I was at a meeting last week where I was discussing 3D analysis and visualization of fluorescent images. Most people are aware of the commercial software that have 3D capabilities, such as Imaris and Arivis, but I was surprised that my colleagues didn’t know about Vaa3D.

Vaa3D (pronunced Waa-three-D) is an open-source 3D analysis suite created by Huanchan Peng, a brain researcher currently working on Big Data solutions in the Allen Institute for Brain Science in Seattle. Vaa3D was built from the ground up to solve the new challenges that came with large 3D and 4D datasets, thanks to new technologies such as light-sheet fluorescence microscopy. It’s much better suited to handle large amounts of data than current commercial software, which were build with much smaller datasets in mind.

I tested Vaa3D on my workstation and it performed much better than Imaris. Some of my datasets, such as whole mouse hippocampi imaged in 3D with two-photon microscopy, are hard to visualize and manipulate with Imaris. Vaa3D opens those in seconds and can do analysis such as cell segmentation without any problems.

Contact me if you need help getting started with Vaa3D!

Étienne