DVID: Distributed Versioned Image-Oriented Dataservice

Frontiers in Neural Circuits
William T Katz, Stephen M Plaza

Abstract

Open-source software development has skyrocketed in part due to community tools like github.com, which allows publication of code as well as the ability to create branches and push accepted modifications back to the original repository. As the number and size of EM-based datasets increases, the connectomics community faces similar issues when we publish snapshot data corresponding to a publication. Ideally, there would be a mechanism where remote collaborators could modify branches of the data and then flexibly reintegrate results via moderated acceptance of changes. The DVID system provides a web-based connectomics API and the first steps toward such a distributed versioning approach to EM-based connectomics datasets. Through its use as the central data resource for Janelia's FlyEM team, we have integrated the concepts of distributed versioning into reconstruction workflows, allowing support for proofreader training and segmentation experiments through branched, versioned data. DVID also supports persistence to a variety of storage systems from high-speed local SSDs to cloud-based object stores, which allows its deployment on laptops as well as large servers. The tailoring of the backend storage to each type of connectomics da...Continue Reading

References

Apr 21, 2009·Bioinformatics·Stephan SaalfeldPavel Tomancak
Apr 29, 2014·Frontiers in Neuroinformatics·Juan Nunez-IglesiasWilliam T Katz
Oct 29, 2014·Nature Neuroscience·Jeff W LichtmanNir Shavit
May 29, 2015·Nature Methods·Tobias PietzschPavel Tomancak
Oct 21, 2015·Proceedings of the National Academy of Sciences of the United States of America·Shin-Ya TakemuraLouis K Scheffer
Nov 4, 2015·IEEE Transactions on Visualization and Computer Graphics·Ali K Ai-AwamiMarkus Hadwiger
Jan 20, 2016·PLoS Computational Biology·John D BlischakGreg Wilson
Jul 19, 2017·ELife·Shin-Ya TakemuraLouis K Scheffer
May 15, 2018·Current Opinion in Neurobiology·Jörgen Kornfeld, Winfried Denk
Jul 18, 2018·Nature Methods·Michał JanuszewskiViren Jain
Nov 30, 2018·Frontiers in Neural Circuits·Ting ZhaoStephen M Plaza

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Citations

Apr 15, 2020·ELife·Alexander Shakeel BatesGregory Sxe Jefferis
Nov 30, 2018·Frontiers in Neural Circuits·Stephen M Plaza, Jan Funke
May 28, 2020·Brain Sciences·Jingbin YuanHua Han
Sep 4, 2020·ELife·Louis K SchefferStephen M Plaza

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Methods Mentioned

BETA
electron microscopy

Software Mentioned

DVCS
git
FlyEM
Google Cloud Storage
Connectomics
CATMAID
polyglot
DataHub
httpie
OpenStack Swift

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