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

被引：109
|
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.
引用
收藏
页数：15
相关论文
共 50 条
  • [41] D-Track-A semi-automatic 3D video-tracking technique to analyse movements and routines of aquatic animals with application to captive dolphins
    Rachinas-Lopes, Patricia
    Ribeiro, Ricardo
    dos Santos, Manuel E.
    Costa, Rui M.
    PLOS ONE, 2018, 13 (08):
  • [42] Automatic cochlear multimodal 3D image segmentation and analysis using atlas-model-based method
    Al-Dhamari, Ibraheem
    Helal, Rania
    Abdelaziz, Tougan
    Waldeck, Stephan
    Paulus, Dietrich
    COCHLEAR IMPLANTS INTERNATIONAL, 2024, 25 (01) : 46 - 58
  • [43] A semi-automatic seed point-based method for separation of individual vertebrae in 3D surface meshes: a proof of principle study
    Peter A. J. Pijpker
    Tim S. Oosterhuis
    Max J. H. Witjes
    Chris Faber
    Peter M. A. van Ooijen
    Jiří Kosinka
    Jos M. A. Kuijlen
    Rob J. M. Groen
    Joep Kraeima
    International Journal of Computer Assisted Radiology and Surgery, 2021, 16 : 1447 - 1457
  • [44] A semi-automatic seed point-based method for separation of individual vertebrae in 3D surface meshes: a proof of principle study
    Pijpker, Peter A. J.
    Oosterhuis, Tim S.
    Witjes, Max J. H.
    Faber, Chris
    van Ooijen, Peter M. A.
    Kosinka, Jiri
    Kuijlen, Jos M. A.
    Groen, Rob J. M.
    Kraeima, Joep
    INTERNATIONAL JOURNAL OF COMPUTER ASSISTED RADIOLOGY AND SURGERY, 2021, 16 (09) : 1447 - 1457
  • [45] Automatic Detection, Segmentation and Characterization of Retinal Horizontal Neurons in Large-scale 3D Confocal Imagery
    Karakaya, Mahmut
    Kerekes, Ryan A.
    Gleason, Shaun S.
    Martins, Rodrigo A. P.
    Dyer, Michael A.
    MEDICAL IMAGING 2011: IMAGE PROCESSING, 2011, 7962
  • [46] A Marked Poisson Process Driven Latent Shape Model for 3D Segmentation of Reflectance Confocal Microscopy Image Stacks of Human Skin
    Ghanta, Sindhu
    Jordan, Michael I.
    Kose, Kivanc
    Brooks, Dana H.
    Rajadhyaksha, Milind
    Dy, Jennifer G.
    IEEE TRANSACTIONS ON IMAGE PROCESSING, 2017, 26 (01) : 172 - 184
  • [47] Eff-3DPSeg: 3D Organ-Level Plant Shoot Segmentation Using Annotation-Efficient Deep Learning
    Luo, Liyi
    Jiang, Xintong
    Yang, Yu
    Samy, Eugene Roy Antony
    Lefsrud, Mark
    Hoyos-Villegas, Valerio
    Sun, Shangpeng
    PLANT PHENOMICS, 2023, 5
  • [48] A model use context complementarity feature fusion learning for semi-supervised 3D medical image segmentation
    Chen, Lei
    Zhao, Yikai
    Yang, Dongxu
    Ma, Yunpeng
    Zhao, Bingjie
    Hou, Jieru
    Liu, Wenhao
    BIOMEDICAL SIGNAL PROCESSING AND CONTROL, 2025, 102
  • [49] 3D spatial and channel reconstruction for large image patch based segmentation of knee anatomical structures on MRI
    Yu, Zeqiu
    Zhao, Xiaoyan
    Singh, Jatin
    Wang, Jing
    Yu, Tong
    Barot, Devansh
    Pu, Jiantao
    MEDICAL IMAGING 2024: IMAGE PROCESSING, 2024, 12926
  • [50] Prior-Knowledge Embedded U-Net-Based Fully Automatic Vessel Wall Volume Measurement of the Carotid Artery in 3D Ultrasound Image
    Yue, Zheng
    Jiang, Jiayao
    Hou, Wenguang
    Zhou, Quan
    David Spence, J.
    Fenster, Aaron
    Qiu, Wu
    Ding, Mingyue
    IEEE TRANSACTIONS ON MEDICAL IMAGING, 2025, 44 (02) : 711 - 727
12345