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Neuroinformatics

, Volume 5, Issue 3, pp 189–203 | Cite as

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
First Online:

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 projection Segmentation Guided region growing Watershed 
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Notes

Acknowledgment

The authors would like to thank Mr. H. M. Cai for the help in testing the data sets using the program of Repulsive Snake Model. They also would like to thank research members of the Life Science Imaging Group of the Center for Bioinformatics (CBI), Harvard Center for Neurodegeneration and Repair (HCNR) and Brigham and Women’s Hospital, Harvard Medical School, for their technical comments. The research is funded by the HCNR, Harvard Medical School (Wong).

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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

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