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Vaa3D specifications


Unique identifier OMICS_10249
Name Vaa3D
Alternative name 3D Visualization-Assisted Analysis
Software type Toolkit/Suite
Interface Graphical user interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Computer skills Medium
Version 3.200
Stability Stable
Maintained Yes


  • DeepNeuron


No version available



  • person_outline Hanchuan Peng
  • person_outline Hanchuan Peng
  • person_outline Fuhui Long

Additional information

Publications for 3D Visualization-Assisted Analysis

Vaa3D citations


Intensify3D: Normalizing signal intensity in large heterogenic image stacks

Sci Rep
PMCID: 5844907
PMID: 29523815
DOI: 10.1038/s41598-018-22489-1

[…] Normalization tool and graphical user interface were designed with MATLAB (Simulink). 3D image rendering was done using the FIJI (ImageJ), 3D viewer plugin. Neuronal reconstruction was performed in Vaa3D (Allen Institute) by N.V. in a “blind manner”. Neuronal diameter analysis was done with NEURON (Yale). External MATLAB and ImageJ scripts that were used in the algorithm are detailed under Suppl […]


3D Imaging and Quantitative Analysis of Vascular Networks: A Comparison of Ultramicroscopy and Micro Computed Tomography

PMCID: 5928875
PMID: 29721067
DOI: 10.7150/thno.22610

[…] also been developed, employing current software tools. Besides the software used in this study, there are many others: Amira (FEI, Munich, Germany), MATLAB (The MathWorks, Inc., Massachusetts, USA), Vaa3D (Howard Hughes Medical Institute, Maryland, USA), AnalyzeDirect (AnalyzeDirect, Inc., Kansas, USA) or Labview (National Instruments, Munich, Germany). Open source software like ImageJ and plugin […]


Development of image analysis software for quantification of viable cells in microchips

PLoS One
PMCID: 5832319
PMID: 29494694
DOI: 10.1371/journal.pone.0193605

[…] ions for open access image analysis, originally developed to solve the needs of particular cases that were subsequently extended for other purposes, such as ImageJ [], BioImageXD [], Icy [], Fiji [], Vaa3D [], CellProfiler [], 3D Slicer [], Image Slicer [], Reconstruct [], FluoRender [], ImageSurfer [], OsiriX [], and IMOD [] among others [].There are also several analytical tools already on the m […]


Neuroanatomical details of the lateral neurons of Drosophila melanogaster support their functional role in the circadian system

PMCID: 5873451
PMID: 29424420
DOI: 10.1002/cne.24406
call_split See protocol

[…] al., ). Besides contrast, brightness and color scheme adjustments, no further manipulations were done to the confocal images, if not stated otherwise.We used the Neuron2‐APP2 implementation from the vaa3D software package for the 3D reconstructions of single cells (Peng, Ruan, Long, Simpson, & Myers, ; Peng, Bria, A., Zhou, Z., Iannello, G., & Long, ; Peng et al., ; Xiao & Peng, ). The tracing fi […]


The Medial Ventrothalamic Circuitry: Cells Implicated in a Bimodal Network

Front Neural Circuits
PMCID: 5812298
PMID: 29479309
DOI: 10.3389/fncir.2018.00009
call_split See protocol

[…] Tokyo, Japan). Images were processed with Fiji (Schindelin et al., ; RRID:SCR_002285). For neuronal reconstruction, Neutube (Feng et al., ) was used. Then, .SWC files were analyzed and animated with Vaa3D (Peng et al., ) and Photoshop CS5. […]


Design and implementation of multi signal and time varying neural reconstructions

Sci Data
PMCID: 5779069
PMID: 29360104
DOI: 10.1038/sdata.2017.207

[…] ese additional dimensions flexibly and precisely while preserving the intuitive simplicity of the original SWC format.Here we present an expanded multichannel file format (ESWC) and the corresponding Vaa3D plugin to acquire multi-signal reconstructions that incorporate subcellular information simultaneously with the overall morphology of the neuron. This application repurposes the ESWC extension p […]


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Vaa3D institution(s)
Allen Institute for Brain Science, Seattle, WA, USA

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