VAST (Volume Annotation and Segmentation Tool): Efficient manual and semi-automatic labeling of large 3D image stacks

Daniel R. Berger; H. Sebastian Seung; Jeff W. Lichtman

doi:10.3389/fncir.2018.00088

VAST (Volume Annotation and Segmentation Tool): Efficient manual and semi-automatic labeling of large 3D image stacks

Daniel R. Berger, H. Sebastian Seung, Jeff W. Lichtman

Research output: Contribution to journal › Article › peer-review

120 Scopus citations

Abstract

Recent developments in serial-section electron microscopy allow the efficient generation of very large image data sets but analyzing such data poses challenges for software tools. Here we introduce Volume Annotation and Segmentation Tool (VAST), a freely available utility program for generating and editing annotations and segmentations of large volumetric image (voxel) data sets. It provides a simple yet powerful user interface for real-time exploration and analysis of large data sets even in the Petabyte range.

Original language	English (US)
Article number	88
Journal	Frontiers in neural circuits
Volume	12
DOIs	https://doi.org/10.3389/fncir.2018.00088
State	Published - Oct 16 2018

All Science Journal Classification (ASJC) codes

Sensory Systems
Cellular and Molecular Neuroscience
Cognitive Neuroscience
Neuroscience (miscellaneous)

Keywords

CLEM
Connectomics
Proofreading
Segmentation
Serial section electron microscopy
TrakEM2
Visualization
Voxel

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10.3389/fncir.2018.00088

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title = "VAST (Volume Annotation and Segmentation Tool): Efficient manual and semi-automatic labeling of large 3D image stacks",

abstract = "Recent developments in serial-section electron microscopy allow the efficient generation of very large image data sets but analyzing such data poses challenges for software tools. Here we introduce Volume Annotation and Segmentation Tool (VAST), a freely available utility program for generating and editing annotations and segmentations of large volumetric image (voxel) data sets. It provides a simple yet powerful user interface for real-time exploration and analysis of large data sets even in the Petabyte range.",

keywords = "CLEM, Connectomics, Proofreading, Segmentation, Serial section electron microscopy, TrakEM2, Visualization, Voxel",

author = "Berger, {Daniel R.} and Seung, {H. Sebastian} and Lichtman, {Jeff W.}",

note = "Publisher Copyright: {\textcopyright} 2018 Berger, Seung and Lichtman.",

year = "2018",

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doi = "10.3389/fncir.2018.00088",

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AU - Seung, H. Sebastian

AU - Lichtman, Jeff W.

PY - 2018/10/16

Y1 - 2018/10/16

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AB - Recent developments in serial-section electron microscopy allow the efficient generation of very large image data sets but analyzing such data poses challenges for software tools. Here we introduce Volume Annotation and Segmentation Tool (VAST), a freely available utility program for generating and editing annotations and segmentations of large volumetric image (voxel) data sets. It provides a simple yet powerful user interface for real-time exploration and analysis of large data sets even in the Petabyte range.

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KW - Connectomics

KW - Proofreading

KW - Segmentation

KW - Serial section electron microscopy

KW - TrakEM2

KW - Visualization

KW - Voxel

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JO - Frontiers in neural circuits

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M1 - 88

ER -

VAST (Volume Annotation and Segmentation Tool): Efficient manual and semi-automatic labeling of large 3D image stacks

Abstract

All Science Journal Classification (ASJC) codes

Keywords

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