Before download

The following V3D-related software packages are free, but you will have to agree to the license terms at this website and their respective license information, 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.

V3D FileIO Matlab Toolbox 1.0

1. ✦This toolbox is for reading/writing V3D basic data file formats (image files .RAW, .TIFF, marker file .marker, point cloud file .apo, neuron file .swc which can indeed be used to describe any complicated graph) in Matlab. This is good for post-analysis of the the image analysis and measurements. Download here.
   

2. ✦Note: you may need libtiff library if you have not already have one in your search path. You may also need to by-pass or update the default Matlab libtiff library file as Matlab uses an old version of libtiff!
   

V3D Plugins

1. ✦Default V3D plugins. You can develop plugin programs to take advantage of the fast volume image rendering, 3D pinpointing, and easy 4D image data management of V3D. Here is source codes v0.95 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.
   

2. •You can now check out the source code of these plugins below. This will also be the location of future plugins’ source code. Use the user account "anonymous" without a password.
   

3.             svn co https://svn.janelia.org/penglab/projects/v3d/trunk/released_plugins my_v3d_plugins
   

4. ✦Other V3D plugins.
   

5. •About 30 V3D plugins (not including the V3D-ITK project below) have been developed by various parties, - we will add a new page which will contain more information of these modules.
   

6. •V3D-ITK project: about another 30 or so plugins, for about 10 typical categories of 3D image processing methods, were preliminarily developed in a V3D-ITK hackathon (June 1-4, 2010) participated by Luis Ibaniz, Yang Yu, Lei Qu, and Hanchuan Peng. The project is a continuing effort to develop a useful open-source library based on ITK and V3D; the “unfinished” source code can be checked-out (as of June 14, 2010) at
   

7.          git clone  git://github.com/luisibanez/ITK-V3D-Plugins.git
   

8. ✦How to compile a plugin and run on the V3D platform.
   

9. •Mac:
   

1. 1.Download Qt 4.5.2 and above. Compile the “Release” version and install it by run the following commands in a Terminal window. (i.e. first run “./configure”, followed by “make” and “sudo make install”).
   

2. 2.Enter the folder that contains your V3D plugin source code and the Qt project file “abc.pro”, - suppose “abc.pro” is the project file name.
   

3. 3.run “qmake abc.pro”
   

4. 4.run “make”
   

5. 5.copy the compiled plugin dynamic library file, which should have a name similar to “abc.dylib”, to a subfolder (say “my_abc”) under the “plugins” folder where you the V3D program installed (typically “/Applications/v3d”).
   

6. 6.Launch V3D program, and you should see a new sub-menu in the plugin menu, called “my_abc”, and you can find the “abc” plugin there.
   

7. 7.If you already launch V3D before you build the plugin, you don’t need to re-start V3D. Instead, you click the plugin menu and choose “Rescan plugins”, and you should find the sub-menu.
   

8. 8.Trouble-shooting. If you follow the above instructions but cannot see the full drop-down menu-list in the sub-menu “my_abc”, you need to check your Qt version, the Release or Debug version in your compilation. You can also try one of the V3D plugin examples. These examples have been tested on many machines and different environments. If they cannot work, you may need to adjust the configuration of Qt and/or the compiling setting on your machine.
   

9. •Linux
   

1. 1.Similar to Mac instructions above, except that the extension of the dynamic library file will be different and the typical V3D folder is the one where unzip the installer.
   

2. 2.Trouble-shooting. For Ubuntu, since many times the g++ and Qt libraries are not installed by default, you may need to ensure you have the correct compiling environment.
   

3. •Windows
   

1. 1.For MinGW 32bit compiler.
   

1. (i)Download Qt 4.4.3 from Nokia’s official Qt website. Compile the “Release” version and install it by run the following commands in a Terminal window. (i.e. first run “./configure”, followed by “make” and “sudo make install”). Then use the “make”, or “mingw32-make”, in a similar way like the above Mac and Linux environment.
   

2. 2.For Visual Studio 2008.
   

1. (i)Download Qt 4.6 from the following website http://code.google.com/p/qt-msvc-installer/ . Ensure that if you have a 32bit system, you will need the 32bit installer; if you have a 64bit Windows system, you should download the 64bit installer.
   

2. (ii)Add Qt’s bin directory to your system PATH environment variable, so that on a command line window you can find “qmake” command.
   

3. (iii)Select and run the 32bit or 64bit command line Terminal in the Visual Studio 2008 folder. This will give you a command line window.
   

4. (iv)Run “qmake abc.pro”, assuming abc.pro is the Qt project name for your plugin.
   

5. (v)run “nmake -f Makefile.Release”. This should compile the plugin.
   

3. 3.copy the compiled plugin dynamic library file, which should have a name similar to “abc.dll”, to a subfolder (say “my_abc”) under the “plugins” folder where you the V3D program installed (or unzipped).
   

4. 4.Launch V3D program, and you should see a new sub-menu in the plugin menu, called “my_abc”, and you can find the “abc” plugin there.
   

5. 5.If you already launch V3D before you build the plugin, you don’t need to re-start V3D. Instead, you click the plugin menu and choose “Rescan plugins”, and you should find the sub-menu.
   

6. 6.Trouble-shooting. If you follow the above instructions but cannot see the full drop-down menu-list in the sub-menu “my_abc”, you need to check your Qt version, the Release or Debug version in your compilation. You can also try one of the V3D plugin examples. These examples have been tested on many machines and different environments. If they cannot work, you may need to adjust the configuration of Qt and/or the compiling setting on your machine.
   

7. •CMake for Linux and Mac
   

1. 1.If you are using CMake, the compilation will be more sophisticated to explain. But you can check out the open-source V3D-ITK project source code and follow the instruction in the README file.
   

2. 2.As of now (June 14, 2010), the open-source V3D-ITK project source code can be checked out using git at the following repository:
   

3.                 git clone  git://github.com/luisibanez/ITK-V3D-Plugins.git
   

3. 3.Feel free to ask about the ongoing V3D-ITK project! See the contact information page.
   

VANO

1. ✦A tri-view based 3D image object annotator. V3D can export the cell segmentation to VANO files and thus get them annotated conveniently. Download here.