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FluoRender

FluoRender Source Code

This is the open-source repository for FluoRender, 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.

Aknowledgements

If you use FluoRender 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."

Author: Yong Wan
Developer: Brig Bagley

Building FluoRender

Requirements: Git, CMake, wxWidgets, boost, Visual Studio 10 (Windows 7+ required), XCode (OSX 10.9+ required)
We recommend building FluoRender outside of the source tree.

OSX

  1. Clone the latest wxWidgets using GIT (git clone git@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=sys --with-libtiff=builtin

    • make

  3. Download and include boost.

  4. In the main FluoRender directory, (containing "CMakeLists.txt" & "fluorender" folder):

    • mkdir build

    • cd build

    • cmake -G Xcode -DwxWidgets_CONFIG_EXECUTABLE="/wxWidgets/mybuild/wx-config" -DwxWidgets_wxrc_EXECUTABLE="/wxWidgets/mybuild/utils/wxrc/wxrc" -DwxWidgets_USE_DEBUG=ON -DwxWidgets_ROOT_DIR="/wxWidgets" -DBoost_INCLUDE_DIR="/boost_1_55_0" -DCMAKE_BUILD_TYPE="Debug" ..

  5. Open the Xcode file generated to build and run FluoRender.

Windows

  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 10 command prompt to build wxWidgets.

    • 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 include boost.

  4. 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.*).

  5. Use the C:\Program Files(x86)\CMake2.8\bin\cmake-gui.exe program to configure build properties and generate your Visual Studio 10 Solution file.

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

    • Choose the FluoRender 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.

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

    • Be sure to set Boost_INCLUDE_DIR to C:\boost_1_55_0 (assuming this is your boost 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 2010 64 bit Command Prompt. Go to the CMakeLists.txt directory.

    • Type cmake -G "Visual Studio 10 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 and the build folder is in the FluoRender 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.

    • 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" should is /machine:X64 NOT /machine:X86.

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

Contact

If there are any problems, email: fluorender@sci.utah.edu