Three-dimensional neurite tracing under globally varying contrast

S. Gulyanon, N. Sharifai, S. Bleykhman, E. Kelly, Michael D. Kim, A. Chiba, G. Tsechpenakis

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

9 Scopus citations


We study the 3D neurite tracing problem in different imaging modalities. We consider that the examined images do not provide sufficient contrast between neurite and background, and the signal-to-noise ratio varies spatially. We first split the stack into box sub-volumes, and inside each box we evolve simultaneously a number of different open-curve snakes. The curves deform based on three criteria: local image statistics, local shape smoothness, and a term that enforces pairwise attraction between snakes, given their spatial proximity and shapes. We validate our method using larva Drosophila sensory neurons imaged with confocal laser scanning microscopy, as well as publicly available datasets.

Original languageEnglish (US)
Title of host publication2015 IEEE 12th International Symposium on Biomedical Imaging, ISBI 2015
PublisherIEEE Computer Society
Number of pages5
ISBN (Electronic)9781479923748
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
ISSN (Print)1945-7928
ISSN (Electronic)1945-8452


Other12th IEEE International Symposium on Biomedical Imaging, ISBI 2015
Country/TerritoryUnited States


  • Drosophila
  • neurite tracing
  • neuron morphology
  • snakes

ASJC Scopus subject areas

  • Biomedical Engineering
  • Radiology Nuclear Medicine and imaging


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