Filament tracing

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

Neuron Tracing 3D (ImageJ)

Workflow
has function
Filament tracing
Neuron image analysis
Feature enhancement
need a thumbnail

Filament Tracing (ImageJ)

Workflow
has function
Filament tracing
Smoothing
Skeletonisation
need a thumbnail

Paintera

Component
Description

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

has topic
Electron microscopy
In-silico reconstruction
has function
Filament tracing
Neuron image analysis
Image reconstruction
Image visualisation
Slice rendering
Surface rendering
Volume rendering
Paintera screenshot
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