Galene is a tool to correct for motion in fluorescence lifetime imaging (FLIM) data. For more information please see [citation].
Precompiled applications are available from http://www.flimfit.org/galene.
For documentation please see http://galene.readthedocs.io.
Instructions to compile from source are provided below, including retrieving the required dependencies.
Requirements
- Windows 7 or greater
- Visual Studio 2015 or greater
- Qt 5.7 or greater, install from https://www.qt.io/download-open-source/
- vcpkg, for installing required dependencies, install from https://github.com/seanwarren/vcpkg
- choco, for installing required dependencies, install from https://chocolatey.org/
- Optionally, CUDA to support GPU processing, install from https://developer.nvidia.com/cuda-downloads
Install the required dependencies using
vcpkg install opencv:x64-windows fftw3:x64-windows boost:x64-windows xalan-c:x64-windows exiv2:x64-windows libraw:x64-windows eigen3:x64-windows proj4:x64-windows hdf5:x64-windows
choco install cmake python2 pip nsis ninja -y
pip install genshi
- Add an environment variable to point CMake to Qt, e.g.
CMAKE_PREFIX_PATH = C:\Qt\5.9\msvc2017_64 - Add an environment variable
VCPKG_ROOTto point to the vcpkg folder
Build steps
- Clone the Galene repository from
https://github.com/flimfit/galene - Run script
build-libs.batto buildbioimageandome-files- run
build-libs.bat --build-debugto also build debug and relwithdebinfo libraries
- run
- Run script
build-flim-ui.bat - A Visual Studio solution will be created in the
Buildsubfolder
Requirements
- MacOS 10.11 or greater
- XCode 8.2 or greater
- Homebrew, install from https://brew.sh
- Optionally, CUDA to support GPU processing, install from https://developer.nvidia.com/cuda-downloads
- Download CUDA 8 for macOS 10.11 or CUDA 9.2 for macOS 10.12 or CUDA 9.2 for macOS 10.13.
Install the required dependencies using
brew install qt cmake opencv boost xerces-c xalan-c exiv2 libraw eigen libpng libtiff proj hdf5 fftw dlib zlib python ninja npm hg
pip install genshi
sudo npm install -g appdmg # to build the disk image
If you have some of the packages installed already, brew upgrade to retrieve the latest packages
Build steps
- Clone the Galene repository from
https://github.com/flimfit/galene - Run script
build-flim-ui.sh
Galene uses the following open source software.
| Package | Licence | |
|---|---|---|
| Qt | http://www.qt.io | LGPL v3 |
| ome-files-cpp | https://www.openmicroscopy.org/ome-files/ | MIT |
| bioimageconvert | https://bitbucket.org/dimin/bioimageconvert/ | MIT |
| dlib | http://dlib.net/ | Boost |
| OpenCV | http://opencv.org/ | BSD |
| boost | http://www.boost.org/ | Boost |
| fftw3 | http://www.fftw.org/ | GPL v2 |
| libhdf5 | https://www.hdfgroup.org/ | BSD |
| QSimpleUpdater | https://github.com/alex-spataru/QSimpleUpdater | DBAD |