Vaa3D statistics

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Citations per year

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chevron_left 3D image visualization Neuron tracing Image-analysis libraries Neuron tracing Morphometric analysis 2D image visualization chevron_right
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Associated diseases


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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


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  • person_outline Hanchuan Peng <>
  • person_outline Hanchuan Peng <>
  • person_outline Fuhui Long <>

Additional information

Publications for 3D Visualization-Assisted Analysis

Vaa3D in pipelines

PMCID: 5087619
PMID: 27578784
DOI: 10.1242/dev.134098

[…] with fiji (; ). imaris software was used for 3d reconstructions. surfaces of clones and the related movies were rendered with chimera from ucsf (). raw data movies of gaudílxbbw were rendered with vaa3d (). quantification of clone size was conducted by thresholding for nuclei and measuring clone volume with the bonej command ‘particle analyser’ (). this clone size was divided by a standard […]

PMCID: 4659165
PMID: 26607933
DOI: 10.1186/s12859-015-0814-7

[…] then, we ran a watershed transform on i in order to generate segmentation masks. we thresholded segmentation masks based on size in order to remove gross mis-segmentations., we ran the vaa3d gvf plugin using 5 diffusion iterations, a fusion threshold of 1, and a minimum region size of 999. we performed an extensive coordinate-wise search over parameter settings, choosing […]

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Vaa3D in publications

PMCID: 5873451
PMID: 29424420
DOI: 10.1002/cne.24406

[…] ). 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, ). […]

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

[…] each tracing point: 7 to reconstruct the arbor morphology and 3+3 to quantify each of the two parallel channels., we implemented this design in a newly developed multichannel_compute plugin for the vaa3d software suite ( specifically, this plugin automatically generates the eswc file from the multichannel image stacks and the corresponding standard swc file (see methods). in addition […]

PMCID: 5815848
PMID: 29412139
DOI: 10.7554/eLife.33420.040

[…] animals were imaged on a custom-built two photon microscope with a 20x (0.95 na) water immersion lens at 2–3.5x scan zoom. the dendrites of single neurons were traced and reconstructed using the vaa3d-neuron 2.0: 3d neuron paint and tracing function in vaa3d ( with manual correction and validation of the tracing (). total dendritic branch length (tdbl) was quantified […]

PMCID: 5617181
PMID: 28953913
DOI: 10.1371/journal.pone.0184972

[…] function, and the negative value around 0° was regarded as belonging to the distribution where the second peak was 18.4°., finally, typical fiber structure was processed by open source software vaa3d, neutu and soax as illustrated in . the tortuosity was not recognized correctly in some locations while the fuzzy regions were ignored. the high curvature regions were overlooked by neutu […]

PMCID: 5606987
PMID: 28931809
DOI: 10.1038/s41467-017-00514-7

[…] compatible with terastitcher. the images were then aligned using image cross-correlation and tiled. after tiling, a multi-resolution image set, compatible with terafly, was stored to disk., vaa3d a freely available software package, was utilized to visualize individual images areas. terafly, a freely available plug in within vaa3d, was used to visualize tiled images produced […]

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

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