Tubular Geodesics using Oriented Flux: An ITK Implementation

Benmansour, Fethallah,Turetken, Engin1*,Fua, Pascal
1.EPFL
Abstract

Abstract

This document describes an ITK implementation of an interactive method for tracing curvilinear structures. The basic tools provided in this framework are an oriented flux-based tubularity measure and a geodesic path tracer that uses the fast marching algorithm. The framework is efficient and requires minimal user interaction to trace curvilinear structures such as vessels and neurites in 2D images and 3D image stacks.

Keywords

Vessel TracingCurvilinear StructuresTubular structuresOptimally Oriented FluxTubularityTubular GeodesicTracingTree-like StructuresReconstructionSegmentationNeurite TracingCenterline ExtractionMinimal Path
Manuscript
Source Code and Data

Source Code and Data

__MACOSXTubularGeodesics._.DS_Store82 B._itkMultiScaleTubularityMeasureImageFilter.h171 B._itkOrientedFluxMatrixImageFilter.hxx171 B._itkOrientedFluxCrossSectionTraceMeasure.hxx216 B._itkPolyLineParametricTubularPath.h171 BTubularGeodesics.DS_Store12 KBCMakeLists.txt4.8 KBIJMacros.txt3.4 KBDeleteCMakeGeneratedFiles.sh557 BPathCompare.cxx3.6 KBREADME.txt1.1 KBdataOP_1.tif923.5 KBOP_1_01.meta340 BOP_1_01.swc8.4 KBOP_1_02.meta339 BOP_1_02.swc8.1 KBOP_1_03.meta339 BOP_1_03.swc7.1 KBOP_1_04.meta340 BOP_1_04.swc5.9 KBReal-DSA-01.jpg51.9 KBReal-DSA-01_01.meta317 BReal-DSA-01_01.swc26.2 KBReal-DSA-01_02.meta316 BReal-DSA-01_02.swc44.2 KBReal-DSA-01_03.meta317 BReal-DSA-01_03.swc34.1 KBSynthetic-02.meta317 BSynthetic-02.png22.3 KBSynthetic-02.swc96.9 KBitkMultiScaleTubularityMeasureImageFilter.cxx17.1 KBitkMultiScaleTubularityMeasureImageFilter.h14.7 KBitkMultiScaleTubularityMeasureImageFilter.hxx23.4 KBitkOrientedFluxCrossSectionTraceMeasure.h5 KBitkOrientedFluxCrossSectionTraceMeasure.hxx4.9 KBitkOrientedFluxMatrixImageFilter.h9.1 KBitkOrientedFluxMatrixImageFilter.hxx17.2 KBitkPolyLineParametricTubularPath.h9.6 KBitkPolyLineParametricTubularPath.hxx31.6 KBitkRK4CharacteristicDirectionsToPathFilter.h8.6 KBitkRK4CharacteristicDirectionsToPathFilter.hxx15.6 KBitkTubularMetricToPathFilter.cxx14.9 KBitkTubularMetricToPathFilter.h7.4 KBoutputs.gitignore71 BitkTubularMetricToPathFilter.hxx9 KB

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