Neuronal nuclei localization in 3D using level set and watershed segmentation from laser scanning microscopy images

Yingxuan Zhu, Eric Olson, Arun Subramanian, David Feiglin, Pramod K. Varshney, Andrzej Krol

Research output: Chapter in Book/Entry/PoemConference contribution

1 Scopus citations


Abnormalities of the number and location of cells are hallmarks of both developmental and degenerative neurological diseases. However, standard stereological methods are impractical for assigning each cell's nucleus position within a large volume of brain tissue. We propose an automated approach for segmentation and localization of the brain cell nuclei in laser scanning microscopy (LSM) embryonic mouse brain images. The nuclei in these images are first segmented by using the level set (LS) and watershed methods in each optical plane. The segmentation results are further refined by application of information from adjacent optical planes and prior knowledge of nuclear shape. Segmentation is then followed with an algorithm for 3D localization of the centroid of nucleus (CN). Each volume of tissue is thus represented by a collection of centroids leading to an approximate 10,000-fold reduction in the data set size, as compared to the original image series. Our method has been tested on LSM images obtained from an embryonic mouse brain, and compared to the segmentation and CN localization performed by an expert. The average Euclidian distance between locations of CNs obtained using our method and those obtained by an expert is 1.58±1.24 μm, a value well within the ̃5 μm average radius of each nucleus. We conclude that our approach accurately segments and localizes CNs within cell dense embryonic tissue.

Original languageEnglish (US)
Title of host publicationMedical Imaging 2008
Subtitle of host publicationImage Processing
StatePublished - 2008
EventMedical Imaging 2008: Image Processing - San Diego, CA, United States
Duration: Feb 17 2008Feb 19 2008

Publication series

NameProgress in Biomedical Optics and Imaging - Proceedings of SPIE
ISSN (Print)1605-7422


OtherMedical Imaging 2008: Image Processing
Country/TerritoryUnited States
CitySan Diego, CA


  • Level set segmentation
  • Neurological diseases
  • Neuronal nucleus centroid localization
  • Neuronal nucleus segmentation
  • Watershed segmentation

ASJC Scopus subject areas

  • Electronic, Optical and Magnetic Materials
  • Atomic and Molecular Physics, and Optics
  • Radiology Nuclear Medicine and imaging
  • Biomaterials


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