Vaa3D Wiki

What is Vaa3D

Vaa3D is an open source 3D/4D/5D image visualization and analysis software for bioimage analysis. It is a cross-platform (Mac, Linux, and Windows) tool for visualizing large-scale (gigabytes, and 64-bit data) image volumes and surface objects. It is also a container of powerful modules/plugins for high dimensional image analysis (cell segmentation, neuron tracing, brain registration, annotation, quantitative measurement and statistics, etc). 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 be used in different ways. It renders 5D (spatial-temporal) data directly in 3D volume-rendering mode; it supports convenient and interactive local and global 3D views at different scales... it has several file IO toolboxes for Matlab, ImageJ/Fiji and Bioformats... Vaa3D can also be driven by Matlab and other programs to display large data in 3D, directly. You can also write your own plugins to take advantage of the Vaa3D platform, and pipeline these modules in both command line scripts and using Vaa3D super-plugins.

Curious about the name? "Vaa3D" is the short-term for “3D Visualization-Assisted Analysis”, a term used in our 2010 Nature Biotechnology paper. See the [Vaa3D publications].

Vaa3D is the new name of the 3D+ visualization software suite developed in Hanchuan Peng lab. It also has a new Chinese name now: ‘挖三维’, which means ‘Mining in 3D’, the intended use of this program.

How to pronounce Vaa3D

The pronunciation of the English name is similar to 'vē-ä-thrē-dē'. The pronunciation of the Chinese name is similar to ‘Wa-San-Wei’.

Why there is a new name

This program was formerly referred to as V3D, which may confuse with other ‘V3D’ names on Internet. Thus from Nov 7, 2011, this program changes to the new name(s) of ‘Vaa3D’ and ‘挖三维’.

Contact & Help

If you have questions, you are encouraged to search for an answer first at the NITRC Vaa3D Discussion Forum. You can also report bugs or request new features there.