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Before download
Vaa3D is free, but you will have to agree to the license & user agreement terms, before downloading, using, running, editing, or changing any portion of codes in this package. Downloading any of the parts of the software means you have read and agreed to the conditions. If you do not agree, please do NOT download.
Questions/comments/bug reports?: Please see the CONTACT page or the new Vaa3D Documentation Site.
Current Release:
Vaa3D 2.9,
Vaa3D-Neuron 2.1,
Plugin Interface 2.1
Vaa3D 2.8~2.9, Vaa3D-Neuron 2.1, Plugin Interface 2.1
Change log (2012 ~ 2014): A major alpha-release of Vaa3D containing a lot of new modules and plugins. This package includes several significant new features such as nice Movie Makers, 3D synchronization of multiple 3D viewers, fast and automated 3D cell segmentation, neuron reconstruction (all-path-pruning methods), terabyte-sized image stack stitching and visualization, convenient plugin creator, among many others. Also note that if your downloaded file(s) cannot be opened correctly, you may have partially downloaded file(s), and in that case you should use the software (e.g. wget) that have the ability to resume the download-breakpoint to finish downloading the entire file.
* Mac
o v2.921: Mac OS X 10.7/10.8/10.9, 64-bit (225.7Mb)
o v2.868: Mac OS X 10.7/10.8/10.9, 64-bit
o To run, you can unzip the packages and run the installer, and then run the program from the /Applications/vaa3d folder.
* Linux
o Note that we just identified an corrupted-file issue with some plugins (e.g. Vaa3D-neuron2 module running on Ubuntu) in the Linux version. You are encouarged to build from the source code directly to avoid some issues running the following binaries. We will fix and make a new release soon.
o v2.921: Linux Redhat, Fedora, and Ubuntu 64-bit (136Mb)
o v2.868: Linux Redhat, Fedora, and Ubuntu 64-bit
o To run, you can unzip the packages and type “./start_vaa3d.sh”. For more information, see the README file in the packages.
* Windows
o v2.801: Windows 7 64-bit (with plugins)
o To run: you can unzip the package and double-click “vaa3d_msvc.exe”.
* Other versions for Windows, Mac, and Linux
o Vaa3D is cross-platform. You can check out the source code and build by yourself (see Source Code section below).
* Command-line execution of Vaa3D program
o The Mac and Linux versions can also be run from command line directly. You only need to locate the actual executable program, called “vaa3d” or “vaa3d64”, and type such program name on a terminal. If you type “vaa3d -h” you will see the help information. You can directly invoke particular plugins from the command line as well. This is particularly useful for large-scale pipeline using the Vaa3D programs and its plugins.
* Matlab File IO toolbox
o In the “matlab_io_basicdatatype” folder after you check out Vaa3D code. See below.
* ImageJ/Fiji File IO toolbox
o In the “imagej_io” folder after you check out Vaa3D code. See below.
o This plugin can be used to read/write Vaa3D’s RAW file (to load 8bit, 16bit and 32bit image data).
* Source code (including standard plugin examples, Vaa3D-ITK project plugins (>100 Vaa3D-ITK plugins), Matlab file IO toolbox, ImageJ/Fiji file IO toolbox, etc.)
o Follow the Vaa3D GoogleCode Documentation Site for source code locations and building instructions. Ensure to read the README file after you get the code. After compiling a new plugin, just put it into the "plugins" folder of the Vaa3D program folder.
o Ensure to read the README files in *each* of the sub-folders after you check out code. Importantly, after you compile a new plugin, you need to move into the "plugins" folder, which should sit in the same folder of the main Vaa3D executable.
Last Release:
Vaa3D 2.707,
Vaa3D-Neuron 2.0,
Plugin Interface 2.1
Vaa3D 2.707, Vaa3D-Neuron 2.0, Plugin Interface 2.1
Change log (Nov 10, 2011): A slightly refined release of this program under the new name, Vaa3D. The various new features of Vaa3D can be seen from the log information of previous releases retained below.
* Mac
o SnowLeopard (Mac OS X 10.6) 64-bit
o To run, you can unzip the packages and run the installer, and then run the program from the /Applications/vaa3d folder.
* Linux
o Linux Redhat and Fedora 64-bit
o To run, you can unzip the packages and type “./start_vaa3d.sh”. For more information, see the README file in the packages.
* Windows
o To run: you can unzip the packages and double-click “vaa3d_msvc.exe”.
* Other versions for Windows, Mac, and Linux
o Vaa3D is cross-platform. You can check out the source code and build by yourself (see Source Code section below).
