Neuroinformatics

, Volume 12, Issue 2, pp 325–339 | Cite as

The Filament Editor: An Interactive Software Environment for Visualization, Proof-Editing and Analysis of 3D Neuron Morphology

  • Vincent J. Dercksen
  • Hans-Christian Hege
  • Marcel Oberlaender
Software Original Article

Abstract

Neuroanatomical analysis, such as classification of cell types, depends on reliable reconstruction of large numbers of complete 3D dendrite and axon morphologies. At present, the majority of neuron reconstructions are obtained from preparations in a single tissue slice in vitro, thus suffering from cut off dendrites and, more dramatically, cut off axons. In general, axons can innervate volumes of several cubic millimeters and may reach path lengths of tens of centimeters. Thus, their complete reconstruction requires in vivo labeling, histological sectioning and imaging of large fields of view. Unfortunately, anisotropic background conditions across such large tissue volumes, as well as faintly labeled thin neurites, result in incomplete or erroneous automated tracings and even lead experts to make annotation errors during manual reconstructions. Consequently, tracing reliability renders the major bottleneck for reconstructing complete 3D neuron morphologies. Here, we present a novel set of tools, integrated into a software environment named ‘Filament Editor’, for creating reliable neuron tracings from sparsely labeled in vivo datasets. The Filament Editor allows for simultaneous visualization of complex neuronal tracings and image data in a 3D viewer, proof-editing of neuronal tracings, alignment and interconnection across sections, and morphometric analysis in relation to 3D anatomical reference structures. We illustrate the functionality of the Filament Editor on the example of in vivo labeled axons and demonstrate that for the exemplary dataset the final tracing results after proof-editing are independent of the expertise of the human operator.

Keywords

Automated neuron tracing Axon Dendrite Alignment of brain sections Barrel cortex 

Supplementary material

12021_2013_9213_MOESM1_ESM.docx (26 kb)
ESM 1(DOCX 26 kb)

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Copyright information

© Springer Science+Business Media New York 2013

Authors and Affiliations

  • Vincent J. Dercksen
    • 1
  • Hans-Christian Hege
    • 1
  • Marcel Oberlaender
    • 2
    • 3
    • 4
  1. 1.Department of Visualization and Data AnalysisZuse Institute BerlinBerlinGermany
  2. 2.Computational Neuroanatomy GroupMax Planck Institute for Biological CyberneticsTuebingenGermany
  3. 3.Digital NeuroanatomyMax Planck Florida InstituteJupiterUSA
  4. 4.Bernstein Center for Computational NeuroscienceTuebingenGermany

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