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3rdParty
3rdParty
 
 
CGAL
CGAL
 
 
ITK
ITK
 
 
debugMATs
debugMATs
 
 
demos
demos
 
 
figuresOut
figuresOut
 
 
testData
testData
 
 
.gitmodules
.gitmodules
 
 
MIJ_wrapper.m
MIJ_wrapper.m
 
 
README.md
README.md
 
 
SDFVals.txt
SDFVals.txt
 
 
analyzeMeshMorphology.m
analyzeMeshMorphology.m
 
 
analyze_getSDFvalues.m
analyze_getSDFvalues.m
 
 
analyze_permeabilityCoefficient.m
analyze_permeabilityCoefficient.m
 
 
denoiseMicroscopyImage.m
denoiseMicroscopyImage.m
 
 
denoise_BM4D_withAnscombe_wrapper.m
denoise_BM4D_withAnscombe_wrapper.m
 
 
denoise_BM4Dwrapper.m
denoise_BM4Dwrapper.m
 
 
denoise_NLMeansPoissonWrapper.m
denoise_NLMeansPoissonWrapper.m
 
 
denoise_anscombeTransform.m
denoise_anscombeTransform.m
 
 
denoise_estimateNoiseWrapper.m
denoise_estimateNoiseWrapper.m
 
 
denoise_guidedFilterWrapper.m
denoise_guidedFilterWrapper.m
 
 
enhance_brightenVessels.m
enhance_brightenVessels.m
 
 
enhance_clipAboveLevel.m
enhance_clipAboveLevel.m
 
 
enhance_sigmoidFilter.m
enhance_sigmoidFilter.m
 
 
exportTheResults.m
exportTheResults.m
 
 
export_figureToDisk.m
export_figureToDisk.m
 
 
export_segmentedVessels_as3D.m
export_segmentedVessels_as3D.m
 
 
export_stack_toDisk.m
export_stack_toDisk.m
 
 
extractCenterline.m
extractCenterline.m
 
 
importMicroscopyFile.m
importMicroscopyFile.m
 
 
import_cellStackToMatrix.m
import_cellStackToMatrix.m
 
 
import_checkImportedData.m
import_checkImportedData.m
 
 
import_checkQuality.m
import_checkQuality.m
 
 
import_parseMetadata.m
import_parseMetadata.m
 
 
init_parallelComputing.m
init_parallelComputing.m
 
 
mesh_CGAL_reconstructionFromPoints.m
mesh_CGAL_reconstructionFromPoints.m
 
 
mesh_checkCGALSystemOutput.m
mesh_checkCGALSystemOutput.m
 
 
mesh_constructCGALparameters.m
mesh_constructCGALparameters.m
 
 
mesh_filterMain.m
mesh_filterMain.m
 
 
mesh_setCGALFilterDefaultParam.m
mesh_setCGALFilterDefaultParam.m
 
 
points_CGAL_filterCall.m
points_CGAL_filterCall.m
 
 
points_filterCGALCombo.m
points_filterCGALCombo.m
 
 
process_SingleFile.m
process_SingleFile.m
 
 
reconstructMeshFromSegmentation.m
reconstructMeshFromSegmentation.m
 
 
reconstruct_fromTIFF.m
reconstruct_fromTIFF.m
 
 
reconstruct_marchingCubes_wrapper.m
reconstruct_marchingCubes_wrapper.m
 
 
registerTheMeshes.m
registerTheMeshes.m
 
 
save_plotToDisk.m
save_plotToDisk.m
 
 
segmentVessels.m
segmentVessels.m
 
 
segment_asetsPreProcessImages.m
segment_asetsPreProcessImages.m
 
 
segment_createRegionFromVessel.m
segment_createRegionFromVessel.m
 
 
segment_enhanceTubularityForImage.m
segment_enhanceTubularityForImage.m
 
 
segment_findEdges.m
segment_findEdges.m
 
 
segment_getPerimeterOfRegion.m
segment_getPerimeterOfRegion.m
 
 
segment_maxFlow_wrapper.m
segment_maxFlow_wrapper.m
 
 
vesselnessFilter.m
vesselnessFilter.m
 
 
vesselness_MDOF_ImageJ_wrapper.m
vesselness_MDOF_ImageJ_wrapper.m
 
 
vesselness_OOF_wrapper.m
vesselness_OOF_wrapper.m
 
 
vesselness_OofOFA_wrapper.m
vesselness_OofOFA_wrapper.m
 
 
visualize_denoising.m
visualize_denoising.m
 
 
visualize_imageQuality.m
visualize_imageQuality.m
 
 
visualize_meshWithColormap.m
visualize_meshWithColormap.m
 
 
visualize_vesselSegmentation.m
visualize_vesselSegmentation.m
 
 
visualize_vesselSegmentationSlices.m
visualize_vesselSegmentationSlices.m
 
 
visualize_vesselnessFilter.m
visualize_vesselnessFilter.m
 
 
visualize_vesselnessWithDenoising.m
visualize_vesselnessWithDenoising.m
 
 

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twoPhotonVessels

In development, hard to keep up with the documentation at the same time

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Analysis for 2-PM vasculature

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