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.

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



Fiji plugin for detecting, tracking and quantifying filopodia

Tumor Blood Vessels: 3D Tubular Network Analysis

Bioimage Analyst

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)

need a thumbnail



Paintera is a general visualization tool for 3D volumetric data and proof-reading in segmentation/reconstruction with a primary focus on neuron reconstruction from electron micrographs in connectomics. It features/supports:

  •  Views of orthogonal 2D cross-sections of the data at arbitrary angles and zoom levels
  •  Mipmaps for efficient display of arbitrarily large data at arbitrary scale levels
  •  Label data
    •  Painting
    •  Manual agglomeration
    •  3D visualization as polygon meshes
      •  Meshes for each mipmap level
      •  Mesh generation on-the-fly via marching cubes to incorporate painted labels and agglomerations in 3D visualization. Marching Cubes is parallelized over small blocks. Only relevant blocks are considered (huge speed-up for sparse label data).

Paintera is implemented in Java and makes extensive use of the UI framework JavaFX

Paintera screenshot


HyphaTracker Workflow

HyphaTracker propose a workflow for time-resolved analysis of conidia germination. Each part of this workflow can also be used independnatly , as a toolbox. It has been tested on bright-field microscopic images of conidial germination. Its purpose is mainly to identify the germlings and to remove crossing hyphae, and measure the dynamics of their growth.


MicrotubuleTracker in FIJI


MTrack is a tool, which detects, tracks, and measures the behavior of fluorescently labeled microtubules imaged by TIRF (total internal reflection fluorescence) microscopy. In such an in vitro reconstitution approach, stabilized, non-dynamic microtubule seeds serve as nucleation points for dynamically growing microtubules.

MTrack is a bi-modular tool. The first module detects and tracks the growing microtubule ends and creates trajectories. The second module uses these trajectories to fit models of dynamic behavior (polymerization and depolymerization velocities, catastrophe and rescue frequencies). It also computes statistics such as length and lifetime distributions when analyzing more than one movie (batch mode).

has topic
Track Filament shaped objects and analyze tracks using Ransac fits.