3D vessel segmentation of synchrotron phase contrast tomography

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Type
Workflow
Supported image dimension
3D
Interaction Level
Semi-automated
Description

Example workflow

has function
Image analysis
has topic
Bioimage informatics
Tomography
Machine learning
has biological terms
blood vessels
Post date
02/04/2019 - 11:07
Last modified
10/17/2019 - 17:07
Workflow steps
Step 1: Preprocess the image
Enhance Local Contrast (CLAHE)
Homogeneity
Step 2: Segmentation of vessels
ilastik - Carving
Watershed segmentation
Step 3: Extract skeleton
Skeletonize3D
Skeletonisation
Step 4: calculate vessel diameter
Local Thickness (ImageJ)
Object feature extraction
Step 5: Plot profile of diameter along the skeleton
MeVisLab XMarkerShortestPath module (Dijsktra shortest path)
Analysis
Reference Publication Link
Structural coronary artery remodelling in the rabbit fetus as a result of intra…