A semi-automatic method for neuron centerline extraction in confocal microscopic image stack

Ping Chang Lee*, Yu-Tai Ching, H. M. Chang, Ann Shyn Chiang

*Corresponding author for this work

Research output: Chapter in Book/Report/Conference proceedingConference contributionpeer-review

9 Scopus citations

Abstract

An algorithm for extracting the centerlines of neurons from 3-D image stack collected from a laser scanning confocal microscope is presented. Recovery of neuronal structure from image stack is critical for quantitative analysis of neuron-morphology. Many methods have been proposed to extract the centerline from the tubular structure in medical images, such as vessels. But the same methods do not work well in processing of neurons. One of the reasons is that the physical limitations of the spatial resolution of the image stack collect by confocal microscopy in the z-direction is much worse than the resolution in x and y directions. In our studied cases the mean voxel size of the image stack is 0.17×0.17×1.0μm3 i.e., the resolution in z-direction cannot reflect the fact that the neuron has a tubular structure. In this paper, we propose an almost automatic neuron-tracing algorithm for a set of confocal microscopic images of neuron. The method is designed based on finding a minimal path in the volume to extract the centerlines of a neuron.

Original languageEnglish
Title of host publication2008 5th IEEE International Symposium on Biomedical Imaging
Subtitle of host publicationFrom Nano to Macro, Proceedings, ISBI
Pages959-962
Number of pages4
DOIs
StatePublished - 10 Sep 2008
Event2008 5th IEEE International Symposium on Biomedical Imaging: From Nano to Macro, ISBI - Paris, France
Duration: 14 May 200817 May 2008

Publication series

Name2008 5th IEEE International Symposium on Biomedical Imaging: From Nano to Macro, Proceedings, ISBI

Conference

Conference2008 5th IEEE International Symposium on Biomedical Imaging: From Nano to Macro, ISBI
CountryFrance
CityParis
Period14/05/0817/05/08

Keywords

  • Centerline extraction
  • Confocal microscopy
  • Minimum path finding
  • Neuronal structure
  • Projection neuron

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