VVD Viewer Source Code

This is the open-source repository for VVD Viewer, an interactive rendering tool for confocal microscopy data visualization. It combines the renderings of multi-channel volume data and polygon mesh data, where the properties of each dataset can be adjusted independently and quickly. The tool is designed especially for neurobiologists, and it helps them better visualize the fluorescent-stained confocal samples. This is a branch of Fluorender (https://github.com/SCIInstitute/fluorender)

https://github.com/takashi310/VVD_Viewer/releases

If you use VVD Viewer in work that leads to published research, we humbly ask that you add the following to the 'Acknowledgments' section of your paper: "This work was made possible in part by software funded by the NIH: Fluorender: An Imaging Tool for Visualization and Analysis of Confocal Data as Applied to Zebrafish Research, R01-GM098151-01."

• Git (https://git-scm.com/)
• CMake 2.6+ (http://www.cmake.org/)
• wxWidgets (https://github.com/wxWidgets/wxWidgets)
• Windows 7+ : Visual Studio 11.0 2012+
• OSX 10.9+ : Latest Xcode and command line tools, homebrew
• Other platforms may work, but are not officially supported.
• Boost 1.59.0+ (http://www.boost.org/users/download/#live)

We recommend building VVD Viewer outside of the source tree.

1. Clone the latest wxWidgets using GIT (git clone https://github.com/wxWidgets/wxWidgets.git).

   • The steps following will assume the wxWidgets root directory is at ~/wxWidgets

2. Build wxWidgets from the command line.

   • cd ~/wxWidgets/

   • mkdir mybuild

   • cd mybuild

   • ../configure --disable-shared --enable-macosx_arch=x86_64 --enable-unicode --with-cocoa --enable-debug --with-macosx-version-min=10.9 --enable-stl --enable-std_containers --enable-std_iostreams --enable-std_string --enable-std_string_conv_in_wxstring --with-libpng --with-libtiff --with-libjpeg

   • make

   • make install

3. Get homebrew, boost, freetype, xz, libtiff, libjpeg, zlib, openssl and curl.

   • ruby -e "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/master/install)"

   • brew install boost

   • brew install freetype

   • brew install xz

   • brew install libtiff

   • brew link libtiff --force

   • brew install jpeg

   • brew link jpeg --force

   • brew install zlib

   • brew link zlib --force

   • brew install openssl

   • brew link openssl --force

   • brew install curl --with-openssl

   • brew link curl --force

4. Get and build VVD Viewer

   • git clone https://github.com/takashi310/VVD_Viewer.git
     

   • mkdir build
     

   • cd build
     

   • cmake ../VVD_Viewer -G Xcode
     

5. Open the Xcode file generated to build and run VVD Viewer.

1. Clone the latest wxWidgets using GIT (git clone git@github.com:wxWidgets/wxWidgets.git).

   • The steps following will assume the wxWidgets repository is at C:\wxWidgets

2. Open a 64 bit Visual Studio command prompt to build wxWidgets. (make sure you use the prompt version you wish to build all dependencies, IE , MSVC 14.0 2015 x64)

   • Go to directory C:\wxWidgets\build\msw

   • Type nmake /f makefile.vc TARGET_CPU=x64 BUILD=debug to build debug libraries.

   • Type nmake /f makefile.vc TARGET_CPU=x64 BUILD=release to build release libraries.

3. Download and build boost.

   • Download boost (http://www.boost.org/users/download/#live) and extract onto your machine.

   • Build boost using bootstrap.exe and b2.exe --toolset=msvc-11.0 --build-type=complete architecture=x86 address-model=64 stage in the boost directory in a MSVC prompt. (change the toolset to the version of MSVC you are using, and omit address-model and architecture for 32-bit)

   • The steps following will assume the boost root directory is at C:\boost_1_59_0 (your version might differ).

   • In a separate directory, checkout a separate boost process library : git clone git@github.com:basisunus/boost_process.git and merge the contents into the boost directory you built in.

4. Build or Download libjpeg, libtiff, openssl, zlib, openssl and curl.

   • If you use Visual Studio 12.0 2013+, also build ffmpeg.

5. You may need to add lines to C:\Program Files (x86)\CMake X.X\share\cmake-x.x\Modules\FindwxWidgets.cmake (x's are your version) for wxWidgets 3.* if it still complains that you haven't installed wxWidgets.

   • Starting about line 277, you will have listed a few sets of library versions to search for like wxbase29${_UCD}${_DBG}
     

   • In 4 places, you will need to add above each line with a "29" a new line that is exactly the same, but with a "31" instead, assuming your version of wxWidgets is 3.1.*).
     

