Use JaneliaSciComp/VVDViewer instead.
This is the open-source repository for VVDViewer, an interactive rendering tool for confocal microscopy data visualization. It combines the rendering 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 for neurobiologists, to better visualize the fluorescent-stained confocal samples. This code base started as a fork of Fluorender.
Click on your operating system to download VVDViewer:
If you get Vulkan-related errors, please try to update your graphics device driver.
https://github.com/JaneliaSciComp/VVDViewer/wiki
Joshua L Lillvis, Hideo Otsuna, Xiaoyu Ding, Igor Pisarev, Takashi Kawase, Jennifer Colonell, Konrad Rokicki, Cristian Goina, Ruixuan Gao, Amy Hu, Kaiyu Wang, John Bogovic, Daniel E Milkie, Linus Meienberg, Brett D Mensh, Edward S Boyden, Stephan Saalfeld, Paul W Tillberg, Barry J Dickson (2022) Rapid reconstruction of neural circuits using tissue expansion and light sheet microscopy eLife 11:e81248
If you use VVDViewer 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."
There are the following mirrored VVDViewer repositories.
https://github.com/JaneliaSciComp/VVDViewer
https://github.com/takashi310/VVD_Viewer
You can get the latest source code and precompiled binary from both repositories.
- 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 VVDViewer outside of the source tree.
-
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
- The steps following will assume the wxWidgets root directory is at
-
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
-
-
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
-
-
Get and build VVDViewer
-
mkdir build
-
cd build
-
cmake ../VVD_Viewer -G Xcode
-
Open the Xcode file generated to build and run VVDViewer.
-
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
- The steps following will assume the wxWidgets repository is at
-
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.
-
-
Download and build boost.
-
Download boost (http://www.boost.org/users/download/#live) and extract onto your machine.
-
Build boost using
bootstrap.exe
andb2.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.
-
-
Build or Download libjpeg, libtiff, openssl, zlib, openssl and curl.
- If you use Visual Studio 12.0 2013+, also build ffmpeg.
-
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.*).
-
-
Download VVDViewer using Git
git clone https://github.com/takashi310/VVD_Viewer.git
-
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 VVDViewer source and build directories (create a new folder for building), and add the locations of boost and wxWidgets.
-
Choose the VVDViewer 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
toC:\wxWidgets\lib\vc_x64_lib
. (this will differ from 32 bit) -
Be sure to set
wxWidgets_ROOT_DIR
toC:\wxWidgets
. -
Be sure to set
Boost_INCLUDE_DIR
toC:\boost_1_59_0
(assuming this is your boost dir). -
Be sure to set
Boost_INCLUDE_DIR
toC:\boost_1_59_0
(assuming this is your boost dir). -
Be sure to set
Boost_CHRONO_LIBRARY_DEBUG
toC:\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
toC:\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
toC:\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
toC:\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
toC:\libcurl
(assuming this is your libcurl dir). -
Be sure to set
CURL_LIBRARY
toC:\libcurl\libcurl.lib
(assuming this is your libcurl dir). -
Be sure to set
JPEG_INCLUDE_DIR
toC:\libjpeg
(assuming this is your libjpeg dir). -
Be sure to set
JPEG_LIBRARY
toC:\libjpeg\jpeg.lib
(assuming this is your libjpeg dir). -
Be sure to set
ZLIB_INCLUDE_DIR
toC:\zlib
(assuming this is your zlib dir). -
Be sure to set
ZLIB_LIBRARY
toC:\zlib\zlib.lib
(assuming this is your zlib dir). -
Be sure to set
LIB_EAY_DEBUG
andLIB_EAY_RELEASE
toC:\openssl\lib\libeay32.lib
(assuming this is your openssl dir). -
Be sure to set
SSL_EAY_DEBUG
andSSL_EAY_RELEASE
toC:\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 inC:\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 VVDViewer 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
- Select your VVDViewer source and build directories (create a new folder for building), and add the locations of boost and wxWidgets.