Segmentation of Synapses in Fluorescent Images using U-Net++ and Gabor-based Anisotropic Diffusion

Yifei Yan, Zhen Qiu, Qi Zhang

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

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Abstract

Objective: Large-scale and automated detection of fluorescent microscopic synaptic images are essential for the understanding of brain function and disorders at the molecular level. However, the quantification of synapses from fluorescent images is challenging due to low signal-to-noise (SNR) and non-synaptic background artefacts. This calls for new tools to be developed for an automatic, high-throughput and robust synapse image segmentation.

Methods: we proposed an automatic synapse segmentation framework using a deep learning method based on a modified U-Net++ and Gabor-based anisotropic diffusion (GAD). The modified U-Net++ was used to segment the non-synaptic regions, while the multiplicative Poisson noise was suppressed and the edge of the synapses was enhanced by the GAD filter. Thereafter, the synapses were segmented by a thresholding method.

Results: The non-synaptic regions were segmented precisely, and the Dice coefficient and Jaccard similarity were 0.833 and 0.719. Our model for synapse segmentation reduced the interference from the non-synaptic tissues and Poisson noise and yielded automatic and accurate segmentation of synapses.

Conclusion: We have proposed an automatic segmentation framework that can accurately segment non-synaptic and synaptic tissues, which may have the potential to automate the quantitative analysis of synapses.
Original languageEnglish
Title of host publicationICMIPE 2021 Conference Proceedings
PublisherIEEE
Number of pages5
ISBN (Print)9781665426084
DOIs
Publication statusPublished - Nov 2021
Event2021 IEEE International Conference on Medical Imaging Physics and Engineering - online, Hefei, China
Duration: 12 Nov 202114 Nov 2021
https://icmipe2021.aconf.cn/en-us/index.html

Conference

Conference2021 IEEE International Conference on Medical Imaging Physics and Engineering
Abbreviated titleICMIPE
Country/TerritoryChina
CityHefei
Period12/11/2114/11/21
Internet address

Keywords

  • synapse
  • image segmentation
  • Gabor-based anisotropic diffusion
  • U-Net++

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