Posted By: Hanchuan Peng - May 25, 2011
Tool/Resource: Vaa3D and Vaa3D-Neuron
Vaa3D Helps Develop Powerful 3D Brain Registration Program

May 25, 2011
Tool/Resource: Vaa3D and Vaa3D-Neuron

The Vaa3D platform helps develop a new 3D brain registration program, BrainAligner, which was published in Nature Methods (May 2011,

BrainAligner is an automatic computer program that registers a (or any) pair of 3D image stacks using landmark matching. It has been primarily used in Janelia Farm’s FlyLight project to align many thousands of laser scanning microscope images, each of which has hundreds of millions pixels and multiple fluorescent colors that highlight various subsets of neurons in a brain as well as the overall brain morphology. The program can be downloaded from

Vaa3D has been used to develop the core algorithm of BrainAligner, as well as a key platform to visualize the registration results of thousands of brain images, using a V3D module called Vaa3D-AtlasViewer.

**** About Vaa3D ****

Vaa3D is a handy, fast, and versatile 3D/4D/5D Image Visualization & Analysis System for Bioimages & Surface Objects. It also provides many unique functions. It supports a very simple and powerful plugin interface and thus can be extended & enhanced easily.

This software has recently been published in Nature Biotechnology (April 2010), received highlights in Nature Methods (May, 2010), Science News (April/May 2010), NIH NITRC (Aug, 2010), and HHMI Annual Report (Dec 2010). Developer hackathons that involved about 10 different research labs were also held recently (July-Aug, 2010).

Vaa3D is a cross-platform (Mac, Linux, and Windows) tool for visualizing large-scale (gigabytes, and 64-bit data) 3D, 4D and 5D image stacks and various surface data. It 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 V3D 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.

In our latest development, 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 even has a Matlab file IO toolbox. Probably most importantly, you can now write your own plugins to take advantage of the Vaa3D platform!

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

Vaa3D official website:
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Vaa3D discussion forum:

* Vaa3D lets you explore & understand your
large 3D/4D/5D images a lot easier!
- fast 3D+ image visualization and analysis,
WYSIWYG, and easy plugin interface:
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