Filament Tracing Tubeness (ImageJ)

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Type
Workflow
Author
Tosí, Sébastien
Requires
ImageJ
Tubeness
Execution Platform
Linux
Mac
Windows
Programming Language
ImageJ Macros
Supported image dimension
3D
Interaction Level
Automated
License/Openness
Free and open source
Description

Blood vessels tracing in 3D image from Tubeness filtering (user defined scale), 3D opening (radius set to 2), thresholding (user defined level) and 3D skeletonization.

has function
Filament tracing
Image segmentation
Feature enhancement
Skeletonisation
has topic
Bioimage informatics
has biological terms
blood vessels
tubular structure
filament
Entry Curator
czhang
Post date
01/23/2020 - 17:22
Last modified
05/17/2023 - 18:50
Workflow steps
Step 1: Enhance tubular structure with Tubeness Filter
Tubeness
Feature enhancement
Step 2: Run Maximum neighbor filter
3D ImageJ Suite
Morphological operation
Step 3: Run Minimum neighbor filter
3D ImageJ Suite
Morphological operation
Step 4: Threshold (binarize) image
ImageJ Threshold
Image segmentation
Step 5: Skeletonize
Skeletonize3D
Image processing
Download Page
Neubias BIAFLOWS workflow of Filament Tracing with ImageJ
has comparison
BIAFLOWS-PROBLEM: VESSEL-TRACING-3D