, Volume 13, Issue 2, pp 227–244 | Cite as

Improved Automatic Centerline Tracing for Dendritic and Axonal Structures

  • David Jiménez
  • Demetrio Labate
  • Ioannis A. Kakadiaris
  • Manos PapadakisEmail author
Original Article


Centerline tracing in dendritic structures acquired from confocal images of neurons is an essential tool for the construction of geometrical representations of a neuronal network from its coarse scale up to its fine scale structures. In this paper, we propose an algorithm for centerline extraction that is both highly accurate and computationally efficient. The main novelties of the proposed method are (1) the use of a small set of Multiscale Isotropic Laplacian filters, acting as self-steerable filters, for a quick and efficient binary segmentation of dendritic arbors and axons; (2) an automated centerline seed points detection method based on the application of a simple 3D finite-length filter. The performance of this algorithm, which is validated on data from the DIADEM set appears to be very competitive when compared with other state-of-the-art algorithms.


Image processing Automated neuron tracing Neuron image segmentation 



This work was supported in part by NSF-DMS 1320910, 0915242, 1008900, 1005799 and by NHARP-003652-0136-2009. I.A. Kakadiaris was also supported by the Hugh Roy and Lillie Cranz Cullen Endowment Fund. We thank our student P. Hernandez-Herrera for allowing us to use the performance test results he obtained with Neuronstudio, ORION and APP2 on numerous data sets. Last, but most certainly not least, we would like to thank the three reviewers for their encouraging comments and their valuable input which helped us improve the quality of the paper.

Supplementary material

12021_2014_9256_MOESM1_ESM.pdf (1.8 mb)
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Copyright information

© Springer Science+Business Media New York 2014

Authors and Affiliations

  • David Jiménez
    • 1
  • Demetrio Labate
    • 2
  • Ioannis A. Kakadiaris
    • 3
  • Manos Papadakis
    • 2
    Email author
  1. 1.Department of MathematicsUniversity of Costa RicaSan Pedro Montes de OcaRepublic of Costa Rica
  2. 2.Department of MathematicsUniversity of HoustonHoustonUSA
  3. 3.Computational Biomedicine Lab, Department of Computer ScienceUniversity of HoustonHoustonUSA

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