Center-extraction-based three dimensional nuclei instance segmentation of fluorescence microscopy images

David Joon Ho, Shuo Han, Chichen Fu, Paul Salama, Kenneth W. Dunn, Edward J. Delp

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

Abstract

Fluorescence microscopy is an essential tool for the analysis of 3D subcellular structures in tissue. An important step in the characterization of tissue involves nuclei segmentation. In this paper, a two-stage method for segmentation of nuclei using convolutional neural networks (CNNs) is described. In particular, since creating labeled volumes manually for training purposes is not practical due to the size and complexity of the 3D data sets, the paper describes a method for generating synthetic microscopy volumes based on a spatially constrained cycle-consistent adversarial network. The proposed method is tested on multiple real microscopy data sets and outperforms other commonly used segmentation techniques.

Original languageEnglish (US)
Title of host publication2019 IEEE EMBS International Conference on Biomedical and Health Informatics, BHI 2019 - Proceedings
PublisherInstitute of Electrical and Electronics Engineers Inc.
ISBN (Electronic)9781728108483
DOIs
StatePublished - May 2019
Event2019 IEEE EMBS International Conference on Biomedical and Health Informatics, BHI 2019 - Chicago, United States
Duration: May 19 2019May 22 2019

Publication series

Name2019 IEEE EMBS International Conference on Biomedical and Health Informatics, BHI 2019 - Proceedings

Conference

Conference2019 IEEE EMBS International Conference on Biomedical and Health Informatics, BHI 2019
CountryUnited States
CityChicago
Period5/19/195/22/19

Fingerprint

Fluorescence microscopy
Fluorescence Microscopy
Microscopic examination
Tissue
Microscopy
Neural networks
Segmentation
Datasets

Keywords

  • Convolutional neural network
  • Fluorescence microscopy
  • Generative adversarial network
  • Instance segmentation
  • Nuclei segmentation

ASJC Scopus subject areas

  • Artificial Intelligence
  • Signal Processing
  • Information Systems and Management
  • Biomedical Engineering
  • Health Informatics
  • Radiology Nuclear Medicine and imaging

Cite this

Ho, D. J., Han, S., Fu, C., Salama, P., Dunn, K. W., & Delp, E. J. (2019). Center-extraction-based three dimensional nuclei instance segmentation of fluorescence microscopy images. In 2019 IEEE EMBS International Conference on Biomedical and Health Informatics, BHI 2019 - Proceedings [8834516] (2019 IEEE EMBS International Conference on Biomedical and Health Informatics, BHI 2019 - Proceedings). Institute of Electrical and Electronics Engineers Inc.. https://doi.org/10.1109/BHI.2019.8834516

Center-extraction-based three dimensional nuclei instance segmentation of fluorescence microscopy images. / Ho, David Joon; Han, Shuo; Fu, Chichen; Salama, Paul; Dunn, Kenneth W.; Delp, Edward J.

2019 IEEE EMBS International Conference on Biomedical and Health Informatics, BHI 2019 - Proceedings. Institute of Electrical and Electronics Engineers Inc., 2019. 8834516 (2019 IEEE EMBS International Conference on Biomedical and Health Informatics, BHI 2019 - Proceedings).

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

Ho, DJ, Han, S, Fu, C, Salama, P, Dunn, KW & Delp, EJ 2019, Center-extraction-based three dimensional nuclei instance segmentation of fluorescence microscopy images. in 2019 IEEE EMBS International Conference on Biomedical and Health Informatics, BHI 2019 - Proceedings., 8834516, 2019 IEEE EMBS International Conference on Biomedical and Health Informatics, BHI 2019 - Proceedings, Institute of Electrical and Electronics Engineers Inc., 2019 IEEE EMBS International Conference on Biomedical and Health Informatics, BHI 2019, Chicago, United States, 5/19/19. https://doi.org/10.1109/BHI.2019.8834516
Ho DJ, Han S, Fu C, Salama P, Dunn KW, Delp EJ. Center-extraction-based three dimensional nuclei instance segmentation of fluorescence microscopy images. In 2019 IEEE EMBS International Conference on Biomedical and Health Informatics, BHI 2019 - Proceedings. Institute of Electrical and Electronics Engineers Inc. 2019. 8834516. (2019 IEEE EMBS International Conference on Biomedical and Health Informatics, BHI 2019 - Proceedings). https://doi.org/10.1109/BHI.2019.8834516
Ho, David Joon ; Han, Shuo ; Fu, Chichen ; Salama, Paul ; Dunn, Kenneth W. ; Delp, Edward J. / Center-extraction-based three dimensional nuclei instance segmentation of fluorescence microscopy images. 2019 IEEE EMBS International Conference on Biomedical and Health Informatics, BHI 2019 - Proceedings. Institute of Electrical and Electronics Engineers Inc., 2019. (2019 IEEE EMBS International Conference on Biomedical and Health Informatics, BHI 2019 - Proceedings).
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