THIS REPOSITORY IS NOW DEPRECATED

Use JaneliaSciComp/VVDViewer instead.

VVDViewer

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.

Download

Click on your operating system to download VVDViewer:

If you get Vulkan-related errors, please try to update your graphics device driver.

Documentation

User Manual

https://github.com/JaneliaSciComp/VVDViewer/wiki

Using VVDViewer for large volume segmentation (by Joshua Lillvis)

https://github.com/JaneliaSciComp/exllsm-circuit-reconstruction/blob/master/docs/NeuronSegmentation.md

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

How to Cite

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."

Source Code

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.

Building VVDViewer

Dependencies

• 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.

OSX

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 VVDViewer

   • 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 VVDViewer.

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 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 VVDViewer 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 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 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 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