Filament tracing operations are image analysis operations in which there is an image of a filamentous structure (it may be a tree-like structure, a filament network or a agglomeration of single 'stick-like' filaments) as input and outputs data that represent the filament, most commonly a skeleton representation of the filaments and their diameters or surfaces.

Synonyms
Tubular structure extraction
biofilament tracing
Curvilinear structure reconstruction
Curvilinear structure detection
neuron image analysis
neuron reconstruction

Filament Tracing LocThresh (ImageJ)

Description

Blood vessels tracing in 3D image from 3D Gaussian blurring (user defined radius), local thresholding (user defined radius and offset) and 3D skeletonization. Dockerized version for BIAFLOWS,

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Filament Tracing Tubeness (ImageJ)

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.

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Neuron Tracing Vaa3D (MOST)

Description

3D Neuron Tracing with a Dockerized version of Vaa3D MOST Raytracer.

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Neuron Tracing 3D (Rivuletpy)

Description

Rivuletpy dockerised workflow for BIAFLOWS.

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Neuron Tracing Vaa3D (App2)

Description

Vaa3d All-Path-Pruning 2.0 (APP2) dockerised workflow for BIAFLOWS.

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Filopodyan

Description

Fiji plugin for detecting, tracking and quantifying filopodia

Tumor Blood Vessels: 3D Tubular Network Analysis

Bioimage Analyst
Developer

In this session, we will implement a simple ImageJ macro to segment and analyze the blood vessel network of a subcutaneous tumor. The analysis is fully performed in 3D, and possible strategies to extract statistics of the network geometry and interactively visualize the results are also discussed and implemented.

Filament Tracing (ImageJ)

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