Synaptic Partner Assignment Using Attentional Voxel Association Networks

Nicholas L. Turner, Kisuk Lee, Ran Lu, Jingpeng Wu, Dodam Ih, H. Sebastian Seung

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

Abstract

Connectomics aims to recover a complete set of synaptic connections within a dataset imaged by volume electron microscopy. Many systems have been proposed for locating synapses, and recent research has included a way to identify the synaptic partners that communicate at a synaptic cleft. We reframe the problem of identifying synaptic partners as directly generating the mask of the synaptic partners from a given cleft. We train a convolutional network to perform this task. The network takes the local image context and a binary mask representing a single cleft as input. It is trained to produce two binary output masks: one which labels the voxels of the presynaptic partner within the input image, and another similar labeling for the postsynaptic partner. The cleft mask acts as an attentional gating signal for the network. We find that an implementation of this approach performs well on a dataset of mouse somatosensory cortex, and evaluate it as part of a combined system to predict both clefts and connections.

Original languageEnglish (US)
Title of host publicationISBI 2020 - 2020 IEEE International Symposium on Biomedical Imaging
PublisherIEEE Computer Society
Pages1209-1213
Number of pages5
ISBN (Electronic)9781538693308
DOIs
StatePublished - Apr 2020
Event17th IEEE International Symposium on Biomedical Imaging, ISBI 2020 - Iowa City, United States
Duration: Apr 3 2020Apr 7 2020

Publication series

NameProceedings - International Symposium on Biomedical Imaging
Volume2020-April
ISSN (Print)1945-7928
ISSN (Electronic)1945-8452

Conference

Conference17th IEEE International Symposium on Biomedical Imaging, ISBI 2020
CountryUnited States
CityIowa City
Period4/3/204/7/20

All Science Journal Classification (ASJC) codes

  • Biomedical Engineering
  • Radiology Nuclear Medicine and imaging

Keywords

  • Brain
  • Connectivity Analysis
  • Machine Learning
  • Microscopy - Electron
  • Pattern Recognition and classification

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  • Cite this

    Turner, N. L., Lee, K., Lu, R., Wu, J., Ih, D., & Seung, H. S. (2020). Synaptic Partner Assignment Using Attentional Voxel Association Networks. In ISBI 2020 - 2020 IEEE International Symposium on Biomedical Imaging (pp. 1209-1213). [9098489] (Proceedings - International Symposium on Biomedical Imaging; Vol. 2020-April). IEEE Computer Society. https://doi.org/10.1109/ISBI45749.2020.9098489