openTSNE can be easily installed from conda-forge with

conda install --channel conda-forge opentsne

Conda package


openTSNE is also available through pip and can be installed with

pip install opentsne

PyPi package

Installing from source

If you wish to install openTSNE from source, please run

python install

in the root directory to install the appropriate dependencies and compile the necessary binary files.

Please note that openTSNE requires a C/C++ compiler to be available on the system. Additionally, numpy must be pre-installed in the active environment.

In order for openTSNE to utilize multiple threads, the C/C++ compiler must support OpenMP. In practice, almost all compilers implement this with the exception of older version of clang on OSX systems.

To squeeze the most out of openTSNE, you may also consider installing FFTW3 prior to installation. FFTW3 implements the Fast Fourier Transform, which is heavily used in openTSNE. If FFTW3 is not available, openTSNE will use numpy’s implementation of the FFT, which is slightly slower than FFTW. The difference is only noticeable with large data sets containing millions of data points.