]]
#* [[TubeTK/Documentation/RegisterUsingImageCenters | RegisterUsingImageCenters]]
#* [[TubeTK/Documentation/RegisterUsingSlidingGeometries | RegisterUsingSlidingGeometries]]
#* [[TubeTK/Documentation/ResampleImage | ResampleImage]]
#* [[TubeTK/Documentation/SampleCLIApplication | SampleCLIApplication]]
#* [[TubeTK/Documentation/SegmentBinaryImageSkeleton | SegmentBinaryImageSkeleton]]
#* [[TubeTK/Documentation/SegmentConnectedComponents | SegmentConnectedComponents]]
#* [[TubeTK/Documentation/SegmentConnectedComponentsUsingParzenPDFs | SegmentConnectedComponentsUsingParzenPDFs]]
#* [[TubeTK/Documentation/SegmentTubes | SegmentTubes]]
#* [[TubeTK/Documentation/SegmentUsingOtsuThreshold | SegmentUsingOtsuThreshold]]
#* [[TubeTK/Documentation/ShrinkImage | ShrinkImage]]
#* [[TubeTK/Documentation/SimulateAcquisitionArtifactsUsingPrior | SimulateAcquisitionArtifactsUsingPrior]]
#* [[TubeTK/Documentation/SubSampleTubes | SubSampleTubes]]
#* [[TubeTK/Documentation/TextCompareCommand | TextCompareCommand]]
#* [[TubeTK/Documentation/TransformTubes | TransformTubes]]
#* [[TubeTK/Documentation/HessianVesselness2D | Hessian Vesselness 2D]]
#* [[TubeTK/Documentation/ExtractCurves2D | Extract Curves 2D]]
#* [[TubeTK/Documentation/ComputeTortuosity | Compute Tortuosity]]
#* [[TubeTK/Documentation/Sliding_Organ_Registration | Sliding Geometries Registration]]
# '''3D Slicer Python Applications'''
#* [[TubeTK/Documentation/InteractivePDFSegmenter | Interactive PDF Segmenter]]


* [[TubeTK/Design | Design discussions]]
= Modules =
* [[TubeTK/Build | Build instructions]]
# Pre-processing
* [[TubeTK/DevelopersGuide | Developers guide]]
#* [[TubeTK/Anisotropic Hybrid Diffusion with Continuous Switch|Anisotropic Hybrid Diffusion with Continuous Switch]]
* [[TubeTK/DevelopersFAQ | Developers FAQ]]
# Object segmentation
* [[TubeTK/GITCheatSheet | GIT Tips and Tricks]]
# Tube extraction
* Applications
#* [[TubeTK/RadiusEstimationFunction|Radius Estimations Functions]]
*# GUI Applications
# Data structures
*# Command-line (CLI) Applications
# Topology analysis
*#* [[TubeTK/HessianVesselness2D | Hessian Vesselness 2D]]
# Editing
*#* [[TubeTK/ExtractCurves2D | Extract Curves 2D]]
# Export
* Modules
#  [[TubeTK/OpenIGTLink|OpenIGTLink]]
*# Pre-processing
# Python
*#* [[TubeTK/Anisotropic Hybrid Diffusion with Continuous Switch]]
#* [http://nbviewer.ipython.org/5925084 Tube NumPy Array]
*# Object segmentation
 
*# Tube extraction
= Related Efforts =
*# Data structures
 
*# Topology analysis
* [[TubeTK/Related Work|Related Work]]
*# Editing
 
*# Export
|}
*#  [[TubeTK/OpenIGTLink | OpenIGTLink]]
 
* [[TubeTK/Reference | References and related works]]
[[Category:TubeTK|Documentation]]
* Miscellaneous
**[http://en.wikipedia.org/wiki/Math_markup Math formula editing in Wiki]
**[http://en.wikipedia.org/wiki/Wikipedia:FAQ/Editing General Wiki Editing FAQ]

Latest revision as of 20:36, 13 October 2015

__NOTITLE__


TubeTK Header.jpg

Home




For Users




For Developers




Report Bugs
Request Features




Contact Us

Applications

  1. GUI Applications
  2. Command-line (CLI) Applications
  3. 3D Slicer Python Applications

Modules

  1. Pre-processing
  2. Object segmentation
  3. Tube extraction
  4. Data structures
  5. Topology analysis
  6. Editing
  7. Export
  8. OpenIGTLink
  9. Python

Related Efforts