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Detecting Synapse Location and Connectivity by Signed Proximity Estimation and Pruning with Deep Nets

  • Toufiq ParagEmail author
  • Daniel Berger
  • Lee Kamentsky
  • Benedikt Staffler
  • Donglai Wei
  • Moritz Helmstaedter
  • Jeff W. Lichtman
  • Hanspeter Pfister
Conference paper
Part of the Lecture Notes in Computer Science book series (LNCS, volume 11134)

Abstract

Synaptic connectivity detection is a critical task for neural reconstruction from Electron Microscopy (EM) data. Most of the existing algorithms for synapse detection do not identify the cleft location and direction of connectivity simultaneously. The few methods that computes direction along with contact location have only been demonstrated to work on either dyadic (most common in vertebrate brain) or polyadic (found in fruit fly brain) synapses, but not on both types. In this paper, we present an algorithm to automatically predict the location as well as the direction of both dyadic and polyadic synapses. The proposed algorithm first generates candidate synaptic connections from voxelwise predictions of signed proximity generated by a 3D U-net. A second 3D CNN then prunes the set of candidates to produce the final detection of cleft and connectivity orientation. Experimental results demonstrate that the proposed method outperforms the existing methods for determining synapses in both rodent and fruit fly brain. (Code at: https://github.com/paragt/EMSynConn).

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Copyright information

© Springer Nature Switzerland AG 2019

Authors and Affiliations

  • Toufiq Parag
    • 1
    Email author
  • Daniel Berger
    • 2
  • Lee Kamentsky
    • 1
  • Benedikt Staffler
    • 3
  • Donglai Wei
    • 1
  • Moritz Helmstaedter
    • 3
  • Jeff W. Lichtman
    • 2
  • Hanspeter Pfister
    • 1
  1. 1.SEASHarvard UniversityCambridgeUSA
  2. 2.MCBHarvard UniversityCambridgeUSA
  3. 3.Max Planck Institute for Brain ResearchFrankfurtGermany

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