Vaa3D Binary Release v3.458

The new release comes with a number of new features/short-cuts for neuron tracing/editing, and new plugins including synapse_detector for synapse detection.

Vaa3D (in Chinese ‘挖三维’) is an Open Source, award-winning visualization and analysis software suite created mainly by Janelia Research Campus, HHMI and Allen Institute for Brain Science. The software performs 3D, 4D and 5D rendering and analysis of very large image data sets, especially those generated using various modern microscopy methods, and associated 3D surface objects.

Vaa3D has been used in hundreds of high profile publications in Nature, Science, Cell, Neuron, IEEE Transactions, etc. It is used as platform software for several of the largest brain research initiatives in the world.

How to run Vaa3D?

-Windows: After downloading the zipped file, unzip and double click the vaa3d_msvc.exe file to run.
-Mac: Download and unzip the file, then move it into /Applications folder, then you can find and right-click on the 'vaa3d64.app' to launch it.
-Linux: After downloading Vaa3D, first run 'tar zxvf [filename]' and then enter the produced folder, and run './start_vaa3d.sh'.

License and references

To use this software package, you agree with the license of the Vaa3D and that you will cite the following papers in your work.

Peng, H., Ruan, Z., Long, F., Simpson, J.H., and Myers, E.W. (2010) "V3D enables real-time 3D visualization and quantitative analysis of large-scale biological image data sets," Nature Biotechnology, Vol. 28, No. 4, pp.348-353. (http://vaa3d.org)
Peng, H., Bria, A., Zhou, Z., Iannello, G., and Long, F. (2014) "Extensible visualization and analysis for multidimensional images using Vaa3D," Nature Protocols, Vol. 9, No. 1, pp. 193-208. (http://vaa3d.org)
Peng, H., et al. (2014) "Virtual finger boosts three-dimensional imaging and microsurgery as well as terabyte volume image visualization and analysis," Nature Communications, Vol. 5, No. 4342, DOI: 10.1038/ncomms5342.
Bria, A., et al. (2016) "TeraFly: real-time 3D visualization and 3D annotation of terabytes of multidimensional volumetric images," Nature Methods, Vol. 13, pp. 192-194, DOI: 10.1038/nmeth.3767.

Vaa3D Binary Release v3.447

Vaa3D binary release v3.447 for Windows, Mac, and Linux (CentOS)

The new release comes with a turbo engine for tracing neurons: UltraTracer and a Deep learning based tracing toolbox: DeepNeuron (Linux only). Read a new Nature Methods paper about UltraTracer (https://www.nature.com/articles/nmeth.4233) and new biorxiv paper abut DeepNeuron (https://www.biorxiv.org/content/early/2018/01/25/254318).

Vaa3D (in Chinese ‘挖三维’) is an Open Source, award-winning visualization and analysis software suite created mainly by Janelia Research Campus, HHMI and Allen Institute for Brain Science. The software performs 3D, 4D and 5D rendering and analysis of very large image data sets, especially those generated using various modern microscopy methods, and associated 3D surface objects.

Vaa3D has been used in hundreds of high profile publications in Nature, Science, Cell, Neuron, IEEE Transactions, etc. It is used as platform software for several of the largest brain research initiatives in the world.

How to run Vaa3D?

-Windows: After downloading the zipped file, unzip and double click the vaa3d_msvc.exe file to run.
-Mac: Download and unzip the file, then move it into /Applications folder, then you can find and right-click on the 'vaa3d64.app' to launch it.
-Linux: After downloading Vaa3D, first run 'tar zxvf [filename]' and then enter the produced folder, and run './start_vaa3d.sh'.

License and references

To use this software package, you agree with the license of the Vaa3D and that you will cite the following papers in your work.

Peng, H., Ruan, Z., Long, F., Simpson, J.H., and Myers, E.W. (2010) "V3D enables real-time 3D visualization and quantitative analysis of large-scale biological image data sets," Nature Biotechnology, Vol. 28, No. 4, pp.348-353. (http://vaa3d.org)
Peng, H., Bria, A., Zhou, Z., Iannello, G., and Long, F. (2014) "Extensible visualization and analysis for multidimensional images using Vaa3D," Nature Protocols, Vol. 9, No. 1, pp. 193-208. (http://vaa3d.org)
Peng, H., et al. (2014) "Virtual finger boosts three-dimensional imaging and microsurgery as well as terabyte volume image visualization and analysis," Nature Communications, Vol. 5, No. 4342, DOI: 10.1038/ncomms5342.
Bria, A., et al. (2016) "TeraFly: real-time 3D visualization and 3D annotation of terabytes of multidimensional volumetric images," Nature Methods, Vol. 13, pp. 192-194, DOI: 10.1038/nmeth.3767.

Vaa3D Binary Release v3.200

Vaa3D binary release v3.200 for Windows, Mac, and Linux (CentOS and Ubuntu)

The new release comes with 100+ (130+ for Linux) plugins / tools for neuroinformatics, Big Data, neuroimaging, etc. It has the powerful built-in TeraFly engine for surfing terabytes of images without stopping, in 3D and on ordinary computers directly. Read a new Nature Methods paper about this technique ( http://www.nature.com/nmeth/journal/v13/n3/full/nmeth.3767.html ).

Vaa3D (in Chinese ‘挖三维’) is an Open Source, award-winning visualization and analysis software suite created mainly by Janelia Research Campus, HHMI and Allen Institute for Brain Science. The software performs 3D, 4D and 5D rendering and analysis of very large image data sets, especially those generated using various modern microscopy methods, and associated 3D surface objects.

Vaa3D has been used in hundreds of high profile publications in Nature, Science, Cell, Neuron, IEEE Transactions, etc. It is used as platform software for several of the largest brain research initiatives in the world.

How to run Vaa3D?

• Windows: After downloading the zipped executable file, unzip and double click the exe file to install and then run.
• Mac: Download and unzip the file, then move it into /Applications folder, then you can find and right-click on the 'vaa3d.app' to launch it.
• Linux: After downloading Vaa3D, first run 'tar zxvf [filename]' and then enter the produced folder, and run './start_vaa3d.sh'.

License and references

To use this software package, you agree with the license of the Vaa3D and that you will cite the following papers in your work.

• Peng, H., Ruan, Z., Long, F., Simpson, J.H., and Myers, E.W. (2010) "V3D enables real-time 3D visualization and quantitative analysis of large-scale biological image data sets," Nature Biotechnology, Vol. 28, No. 4, pp.348-353. (http://vaa3d.org)
• Peng, H., Bria, A., Zhou, Z., Iannello, G., and Long, F. (2014) "Extensible visualization and analysis for multidimensional images using Vaa3D," Nature Protocols, Vol. 9, No. 1, pp. 193-208. (http://vaa3d.org)
• Peng, H., et al. (2014) "Virtual finger boosts three-dimensional imaging and microsurgery as well as terabyte volume image visualization and analysis," Nature Communications, Vol. 5, No. 4342, DOI: 10.1038/ncomms5342.
• Bria, A., et al. (2016) "TeraFly: real-time 3D visualization and 3D annotation of terabytes of multidimensional volumetric images," Nature Methods, Vol. 13, pp. 192-194, DOI: 10.1038/nmeth.3767.

Vaa3D Binary Release v3.100

Vaa3D binary releases v3.100 for Windows, Mac, and Linux (CentOS and Ubuntu).

Vaa3D Preview v3.111 w/o plugins

This is a version to demonstrate the Vaa3D-TeraFly capability (for all platforms: Mac, Linux and Windows), w/o inclusion of various Vaa3D plugins. A new version is planned in the near future to include all modules.