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CAVE : Connectome Annotation Versioning Engine

Dorkenwald, Sven ; Schneider-Mizell, Casey M. ; Brittain, Derrick ; Halageri, Akhilesh ; Jordan, Chris ; Kemnitz, Nico ; Castro, Manual A. ; Silversmith, William ; Maitin-Shephard, Jeremy and Troidl, Jakob , et al. (2025) In Nature Methods 22(5). p.1112-1120
Abstract

Advances in electron microscopy, image segmentation and computational infrastructure have given rise to large-scale and richly annotated connectomic datasets, which are increasingly shared across communities. To enable collaboration, users need to be able to concurrently create annotations and correct errors in the automated segmentation by proofreading. In large datasets, every proofreading edit relabels cell identities of millions of voxels and thousands of annotations like synapses. For analysis, users require immediate and reproducible access to this changing and expanding data landscape. Here we present the Connectome Annotation Versioning Engine (CAVE), a computational infrastructure that provides scalable solutions for... (More)

Advances in electron microscopy, image segmentation and computational infrastructure have given rise to large-scale and richly annotated connectomic datasets, which are increasingly shared across communities. To enable collaboration, users need to be able to concurrently create annotations and correct errors in the automated segmentation by proofreading. In large datasets, every proofreading edit relabels cell identities of millions of voxels and thousands of annotations like synapses. For analysis, users require immediate and reproducible access to this changing and expanding data landscape. Here we present the Connectome Annotation Versioning Engine (CAVE), a computational infrastructure that provides scalable solutions for proofreading and flexible annotation support for fast analysis queries at arbitrary time points. Deployed as a suite of web services, CAVE empowers distributed communities to perform reproducible connectome analysis in up to petascale datasets (~1 mm3) while proofreading and annotating is ongoing.

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organization
publishing date
type
Contribution to journal
publication status
published
subject
in
Nature Methods
volume
22
issue
5
pages
9 pages
publisher
Nature Publishing Group
external identifiers
  • pmid:40205066
  • scopus:105002172706
ISSN
1548-7091
DOI
10.1038/s41592-024-02426-z
language
English
LU publication?
yes
id
9501e250-73d4-4bde-a555-a0602fa81aca
date added to LUP
2025-09-02 13:10:22
date last changed
2025-10-14 17:32:07
@article{9501e250-73d4-4bde-a555-a0602fa81aca,
  abstract     = {{<p>Advances in electron microscopy, image segmentation and computational infrastructure have given rise to large-scale and richly annotated connectomic datasets, which are increasingly shared across communities. To enable collaboration, users need to be able to concurrently create annotations and correct errors in the automated segmentation by proofreading. In large datasets, every proofreading edit relabels cell identities of millions of voxels and thousands of annotations like synapses. For analysis, users require immediate and reproducible access to this changing and expanding data landscape. Here we present the Connectome Annotation Versioning Engine (CAVE), a computational infrastructure that provides scalable solutions for proofreading and flexible annotation support for fast analysis queries at arbitrary time points. Deployed as a suite of web services, CAVE empowers distributed communities to perform reproducible connectome analysis in up to petascale datasets (~1 mm<sup>3</sup>) while proofreading and annotating is ongoing.</p>}},
  author       = {{Dorkenwald, Sven and Schneider-Mizell, Casey M. and Brittain, Derrick and Halageri, Akhilesh and Jordan, Chris and Kemnitz, Nico and Castro, Manual A. and Silversmith, William and Maitin-Shephard, Jeremy and Troidl, Jakob and Pfister, Hanspeter and Gillet, Valentin and Xenes, Daniel and Bae, J. Alexander and Bodor, Agnes L. and Buchanan, Jo Ann and Bumbarger, Daniel J. and Elabbady, Leila and Jia, Zhen and Kapner, Daniel and Kinn, Sam and Lee, Kisuk and Li, Kai and Lu, Ran and Macrina, Thomas and Mahalingam, Gayathri and Mitchell, Eric and Mondal, Shanka Subhra and Mu, Shang and Nehoran, Barak and Popovych, Sergiy and Takeno, Marc and Torres, Russel and Turner, Nicholas L. and Wong, William and Wu, Jingpeng and Yin, Wenjing and Yu, Szi Chieh and Reid, R. Clay and da Costa, Nuno Maçarico and Seung, H. Sebastian and Collman, Forrest}},
  issn         = {{1548-7091}},
  language     = {{eng}},
  number       = {{5}},
  pages        = {{1112--1120}},
  publisher    = {{Nature Publishing Group}},
  series       = {{Nature Methods}},
  title        = {{CAVE : Connectome Annotation Versioning Engine}},
  url          = {{http://dx.doi.org/10.1038/s41592-024-02426-z}},
  doi          = {{10.1038/s41592-024-02426-z}},
  volume       = {{22}},
  year         = {{2025}},
}