Three-dimensional neurite tracing under globally varying contrast

S. Gulyanon, N. Sharifai, S. Bleykhman, E. Kelly, M. D. Kim, Akira Chiba, G. Tsechpenakis

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

9 Citations (Scopus)

Abstract

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 publicationProceedings - International Symposium on Biomedical Imaging
PublisherIEEE Computer Society
Pages875-879
Number of pages5
Volume2015-July
ISBN (Print)9781479923748
DOIs
StatePublished - Jul 21 2015
Event12th IEEE International Symposium on Biomedical Imaging, ISBI 2015 - Brooklyn, United States
Duration: Apr 16 2015Apr 19 2015

Other

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

Fingerprint

Snakes
Neurites
Neurons
Signal to noise ratio
Microscopic examination
Statistics
Scanning
Imaging techniques
Lasers
Signal-To-Noise Ratio
Sensory Receptor Cells
Confocal Microscopy
Drosophila
Larva
Datasets

Keywords

  • Drosophila
  • neurite tracing
  • neuron morphology
  • snakes

ASJC Scopus subject areas

  • Biomedical Engineering
  • Radiology Nuclear Medicine and imaging

Cite this

Gulyanon, S., Sharifai, N., Bleykhman, S., Kelly, E., Kim, M. D., Chiba, A., & Tsechpenakis, G. (2015). Three-dimensional neurite tracing under globally varying contrast. In Proceedings - International Symposium on Biomedical Imaging (Vol. 2015-July, pp. 875-879). [7164010] IEEE Computer Society. https://doi.org/10.1109/ISBI.2015.7164010

Three-dimensional neurite tracing under globally varying contrast. / Gulyanon, S.; Sharifai, N.; Bleykhman, S.; Kelly, E.; Kim, M. D.; Chiba, Akira; Tsechpenakis, G.

Proceedings - International Symposium on Biomedical Imaging. Vol. 2015-July IEEE Computer Society, 2015. p. 875-879 7164010.

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

Gulyanon, S, Sharifai, N, Bleykhman, S, Kelly, E, Kim, MD, Chiba, A & Tsechpenakis, G 2015, Three-dimensional neurite tracing under globally varying contrast. in Proceedings - International Symposium on Biomedical Imaging. vol. 2015-July, 7164010, IEEE Computer Society, pp. 875-879, 12th IEEE International Symposium on Biomedical Imaging, ISBI 2015, Brooklyn, United States, 4/16/15. https://doi.org/10.1109/ISBI.2015.7164010
Gulyanon S, Sharifai N, Bleykhman S, Kelly E, Kim MD, Chiba A et al. Three-dimensional neurite tracing under globally varying contrast. In Proceedings - International Symposium on Biomedical Imaging. Vol. 2015-July. IEEE Computer Society. 2015. p. 875-879. 7164010 https://doi.org/10.1109/ISBI.2015.7164010
Gulyanon, S. ; Sharifai, N. ; Bleykhman, S. ; Kelly, E. ; Kim, M. D. ; Chiba, Akira ; Tsechpenakis, G. / Three-dimensional neurite tracing under globally varying contrast. Proceedings - International Symposium on Biomedical Imaging. Vol. 2015-July IEEE Computer Society, 2015. pp. 875-879
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