Previous Release Logs:
Vaa3D 2.706, Vaa3D-Neuron 2.0, Plugin Interface 2.1
Change log (Nov 7, 2011): This first release of this program under the new name, Vaa3D. The various new features of Vaa3D can be seen from the log information of previous releases retained below.
* Mac
o SnowLeopard (Mac OS X 10.6) 64-bit
o To run, you can unzip the packages and run the installer, and then run the program from the /Applications/vaa3d folder.
* Linux
o Linux Redhat and Fedora 64-bit
o To run, you can unzip the packages and type “./start_vaa3d.sh”. For more information, see the README file in the packages.
* Windows
o To run: you can unzip the packages and double-click “vaa3d_msvc.exe”.
Vaa3D 2.687, Vaa3D-Neuron 2.0, Plugin Interface 2.1
Change log (Aug 10, 2011): This version is a major upgrade of the previous versions. Now Vaa3D has a powerful color manager for tri-view window, has the new user-definable toolbar functions, web-service engine, and a number of new plugins (you can just explore by yourself!).
Note that as the Vaa3D plugin interface is still being continuously enhanced, if you would like to write plugins for Vaa3D, you need to ensure you check out the latest version of the source code.
Vaa3D 2.603, Vaa3D-Neuron 2.0, Plugin Interface 2.1
Change log (Jan 6, 2011): A major upgrade of the Vaa3D main program and make the plugin interface even easier and more powerful. Allow multi-thread data loading whenever possible. Add web file fetching and load function. Enable 16/32 bit direct 3D visualization and 3D WYSIWYG for such data. Fixed some bugs and enhanced the interaction performance. More comprehensive plugin interface.
Vaa3D now is open source, along with more than 100 plugins developed by various people. Some featured plugins that can be very useful include Simple Movie Maker, 5D Stack Converter, Fast Distance Transform, Multi-thread Image Loading, Vaa3D Example Plugin for Push Image and Objects, etc. You can also check out the latest source code, or download pre-compiled versions below.
Note that as the Vaa3D plugin interface is still being continuously enhanced, if you would like to write plugins for Vaa3D, you need to ensure you check out the latest version of the source code.
Special note about large image files (>2G bytes): The new, and default, image data reader uses LIBTIFF to read files and thus has the limitation to load >2G image files. If you want to do so, you can rename or remove this data reader, which is a plugin called "multithreaded_imgloading" under the "plugins" sub-folder in your Vaa3D folder. Then you need to also change preferences by selecting the main menu "File->Adjust Preferences->Use LibTiff (ON) or MYLIB (OFF)" to be OFF.
Known problems and fix: There is a bug introduced in 5D data rendering; some plugins may appear less organized. The bug has been fixed and the plugins' menus have been rearranged and improved in a newer version v2.607. You can check out the latest source code (see link below) and build your own version. Check the Vaa3D Discussion Forum for the latest information.
Vaa3D 2.526, Vaa3D-Neuron 2.0, Plugin Interface 2.1
Change log (Sept 8, 2010): A major upgrade of both the Vaa3D main program and the plugin interface. Fixed a number of small bugs or enhanced the interaction performance. Added optional method to load >2G TIF/LSM files directly using mylib. Add 3D 1-click or 1-stroke zoom-in of any 3D content. Much more powerful plugin interface.
Vaa3D now is entirely open source, along with more than 100 plugins developed by people from different institutes and companies (e.g. Janelia Farm-HHMI, Kitware, EPFL, Institut Pasteur, UNC Chapel Hill, etc.). You can download the latest source code, or pre-compiled versions below. Note that as the Vaa3D plugin interface is still being continuously enhanced, if you would like to write plugins for Vaa3D, you need to ensure you use the latest version of the source code.
V3D 2.485, V3D-Neuron 2.0, Plugin Interface 0.96
Change log (July 27, 2010): Add new controls to the 3D viewer that allows a user to precisely control the orientation of the 3d displayed image/surface, thus further make it easy to compare different views. Also add support to the pixel resolutions through the Vaa3D plugin interface. Also fix bugs in displaying the maximum values in the volume-cut sliders, marker/curve definition for one single slice. This version is the one currently being used by the Vaa3D Hackathon meeting from July 26-Aug 8, Janelia Farm, HHMI.
