SynEM, automated synapse detection for connectomics

Benedikt StafflerMoritz Helmstaedter


Nerve tissue contains a high density of chemical synapses, about 1 per µm(3) in the mammalian cerebral cortex. Thus, even for small blocks of nerve tissue, dense connectomic mapping requires the identification of millions to billions of synapses. While the focus of connectomic data analysis has been on neurite reconstruction, synapse detection becomes limiting when datasets grow in size and dense mapping is required. Here, we report SynEM, a method for automated detection of synapses from conventionally en-bloc stained 3D electron microscopy image stacks. The approach is based on a segmentation of the image data and focuses on classifying borders between neuronal processes as synaptic or non-synaptic. SynEM yields 97% precision and recall in binary cortical connectomes with no user interaction. It scales to large volumes of cortical neuropil, plausibly even whole-brain datasets. SynEM removes the burden of manual synapse annotation for large densely mapped connectomes.


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Aug 9, 2013·Nature·Moritz HelmstaedterWinfried Denk
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Apr 14, 2015·Nature Methods·Shawn Mikula, Winfried Denk
Aug 2, 2015·Cell·Narayanan KasthuriJeff William Lichtman
Aug 4, 2015·Nature Communications·Yunfeng HuaMoritz Helmstaedter
Sep 25, 2015·Neuron·Manuel BerningMoritz Helmstaedter
Dec 1, 2015·ELife·Thomas M BartolTerrence J Sejnowski
Feb 6, 2017·Science·Luisa de VivoChiara Cirelli
Mar 3, 2017·Nature Methods·Sven DorkenwaldJoergen Kornfeld
Jun 13, 2017·Nature Methods·Kevin M BoergensMoritz Helmstaedter

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Sep 30, 2017·Nature·Helene SchmidtMoritz Helmstaedter
Oct 28, 2019·Science·Alessandro MottaMoritz Helmstaedter
May 28, 2019·Frontiers in Neuroinformatics·Xue Fan, Henry Markram
Nov 5, 2019·Frontiers in Neural Circuits·Yoshiyuki Kubota
Nov 14, 2018·Frontiers in Neural Circuits·Gary B HuangStephen M Plaza
Nov 10, 2018·Frontiers in Neural Circuits·Adrian A Wanner, Ashwin Vishwanathan
Dec 5, 2020·Science·Anjali GourMoritz Helmstaedter
May 15, 2021·Nature Communications·Emmanuel KlingerMoritz Helmstaedter

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