A tool for compensating for motion in FLIM data
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README.md

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

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

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