Vaa3D and Vaa3D-Neuron Releases

vaa3d Vaa3D 3.2

hanchuan@stage.nitrcce.org (Hanchuan Peng) — Thu, 23 Jun 2016 20:50:00 GMT

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

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.

[b]How to run Vaa3D?[/b]

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'.

[b]License and references[/b]

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 Vaa3D-2.938

xiaoxiao@stage.nitrcce.org (Xiaoxiao Liu) — Fri, 13 Mar 2015 21:34:00 GMT

vaa3d v2.475

hanchuan@stage.nitrcce.org (Hanchuan Peng) — Thu, 24 Jun 2010 21:03:00 GMT

vaa3d V3D 2.466, V3D-Neuron 2.0, Plugin Interface 0.92

hanchuan@stage.nitrcce.org (Hanchuan Peng) — Sat, 15 May 2010 5:01:00 GMT

This is a major release of V3D.

Now V3D supports 3D curve drawing from an image directly! See details below.

For different Mac 32/64bit, Windows 32/64bit, and Linux 32/64bit versions, see a few notes:

* Mac
o Mac Pro (Maci) with Leopard/Snow Leopard OS (Mac OS 10.5/10.6), 32bit (On Leopard, 32bit runs faster than the 64bit version)
o Mac Pro (Maci) with Leopard/Snow Leopard OS (Mac OS 10.5/10.6), 64bit (Due to some 64-bit QT problems in event handling, on some machines sometimes the keyboard input in the tri-view window may be blocked if a 3D viewer has not been launched, - open a 3D viewer and return to the tri-view may fix the problem)
o We no longer support older Mac OS X versions (e.g. Tiger, OS X 10.4) or G4/G5 CPUs. You can download the older versions of V3D, e.g. v2.452, that support them. (see V3D official site links http:/penglab.janelia.org/pro/v3d).

* Windows
o Windows XP/Vista/7, 32bit (generated using MinGW 32bit compiler)
o Windows 7, 64bit (generated using VC 2008 compiler and may be less stable than the above 32bit version)

* Linux
o Linux Redhat and Fedora 64-bit
o Linux Ubuntu (9.1) 64-bit
o Linux Ubuntu (10.04) 32-bit
o To run each of the above Linux releases, you will need to follow the respective step-by-step instructions in the respective README file (after you unzip the package) to ensure you have the library files set up correctly. If you still have a problem, you either have some missing system library files or have incompatibility of the Linux versions. For the former, you can run the “ldd v3d” command in the V3D folder to determine which library file(s) are missing, and then figure out some ways to install these system files (e.g. in Ubuntu, use the apt-get command). For the latter case, you will need to ensure you have an appropriate Linux version (either by upgrading or some other ways).

* Plugin example source code v0.92
o source codes v0.92 for all platforms (Read the README in the zipped file for instructions) After compiling a new plugin, just put it into the "plugins" folder of the V3D program folder.