3D axon structure extraction and analysis in confocal fluorescence microscopy images

Yong Zhang, Xiaobo Zhou, Ju Lu, Jeff Lichtman, Donald Adjeroh, Stephen T.C. Wong

Research output: Contribution to journalArticlepeer-review

16 Scopus citations


The morphological properties of axons, such as their branching patterns and oriented structures, are of great interest for biologists in the study of the synaptic connectivity of neurons. In these studies, researchers use triple immunofluorescent confocal microscopy to record morphological changes of neuronal processes. Three-dimensional (3D) microscopy image analysis is then required to extract morphological features of the neuronal structures. In this article, we propose a highly automated 3D centerline extraction tool to assist in this task. For this project, the most difficult part is that some axons are overlapping such that the boundaries distinguishing them are barely visible. Our approach combines a 3D dynamic programming (DP) technique and marker-controlled watershed algorithm to solve this problem. The approach consists of tracking and updating along the navigation directions of multiple axons simultaneously. The experimental results show that the proposed method can rapidly and accurately extract multiple axon centerlines and can handle complicated axon structures such as cross-over sections and overlapping objects.

Original languageEnglish (US)
Pages (from-to)1899-1927
Number of pages29
JournalNeural Computation
Issue number8
StatePublished - Aug 2008

ASJC Scopus subject areas

  • Arts and Humanities (miscellaneous)
  • Cognitive Neuroscience


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