title: A distance-field based automatic neuron tracing method.
abstract: BACKGROUND
  Automatic 3D digital reconstruction (tracing) of neurons embedded in noisy microscopic images is challenging, especially when the cell morphology is complex.
  
  
  RESULTS
  We have developed a novel approach, named DF-Tracing, to tackle this challenge. This method first extracts the neurite signal (foreground) from a noisy image by using anisotropic filtering and automated thresholding. Then, DF-Tracing executes a coupled distance-field (DF) algorithm on the extracted foreground neurite signal and reconstructs the neuron morphology automatically. Two distance-transform based "force" fields are used: one for "pressure", which is the distance transform field of foreground pixels (voxels) to the background, and another for "thrust", which is the distance transform field of the foreground pixels to an automatically determined seed point. The coupling of these two force fields can "push" a "rolling ball" quickly along the skeleton of a neuron, reconstructing the 3D cell morphology.
  
  
  CONCLUSIONS
  We have used DF-Tracing to reconstruct the intricate neuron structures found in noisy image stacks, obtained with 3D laser microscopy, of dragonfly thoracic ganglia. Compared to several previous methods, DF-Tracing produces better reconstructions.
authors.affiliation: Janelia Farm Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA.
authors.forename: Jinzhu
authors.initials: J
authors.lastname: Yang
authors.forename: Paloma T
authors.initials: PT
authors.lastname: Gonzalez-Bellido
authors.forename: Hanchuan
authors.initials: H
authors.lastname: Peng
mesh_terms: D000465:Algorithms; D000818:Animals; D016880:Anisotropy; D021621:Imaging, Three-Dimensional / Q000379:methods*; D018613:Microscopy, Confocal; D016501:Neurites / Q000648:ultrastructure; D009474:Neurons / Q000166:cytology*; D063191:Odonata / Q000166:cytology