3D vessel segmentation of synchrotron phase contrast tomography

need a thumbnail
Type
Workflow
Post date
02/04/2019 - 11:07
Last modified
02/04/2019 - 11:45
Workflow steps
Step 1: Preprocess the image
Enhance Local Contrast (CLAHE)
Step 2: Segmentation of vessels
ilastik - Carving
Step 3: Extract skeleton
Skeletonize3D
Step 4: calculate vessel diameter
Local Thickness (ImageJ)
Step 5: Plot profile of diameter along the skeleton
MeVisLab XMarkerShortestPath module (Dijsktra shortest path)