VAST (Volume Annotation and Segmentation Tool): Efficient Manual and Semi-Automatic Labeling of Large 3D Image Stacks

被引：119
作者：
Berger, Daniel R. [1 ]
Seung, H. Sebastian [2 ]
Lichtman, Jeff W. [1 ]
机构：
[1] Harvard Univ, Dept Mol & Cellular Biol, Cambridge, MA 02138 USA
[2] Princeton Univ, Dept Comp Sci, Princeton Neurosci Inst, Princeton, NJ 08544 USA
来源：
FRONTIERS IN NEURAL CIRCUITS | 2018年 / 12卷
基金：
美国国家卫生研究院;
关键词：
connectomics; segmentation; visualization; serial section electron microscopy; CLEM; proofreading; TrakEM2; voxel; SCANNING-ELECTRON-MICROSCOPY; DIRECTION-SELECTIVITY; WIRING SPECIFICITY; HIGH-RESOLUTION; CIRCUIT; NETWORK; RECONSTRUCTION; ANATOMY; SYSTEM;
D O I：
10.3389/fncir.2018.00088
中图分类号：
Q189 [神经科学];
学科分类号：
071006 ;
摘要：
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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页数：15
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共 47 条
[1]   NeuroBlocks - Visual Tracking of Segmentation and Proofreading for Large Connectomics Projects [J].
Al-Awami, Ali K. ;
Beyer, Johanna ;
Haehn, Daniel ;
Kasthuri, Narayanan ;
Lichtman, Jeff W. ;
Pfister, Hanspeter ;
Hadwiger, Markus .
IEEE TRANSACTIONS ON VISUALIZATION AND COMPUTER GRAPHICS, 2016, 22 (01) :738-746
[2]   Digital Museum of Retinal Ganglion Cells with Dense Anatomy and Physiology [J].
Bae, J. Alexander ;
Mu, Shang ;
Kim, Jinseop S. ;
Turner, Nicholas L. ;
Tartavull, Ignacio ;
Kemnitz, Nico ;
Jordan, Chris S. ;
Norton, Alex D. ;
Silversmith, William M. ;
Prentki, Rachel ;
Sorek, Marissa ;
David, Celia ;
Jones, Devon L. ;
Bland, Doug ;
Sterling, Amy L. R. ;
Park, Jungman ;
Briggman, Kevin L. ;
Seung, H. Sebastian .
CELL, 2018, 173 (05) :1293-+
[3]   Nanoconnectomic upper bound on the variability of synaptic plasticity [J].
Bartol, Thomas M., Jr. ;
Bromer, Cailey ;
Kinney, Justin ;
Chirillo, Michael A. ;
Bourne, Jennifer N. ;
Harris, Kristen M. ;
Sejnowski, Terrence J. .
ELIFE, 2015, 4
[4]   Network anatomy and in vivo physiology of visual cortical neurons [J].
Bock, Davi D. ;
Lee, Wei-Chung Allen ;
Kerlin, Aaron M. ;
Andermann, Mark L. ;
Hood, Greg ;
Wetzel, Arthur W. ;
Yurgenson, Sergey ;
Soucy, Edward R. ;
Kim, Hyon Suk ;
Reid, R. Clay .
NATURE, 2011, 471 (7337) :177-U59
[5]   webKnossos: efficient online 3D data annotation for connectomics [J].
Boergens, Kevin M. ;
Berning, Manuel ;
Bocklisch, Tom ;
Braeunlein, Dominic ;
Drawitsch, Florian ;
Frohnhofen, Johannes ;
Herold, Tom ;
Otto, Philipp ;
Rzepka, Norman ;
Werkmeister, Thomas ;
Werner, Daniel ;
Wiese, Georg ;
Wissler, Heiko ;
Helmstaedter, Moritz .
NATURE METHODS, 2017, 14 (07) :691-+
[6]   Volume electron microscopy for neuronal circuit reconstruction [J].
Briggman, Kevin L. ;
Bock, Davi D. .
CURRENT OPINION IN NEUROBIOLOGY, 2012, 22 (01) :154-161
[7]   Wiring specificity in the direction-selectivity circuit of the retina [J].
Briggman, Kevin L. ;
Helmstaedter, Moritz ;
Denk, Winfried .
NATURE, 2011, 471 (7337) :183-U67
[8]   TrakEM2 Software for Neural Circuit Reconstruction [J].
Cardona, Albert ;
Saalfeld, Stephan ;
Schindelin, Johannes ;
Arganda-Carreras, Ignacio ;
Preibisch, Stephan ;
Longair, Mark ;
Tomancak, Pavel ;
Hartenstein, Volker ;
Douglas, Rodney J. .
PLOS ONE, 2012, 7 (06)
[9]   Semi-automated reconstruction of neural circuits using electron microscopy [J].
Chklovskii, Dmitri B. ;
Vitaladevuni, Shiv ;
Scheffer, Louis K. .
CURRENT OPINION IN NEUROBIOLOGY, 2010, 20 (05) :667-675
[10]   Serial block-face scanning electron microscopy to reconstruct three-dimensional tissue nanostructure [J].
Denk, W ;
Horstmann, H .
PLOS BIOLOGY, 2004, 2 (11) :1900-1909
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