Galene

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.

Building on Windows

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_ROOT to point to the vcpkg folder

Build steps

• Clone the Galene repository from https://github.com/flimfit/galene
• Run script build-libs.bat to build bioimage and ome-files
  • run build-libs.bat --build-debug to also build debug and relwithdebinfo libraries
• Run script build-flim-ui.bat
• A Visual Studio solution will be created in the Build subfolder

Building on Mac

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

Acknowledgements

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