Part-wise neuron segmentation using artificial templates

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

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

Abstract

Our goal is to analyze neuronal morphology during development using artificially created templates. Such templates serve as input from the domain expertise: a standardized representation of the neuron, independent from imaging modalities and resolution, is what a neurobiologist can provide from knowledge and qualitative observations in the microscope. A template is divided into context-specific (topology, shape, and/or function) compartments, and our task is to segment input neuron volumes from their surroundings and partition them accordingly. We solve this problem using a global-to-local approach. We first employ a global transformation that serves as part-wise alignment of the template with the input volume. Then, we use local, deformable compartment shape registration using MRF-based free-form deformations. We validated our results using aCC motorneuron image stacks from larva Drosophila, at multiple developmental instances and different spatial resolutions.

Original languageEnglish (US)
Title of host publication2018 IEEE 15th International Symposium on Biomedical Imaging, ISBI 2018
PublisherIEEE Computer Society
Pages640-644
Number of pages5
Volume2018-April
ISBN (Electronic)9781538636367
DOIs
StatePublished - May 23 2018
Event15th IEEE International Symposium on Biomedical Imaging, ISBI 2018 - Washington, United States
Duration: Apr 4 2018Apr 7 2018

Other

Other15th IEEE International Symposium on Biomedical Imaging, ISBI 2018
CountryUnited States
CityWashington
Period4/4/184/7/18

Fingerprint

Neurons
Drosophila
Larva
Microscopes
Topology
Imaging techniques

Keywords

  • Free-form deformations
  • Markov Random Fields
  • Neuron morphology
  • Registration
  • Segmentation

ASJC Scopus subject areas

  • Biomedical Engineering
  • Radiology Nuclear Medicine and imaging

Cite this

Gulyanon, S., Sharifai, N., Kim, M. D., Chiba, A., & Tsechpenakis, G. (2018). Part-wise neuron segmentation using artificial templates. In 2018 IEEE 15th International Symposium on Biomedical Imaging, ISBI 2018 (Vol. 2018-April, pp. 640-644). IEEE Computer Society. https://doi.org/10.1109/ISBI.2018.8363656

Part-wise neuron segmentation using artificial templates. / Gulyanon, S.; Sharifai, N.; Kim, M. D.; Chiba, Akira; Tsechpenakis, G.

2018 IEEE 15th International Symposium on Biomedical Imaging, ISBI 2018. Vol. 2018-April IEEE Computer Society, 2018. p. 640-644.

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

Gulyanon, S, Sharifai, N, Kim, MD, Chiba, A & Tsechpenakis, G 2018, Part-wise neuron segmentation using artificial templates. in 2018 IEEE 15th International Symposium on Biomedical Imaging, ISBI 2018. vol. 2018-April, IEEE Computer Society, pp. 640-644, 15th IEEE International Symposium on Biomedical Imaging, ISBI 2018, Washington, United States, 4/4/18. https://doi.org/10.1109/ISBI.2018.8363656
Gulyanon S, Sharifai N, Kim MD, Chiba A, Tsechpenakis G. Part-wise neuron segmentation using artificial templates. In 2018 IEEE 15th International Symposium on Biomedical Imaging, ISBI 2018. Vol. 2018-April. IEEE Computer Society. 2018. p. 640-644 https://doi.org/10.1109/ISBI.2018.8363656
Gulyanon, S. ; Sharifai, N. ; Kim, M. D. ; Chiba, Akira ; Tsechpenakis, G. / Part-wise neuron segmentation using artificial templates. 2018 IEEE 15th International Symposium on Biomedical Imaging, ISBI 2018. Vol. 2018-April IEEE Computer Society, 2018. pp. 640-644
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