A command-line interface for wrangling data from CyCIF images
Cyftools can currently only be built from source. It requires a few dependencies to be installed to compile, see instructions below.
Clone the project recursively (it has submodules):
git clone --recursive [email protected]:walaj/cyftools
Install the following dependencies:
- libjpeg
- hdf5
- eigen3
- libomp
- cgal
- boost
- mlpack
- libbdplus
- armadillo
On OSX this can be done with:
brew install libjpeg hdf5 eigen libomp cgal boost mlpack libbdplus armadillo
You will also need supervised-lda, which needs to be in $HOME/git/supervised-lda, so run:
mkdir -p $HOME/git
git clone [email protected]:angeloskath/supervised-lda $HOME/git/supervised-lda
Then follow the instructions here to build it from source (might need to install cmake first as well).
On MacBook ARM architectures the make check on supervised-lda might fail with stuff like:
test_approximate_supervised_expectation_step.cpp:166:5: error: reference to 'VectorX' is ambiguous`
fatal error: too many errors emitted, stopping now [-ferror-limit=]
Running sudo make install and then cp build/libldaplusplus.dylib lib/ got it to work anyway - cyftools expects the library to be in $HOME/git/supervised-lda/lib/libldaplusplus.dylib rather than build.
From root of repo:
cd src
make all