Neuroinformatics

, Volume 5, Issue 3, pp 189–203

Automated Axon Tracking of 3D Confocal Laser Scanning Microscopy Images Using Guided Probabilistic Region Merging

  • Ranga Srinivasan
  • Xiaobo Zhou
  • Eric Miller
  • Ju Lu
  • Jeff Litchman
  • Stephen T. C. Wong
Article

DOI: 10.1007/s12021-007-0013-4

Cite this article as:
Srinivasan, R., Zhou, X., Miller, E. et al. Neuroinform (2007) 5: 189. doi:10.1007/s12021-007-0013-4

Abstract

This paper presents a new algorithm for extracting the centerlines of the axons from a 3D data stack collected by a confocal laser scanning microscope. Recovery of neuronal structures from such datasets is critical for quantitatively addressing a range of neurobiological questions such as the manner in which the branching pattern of motor neurons change during synapse elimination. Unfortunately, the data acquired using fluorescence microscopy contains many imaging artifacts, such as blurry boundaries and non-uniform intensities of fluorescent radiation. This makes the centerline extraction difficult. We propose a robust segmentation method based on probabilistic region merging to extract the centerlines of individual axons with minimal user interaction. The 3D model of the extracted axon centerlines in three datasets is presented in this paper. The results are validated with the manual tracking results while the robustness of the algorithm is compared with the published repulsive snake algorithm.

Keywords

Maximum intensity projectionSegmentationGuided region growingWatershed

Copyright information

© Humana Press Inc. 2007

Authors and Affiliations

  • Ranga Srinivasan
    • 1
    • 2
  • Xiaobo Zhou
    • 1
    • 4
  • Eric Miller
    • 3
  • Ju Lu
    • 5
  • Jeff Litchman
    • 5
  • Stephen T. C. Wong
    • 1
    • 4
  1. 1.Harvard Center for Neurodegeneration and Repair–Center for BioinformaticsHarvard Medical SchoolBostonUSA
  2. 2.Department of Electrical and Computer EngineeringNortheastern UniversityBostonUSA
  3. 3.Department of Electrical and Computer EngineeringTufts UniversityMedfordUSA
  4. 4.Functional and Molecular Imaging Center, Department of RadiologyBrigham and Women’s Hospital and Harvard Medical SchoolBostonUSA
  5. 5.Department of Molecular and Cellular BiologyHarvard UniversityCambridgeUSA