A Swiss Army Knife for exploring Big-Big Image Data!


Vaa3D visualizes and explores big 3D/4D/5D images with giga-voxels and even tera-voxels, within seconds or sub-seconds!


Vaa3D extracts complex surface objects from images, and performs comprehensive analyses such as brain connectome mapping.


100+ plugins for image acquisition, microsurgery, data management and analysis, and massive-scale pipelining.

What is 'Vaa3D'?

'Vaa3D' is short for the “3D Visualization-Assisted Analysis” software suite. This term was first used in a 2010 Nature Biotech article (DOI: 10.1038/nbt.1612). The software has been featured in HHMI News, Allen Institute News, Nature Methods Highlights, Science News, among others. This software is currently maintained by both HHMI - Janelia Research Campus and the Allen Institute for Brain Science, and is used in a number of projects worldwide.

How to pronounce 'Vaa3D'?

Vaa3D should be pronounced like 'wa-three-d'. A sound file can be downloaded here. Vaa3D has a Chinese name: ‘挖三维’, which means ‘Mining in 3D’, the intended use of this software. The pronunciation of the Chinese name is similar to ‘Wa-San-Wei’.

What Vaa3D does

Vaa3D is a handy, fast, and versatile 3D/4D/5D Image Visualization and Analysis System for Bioimages and Surface Objects. It also provides many unique functions that you may not find in other software. It is Open Source, and supports a very simple and powerful plugin interface and thus can be extended and enhanced easily.

Vaa3D is cross-platform (Mac, Linux, and Windows). This software suite is powerful for visualizing large- or massive-scale (giga-voxels and even tera-voxels) 3D image stacks and various surface data. Vaa3D is also a container of powerful modules for 3D image analysis (cell segmentation, neuron tracing, brain registration, annotation, quantitative measurement and statistics, etc) and data management. This makes Vaa3D suitable for various bioimage informatics applications, and a nice platform to develop new 3D image analysis algorithms for high-throughput processing. In short, Vaa3D streamlines the workflow of visualization-assisted analysis.

Vaa3D can render 5D (spatial-temporal) data directly in 3D volume-rendering mode; it supports convenient and interactive local and global 3D views at different scales... it comes with a number of plugins and toolboxes. Importantly, you can now write your own plugins to take advantage of the Vaa3D platform, possibly within minutes!

Please contact us if you want to learn more, provide feedbacks, or become a part of this exciting developing team!