Automated cell segmentation with 3D fluorescence microscopy images

Jun Kong, Fusheng Wang, George Teodoro, Yanhui Liang, Yangyang Zhu, Carol Tucker-Burden, Daniel J. Brat

Research output: Chapter in Book/Report/Conference proceedingConference contribution

13 Scopus citations

Abstract

A large number of cell-oriented cancer investigations require an effective and reliable cell segmentation method on three dimensional (3D) fluorescence microscopic images for quantitative analysis of cell biological properties. In this paper, we present a fully automated cell segmentation method that can detect cells from 3D fluorescence microscopic images. Enlightened by fluorescence imaging techniques, we regulated the image gradient field by gradient vector flow (GVF) with interpolated and smoothed data volume, and grouped voxels based on gradient modes identified by tracking GVF field. Adaptive thresholding was then applied to voxels associated with the same gradient mode where voxel intensities were enhanced by a multiscale cell filter. We applied the method to a large volume of 3D fluorescence imaging data of human brain tumor cells with (1) small cell false detection and missing rates for individual cells; and (2) trivial over and under segmentation incidences for clustered cells. Additionally, the concordance of cell morphometry structure between automated and manual segmentation was encouraging. These results suggest a promising 3D cell segmentation method applicable to cancer studies.

Original languageEnglish (US)
Title of host publication2015 IEEE 12th International Symposium on Biomedical Imaging, ISBI 2015
PublisherIEEE Computer Society Press
Pages1212-1215
Number of pages4
Volume2015-July
ISBN (Electronic)9781479923748
DOIs
StatePublished - Jul 21 2015
Event12th IEEE International Symposium on Biomedical Imaging, ISBI 2015 - Brooklyn, United States
Duration: Apr 16 2015Apr 19 2015

Publication series

NameProceedings - International Symposium on Biomedical Imaging
Volume2015-July
ISSN (Print)1945-7928
ISSN (Electronic)1945-8452

Other

Other12th IEEE International Symposium on Biomedical Imaging, ISBI 2015
CountryUnited States
CityBrooklyn
Period4/16/154/19/15

Keywords

  • 3D Cell Analysis
  • Fluorescence Microscopy Image
  • Gradient Vector Flow

ASJC Scopus subject areas

  • Biomedical Engineering
  • Radiology Nuclear Medicine and imaging

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