6. Download VVD Viewer using Git git clone https://github.com/takashi310/VVD_Viewer.git

7. Use the C:\Program Files(x86)\CMake2.8\bin\cmake-gui.exe program to configure build properties and generate your Visual Studio Solution file. (Remember to keep your MSVC version consistent)

   • Select your VVD Viewer source and build directories (create a new folder for building), and add the locations of boost and wxWidgets.
     

   • Choose the VVD Viewer main folder for source and create a new folder for the build.
     

   • Click Configure. NOTE: You may need to display advanced options to set below options.
     

   • Choose the build type CMAKE_BUILD_TYPE to be "Debug" or "Release"
     

   • Be sure to set wxWidgets_LIB_DIR to C:\wxWidgets\lib\vc_x64_lib. (this will differ from 32 bit)

   • Be sure to set wxWidgets_ROOT_DIR to C:\wxWidgets.

   • Be sure to set Boost_INCLUDE_DIR to C:\boost_1_59_0 (assuming this is your boost dir).
     

   • Be sure to set Boost_INCLUDE_DIR to C:\boost_1_59_0 (assuming this is your boost dir).
     

   • Be sure to set Boost_CHRONO_LIBRARY_DEBUG to C:\boost_1_59_0\x64\lib\libboost_chrono-vc110-mt-gd-1_59.lib (assuming this is your boost dir).
     

   • Be sure to set Boost_CHRONO_LIBRARY_RELEASE to C:\boost_1_59_0\x64\lib\libboost_chrono-vc110-mt-s-1_59.lib (assuming this is your boost dir).
     

   • Be sure to set Boost_SYSTEM_LIBRARY_DEBUG to C:\boost_1_59_0\x64\lib\libboost_system-vc110-mt-gd-1_59.lib (assuming this is your boost dir).
     

   • Be sure to set Boost_SYSTEM_LIBRARY_RELEASE to C:\boost_1_59_0\x64\lib\libboost_system-vc110-mt-s-1_59.lib (assuming this is your boost dir).
     

   • Be sure to set CURL_INCLUDE_DIR to C:\libcurl (assuming this is your libcurl dir).
     

   • Be sure to set CURL_LIBRARY to C:\libcurl\libcurl.lib (assuming this is your libcurl dir).
     

   • Be sure to set JPEG_INCLUDE_DIR to C:\libjpeg (assuming this is your libjpeg dir).
     

   • Be sure to set JPEG_LIBRARY to C:\libjpeg\jpeg.lib (assuming this is your libjpeg dir).
     

   • Be sure to set ZLIB_INCLUDE_DIR to C:\zlib (assuming this is your zlib dir).
     

   • Be sure to set ZLIB_LIBRARY to C:\zlib\zlib.lib (assuming this is your zlib dir).
     

   • Be sure to set LIB_EAY_DEBUG and LIB_EAY_RELEASE to C:\openssl\lib\libeay32.lib (assuming this is your openssl dir).
     

   • Be sure to set SSL_EAY_DEBUG and SSL_EAY_RELEASE to C:\openssl\lib\ssleay32.lib (assuming this is your openssl dir).
     

   • If you use Visual Studio 12.0 2013+, delete all files in VVD_Viewer\fluorender\ffmpeg\Win64 and copy your ffmpeg files in C:\ffmpeg (assuming this is your ffmpeg dir).
     

   • Click Generate.

   • You may also generate using the command prompt, but you must explicitly type the paths for the cmake command.
     

   • Open Visual Studio Command Prompt. Go to the CMakeLists.txt directory.
     

   • Type cmake -G "Visual Studio 14 2015 Win64" -DwxWidgets_LIB_DIR="C:\wxWidgets\lib\vc_x64_lib" -DwxWidgets_ROOT_DIR="C:\wxWidgets" -DBoost_INCLUDE_DIR="C:\boost_1_55_0" -DCMAKE_BUILD_TYPE="Debug" .. in your build directory (again assuming these are your directory locations / Generator versions, and the build folder is in the VVD Viewer root directory).
     

   • Open the Visual Studio SLN file generated by CMake (found in your "build" directory).
     

   • Build the solution. Use CMake to generate both "Release" and "Debug" configurations if you wish to build both in Visual Studio.
     
     Notes for Visual Studio

   • Visual Studio may not set the correct machine target when building 64 bit. Check Project Properties -> Configuration Properties -> Linker -> Command line. Make sure "Additional Options" is /machine:X64 NOT /machine:X86.
     

   • You may need to right-click VVD_Viewer project on the Solution Explorer to "Set as StartUp Project" for it to run.
     

   • If you are building on Windows 8 or later, you will need to set a Visual Studio Graphics Option. This enables the application to build in higher definition.
     Project Properties -> Manifest Tool -> Input and Output -> Enable DPI Awareness -> Yes