Installation

The Spatialign package is developed based on the pytorch framework and can be implemented on both CPU and GPU.

We recommend running the package on GPU. Please ensure that pytorch and CUDNN are installed correctly.

To run Spatialign, all dependencies included in the file ‘requirement.txt’ need to be installed.

We provide two ways to install the package of Spatialign.

Please note that the current Spatialign version offers full support of Linux operating system. Further version for other operating systems would be released soon.

1. Python

Install through Pypi.

pip install spatialign

or downloading the package from GitHub repository.

pip install spatialign-0.1.3-py3-none-linux_x86_64.whl

or

git clone https://github.com/STOmics/Spatialign.git

cd Spatialign

python setup.py install

2. Anaconda

For convenience, we suggest using a separate conda environment for running Spatialign. Please ensure Annaconda3 is installed.

Create conda environment and install Spatialign package.

# create an environment called Spatialign
conda create -n Spatialign python=3.8

# activate your environment
conda activate Spatialign

# install package

pip install spatialign

or

git clone https://github.com/STOmics/Spatialign.git

cd Spatialign

python setup.py build

python setup.py install --user

#To use the environment in jupyter notebook, add python kernel for this environment.

pip install ipykernel

python -m ipykernel install --user --name=spatialign