V3D 2.475, V3D-Neuron 2.0, Plugin Interface 0.95
Change log (June 17, 2010): A major plugin-interface upgrade. Besides the major new functions introduced in a recent release (v2.466, see release note below), this release adds the support of a more comprehensive plugin interface, which lets a plugin read and write the 3D curve and neuron, besides the 3D markers and a region of interest, that are associated with an image. Starting from this version, Vaa3D also comes with a new plugin, “ImageIO_bioformat”, to read dozens of image file formats such as PNG, JPEG, BMP, ZVI, AVI, etc. Thus the default set of Vaa3D release includes a bunch of plugins, for example
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•conversion a 4D stack to 5D time series (and vice versa),
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•ImageIO_bioformat: read dozens of image file formats, or batch-convert to tiff stacks (based on LOCI Bio-formats Java library, which has great, but varying ability depending on platforms to read different file formats),
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•fast (linear-time) image distance transform in both 2D and 3D,
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•demo programs of the single-image and multi-image plugin interfaces, etc.
The source code of these default plugins can be downloaded below.
This version is the best to support the ongoing Open-Source Vaa3D-ITK project, which tries to convert some commonly useful ITK filters to Vaa3D-plugins. As of now (June 2010), the source code of the Vaa3D-ITK project can be checked out using git. For more information, see the Toolbox page.
Vaa3D 2.466 and Vaa3D-Neuron 2.0
Change log (May 15, 2010): A major release of Vaa3D that now includes the Vaa3D-Neuron 2.0 (alpha) tracing. Vaa3D-Neuron 2.0 includes a 3D paint-and-trace function that lets a user trace very complicated structure and proofread it immediately. Combined with the graph-augmented deformable model and shortest-path merging algorithms in Vaa3D-Neuron 1.0 (see v2.451 release note below and the respective papers), Vaa3D-Neuron 2.0 in principle can trace any complicated morphological structure of a neuron (or other fibrous structures) within a reasonably short time. The 3D paint-and-tracing function is built upon a one-stroke-drawing for a 3D curve, an important extension to the 3D pinpointing functions of Vaa3D. Vaa3D-Neuron 2.0 can automatically connect individual 3D curves if their end-points are close to another curve, thus complete the neuron reconstruction. Also note that this novel 3D curve drawing function can be used to profile the image voxel intensity along any 3D trajectory a user can see in the 3D space. Therefore this version of Vaa3D lets a user directly produce quantitative measurement along any 3D [curved] path in the 3D space. For demos, watch movies at the Tutorial Movies page.
This release also includes 10 updated plugins, including for example
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•conversion a 4D stack to 5D time series (and vice versa),
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•fast (linear-time) image distance transform in both 2D and 3D,
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•demo programs of the single-image and multi-image plugin interfaces, etc.
The source codes can be downloaded below as well.
v2.465
Change log (April 16, 2010): New features of Vaa3D-Neuron such as post-merging branches, estimation of radius based on XY plane only or complete XYZ information, using z-thickness a weighting factor for radius estimation; also fixed bugs on one-slice marker definition, image rotation, etc.
v2.452
Change log (Mar 17, 2010): In addition to the recently released Vaa3D-Neuron 1.0 (see release note on v2.451 below), the 3D image atlas viewer/blender menu is provided. The 3D image atlas can be used to browse and blend a large image archive, based on a spreadsheet which contains linking information to the actual files.
Vaa3D v2.451; Vaa3D-Neuron 1.0
Change log (Feb 15, 2010): V3D-Neuron 1.0 is formally included in this release. This module supports easy 3D marker-based neuron tracing/reconstruction and proofreading/editing. The Vaa3D GUI interface has also been slightly changed to add more convenience.
v2.430
Change log (Dec 5, 2009): This version supports a new 3D image visualization engine that has both synchronized and asynchronized modes to render 3D/4D/5D images. This version also supports transparent surface display and contour-only modes ('Ctrl/Cmd-P', 'Alt/Option-P' short keys), faster 3D pinpointing using continuous 1-clicks until 'Esc' key is pressed, highlighting search results in the object manager, 'Alt/Option'-L short key for better neuron (swc) display, allow sub-volume image processing without doing that in a separate local 3D viewer window, alpha-test version of the AutoMarker function, and others. The plugin programming interface is further enhanced.
v2.323
Change log (Sept 3, 2009): This version supports 5D rendering (true 3D volume rendering in temporal domain and with multiple colors)! This version also supports user-developed plugins with which a user can take advantage of the powerful Vaa3D platform and adds his/her own modules! You can download the example plugin source codes below. Also with this release we provide a Matlat toolbox that can read and write most used Vaa3D data file formats (see Related Software below).
