Vaa3D and Vaa3D-Neuron News

Vaa3D v3.2 (w TeraFly engine and 130+ plugins) is released

Hanchuan Peng — Fri, 20 May 2016 1:03:15 GMT

Vaa3D (http://vaa3d.org) version 3.2 for Windows, Mac and Linux has just been released. The new release comes with 130+ 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 led to 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.

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

[1] 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)

[2] 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)

[3] 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.

[4] 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 on GitHub Now!

Hanchuan Peng — Tue, 02 Feb 2016 1:52:16 GMT

Visit Vaa3D's new github code repository!

https://github.com/Vaa3D

Vaa3D v2.920 released!

Hanchuan Peng — Tue, 21 Oct 2014 12:58:40 GMT

Cool new features of the Vaa3D system can be found at the new download site

http://home.penglab.com/proj/vaa3d/

New Vaa3D paper is published in Nature Protocols

Hanchuan Peng — Mon, 06 Jan 2014 11:39:11 GMT

Vaa3D was just published as a featured protocol in Nature, open-access to everyone, on the topic of visualization and analysis of multi-dimensional images and surface obejcts.

http://www.nature.com/nprot/journal/v9/n1/full/nprot.2014.011.html

Vaa3D version 2.865 is released

Hanchuan Peng — Mon, 30 Dec 2013 3:51:08 GMT

The Vaa3D version v2.865 ( http://vaa3d.org ) has been released on Dec 28, 2013.

This software suite has powerful modules for 3D visualization and analysis of multi-dimensional images and surface objects. This new release includes several significant new features such as

** nice 3D movie makers;
* 3D synchronization of multiple 3D viewers;
* fast and automated 3D cell segmentation;
** automated neuron reconstruction (all-path-pruning methods);
* terabyte-sized image stack stitching (terastitcher);
** terabyte-sized image stack visualization and annotation (terafly);
* convenient plugin creator.
* many others.

Vaa3D (Peng et al, Nature Biotechnology, 2010) is a handy, fast, and versatile 3D/4D/5D Image Visualization & Analysis System for Bioimages & Surface Objects. It also provides many unique functions. It is also Open Source, supports a very simple and powerful plugin interface and thus can be extended & enhanced easily.

Vaa3D is a cross-platform (Mac, Linux, and Windows) tool for visualizing large-scale (gigabytes, and 64-bit data) 3D 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 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.

Download the software at http://vaa3d.org .

Vaa3D Helps win the Annual Andor Insight Best Image Award

Hanchuan Peng — Tue, 02 Jul 2013 3:15:44 GMT

Congrats to Fernando Amat, who used Vaa3D in his new award fron Andor:

http://www.theinsightawards.com/#!/entry/1736749.

Vaa3D-Neuron2 Released (April 19, 2013)

Hanchuan Peng — Wed, 24 Apr 2013 2:47:59 GMT

The Vaa3D-Neuron2 Tool, integrated in the Vaa3D platform, has been released on April 19, 2013.

This software suite is able to reconstruct the 3D morphology of a neuron from 3D image completely automatically.

If a user chooses to supply some starting locations of the tracing, the software is also able to incorporate such information automatically. This also combines with other semi-automatic tools, such as Vaa3D's 3D-WYSIWYG functions, for semi-automatic reconstruction of a neuron.

** How to use: Open an image in Vaa3D, see it in a 3D viewer window and then right-click the mouse, a pop-up menu will be displayed to guide how to use the Vaa3D-Neuron2 tool.

** Source code repository: svn co https://svn.janelia.org/penglab/projects/vaa3d_tools

The All-Path-Pruning-2 paper is published in Bioinformatics

Hanchuan Peng — Sun, 21 Apr 2013 5:34:50 GMT

The paper for the just released source code of the automated 3D neuron tracing method is published.

http://bioinformatics.oxfordjournals.org/cgi/reprint/btt170?%20%20%20%20%20%20%20%20%20%20%20%20%20%20%20%20%20%20%20%20%20%20%20%20%20%20%20%20ijkey=GfA2Hy6oaEtsp8F&keytype=ref

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APP2: Automatic Tracing of 3D Neuron Morphology Based on Hierarchical Pruning of Gray-Weighted Image Distance-Trees

Hang Xiao1,2,4 and
Hanchuan Peng1,3,4,*

+ Author Affiliations

1 Janelia Farm Research Campus, Howard Hughes Medical Institute
2 CAS-MPG Partner Institute for Computational Biology
3 Allen Institute for Brain Science
4 Equal contribution

↵*To whom correspondence should be addressed. Hanchuan Peng, E-mail: hanchuanp@alleninstitute.org

Abstract

Motivation: Tracing of neuron morphology is an essential technique in computational neuroscience. However, despite a number of existing methods, few open-source techniques are completely or sufficiently automated and at the same time are able to generate robust results for real 3D microscopy images.

Results: We developed APP2 (all-path-pruning 2.0) for 3D neuron tracing. The most important idea is to prune an initial reconstruction tree of a neuron's morphology using a long-segment-first hierarchical procedure instead of the original termini-first-search process in APP. To further enhance the robustness of APP2, we compute the distance-transform of all image-voxels directly for a gray-scale image, without the need to binarize the image before invoking the conventional distance-transform. We also design a fast-marching algorithm based method to compute the initial reconstruction trees without pre-computing a large graph. This method allows us to trace large images. We bench-tested APP2 on about 700 3D microscopic images and found APP2 can generate more satisfactory results in most cases than several previous methods.

Availability: The software has been implemented as an open-source Vaa3D plugin. The source code is available in the Vaa3D code repository http://vaa3d.org.

* Contact: hanchuanp@alleninstitute.org

Vaa3D v2.801 Released

Hanchuan Peng — Tue, 04 Sep 2012 2:11:00 GMT

A new binary version (v2.801) of the 3D visualization and analysis tool, Vaa3D, was just released.

http://www.vaa3d.org

This is a new alpha release containing new modules and over 160 plugins.

The Documentation site for Vaa3D is

http://code.google.com/p/vaa3d/

Vaa3D also comes with a Chinese name: æŒ–ä¸‰ç»´, which means 'Mining in 3D'. The pronunciation of the Chinese name is similar to 'wa-san-wei'.

<2012-08-29>

Vaa3D and Vaa3D-Neuron now documented on GoogleCode

Hanchuan Peng — Wed, 18 Apr 2012 1:33:53 GMT

A lot of documentation information of the 3D visualization and analysis tool, Vaa3D, are now hosted at GoogleCode.

http://code.google.com/p/vaa3d/

A short list of content includes:

* How to Use Vaa3D
* Basic use guide
* Demo movies
* User manual
* Command line access
* Test data
* Discussion forums
* Neuron tracing
* Get & build source code
* FAQ
* Plugins
* Overview
* Plugins list
* Command line access
* Write a plugin: example
* Compile plugins
* Plugin-API details
* Toolboxes
* Matlab I/O
* ImageJ/Fiji
* Bioformats
* Data structures
* About
* Publications