, 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


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.


Automated neuron tracing Axon Dendrite Alignment of brain sections Barrel cortex 



We thank Bert Sakmann and Philip J. Broser for advice and assistance during early stages of the project; Wolfgang Holler and Britta Weber for their contribution to the Filament Editor; Marianne Krabi and Jonas Hörsch for assisting with the analysis functionality; Norbert Lindow for providing the LineRayCaster. Randy M. Bruno and Christiaan P.J. de Kock for supplying biocytin-labeled neurons; Lothar Baltruschat, Richard Smith, Kevin Pels, and Ariel Lee for proof-editing; Hans-Joachim Wagner and the entire staff of the Anatomy Institute of the University of Tuebingen for their generous support. Funding was provided by the Bernstein Center for Computational Neuroscience, Tuebingen (funded by the German Federal Ministry of Education and Research (BMBF; FKZ: 01GQ1002)) (MO), by the Max Planck Institute for Biological Cybernetics, Tuebingen (MO), by the Max Planck Florida Institute for Neuroscience, Jupiter (MO), by the Werner Reichardt Center for Integrative Neuroscience, Tuebingen (MO), by the Zuse Institute Berlin (VJD, HCH) and the Max Planck Institute of Neurobiology, Martinsried (VJD). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

Author Contributions

Conceived and designed the project: MO. Developed the Filament Editor and associated functionalities: VJD. Analyzed the data and wrote the paper: VJD, HCH, MO.

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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