Neuron Tracing 3D (ImageJ)

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Type
Workflow
Author
Tosí, Sébastien
Chessel, Anatole
Requires
ImageJ
Execution Platform
Linux
Mac
Windows
Implementation Type
plugin
Programming Language
ImageJ Macros
Supported image dimension
3D
Interaction Level
Automated
License/Openness
Free and open source
has function
Filament tracing
Neuron image analysis
Feature enhancement
has biological terms
neuron
Entry Curator
lascholz
Post date
02/26/2019 - 15:39
Last modified
02/26/2019 - 16:53
Workflow steps
Step 1: Run Filament Enhancement (Sato Tubeness)
Tubeness
Step 2: Get maximum pixel value
ImageJ Built-in Macro Functions
Step 3: Threshold enhanced image
Thresholder (ImageJ)
Step 4: Perform Morphological Opening with Maximum (3D) followed by Minimum (3D)
Maximum (3D) VIB Protocol
Step 5: Perform Morphological Opening with Maximum (3D) followed by Minimum (3D)
Minimum (3D) Filter VIB Protocol
Step 6: Run Fill Holes 3D
3D Fill holes (mcib3d)
Step 7: Skeletonize binary mask
Skeletonize3D
Step 8: Analyze Skeleton
ImageJ Analyze Skeleton
Download Page
Neubias BIAFLOWS workflow of Neuron Tracing 3D with ImageJ
has comparison
BIAFLOWS Neuron Tracing 3D project