Effective automated pipeline for 3D reconstruction of synapses based on deep learning

BMC Bioinformatics
Chi XiaoHua Han

Abstract

The locations and shapes of synapses are important in reconstructing connectomes and analyzing synaptic plasticity. However, current synapse detection and segmentation methods are still not adequate for accurately acquiring the synaptic connectivity, and they cannot effectively alleviate the burden of synapse validation. We propose a fully automated method that relies on deep learning to realize the 3D reconstruction of synapses in electron microscopy (EM) images. The proposed method consists of three main parts: (1) training and employing the faster region convolutional neural networks (R-CNN) algorithm to detect synapses, (2) using the z-continuity of synapses to reduce false positives, and (3) combining the Dijkstra algorithm with the GrabCut algorithm to obtain the segmentation of synaptic clefts. Experimental results were validated by manual tracking, and the effectiveness of our proposed method was demonstrated. The experimental results in anisotropic and isotropic EM volumes demonstrate the effectiveness of our algorithm, and the average precision of our detection (92.8% in anisotropy, 93.5% in isotropy) and segmentation (88.6% in anisotropy, 93.0% in isotropy) suggests that our method achieves state-of-the-art results. ...Continue Reading

References

Aug 12, 2006·IEEE Transactions on Image Processing : a Publication of the IEEE Signal Processing Society·N K Bose, Nilesh A Ahuja
Nov 24, 2006·The Journal of Neuroscience : the Official Journal of the Society for Neuroscience·Kristen M HarrisJamie Hurlburt
Mar 21, 2008·The Journal of Neuroscience : the Official Journal of the Society for Neuroscience·Graham KnottBen Lich
Nov 14, 2008·Nature·Sonja B HoferMark Hübener
May 25, 2010·BMC Bioinformatics·Benjamin SchmidMartin Heisenberg
Sep 28, 2010·Neuron·Yuriy MishchenkoDmitri B Chklovskii
Mar 11, 2011·Nature·Kevin L BriggmanWinfried Denk
Oct 15, 2011·IEEE Transactions on Medical Imaging·Aurélien LucchiPascal Fua
Jun 19, 2013·IEEE Transactions on Medical Imaging·Carlos BeckerPascal Fua
Jul 3, 2013·Bioinformatics·Saket NavlakhaZiv Bar-Joseph
Aug 9, 2013·Nature·Moritz HelmstaedterWinfried Denk
Feb 17, 2015·International Journal of Computer Assisted Radiology and Surgery·Erik SmistadFrank Lindseth
Aug 2, 2015·Cell·Narayanan KasthuriJeff William Lichtman
Jun 14, 2016·IEEE Transactions on Pattern Analysis and Machine Intelligence·Shaoqing RenJian Sun
Feb 1, 2017·Nature Methods·Thorsten BeierFred A Hamprecht
Mar 3, 2017·Nature Methods·Sven DorkenwaldJoergen Kornfeld
Jul 15, 2017·ELife·Benedikt StafflerMoritz Helmstaedter

❮ Previous
Next ❯

Citations

Jul 8, 2020·ACS Omega·Ekaterina A SosninaMaxim V Fedorov

❮ Previous
Next ❯

Methods Mentioned

BETA
optical microscopy
electron microscopy
scanning electron microscopy
transmission electron microscopy
feature extraction

Software Mentioned

ImageJ
ImageNet
GraphCut
SyConn
CNN
Faster
Sun
Net
GeForce
Caffe R CNN

Related Concepts

Trending Feeds

COVID-19

Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

Blastomycosis

Blastomycosis fungal infections spread through inhaling Blastomyces dermatitidis spores. Discover the latest research on blastomycosis fungal infections here.

Nuclear Pore Complex in ALS/FTD

Alterations in nucleocytoplasmic transport, controlled by the nuclear pore complex, may be involved in the pathomechanism underlying multiple neurodegenerative diseases including Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. Here is the latest research on the nuclear pore complex in ALS and FTD.

Applications of Molecular Barcoding

The concept of molecular barcoding is that each original DNA or RNA molecule is attached to a unique sequence barcode. Sequence reads having different barcodes represent different original molecules, while sequence reads having the same barcode are results of PCR duplication from one original molecule. Discover the latest research on molecular barcoding here.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Evolution of Pluripotency

Pluripotency refers to the ability of a cell to develop into three primary germ cell layers of the embryo. This feed focuses on the mechanisms that underlie the evolution of pluripotency. Here is the latest research.

Position Effect Variegation

Position Effect Variagation occurs when a gene is inactivated due to its positioning near heterochromatic regions within a chromosome. Discover the latest research on Position Effect Variagation here.

STING Receptor Agonists

Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.

Microbicide

Microbicides are products that can be applied to vaginal or rectal mucosal surfaces with the goal of preventing, or at least significantly reducing, the transmission of sexually transmitted infections. Here is the latest research on microbicides.

Related Papers

Conference Proceedings : ... Annual International Conference of the IEEE Engineering in Medicine and Biology Society
Jung Uk Kim Yong Man Ro
Medical Image Computing and Computer-assisted Intervention : MICCAI
Carlos BeckerPascal Fua
© 2022 Meta ULC. All rights reserved