v2.223
Change log (July 29, 2009): This is a preview (alpha-test) version of Vaa3D. Among a number of enhancements over the last stable release 2.033 (you can try and find the differences!), the most useful function is that now the user can select an roi (region of interest) in the tri-view and then generate a local 3D viewer for that region only. Also with this release we provide a Matlab toolbox that can read and write most used Vaa3D data file formats (see Related Software below).
v2.033
Change log (May 4, 2009): A number of enhancements and bug fixes. Enable user preferences of automatic flip image for different coordinate systems when opening an image, automatic open 3D viewer, set default marker size and change displayed size, change looking-glass size, fix bug of refreshing display events, enable 3D line drawing and intensity profiling of line for all color channels, update the layout of 3D viewer control panel, enable display marker label in 3D viewer, enable surface objects stretch together with 3D rendered volume image when Z-thickness changes, enable neuron names and comments annotation saved in SWC file, enable neuron comparison and can compute distance/similarity scores between neurons, enables display neuron structure/morphological features, enable display individual neuron node information, enable display surface mesh area/size information, save surface mesh display status in V3DS file for faster reuse, enable image cropping for both of region of interest and region of non-interest, fast fill/flood non-interest image region with certain values, add a new cell segmentation and counting program, add new 3D image registration methods, enable 3D neuron interactive reconstruction, enable reading some simple electron microscopy MRC files, fix bugs in marker location display, etc.
v1.999
Change log (Feb 15, 2009): Enable landmark defining in any zoom-in/out tri-view; enhance the z-thickness in 3D viewer as double spinbox and up-to 10x change.
v1.998
Change log (Feb 13, 2009): Add big image panning-around, color inversion, voxel intensity rescaling functions in main window. Also refine frontal plane cut for both MIP, alpha blending and cross-sectional views in 3D viewer. Turn the 3D image registration, segmentation, neuron tracing modules as customary modules. Bug fix of the image flipping.
v1.986
Change log (Dec 22, 2008): Redesign the main window menu. Add regional statistics in landmark dialog which can be used for 3D measurements. Add volume image colormap. Fix some small bugs. Release a preliminary 64-bit Redhat/Fedora version.
v1.983
Change log (Dec 15, 2008): Many updates. Add atlas viewer and landmark manager in main GUI. Add 3D cell segmentation as a standard module. Add exporting function to transfer cell/nuclei segmentation results to VANO/WANO software. Linux versions (Redhat and Ubuntu) are released internally.
v1.972
Change log (Nov 15, 2008): Enable flexible color-picker for surface and other objects (neurons, point clouds); enable zoom-in and zoom-out modes for the tri-view in main window; enable drag-and-drop for Windows PCs; enable viewing and color changing for multiple neurons.
v1.962
Change log (Nov 11, 2008): A lot of changes! Bug fixes, adding cutting planes to surface and objects, adding compression mode for volume rendering and Ctrl-C switches, clock-type rotation buttons, 3D rotation state machine updates, drag-and-drop into the 3D viewer, etc.
v1.950
Change log (Oct 8, 2008): Make the 3D image registration module a default for general release; significant optimization on the memory use for 3D rendering; change the Help text to html. Note that from this release Vaa3D makes two different versions for Mac Intel CPU based Tiger (OS 10.4) system, one with multisampling supporting from the video card, another without multisampling support from the video card (e.g. NVIDIA GeForce 7300GT). The one w/o multisampling will should run well except that the 3D viwer may not draw lines and objects smoothly enough (i.e. with sawtooth); on the other hand machines without an apporpriate video card may crash or hang when the multisampling-supporting version is used for 3D rendering.
v1.949
Change log: Enable the direct opening apo, swc, v3ds, and obj file formats in 3D viewer; get around a Graphics card hardware bug related to multisampling in certain Maci/Tiger machine.
v1.947
Change log: add creating surface from any RGB channel of the currently viewed volume data.
v1.946
Change log: add the recent-file history, image permutation and reshape, image flipping, grayscale2color color channel splitting, disable 16-bit TIFF auto-bit-shifting in reading, add channel-display switch in 3D viewer, better layout of some 3D viewer controls, and fix the potential memory allocation crashes in image analysis.
v1.945
Change log: enhance the handling of memory allocation exception in creating the 3D viewer.
v1.943
Change log (July 29, 2009): porting to windows system. This is a preview (alpha-test) version of Vaa3D. Among a number of enhancements over the last stable release 2.033 (you can try and find the differences!), the most useful function is that now the user can select an roi (region of interest) in the tri-view and then generate a local 3D viewer for that region only. Also with this release we provide a Matlab toolbox that can read and write most used Vaa3D data file formats (see Related Software section below).
Other earlier versions: 2006-2008 developed by Hanchuan Peng.
